Novel RNA-guided nucleases and proteins for polymerase editing

Abstract

Compositions and methods for binding to a target sequence of interest are provided. The compositions find use in cleaving or modifying a target sequence of interest, visualizing a target sequence of interest, and modifying the expression of a sequence of interest. Compositions comprise RNA-guided nuclease (RGN) polypeptides, polymerase editors (PEs), guide RNAs, and polynucleotides encoding the same. Vectors and host cells comprising the polynucleotides are also provided. Further provided are RGN systems for binding and modifying a target sequence of interest, wherein the RGN system comprises an RNA-guided nuclease polypeptide and one or more guide RNAs, as well as PE systems for modifying a target sequence of interest, wherein the PE system comprises a polymerase, a RGN polypeptide, and one or more polymerase editing guide RNAs.

Description

[0001]NOVEL RNA-GUIDED NUCLEASES AND PROTEINS FOR POLYMERASE EDITING CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to U.S. Provisional Application No.63 / 552,421, filed February 12, 2024, and to U.S. Provisional Application No.63 / 559,159, filed February 28, 2024, each of which is incorporated by referenced herein in its entirety. REFERENCE TO A SEQUENCE LISTING SUBMITTED ELECTRONICALLY AS AN XML FILE The instant application contains a Sequence Listing which has been submitted in xml format and is hereby incorporated by reference in its entirety. Said xml copy, created on February 11, 2025, is named L103438_1390WO_0330_1_SL, and is 4,005,847 bytes in size. FIELD OF THE INVENTION The present invention relates to the field of molecular biology and gene editing. BACKGROUND OF THE INVENTION Targeted genome editing or modification is rapidly becoming an important tool for basic and applied research. Initial methods involved engineering nucleases such as meganucleases, zinc finger fusion proteins or TALENs, requiring the generation of chimeric nucleases with engineered, programmable, sequence-specific DNA-binding domains specific for each particular target sequence. RNA-guided nucleases (RGNs), such as the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (Cas) proteins of the CRISPR-Cas bacterial system, allow for the targeting of specific sequences by complexing the nucleases with guide RNA that specifically hybridizes with a particular target sequence. Producing target-specific guide RNAs is less costly and more efficient than generating chimeric nucleases for each target sequence. Such RNA-guided nucleases can be used to edit genomes optionally through the introduction of a sequence-specific, double-stranded break that is repaired via error-prone non-homologous end-joining (NHEJ) to introduce a mutation at a specific genomic location. Alternatively, heterologous DNA may be introduced into the genomic site via homology-directed repair. RNA-guided nucleases (RGNs) can also be used for base editing when fused with a deaminase or prime editing when fused with reverse transcriptase. Prime editing is a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using an RNA-guided DNA binding protein (e.g., RGN) working in association with a reverse transcriptase (described in, e.g., US 11,447,770B1; WO2021072328; WO2021226558; WO2020156575; WO2021042047; US11193123; each 1 Atty Dkt No: L1034381390WO (0330.1) incorporated by reference in its entirety herein). The prime editing system uses an RGN that is a nickase and a polymerase, and the system is programmed with a prime editing guide RNA that comprises a primer binding site (PBS) and a DNA synthesis template that serves as the template for the replacement strand comprising the edit. The prime editor nicks the non-target strand upstream of the sequence to be edited and upstream of the PAM, creating a 3' flap on the non-target strand. The PBS is complementary to the 3' flap of the non-target strand and hybridrization of the PBS and 3' flap of the non-target strand allows for the polymerization of the replacement strand containing the edit using the DNA synthesis template. BRIEF SUMMARY OF THE INVENTION Compositions and methods for binding and modifying a target sequence of interest in a target polynucleotide are provided. The compositions find use in cleaving or modifying a target polynucleotide of interest, detection of a target sequence of interest, and modifying the expression of a gene of interest comprising a target sequence. Compositions comprise RNA-guided nuclease (RGN) polypeptides, polymerase editors (PEs), guide RNAs (gRNAs), polynucleotides encoding the same, vectors and host cells comprising the polynucleotides, and pharmaceutical compositions comprising the same. Also provided are RGN systems and ribonucleoprotein complexes for binding a target sequence of interest, wherein the RGN system and ribonucleoprotein complex comprises an RNA- guided nuclease polypeptide and one or more guide RNAs. Polymerase editor (PE) systems comprising one or more polymerase editing guide RNAs (PEgRNAs), a polymerase, and an RGN polypeptide are also provided. Thus, methods disclosed herein are drawn to binding a target sequence of interest in a target polynucleotide, and in some embodiments, cleaving or modifying the target polynucleotide of interest. The target polynucleotide of interest can be modified, for example, as a result of non-homologous end joining, homology-directed repair with an introduced donor sequence, base editing, or polymerase editing. DETAILED DESCRIPTION Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended embodiments. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation. 2 Atty Dkt No: L1034381390WO (0330.1) I. Overview Provided herein are RNA-guided nuclease (RGN) variants of the APG07433.1 RGN disclosed in International Appl. Publ. No. WO 2019 / 236566, which is herein incorporated by reference in its entirety, that are capable of recognizing a protospacer adjacent motif (PAM) 3' of a target sequence having the nucleotide sequence nnnnCY, nnnnCT, nnnnC, or nnnnCM, instead of the parental APG07433.1 PAM of nnnnCC. One such APG07433.1 variant is LPG10221, which is set forth as SEQ ID NO: 1, comprises five mutations within the PAM-interacting domain of APG07433.1; specifically, D1020S, S1021G, D1022N, R1023K, and N1025E; and recognizes a PAM having the nucleotide sequence nnnnCY. LPG10209, set forth as SEQ ID NO: 579, has a R1023Q mutation and recognizes a PAM having the nucleotide sequence nnnnC. LPG10210, set forth as SEQ ID NO: 584, has S1021T and R1023N mutations and recognizes a PAM having the nucleotide sequence nnnnCM (where M is C or A). LPG10212, set forth as SEQ ID NO: 583, has a S1021N and R1023N mutations and recognizes a PAM having the nucleotide sequence nnnnC. LPG10213, set forth as SEQ ID NO: 591, comprises four mutations; specifically S975Q, D1020A, D1022G, R1023Q; and recognizes a PAM having the nucleotide sequence nnnnCT. The RGNs disclosed herein can alter gene expression by modifying a target polynucleotide comprising a target sequence. In specific embodiments, the RGNs are directed to a target sequence (e.g., target DNA sequence) by a guide RNA (gRNA) as part of a CRISPR RGN system. The RGNs are considered “RNA-guided” because guide RNAs form a complex with the RGNs to direct the RGN to bind to a target sequence and, in some embodiments, introduce a double-stranded break at the target sequence (e.g., target DNA sequence), whereas in other embodiments, introduce a single- stranded break (“nick”) at the target sequence (e.g., target DNA sequence). After the target sequence has been cleaved, the break can be repaired such that the sequence of the target polynucleotide is modified during the repair process. Thus, provided herein are methods for using the RGNs to modify a target polynucleotide in a host cell. For example, RGNs can be used to modify a target sequence at a genomic locus of eukaryotic cells or prokaryotic cells. Also provided herein are polymerase editors, polymerase editor systems, and methods of using the same for editing a target DNA molecule, wherein the polymerase editor systems comprise a DNA polymerase and the novel RGN LPG10221 (set forth as SEQ ID NO: 1) as described herein, or an active variant or fragment thereof, the novel RGN LPG10209 (set forth as SEQ ID NO: 579) as described herein, or an active variant or fragment thereof, the novel RGN LPG10210 (set forth as SEQ ID NO: 584) as described herein, or an active variant or fragment thereof, the novel RGN LPG10212 (set forth as SEQ ID NO: 583) as described herein, or an active variant or fragment thereof, the novel RGN LPG10213 (set forth as SEQ ID NO: 591) as described herein, or an active variant or fragment thereof, the RGN APG05586 (set forth as SEQ ID NO: 2 and previously described in International Appl. Publ. No. WO 2021 / 217002, which is herein incorporated by reference in its 3 Atty Dkt No: L1034381390WO (0330.1) entirety) or an active variant or fragment thereof, the RGN APG07433.1 (set forth as SEQ ID NO: 7 and previously described in International Appl. Publ. No. WO 2019 / 236566, which is herein incorporated by reference in its entirety) or an active variant or fragment thereof, the RGN APG01604 (set forth as SEQ ID NO: 565 and previously described in International Appl. Publ. No. WO 2021 / 217002, which is herein incorporated by reference in its entirety) or an active variant or fragment thereof, or the RGN LPG10145 (set forth as SEQ ID NO: 566 and previously described in International Appl. Publ. No. WO 2023 / 139557, which is herein incorporated by reference in its entirety) or an active variant or fragment thereof, such as those RGN LPG10145 variants set forth as SEQ ID NOs: 1165-1179 and previously described in U.S. Provisional Appl. No.63 / 516,127, filed July 27, 2023, which is herein incorporated by reference in its entirety. As used herein, a “polymerase editor” or “PE” refers to a protein or a plurality of proteins comprising an RGN and a polymerase that, along with a polymerase editing guide RNA (PEgRNA) that comprises an extension arm comprising a primer binding site (PBS) and a DNA synthesis template comprising a desired edit, is capable of editing a double-stranded polynucleotide through the replacement of a target sequence using the DNA synthesis template as a template for the polymerase. In certain embodiments, the RGN and the polymerase are operably linked (by fusion or insertion). In other embodiments, the RGN and the polymerase are not operably linked. In one particular embodiment, the RGN and the polymerase are two separate polypeptides. In some embodiments, the polymerase editor does not require the introduction of a double-stranded break, but rather utilizes an RGN nickase that nicks the non-target strand upstream of the sequence to be edited and upstream of the PAM, creating a 3' flap on the non-target strand. The PBS of the PEgRNA is complementary to the 3' flap of the non-target strand and hybridrization of the PBS and 3' flap of the non-target strand allows for the polymerization of the replacement strand containing the edit using the DNA synthesis template and polymerase. Those polymerase editors that utilize a reverse transcriptase as the polymerase are referred to herein as “RT editors” or “RTEs”. II. Polymerase Editors The presently disclosed polymerase editors comprise a polymerase (e.g., reverse transcriptase) and an RGN polypeptide. The polymerase (e.g., reverse transcriptase) includes but is not limited to the polymerases (e.g., reverse transcriptases) described herein and variants or fragments thereof, including but not limited to a reverse transcriptase having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or more identity to any one of SEQ ID NOs: 174, 175, and 2127-2131. The RGN can include, but is not limited to the RGNs described herein and variants or fragments thereof, including but not limited to an RGN having at least 50%, at least 60%, at least 70%, at least 80%, at 4 Atty Dkt No: L1034381390WO (0330.1) least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or more identity to SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179. A. RNA-guided nucleases The polymerase editors (PEs) or PE systems disclosed herein include the LPG10221, LPG10209, LPG10210, LPG10212, and LPG10213 (all described in more detail herein), APG07433.1, APG05586, LPG10145, and APG01604 RGNs or active variants or fragments thereof that retain the ability to bind to a target sequence in an RNA-guided sequence-specific manner. In some of these embodiments, the active fragment or variant of the LPG10221, LPG10209, LPG10210, LPG10212, LPG10213, APG07433.1, APG05586, LPG10145, and APG01604 RGN is capable of cleaving a single strand of a double-stranded target sequence. In some embodiments, an active variant of the LPG10221, LPG10209, LPG10210, LPG10212, LPG10213 APG05586, APG07433.1, LPG10145, and APG01604 RGN comprises an amino acid sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179, respectively. In some embodiments, the PE or PE system comprises an active variant of the LPG10221 RGN that comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10221 RGN comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10221 RGN comprises an amino acid sequence having at least 98% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10221 RGN comprises an amino acid sequence having at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, the PE or PE system comprises an active variant of the LPG10209 RGN that comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 579 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10209 RGN comprises an amino acid sequence having at least 95% 5 Atty Dkt No: L1034381390WO (0330.1) sequence identity to the amino acid sequence set forth in SEQ ID NO: 579 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10209 RGN comprises an amino acid sequence having at least 98% sequence identity to the amino acid sequence set forth in SEQ ID NO: 579 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA- guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10209 RGN comprises an amino acid sequence having at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NO: 579 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, the PE or PE system comprises an active variant of the LPG10210 RGN that comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 584 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10210 RGN comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth in SEQ ID NO: 584 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10210 RGN comprises an amino acid sequence having at least 98% sequence identity to the amino acid sequence set forth in SEQ ID NO: 584 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA- guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10210 RGN comprises an amino acid sequence having at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NO: 584 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, the PE or PE system comprises an active variant of the LPG10212 RGN that comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 583 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10212 RGN comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth in SEQ ID NO: 583 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10212 RGN comprises an amino acid sequence having at least 98% sequence identity to the amino acid sequence set forth in SEQ ID NO: 583 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA- guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10212 RGN comprises an amino acid sequence having at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NO: 583 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. 6 Atty Dkt No: L1034381390WO (0330.1) In some embodiments, the PE or PE system comprises an active variant of the LPG10213 RGN that comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 591 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10213 RGN comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth in SEQ ID NO: 591 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10213 RGN comprises an amino acid sequence having at least 98% sequence identity to the amino acid sequence set forth in SEQ ID NO: 591 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA- guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10213 RGN comprises an amino acid sequence having at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NO: 591 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, the PE or PE system comprises an active variant of the APG05586 RGN that comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 2 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the APG05586 RGN comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth in SEQ ID NO: 2 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the APG05586 RGN comprises an amino acid sequence having at least 98% sequence identity to the amino acid sequence set forth in SEQ ID NO: 2 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the APG05586 RGN comprises an amino acid sequence having at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NO: 2 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, the PE or PE system comprises an active variant of the APG07433.1 RGN that comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 7 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the APG07433.1 RGN comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth in SEQ ID NO: 7 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the APG07433.1 RGN comprises an amino acid sequence having at least 98% sequence identity to the amino acid sequence set forth in SEQ ID NO: 7 7 Atty Dkt No: L1034381390WO (0330.1) and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the APG07433.1 RGN comprises an amino acid sequence having at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NO: 7 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, the PE or PE system comprises an active variant of the LPG10145 RGN that comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 566 or 1165-1179 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10145 RGN comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth in SEQ ID NO: 566 or 1165-1179 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10145 RGN comprises an amino acid sequence having at least 98% sequence identity to the amino acid sequence set forth in SEQ ID NO: 566 or 1165-1179 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the LPG10145 RGN comprises an amino acid sequence having at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NO: 566 or 1165-1179 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 566, it comprises at least one of the following amino acid residues: a) an R at a position corresponding to amino acid position 55 in SEQ ID NO: 566; b) an R at a position corresponding to amino acid position 647 in SEQ ID NO: 566; c) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 566; d) an R at a position corresponding to amino acid position 822 in SEQ ID NO: 566; e) an R at a position corresponding to amino acid position 856 in SEQ ID NO: 566; and f) an R at a position corresponding to amino acid position 969 in SEQ ID NO: 566. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1165, it comprises: a) an R at a position corresponding to amino acid position 55 in SEQ ID NO: 1165; b) an R at a position corresponding to amino acid position 647 in SEQ ID NO: 1165; c) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1165; and d) an R at a position corresponding to amino acid position 969 in SEQ ID NO: 1165. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1166, it comprises: 8 Atty Dkt No: L1034381390WO (0330.1) a) an R at a position corresponding to amino acid position 647 in SEQ ID NO: 1166; b) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1166; c) an R at a position corresponding to amino acid position 856 in SEQ ID NO: 1166; and d) an R at a position corresponding to amino acid position 969 in SEQ ID NO: 1166. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1167, it comprises: a) an R at a position corresponding to amino acid position 55 in SEQ ID NO: 1167; b) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1167; c) an R at a position corresponding to amino acid position 856 in SEQ ID NO: 1167; and d) an R at a position corresponding to amino acid position 969 in SEQ ID NO: 1167. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1168, it comprises: a) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1168; b) an R at a position corresponding to amino acid position 856 in SEQ ID NO: 1168; and c) an R at a position corresponding to amino acid position 969 in SEQ ID NO: 1168. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1169, it comprises: a) an R at a position corresponding to amino acid position 55 in SEQ ID NO: 1169; b) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1169; and c) an R at a position corresponding to amino acid position 969 in SEQ ID NO: 1169. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1170, it comprises: a) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1170; and b) an R at a position corresponding to amino acid position 969 in SEQ ID NO: 1170. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1171, it comprises: a) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1171; and b) an R at a position corresponding to amino acid position 856 in SEQ ID NO: 1171. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1172, it comprises: a) an R at a position corresponding to amino acid position 55 in SEQ ID NO: 1172; b) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1172; and c) an R at a position corresponding to amino acid position 822 in SEQ ID NO: 1172. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1173, it comprises: a) an R at a position corresponding to amino acid position 55 in SEQ ID NO: 1173; b) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1173; and 9 Atty Dkt No: L1034381390WO (0330.1) c) an R at a position corresponding to amino acid position 822 in SEQ ID NO: 1173. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1174, it comprises: a) an R at a position corresponding to amino acid position 55 in SEQ ID NO: 1174; b) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1174; c) an R at a position corresponding to amino acid position 822 in SEQ ID NO: 1174; and d) an R at a position corresponding to amino acid position 969 in SEQ ID NO: 1174. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1175, it comprises: a) an R at a position corresponding to amino acid position 55 in SEQ ID NO: 1175; b) an R at a position corresponding to amino acid position 647 in SEQ ID NO: 1175; c) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1175; and d) an R at a position corresponding to amino acid position 822 in SEQ ID NO: 1175. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1176, it comprises: a) an R at a position corresponding to amino acid position 55 in SEQ ID NO: 1175; b) an R at a position corresponding to amino acid position 674 in SEQ ID NO: 1175; c) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1175; d) an R at a position corresponding to amino acid position 822 in SEQ ID NO: 1175; and e) an R at a position corresponding to amino acid position 969 in SEQ ID NO: 1175. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1177, it comprises: a) an R at a position corresponding to amino acid position 647 in SEQ ID NO: 1177; b) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1177; c) an R at a position corresponding to amino acid position 822 in SEQ ID NO: 1177; and d) an R at a position corresponding to amino acid position 969 in SEQ ID NO: 1177. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1178, it comprises: a) an R at a position corresponding to amino acid position 647 in SEQ ID NO: 1178; b) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1178; and c) an R at a position corresponding to amino acid position 822 in SEQ ID NO: 1178. In embodiments wherein the PE or PE system comprises an RGN having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1179, it comprises: a) an R at a position corresponding to amino acid position 55 in SEQ ID NO: 1179; b) an R at a position corresponding to amino acid position 647 in SEQ ID NO: 1179; c) an R at a position corresponding to amino acid position 778 in SEQ ID NO: 1179; d) an R at a position corresponding to amino acid position 822 in SEQ ID NO: 1179; and 10 Atty Dkt No: L1034381390WO (0330.1) e) an R at a position corresponding to amino acid position 856 in SEQ ID NO: 1179. In some embodiments, the PE or PE system comprises an active variant of the APG01604 RGN that comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth in SEQ ID NO: 565 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the APG01604 RGN comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth in SEQ ID NO: 565 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. In some embodiments, an active variant of the APG01604 RGN comprises an amino acid sequence having at least 98% sequence identity to the amino acid sequence set forth in SEQ ID NO: 565 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA- guided sequence-specific nicking activity. In some embodiments, an active variant of the APG01604 RGN comprises an amino acid sequence having at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NO: 565 and retains RNA-guided sequence-specific binding activity, and in some embodiments, RNA-guided sequence-specific nicking activity. The PE or PE system can comprise an active fragment of the LPG10221, APG07433.1, APG05586, APG01604, LPG10145, LPG10209, LPG10212, LPG10210, or LPG10213 RGN that comprises at least 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, or more contiguous amino acid residues of the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179, respectively. A PE or PE system of the disclosure comprises an RGN that binds to a target sequence, e.g., such as those that are disclosed herein. In some embodiments, the PE or PE system comprises an RGN, or an active variant or fragment thereof, that recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNNNCY 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G and wherein Y is C or T / U). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 1 (LPG10221), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNCY 3' of the target sequence on its non-target strand. A PE or PE system of the disclosure comprises an RGN that binds to a target sequence, e.g., such as those that are disclosed herein. In some embodiments, the PE or PE system comprises an RGN, or an active variant or fragment thereof, that recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNNNC 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 579 (LPG10209), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNC 3' of the target sequence on its non-target strand. In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 583 (LPG10212), or an active variant 11 Atty Dkt No: L1034381390WO (0330.1) or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNC 3' of the target sequence on its non-target strand. A PE or PE system of the disclosure comprises an RGN that binds to a target sequence, e.g., such as those that are disclosed herein. In some embodiments, the PE or PE system comprises an RGN, or an active variant or fragment thereof, that recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNNNCM 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G and wherein M is C or A). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 584 (LPG10210), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNCM 3' of the target sequence on its non-target strand. A PE or PE system of the disclosure comprises an RGN that binds to a target sequence, e.g., such as those that are disclosed herein. In some embodiments, the PE or PE system comprises an RGN, or an active variant or fragment thereof, that recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNNNCT 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 591 (LPG10213), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNCT 3' of the target sequence on its non-target strand. A PE or PE system of the disclosure comprise an RGN that binds to a target sequence, e.g., such as those that are disclosed herein. In some embodiments, the PE or PE system comprises an RGN, or an active variant or fragment thereof, that recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNRYA 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G, R is G or A, and Y is C or T / U). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 2 (APG05586), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNRYA 3' of the target sequence on its non-target strand. A PE or PE system of the disclosure comprise an RGN that binds to a target sequence, e.g., such as those that are disclosed herein. In some embodiments, the PE or PE system comprises an RGN, or an active variant or fragment thereof, that recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNNNCC 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G, R is G or A, and Y is C or T / U). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 7 (APG07743.1), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNCC 3' of the target sequence on its non-target strand. A PE or PE system of the disclosure comprise an RGN that binds to a target sequence, e.g., such as those that are disclosed herein. In some embodiments, the PE or PE system comprises an RGN, or an active variant or fragment thereof, that recognizes a protospacer adjacent motif (PAM) 12 Atty Dkt No: L1034381390WO (0330.1) having a consensus nucleotide sequence of NNGRR 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G, R is G or A, and R is A or G). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 565 (APG01604), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNGRR 3' of the target sequence on its non-target strand. A PE or PE system of the disclosure comprise an RGN that binds to a target sequence, e.g., such as those that are disclosed herein. In some embodiments, the PE or PE system comprises an RGN, or an active variant or fragment thereof, that recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNGG 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G, R is G or A). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 566 (LPG10145) or 1165-1179, or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNGG 3' of the target sequence on its non-target strand. As used herein in reference to a PAM recognition nucleotide motif, Y refers to cytosine (C) or thymine / uracil (T / U); N refers to adenine (A) or cytosine (C) or thymine / uracil (T / U) or guanine (G); R refers to adenine (A) or guanine (G); V refers to adenine (A) or cytosine (C) or guanine (G); M refers to adenine (A) or cytosine (C). In some embodiments, an active fragment or variant of an RGN recognizing such PAM sequences is capable of binding and in some embodiments, cleaving or nicking a target sequence. A PE or PE system of the disclosure can comprise an RGN, or an active variant or fragment thereof, that has a PAM-interacting (PI) domain that contributes to recognition of a PAM site in a target polynucleotide. The PI domain can comprise 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150 or more amino acid residues. In some embodiments, the PI domain of an RGN, or an active variant or fragment thereof, of the disclosure is located within the carboxy (C)-terminal region of the RGN. The C-terminal region comprising the PI domain of an RGN, or an active variant or fragment thereof, of the disclosure can include the C- terminal 151 amino acid residues, the C-terminal 150 amino acid residues, the C-terminal 140 amino acid residues, the C-terminal 135 amino acid residues, the C-terminal 132 amino acid residues, the C- terminal 130 amino acid residues, the C-terminal 125 amino acid residues, the C-terminal 120 amino acid residues, the C-terminal 110 amino acid residues, the C-terminal 100 amino acid residues, the C- terminal 90 amino acid residues, the C-terminal 80 amino acid residues, the C-terminal 70 amino acid residues, the C-terminal 60 amino acid residues, the C-terminal 50 amino acid residues, the C- terminal 40 amino acid residues, the C-terminal 30 amino acid residues, the C-terminal 20 amino acid residues, or the C-terminal 10 amino acid residues of the RGN. In some embodiments, the PI domain of an RGN, or an active variant or fragment thereof, of the disclosure is within or includes amino acid residues 939-1071 or 999-1150 of the RGN. In some embodiments, the PI domain of an RGN having the amino acid sequence set forth as SEQ ID NO: 1, 7, 565, 566, 579, 583, 584, 591, or 1165-1179, or 13 Atty Dkt No: L1034381390WO (0330.1) an active variant or fragment thereof, is within or includes amino acid residues 939-1071 of the RGN. In some embodiments, the PI domain of an RGN having at least 90% sequence identity to any one of SEQ ID NOs: 1, 7, 579, 583, 584, or 591 has the amino acid sequence set forth as SEQ ID NO: 575. In some embodiments, the PI domain of an RGN having the amino acid sequence set forth as SEQ ID NO: 2, or an active variant or fragment thereof, is within or includes amino acid residues 999-1150 of the RGN. In some embodiments, the PI domain of an RGN having at least 90% sequence identity to SEQ ID NO: 2 has the amino acid sequence set forth as SEQ ID NO: 1186. In some embodiments, the PI domain of an RGN having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 565 has the amino acid sequence set forth as SEQ ID NO: 1187. In some embodiments, the PI domain of an RGN having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 566 or 1165-1179 has the amino acid sequence set forth as SEQ ID NO: 1188. A PE or PE system provided herein can comprise an RGN comprising at least one nuclease domain (e.g., DNase, RNase domain) and at least one RNA recognition and / or RNA binding domain to interact with guide RNAs. In some embodiments, the RGN of the PE or PE system comprises only one active nuclease domain and thus functions as a nickase. In some embodiments, the RGN nuclease domain that is active is an RGN nickase is a RuvC domain. In some embodiments, the RGN comprises an inactivated HNH nuclease domain. Further domains that can be found in RGNs include, but are not limited to: DNA binding domains, helicase domains, protein-protein interaction domains, and dimerization domains. In some embodiments, the RGNs can comprise at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to one or more of a DNA binding domain, helicase domain, protein-protein interaction domain, and dimerization domain. In various embodiments, a target sequence is bound by an RGN of a PE or PE system provided herein. In those instances wherein the target sequence is double-stranded (e.g., double- stranded DNA), the target strand of the target sequence hybridizes with the guide RNA associated with the RGN. The target strand and / or the non-target strand of the target sequence (e.g., target DNA sequence) can then be subsequently cleaved by the RGN if the polypeptide possesses nuclease activity. The terms “cleave” or “cleavage” refer to the hydrolysis of at least one phosphodiester bond within the backbone of one or both strands of a double-stranded target sequence (e.g., target DNA sequence) that can result in either single-stranded or double-stranded breaks within the target sequence. RGNs can cleave nucleotides within a polynucleotide, functioning as an endonuclease or can be an exonuclease, removing successive nucleotides from the end (the 5' and / or the 3' end) of a polynucleotide. In some embodiments, RGNs can cleave nucleotides of a target polynucleotide within any position of a polynucleotide and thus function as both an endonuclease and exonuclease. The cleavage of a target polynucleotide by RGNs can result in staggered breaks or blunt ends. A staggered cut in a polynucleotide leads to two sticky ends or overhanging ends, and is formed when the nuclease 14 Atty Dkt No: L1034381390WO (0330.1) cuts each strand of a polynucleotide such that the cuts are not directly opposite each other. For each sticky end of the cut polynucleotide, one strand (i.e. the overhanging strand) is longer than the other (typically by at least a few nucleotides), such that the longer strand has bases which are left unpaired. The longer strand of an overhanging end of a cleaved polynucleotide can have one unpaired nucleotide, two unpaired nucleotides, 3 unpaired nucleotides, 4 unpaired nucleotides, 5 unpaired nucleotides, or more unpaired nucleotides. In some embodiments, the longer strand of an overhanging end of a cleaved polynucleotide can have one unpaired nucleotide. The overhanging end of a cleaved polynucleotide can be a 3′ overhang or a 5′ overhang. In some embodiments, the overhanging end of a cleaved polynucleotide is a 3′ overhang. In some embodiments, the overhanging end of a cleaved polynucleotide is a 5′ overhang. In some embodiments, an RGN, or an active variant or fragment thereof, of the disclosure cleaves a target polynucleotide to form a staggered cut, wherein the staggered cut creates a 3′ overhang with one unpaired nucleotide. By contrast, a blunt cut generates two blunt ends, such that each blunt end of the cut polynucleotide has both strands that are of equal length – i.e. there are no unpaired bases on either strand of a blunt end. RGNs of the presently disclosed PEs and PE systems can be wild-type sequences derived from bacterial or archaeal species. Alternatively, the RGNs can be variants or fragments of wild-type polypeptides. The wild-type RGN can be modified to alter nuclease activity or alter PAM specificity, for example. In some embodiments, the RGN is not naturally-occurring. In some embodiments, the RGNs of the presently disclosed PEs and PE systems function as a nickase, only cleaving a single strand of a double-stranded target sequence (e.g., target DNA sequence). Such RGNs have a single functioning nuclease domain. In particular embodiments, the nickase is capable of cleaving the target strand (has an active HNH domain) or the non-target strand (has an active RuvC domain) of the double-stranded target sequence (e.g., target DNA sequence). In order to effect the nicking of a single strand of a double-stranded target polynucleotide (e.g., target DNA), at least one inactivating mutation (also referred to herein as a mutation that reduces nuclease activity) can be introduced into a nuclease domain of an RGN. For example, in order to reduce the activity of or inactivate the HNH domain of LPG10221, APG07433.1, LPG10209, LPG10210, LPG10212, or LPG10213, one or more of the following catalytic amino acid residues can be mutated to an alanine, for example, or another non-conserved amino acid residue: D603, H604, N618, N627. In order to reduce the activity of or inactivate the HNH domain of APG05586, one or more of the following catalytic amino acid residues can be mutated to an alanine, for example, or another non- conserved amino acid residue: D600, H601, N615, N624. More than one mutation that reduces nuclease activity can be introduced into a nuclease domain of an RGN in order to further reduce or eliminate its activity. Thus, in some embodiments, the HNH nuclease domain of an RGN of a PE or PE system comprises an alanine (or another non-conserved amino acid residue) at a position corresponding to 604 and an alanine (or another non-conserved amino acid residue) at a position corresponding to 627 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; an alanine (or another non- 15 Atty Dkt No: L1034381390WO (0330.1) conserved amino acid residue) at a position corresponding to 601 and an alanine (or another non- conserved amino acid residue) at a position corresponding to 624 of SEQ ID NO: 2; an alanine (or another non-conserved amino acid residue) at a position corresponding to 559 and an alanine (or another non-conserved amino acid residue) at a position corresponding to 582 of SEQ ID NO: 565; or an alanine (or another non-conserved amino acid residue) at a position corresponding to 611 and an alanine (or another non-conserved amino acid residue) at a position corresponding to 634 of SEQ ID NO: 566 or 1165-1179. Non-limiting examples of DNA constructs encoding a PE comprising an RGN nickase with double mutations within the HNH domain are set forth as SEQ ID NO: 1182 (comprising APG07433.1 HNH double mutant) and 1183 (comprising APG05586 HNH double mutant). In some embodiments, the RGN nickase comprises the sequence set forth as SEQ ID NO: 8, 106, 365, 367, 368, 396, 567, 568, 569, or 570, or an active fragment or variant thereof, such as one having at least at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one of SEQ ID NOs: 8, 106, 365, 367, 368, 396, 567, 568, 569, or 570. RGN nickases with inactivated HNH domains can be used for polymerase editing and can be fused to a polymerase as described herein. In some embodiments, all or part of an HNH domain of an RGN polypeptide is replaced with a polymerase (e.g., DNA polymerase) to generate a PE. In other embodiments, the RGN of the presently disclosed PEs and PE systems lacks nuclease activity altogether and is referred to herein as nuclease-dead or nuclease inactive. In some embodiments, nuclease-dead or nuclease inactive versions of the enzymes are used for modifying a nucleic acid, such as in base editing as described herein. Any method known in the art for introducing mutations into an amino acid sequence, such as PCR-mediated mutagenesis and site-directed mutagenesis, can be used for generating nickases or nuclease-dead RGNs. See, e.g., U.S. Publ. No. 2014 / 0068797 and U.S. Pat. No.9,790,490; each of which is incorporated by reference in its entirety. B. Polymerase Provided herein are polymerases (e.g., DNA polymerases, reverse transcriptases, etc.) that can be used in the described PEs or PE systems. As used herein, a “polymerase” is an enzyme that catalyzes the formation of a nucleic acid polymer. A polymerase can be an RNA polymerase (catalyzing an RNA polymer) or a DNA polymerase (catalyzing a DNA polymer). In some embodiments, the polymerase of the polymerase editor or system is a DNA polymerase. The PE or PE system can comprise a DNA-dependent DNA polymerase (uses DNA as a template) or an RNA- dependent DNA polymerase (uses RNA as a template). In some embodiments, the DNA polymerase of the presently disclosed PEs and PE systems is an RNA-dependent DNA polymerase (i.e., reverse transcriptase). The reverse transcriptase used in the presently disclosed compositions and methods can be any known in the art, including but not limited to that of the Moloney murine leukemia virus 16 Atty Dkt No: L1034381390WO (0330.1) (MMLV), the sequence of which is set forth as SEQ ID NO: 174, or an active variant thereof, such as one having at least at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 174. A MMLV RT having any one of the following mutations can also be used in the presently disclosed PEs or PE systems: D200N, L603W, T330P, T306K, and W313F. Thus, the PEs or PE system can comprise an RT having at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 174, wherein the RT comprises at least one of the following amino acid residues: a) an N at a position corresponding to 200 of SEQ ID NO: 174, b) a W at a position corresponding to position 603 of SEQ ID NO: 174, c) a P at a position corresponding to position 330 of SEQ ID NO: 174, d) a K at a position corresponding to position 306 of SEQ ID NO: 174, and e) an F at a position corresponding to 313 of SEQ ID NO: 174. A reverse transcriptase can be used wherein the RNase H domain (which is a processive 5’ and 3’ ribonuclease specific for the RNA strand of RNA-DNA hybrids) has been inactivated or removed. In some embodiments, the reverse transcriptase lacks the RNase H domain, wherein it is truncated immediately after an amino acid at a position corresponding to 497 in SEQ ID NO: 174. Thus, the RT of the presently disclosed PEs and PE systems can have at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 175. An RT of the presently disclosed PEs and PE systems can have at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one of SEQ ID NOs: 2127-2131. In some embodiments, an RT of the presently disclosed PEs and PE systems has an amino acid sequence set forth as any one of SEQ ID NOs: 2127-2131. C. Various Formats of Polymerase Editors The presently disclosed polymerase editors can be provided in trans, wherein the polymerase (e.g., reverse transcriptase) and RGN are two separate polypeptides. In some embodiments, the polymerase (e.g., reverse transcriptase) and the RGN polypeptide are transcribed together and have a sequence encoding a self-cleaving peptide (e.g., 2A peptide such as P2A) in between, such that translation results in two separate polypeptides. Any self-cleaving peptide known in the art can be used in such embodiments, including but not limited to, 2A peptides, which is a class of 18-22 amino acid long peptides that may function through ribosomal skipping during translation. Non-limiting examples of 2A peptides are T2A, P2A, E2A, and F2A. Alternatively, the presently disclosed polymerase editors can comprise a polymerase operably fused to an RGN, wherein the polymerase and RGN are fused to each other end-to-end or wherein the polymerase is inserted into the RGN polypeptide, such as those inlaid base editors described in International Appl. No. PCT / IB2023 / 061192 filed November 6, 2023, which is herein incorporated by reference in its entirety. In an end-to-end fusion, the polymerase can be fused to the amino terminus 17 Atty Dkt No: L1034381390WO (0330.1) of the RGN or the carboxy terminus of the RGN. The term “inserted into” or “inserted within” refers to a polypeptide (e.g., polymerase) being located at or present within a specified location of the polypeptide (e.g., RGN) that it is inserted into. For example, a DNA polymerase inserted within an RGN polypeptide of SEQ ID NO: 2 at amino acid position corresponding to position 678 of SEQ ID NO: 2 means the DNA polymerase is located or present at that position. In those embodiments wherein the polymerase (e.g., reverse transcriptase) is inserted within an RGN polypeptide, the polymerase is inserted between surface amino acid residues. The polymerase can be inserted within or between a linker domain 2, a wedge (WED) domain, a RuvC domain, an HNH domain, a Rec-2 domain, or a PAM-interacting (PI) domain. In some embodiments, the RuvC domain is the RuvCIII domain. A Rec or recognition lobe mediates nucleic acid binding through multiple Rec domains (e.g., Rec1-3) by sensing nucleic acids, regulates the HNH conformational transition, and locks the catalytic HNH domain at the cleavage site. A wedge domain is responsible for the recognition of guide RNA scaffolds. Non-limiting examples of domains within an RGN include: RuvC-I from amino acid residues 1-54; BH from amino acid residues 55-83; REC1 from amino acid residues 84-244; REC2 from amino acid residues 245-462; RuvC-II from amino acid residues 463-521; L1 from amino acid residues 522-552; HNH from amino acid residues 553-672; L2 from amino acid residues 673-685; RuvC-III from amino acid residues 686-833; WED from amino acid residues 834-938; and PI from amino acid residues 939-1071; all in reference to LPG10221, APG07433.1, LPG10209, LPG10210, LPG10212, or LPG10213, which are set forth as SEQ ID NOs: 1, 7, 579, 584, 583, and 591, respectively. APG05586 (set forth as SEQ ID NO: 2) has the following domains: RuvC-I from amino acid residues 1-33; BH from amino acid residues 34-71; REC1 from amino acid residues 72-232; REC2 from amino acid residues 233-468; RuvC-II from amino acid residues 469-517; L1 from amino acid residues 518-552; HNH from amino acid residues 553-672; L2 from amino acid residues 673-687; RuvC-III from amino acid residues 688-837; WED from amino acid residues 838-998; and PI from amino acid residues 999-1150. LPG10145 (set forth as SEQ ID NO: 566) and variants thereof (set forth as SEQ ID NOs: 1165-1179) have the following domains: RuvC-I from amino acid residues 1-42; BH from amino acid residues 43-79; REC1 from amino acid residues 80-236; REC2 from amino acid residues 237-476; RuvC-II from amino acid residues 477- 524; L1 from amino acid residues 525-560; HNH from amino acid residues 561-676; L2 from amino acid residues 677-690; RuvC-III from amino acid residues 691-828; WED from amino acid residues 829-976; and PI from amino acid residues 977-1130. APG01604 (set forth as SEQ ID NO: 565) has the following domains: RuvC-I from amino acid residues 1-40; BH from amino acid residues 41-74; REC1 from amino acid residues 75-223; REC2 from amino acid residues 224-430; RuvC-II from amino acid residues 431-483; L1 from amino acid residues 484-516; HNH from amino acid residues 517-631; L2 from amino acid residues 632-651; RuvC-III from amino acid residues 652-775; WED from amino acid residues 776-909; and PI from amino acid residues 910-1052. 18 Atty Dkt No: L1034381390WO (0330.1) A PAM-interacting domain is the domain that binds to the PAM sequence. The general domains of RGN proteins can be determined via structural comparison to RGN proteins with defined domains. In those embodiments wherein the PE comprises an RGN having at least 90% sequence identity to SEQ ID NO: 1 or 7, the polymerase can be inserted within the RGN immediately after the amino acid position selected from the group consisting of: i) amino acid position corresponding to position 30 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; ii) amino acid position corresponding to position 642 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; iii) amino acid position corresponding to position 670 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; iv) amino acid position corresponding to position 737 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; v) amino acid position corresponding to position 772 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; vi) amino acid position corresponding to position 775 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; vii) amino acid position corresponding to position 778 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; viii) amino acid position corresponding to position 802 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; ix) amino acid position corresponding to position 900 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; and x) amino acid position corresponding to position 910 of SEQ ID NO: 1, 7, 579, 583, 584, or 591. In those embodiments wherein the PE comprises an RGN having at least 90% sequence identity to SEQ ID NO: 2, the polymerase can be inserted within the RGN immediately after the amino acid position selected from the group consisting of: i) amino acid position corresponding to position 342 of SEQ ID NO: 2; ii) amino acid position corresponding to position 518 of SEQ ID NO: 2; iii) amino acid position corresponding to position 630 of SEQ ID NO: 2; iv) amino acid position corresponding to position 661 of SEQ ID NO: 2; v) amino acid position corresponding to position 678 of SEQ ID NO: 2; vi) amino acid position corresponding to position 736 of SEQ ID NO: 2; vii) amino acid position corresponding to position 778 of SEQ ID NO: 2; viii) amino acid position corresponding to position 788 of SEQ ID NO: 2; 19 Atty Dkt No: L1034381390WO (0330.1) ix) amino acid position corresponding to position 922 of SEQ ID NO: 2; and x) amino acid position corresponding to position 1109 of SEQ ID NO: 2. In those embodiments wherein the PE comprises an RGN having at least 90% sequence identity to SEQ ID NO: 565, the polymerase can be inserted within the RGN immediately after the amino acid position selected from the group consisting of: i) amino acid position corresponding to position 597 of SEQ ID NO: 565; ii) amino acid position corresponding to position 631 of SEQ ID NO: 565; iii) amino acid position corresponding to position 725 of SEQ ID NO: 565; iv) amino acid position corresponding to position 739 of SEQ ID NO: 565; and v) amino acid position corresponding to position 744 of SEQ ID NO: 565. In those embodiments wherein the PE comprises an RGN having at least 90% sequence identity to SEQ ID NO: 566 or 1165-1179, the polymerase can be inserted within the RGN immediately after the amino acid position selected from the group consisting of: i) amino acid position corresponding to position 347 of SEQ ID NO: 566 or 1165-1179; ii) amino acid position corresponding to position 524 of SEQ ID NO: 566 or 1165-1179; iii) amino acid position corresponding to position 640 of SEQ ID NO: 566 or 1165-1179; iv) amino acid position corresponding to position 666 of SEQ ID NO: 566 or 1165-1179; v) amino acid position corresponding to position 680 of SEQ ID NO: 566 or 1165-1179; vi) amino acid position corresponding to position 740 of SEQ ID NO: 566 or 1165-1179; vii) amino acid position corresponding to position 785 of SEQ ID NO: 566 or 1165-1179; viii) amino acid position corresponding to position 910 of SEQ ID NO: 566 or 1165-1179; and ix) amino acid position corresponding to position 1077 of SEQ ID NO: 566 or 1165- 1179. The polymerase may be fused directly to the RGN polypeptide or a linker sequence can connect the polymerase and the RGN polypeptide. In those embodiments wherein the polymerase is inserted into the RGN polypeptide, there can be linker sequences on one or both ends of the polymerase sequence. Any suitable linker sequence can be used to connect the polymerase and RGN polypeptide (or a fragment thereof), but one suitable linker sequence comprises one or more copies of SGGS (SEQ ID NO: 2126). In some embodiments, the linker sequence comprises 1 SGGS sequence, 2 SGGS sequences (SEQ ID NO: 2120), 3 SGGS sequences, 4 SGGS sequences, or more, such that the linker sequence can be 4, 8, 12, or 16 amino acids long. The linker between the polymerase and RGN (or fragments thereof) can be 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, or more nucleotides in length. The linker sequence separating the polymerase and RGN (or a fragment thereof) can also comprise a nuclear localization sequence (NLS), such as but not limited to those disclosed elsewhere 20 Atty Dkt No: L1034381390WO (0330.1) herein, namely any one of SEQ ID NOs: 107, 108, 109, 2086-2101, 2118, and 2119, wherein the nuclear localization sequences can be connected by linkers (such as SGGS). In some embodiments, the linker sequence separating the polymerase and RGN (or a fragment thereof) comprises more than one nuclear localization sequences, such as 2, 3, or more nuclear localization sequences. In some embodiments, a linker has a formula of -(SGGS)x-NLSm-(SGGS)y-NLSn-(SGGS)z-, wherein each of x, y, or z is 0, 1, 2, 3, or 4; and wherein each of m or n is 0 or 1. In certain embodiments, the linker has a formula of -(SGGS)x-NLSm-(SGGS)y-NLSn-(SGGS)z-, wherein each of x or z is 0, 1, 2, 3, or 4, and y is 0; and wherein one of m or n is 0, and the other is 1. In other embodiments, the linker has a formula of -(SGGS)x-NLSm-(SGGS)y-NLSn-(SGGS)z-, wherein each of x, y, or z is 0, 1, 2, 3, or 4; and wherein each of m or n is 1, and y is not 0. In some embodiments, x, y, or z are not all 0. The presently disclosed RGNs, polymerases, or PEs can comprise at least one nuclear localization signal (NLS) to enhance transport of the protein to the nucleus of a cell. Nuclear localization signals are known in the art and generally comprise a stretch of basic amino acids (see, e.g., Lange et al., J. Biol. Chem. (2007) 282:5101-5105). In some embodiments, the RGN, polymerase, or PE comprises 2, 3, 4, 5, 6 or more nuclear localization signals. The nuclear localization signal(s) can be a heterologous NLS. As used herein, “heterologous”, in reference to a polypeptide that is heterologous to another polypeptide (e.g., polymerase, RGN, PE), is a polypeptide that is not operably fused to the presently described, e.g., polymerases, RGNs, or PEs, in nature. The heterologous polypeptide can originate from a foreign species or from the same species. The heterologous polypeptide can be in its native form or is substantially modified from its native form in composition and / or genomic locus by deliberate human intervention. The heterologous polypeptide can be any polypeptide, including but not limited to a localization signal, cell-penetrating domain, detectable label (e.g., fluorescent protein), or purification tag. Non-limiting examples of nuclear localization signals useful for the presently disclosed RGNs, polymerases, or PEs are the nuclear localization signals of SV40 Large T-antigen, nucleoplasmin, c-Myc (see, e.g., Ray et al. (2015) Bioconjug Chem 26(6):1004-7), ADAR2, POLD1, and the NLSes disclosed in Table 40. In some embodiments, the RGN, polymerase, or PE comprises the NLS sequence set forth as SEQ ID NO: 107, 108, 109, 2086-2101, 2118, and / or 2119. The RGN, polymerase, or PE can comprise one or more NLS sequences at its N-terminus, C- terminus, or both the N-terminus and C-terminus. For example, the RGN, polymerase, or PE can comprise two NLS sequences at the N-terminal region and four NLS sequences at the C-terminal region. As another example, the RGN, polymerase, or PE can comprise one NLS sequence at the N-terminal region and one NLS sequence at the C-terminal region. In some embodiments, a peptide linker (e.g., SGGS (SEQ ID NO: 2126), SGGSSGGS (SEQ ID NO: 2120), etc.) can connect the NLS to the RGN, polymerase, or fusion protein. Other localization signal sequences known in the art that localize polypeptides to particular subcellular location(s) can also be used to target the RGNs, polymerases, or PEs, including, but not 21 Atty Dkt No: L1034381390WO (0330.1) limited to, plastid localization sequences, mitochondrial localization sequences, and dual-targeting signal sequences that target to both the plastid and mitochondria (see, e.g., Nassoury and Morse (2005) Biochim Biophys Acta 1743:5-19; Kunze and Berger (2015) Front Physiol dx.doi.org / 10.3389 / fphys.2015.00259; Herrmann and Neupert (2003) IUBMB Life 55:219-225; Soll (2002) Curr Opin Plant Biol 5:529-535; Carrie and Small (2013) Biochim Biophys Acta 1833:253- 259; Carrie et al. (2009) FEBS J 276:1187-1195; Silva-Filho (2003) Curr Opin Plant Biol 6:589-595; Peeters and Small (2001) Biochim Biophys Acta 1541:54-63; Murcha et al. (2014) J Exp Bot 65:6301- 6335; Mackenzie (2005) Trends Cell Biol 15:548-554; Glaser et al. (1998) Plant Mol Biol 38:311- 338). RGNs, polymerases, or PEs can comprise at least one cell-penetrating domain that facilitates cellular uptake of the RGN, polymerase, or PE. Cell-penetrating domains are known in the art and generally comprise stretches of positively charged amino acid residues (i.e., polycationic cell- penetrating domains), alternating polar amino acid residues and non-polar amino acid residues (i.e., amphipathic cell-penetrating domains), or hydrophobic amino acid residues (i.e., hydrophobic cell- penetrating domains) (see, e.g., Milletti F. (2012) Drug Discov Today 17:850-860). A non-limiting example of a cell-penetrating domain is the trans-activating transcriptional activator (TAT) from the human immunodeficiency virus 1. The nuclear localization signal, plastid localization signal, mitochondrial localization signal, dual-targeting localization signal, and / or cell-penetrating domain can be located at the amino-terminus (N-terminus), the carboxyl-terminus (C-terminus), and / or in an internal location of the RGN, polymerase, or PE. RGNs, polymerases, or PEs can also comprise a purification tag, which is any molecule that can be utilized to isolate a protein or fused protein from a mixture (e.g., biological sample, culture medium). Non-limiting examples of purification tags include biotin, myc, maltose binding protein (MBP), glutathione-S-transferase (GST), and 3X FLAG tag. Non-limiting examples of PEs include those of any one of SEQ ID NOs: 9-11, 111-130, 137- 173, 364, 774-787, 790-814, 817-901, 926, 1143-1155, 1164, 1182-1185, 1189-2085, and 2121-2125 and active variants and fragments thereof, such as one having at least at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one of SEQ ID NOs: 9-11, 111-130, 137-173, 364, 774-787, 790-814, 817-901, 926, 1143-1155, 1164, 1182- 1185, 1189-2085, and 2121-2125. In some embodiments, a PE of the disclosure include those of any one of SEQ ID NOs: 364, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 1432, 1443, 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718, and active variants and fragments thereof, such as one having at least at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one of SEQ ID NOs: 364, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 22 Atty Dkt No: L1034381390WO (0330.1) 1432, 1443, 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718. D. Guide RNA The present disclosure provides guide RNAs and polynucleotides encoding the same that target an associated RNA-guided nuclease (RGN) or a PE comprising such an RGN to a target sequence. The term “guide RNA” refers to a nucleotide sequence having sufficient complementarity with a target nucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of an associated RGN to the target nucleotide sequence. More specifically, when the target nucleotide sequence is double-stranded as is the case with DNA, the target nucleotide sequence comprises a target strand and a non-target strand (which comprises the PAM sequence). In these embodiments, the guide RNA has sufficient complementarity with the target strand of a double- stranded target sequence (e.g., target DNA sequence) such that the guide RNA hybridizes with the target strand and directs sequence-specific binding of an associated RGN to the target sequence (e.g., target DNA sequence). Therefore, in some embodiments, a guide RNA includes a spacer that is identical to the sequence of the non-target strand except that uracil (U) replaces thymidine (T) in the guide RNA. In embodiments where multiplex gene editing is used and there are multiple guide RNAs, each of the one or more guide RNA has sufficient complementarity with the target strand of a particular target sequence and is capable of hybridizing to the target strand of that target sequence. Thus, “a corresponding target sequence” for a guide RNA refers to the target sequence that the guide RNA has sufficient complementarity with and is capable of hybridizing to. An RGN’s respective guide RNA is one or more RNA molecules (generally, one or two), that can bind to the RGN and guide the RGN to bind to a particular target sequence, and in those embodiments wherein the RGN has nickase or nuclease activity, also cleave the target strand and / or the non-target strand. In general, a guide RNA comprises a CRISPR RNA (crRNA) and a trans- activating CRISPR RNA (tracrRNA), although some RGNs do not require a tracrRNA. A guide RNA of the disclosure (e.g., a crRNA) can comprise at least one chemical modification. The at least one chemical modification includes: a bridged nucleic acid (BNA) modification; 2'-O-methyl (2'-O-Me) modification; 2'-O-methoxy-ethyl (2'MOE) modification; 2'- fluoro (2'-F) modification; 2'F-4'Cα-OMe modification; 2',4'-di-Cα-OMe modification; 2'-O-methyl 3'phosphorothioate (MS) modification; 2'-O-methyl 3'thiophosphonoacetate (MSP) modification; 2'- O-methyl 3'phosphonoacetate (MP) modification; and phosphorothioate (PS) modification; or a combination thereof. In some embodiments, the BNA comprises a 2′,4′ BNA modification. In some embodiments, the 2′,4′ BNA modification is selected from the group consisting of: locked nucleic acid (LNA) modification, BNANC[N-Me] modification, 2′-O,4′-C-ethylene bridged nucleic acid (2′,4′- ENA) modification, and S-constrained ethyl (cEt) modification. In some embodiments, the 2′,4′ BNA 23 Atty Dkt No: L1034381390WO (0330.1) is a LNA modification. In some embodiments, the 2′,4′ BNA is a cEt modification. In some embodiments, the at least one chemical modification comprises a BNA modification, 2'-O-Me modification, or PS modification. Chemical modifications of spacers, crRNA repeats, crRNAs, tracrRNAs, and guide RNAs are described in International application no. PCT / IB2023 / 058418, filed August 25, 2023, which is hereby incorporated by reference in its entirety herein. The present disclosure provides guide RNAs comprising CRISPR RNAs (crRNAs). A crRNA comprises a spacer and a CRISPR repeat. The “spacer” has a nucleotide sequence that directly hybridizes with the target strand of a target sequence (e.g., target DNA sequence) of interest. The spacer is engineered to have full or partial complementarity with the target strand of a target sequence of interest. In some embodiments, the spacer can comprise from about 8 nucleotides to about 30 nucleotides, or more. For example, the spacer can be about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, or more nucleotides in length. In some embodiments, the spacer is 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides in length. In some embodiments, the spacer is about 10 to about 26 nucleotides in length, or about 12 to about 30 nucleotides in length. In some embodiments, the spacer is about 25 nucleotides in length. In some embodiments, the degree of complementarity between a spacer and the target strand of a target sequence (e.g., target DNA sequence), when optimally aligned using a suitable alignment algorithm, is between 50% and 99% or more, including but not limited to about or more than about 50%, about 60%, about 70%, about 75%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more. In some embodiments, the degree of complementarity between a spacer and the target strand of a target sequence (e.g., target DNA sequence), when optimally aligned using a suitable alignment algorithm, is 50%, 60%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more. In some embodiments, the spacer can be identical in sequence to the non-target strand of a target sequence. In some of those embodiments wherein the target sequence is a target DNA sequence, the spacer can be identical in sequence to the non-target strand of the target DNA sequence, with the exception of the thymidines (Ts) in the non-target strand being replaced by uracils (Us) in the spacer. In particular embodiments, the spacer is free of secondary structure, which can be predicted using any suitable polynucleotide folding algorithm known in the art, including but not limited to mFold (see, e.g., Zuker and Stiegler (1981) Nucleic Acids Res.9:133-148) and RNAfold (see, e.g., Gruber et al. (2008) Cell 106(1):23-24). Along with a spacer, a crRNA further comprises a CRISPR RNA (crRNA) repeat. Generally, a crRNA repeat comprises a nucleotide sequence that forms a structure, either on its own or in concert with a hybridized tracrRNA, that is recognized by the RGN polypeptide. For LPG10221, LPG10209, 24 Atty Dkt No: L1034381390WO (0330.1) LPG10210, LPG10212, LPG10213, APG07433.1, APG05586, APG01604, and LPG10145 guide crRNAs, the spacer is 5′ of the crRNA repeat. In various embodiments, the crRNA repeat can comprise from about 8 nucleotides to about 30 nucleotides, or more. For example, the crRNA repeat can be about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, or more nucleotides in length. In particular embodiments, the crRNA repeat is 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides in length. In some embodiments, a crRNA repeat of the disclosure comprises a total length of 19 to 40 nucleotides (nt). In some embodiments, a crRNA repeat of the disclosure comprises a total length of at most 19 nt, 20 nt, 21 nt, 22 nt, 23 nt, 24 nt, 25 nt, 26 nt, 27 nt, 28 nt, 29 nt, or 30 nt. In some embodiments, the crRNA repeat is about 19 nt or 21 nt. A crRNA repeat of the disclosure can include a consensus repeat of the CRISPR array found in the genome of the organism from which the crRNA repeat is obtained. In some embodiments, the crRNA repeat comprises the nucleotide sequence set forth as SEQ ID NO: 3, 5, 470, 471, 475, 476, 571, 573, or 1180, or an active variant or fragment thereof, that when comprised within a guide RNA, is capable of directing the sequence-specific binding of an associated RGN provided herein to a target sequence of interest. In some embodiments, an active crRNA repeat variant of a wild-type sequence comprises a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the nucleotide sequence set forth as SEQ ID NO: 3, 5, 470, 471, 475, 476, 571, 573, or 1180. In some embodiments, an active crRNA repeat fragment of a wild-type sequence comprises at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous nucleotides of the nucleotide sequence set forth as SEQ ID NO: 3, 5, 470, 471, 475, 476, 571, 573, or 1180. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 1, 7, 579, 583, 584, or 591, the crRNA repeat of the associated gRNA can have the nucleotide sequence set forth as SEQ ID NOs: 3, 470, or 471, or an active variant or fragment thereof. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 2, the crRNA repeat of the associated gRNA can have the nucleotide sequence set forth as SEQ ID NO: 5, 475, or 476, or an active variant or fragment thereof. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 565, the crRNA repeat of the associated gRNA can have the nucleotide sequence set forth as SEQ ID NO: 571, or an active variant or fragment thereof. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 566 or 1165- 1179, the crRNA repeat of the associated gRNA can have the nucleotide sequence set forth as SEQ ID NO: 573 or 1180 or an active variant or fragment thereof. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 3 or differs from SEQ ID NO: 3 by 1 to 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 3 by 5 nucleotides. In some embodiments, a 25 Atty Dkt No: L1034381390WO (0330.1) crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 3 by 4 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 3 by 3 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 3 by 2 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 3 by 1 nucleotide. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 3. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 5 or differs from SEQ ID NO: 5 by 1 to 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 5 by 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 5 by 4 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 5 by 3 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 5 by 2 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 5 by 1 nucleotide. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 5. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 470 or differs from SEQ ID NO: 470 by 1 to 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 470 by 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 470 by 4 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 470 by 3 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 470 by 2 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 470 by 1 nucleotide. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 470. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 471 or differs from SEQ ID NO: 471 by 1 to 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 471 by 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 471 by 4 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 471 by 3 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 471 by 2 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 471 by 1 nucleotide. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 471. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 475 or differs from SEQ ID NO: 475 by 1 to 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 475 by 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 475 by 4 nucleotides. In 26 Atty Dkt No: L1034381390WO (0330.1) some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 475 by 3 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 475 by 2 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 475 by 1 nucleotide. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 475. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 476 or differs from SEQ ID NO: 476 by 1 to 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 476 by 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 476 by 4 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 476 by 3 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 476 by 2 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 476 by 1 nucleotide. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 476. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 571 or differs from SEQ ID NO: 571 by 1 to 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 571 by 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 571 by 4 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 571 by 3 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 571 by 2 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 571 by 1 nucleotide. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 571. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 573 or differs from SEQ ID NO: 573 by 1 to 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 573 by 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 573 by 4 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 573 by 3 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 573 by 2 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 573 by 1 nucleotide. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 573. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 1180 or differs from SEQ ID NO: 1180 by 1 to 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 1180 by 5 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 1180 by 4 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ 27 Atty Dkt No: L1034381390WO (0330.1) ID NO: 1180 by 3 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 1180 by 2 nucleotides. In some embodiments, a crRNA repeat has a nucleotide sequence that differs from SEQ ID NO: 1180 by 1 nucleotide. In some embodiments, a crRNA repeat has the nucleotide sequence set forth as SEQ ID NO: 1180. In some embodiments, the crRNA is not naturally-occurring. In some of these embodiments, the specific crRNA repeat is not linked to the engineered spacer in nature and the crRNA repeat is considered heterologous to the spacer. In certain embodiments, the spacer is an engineered sequence that is not naturally occurring. LPG10221, LPG10209, LPG10210, LPG10212, LPG10213, APG07443.1, APG05586, APG01604, and LPG10145 (and variants thereof) utilize guide RNAs that comprise a crRNA and a trans-activating CRISPR RNA (tracrRNA). A tracrRNA molecule comprises a nucleotide sequence comprising a region that has sufficient complementarity to hybridize to a CRISPR repeat of a crRNA, which is referred to herein as the anti-repeat. In some embodiments, the tracrRNA molecule further comprises a region with secondary structure (e.g., stem-loop) or forms secondary structure upon hybridizing with its corresponding crRNA. In particular embodiments, the region of the tracrRNA that is fully or partially complementary to a CRISPR repeat is at the 5' end of the molecule and the 3' end of the tracrRNA comprises secondary structure. This region of secondary structure generally comprises several hairpin structures, including the nexus hairpin, which is found adjacent to the anti- repeat. The nexus forms the core of the interactions between the guide RNA and the RGN, and is at the intersection between the guide RNA, the RGN, and the target DNA. The nexus hairpin often has a conserved nucleotide sequence in the base of the hairpin stem, with the motif UNANNC found in many nexus hairpins in tracrRNAs. In embodiments, guide RNAs or RGN systems of the disclosure use tracrRNAs that comprise non-canonical sequences in the base of the hairpin stem of their nexus hairpins, including UNANNG, CNANNC, CNANNU, UNANNU, CNANNG, and CNCNNU. There are often terminal hairpins at the 3' end of the tracrRNA that can vary in structure and number, but often comprise a GC-rich Rho-independent transcriptional terminator hairpin followed by a string of U’s at the 3' end. See, for example, Briner et al. (2014) Molecular Cell 56:333-339, Briner and Barrangou (2016) Cold Spring Harb Protoc; doi: 10.1101 / pdb.top090902, and U.S. Publication No. 2017 / 0275648, each of which is herein incorporated by reference in its entirety. In various embodiments, the anti-repeat region of the tracrRNA that is fully or partially complementary to the CRISPR repeat comprises from about 8 nucleotides to about 30 nucleotides, or more. For example, the region of base pairing between the tracrRNA anti-repeat and the CRISPR repeat can be about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, or more nucleotides in length. In particular embodiments, the region of base pairing between the tracrRNA anti-repeat and the CRISPR repeat is 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides in length. 28 Atty Dkt No: L1034381390WO (0330.1) In some embodiments, the degree of complementarity between a CRISPR repeat and its corresponding tracrRNA anti-repeat, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, about 60%, about 70%, about 75%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more. In particular embodiments, the degree of complementarity between a CRISPR repeat and its corresponding tracrRNA anti-repeat, when optimally aligned using a suitable alignment algorithm, is 50%, 60%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more. In various embodiments, the entire tracrRNA can comprise from about 60 nucleotides to more than about 210 nucleotides. For example, the tracrRNA can be about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 85, about 90, about 95, about 100, about 105, about 110, about 115, about 120, about 125, about 130, about 135, about 140, about 150, about 160, about 170, about 180, about 190, about 200, about 210, or more nucleotides in length. In particular embodiments, the tracrRNA is 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 150, 160, 170, 180, 190, 200, 210 or more nucleotides in length. In particular embodiments, the tracrRNA is about 57 to about 115 nucleotides in length, including about 57, about 58, about 59, about 60, about 61, about 62, about 63, about 64, about 65, about 66, about 67, about 68, about 69, about 70, about 71, about 72, about 73, about 74, about 75, about 76, about 77, about 78, about 79, about 80, about 81, about 82, about 83, about 84, about 85, about 86, about 87, about 88, about 89, about 90, about 91, about 92, about 93, about 94, about 95, about 96, about 97, about 98, about 99, about 100, about 101, about 102, about 103, about 104, about 105, about 106, about 107, about 108, about 109, about 110, about 111, about 112, about 113, about 114, and about 115 nucleotides in length. In particular embodiments, the tracrRNA is 59 to 115 nucleotides in length, including 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, and 115 nucleotides in length. In particular embodiments, the tracrRNA comprises the nucleotide sequence of SEQ ID NO: 4, 6, 472, 473, 474, 477, 478, 479, or 480, or an active variant or fragment thereof that when comprised within a guide RNA is capable of directing the sequence-specific binding of an associated RNA-guided nuclease provided herein to a target DNA sequence of interest. In certain embodiments, an active tracrRNA sequence variant comprises a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the nucleotide sequence set forth as SEQ ID NO: 4, 6, 472, 473, 474, 477, 478, 479, 480, 572, 574, or 1181. In certain embodiments, an active tracrRNA sequence fragment comprises at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, or 75, or more 29 Atty Dkt No: L1034381390WO (0330.1) contiguous nucleotides of the nucleotide sequence set forth as SEQ ID NO: 4, 6, 472, 473, 474, 477, 478, 479, 480, 572, 574, or 1181. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 1, 7, 579, 583, 584, or 591, the tracrRNA of the associated gRNA can have the nucleotide sequence set forth as SEQ ID NOs: 4, 472, 473, or 474, or an active variant or fragment thereof. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 2, the tracrRNA of the associated gRNA can have the nucleotide sequence set forth as SEQ ID NO: 6, 477, 478, 479, or 480, or an active variant or fragment thereof. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 565, the tracrRNA of the associated gRNA can have the nucleotide sequence set forth as SEQ ID NO: 572, or an active variant or fragment thereof. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 566 or 1165-1179, the tracrRNA of the associated gRNA can have the nucleotide sequence set forth as SEQ ID NO: 574 or 1181, or an active variant or fragment thereof. The guide RNA can be a single guide RNA or a dual-guide RNA system. A single guide RNA comprises the crRNA and optionally tracrRNA on a single molecule of RNA, whereas a dual- guide RNA system comprises a crRNA and a tracrRNA present on two distinct RNA molecules, hybridized to one another through at least a portion of the CRISPR repeat sequence of the crRNA and at least a portion of the tracrRNA, which may be fully or partially complementary to the CRISPR repeat sequence of the crRNA. In some of those embodiments wherein the guide RNA is a single guide RNA, the crRNA and optionally tracrRNA are connected by a linker nucleotide sequence. In general, the linker nucleotide sequence between a crRNA and a tracrRNA is one that does not include complementary bases in order to avoid the formation of secondary structure within or comprising nucleotides of the linker nucleotide sequence. In some embodiments, the linker nucleotide sequence between the crRNA and tracrRNA is at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, or more nucleotides in length. In some embodiments, the linker nucleotide sequence between the crRNA and tracrRNA is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more nucleotides in length. In some embodiments, the linker nucleotide sequence of a single guide RNA is at least 4 nucleotides in length. In some embodiments, the linker nucleotide sequence of a single guide RNA is 4 nucleotides in length. In some embodiments, the linker nucleotide sequence is AAAG. In some embodiments, the guide RNA is a single guide RNA (sgRNA) having the backbone sequence (comprising a crRNA repeat, an optional linker nucleotide sequence, and a tracrRNA) of any one of SEQ ID NOs: 206, 209, 212, 310, 326, 330, 481-483, 1162, and 1163, or an active variant or fragment thereof. In certain embodiments, an active sgRNA backbone sequence variant comprises a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one of the nucleotide sequences set forth as SEQ ID NO: 206, 209, 212, 310, 326, 330, 481-483, 1162, and 30 Atty Dkt No: L1034381390WO (0330.1) 1163. In certain embodiments, an active sgRNA backbone sequence fragment comprises at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, or more contiguous nucleotides of any one of the nucleotide sequences set forth as SEQ ID NO: 206, 209, 212, 310, 326, 330, 481-483, 1162, and 1163. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 1, 7, 579, 583, 584, or 591, the sgRNA backbone can have any one of the nucleotide sequences set forth as SEQ ID NOs: 206 and 481-483, or an active variant or fragment thereof. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 2, the sgRNA backbone can have any one of the nucleotide sequences set forth as SEQ ID NOs: 209, 212, 310, 326, and 330, or an active variant or fragment thereof. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 565, the sgRNA backbone can have the nucleotide sequence set forth as SEQ ID NO: 1162, or an active variant or fragment thereof. In those embodiments wherein the RGN has the amino acid sequence set forth as SEQ ID NO: 566 or 1165- 1179, the sgRNA backbone can have the nucleotide sequence set forth as SEQ ID NO: 1163, or an active variant or fragment thereof. Two polynucleotide sequences can be considered to be substantially complementary when the two sequences hybridize to each other under stringent conditions. Likewise, an RGN is considered to bind to a particular target sequence within a sequence-specific manner if the guide RNA bound to the RGN binds to a target sequence under stringent conditions. By "stringent conditions" or "stringent hybridization conditions" is intended conditions under which the two polynucleotide sequences will hybridize to each other to a detectably greater degree than to other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is at least about 30°C for short sequences (e.g., 10 to 50 nucleotides) and at least about 60°C for long sequences (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulfate) at 37°C, and a wash in 1X to 2X SSC (20X SSC = 3.0 M NaCl / 0.3 M trisodium citrate) at 50 to 55°C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37°C, and a wash in 0.5X to 1X SSC at 55 to 60°C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0.1X SSC at 60 to 65°C. Optionally, wash buffers may comprise about 0.1% to about 1% SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium. 31 Atty Dkt No: L1034381390WO (0330.1) The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched sequence. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: Tm = 81.5°C + 16.6 (log M) + 0.41 (%GC) - 0.61 (% form) - 500 / L; where M is the molarity of monovalent cations, %GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. Generally, stringent conditions are selected to be about 5°C lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and / or wash at 1, 2, 3, or 4°C lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and / or wash at 6, 7, 8, 9, or 10°C lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and / or wash at 11, 12, 13, 14, 15, or 20°C lower than the thermal melting point (Tm). Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and / or wash solutions are inherently described. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology— Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, New York); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley- Interscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, New York). The term “sequence specific” can also refer to the binding of a RGN polypeptide or PE to a target sequence at a greater affinity than binding to a randomized background sequence. The guide RNA can be synthesized chemically or via in vitro transcription. Assays for determining sequence-specific binding between an RGN and a guide RNA are known in the art and include, but are not limited to, in vitro binding assays between an expressed RGN and the guide RNA, which can be tagged with a detectable label (e.g., biotin) and used in a pull-down detection assay in which the guide RNA:RGN complex is captured via the detectable label (e.g., with streptavidin beads). A control guide RNA with an unrelated sequence or structure to the guide RNA can be used as a negative control for non-specific binding of the RGN to RNA. The guide RNA can be introduced into a target cell, organelle, or embryo as an RNA molecule. In some embodiments, a nucleotide sequence encoding the guide RNA is introduced into a target cell, organelle, or embryo. In some embodiments, the nucleotide sequence encoding a guide RNA is operably linked to a promoter (e.g., an RNA polymerase III promoter). The promoter can be a native promoter or heterologous to the guide RNA-encoding nucleotide sequence. In some embodiments, the guide RNA can be introduced into a target cell, organelle, or embryo as a ribonucleoprotein complex, as described herein, wherein the guide RNA is bound to an RGN polypeptide. 32 Atty Dkt No: L1034381390WO (0330.1) The guide RNA directs an associated RGN to a particular target nucleotide sequence of interest through hybridization of the guide RNA to the target sequence of interest. The target sequence can be bound (and in some embodiments, cleaved) by an RGN in vitro or in a cell. A target sequence is within a target polynucleotide and can comprise DNA, RNA, or a combination of both and can be single-stranded or double-stranded. A target sequence can be genomic DNA (i.e., chromosomal DNA), plasmid DNA, or an RNA molecule (e.g., messenger RNA, ribosomal RNA, transfer RNA, micro RNA, small interfering RNA). In those embodiments wherein the target sequence is a chromosomal sequence, the chromosomal sequence can be a nuclear, plastid, or mitochondrial chromosomal sequence. In the presently disclosed compositions and methods, the target sequence is within a target polynucleotide that is double-stranded (e.g., a target DNA sequence). In some embodiments, the target sequence is unique in the target genome. In some embodiments, the target sequence is double-stranded and comprises a target strand and a non-target strand. The target sequence is adjacent to a protospacer adjacent motif (PAM) and the non-target strand of the target sequence is the strand that comprises the PAM. The PAM is immediately adjacent to the target sequence and often comprise Ns, which represent any nucleotide. In some embodiments, the PAM comprises about 1 to about 10 Ns, including about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, or about 10 Ns. In particular embodiments, a PAM comprises 1 to 10 Ns, including 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 Ns. In general, the PAM can be 5' or 3' of the target sequence on its non-target strand. The PAM of the presently disclosed RGNs is immediately 3' of the target sequence on its non-target strand. Generally, the PAM is a consensus sequence of about 3-4 nucleotides, but in particular embodiments it can be 2, 3, 4, 5, 6, 7, 8, 9, or more nucleotides in length. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 1, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCY. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 1, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCY, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 2, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNRYA. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 2, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNRYA, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 5, 475, and 476, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 6, 477, 478, 479, and 480, or an active variant or fragment thereof. 33 Atty Dkt No: L1034381390WO (0330.1) In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 7, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCC. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 7, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCC, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 579, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNC. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 579, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNC, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 583, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNC. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 583, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNC, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 584, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCM. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 584, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCM, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 591, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCT. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 591, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCT, when bound to a 34 Atty Dkt No: L1034381390WO (0330.1) guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 565, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNGRR. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 565, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNGRR, when bound to a guide RNA comprising a crRNA repeat sequence of SEQ ID NO: 571, or an active variant or fragment thereof, and a tracrRNA sequence of SEQ ID NO: 572, or an active variant or fragment thereof. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 566 or 1165-1179, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNGG. In some embodiments, an RGN having the amino acid sequence set forth as SEQ ID NO: 566 or 1165-1179, or an active variant or fragment thereof, binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNGG, when bound to a guide RNA comprising a crRNA repeat sequence of SEQ ID NO: 573 or 1180, or an active variant or fragment thereof, and a tracrRNA sequence of SEQ ID NO: 574 or 1181, or an active variant or fragment thereof. It is well-known in the art that PAM sequence specificity for a given nuclease enzyme is affected by enzyme concentration (see, e.g., Karvelis et al. (2015) Genome Biol 16:253), which may be modified by altering the promoter used to express the RGN, or the amount of ribonucleoprotein complex delivered to a target cell, organelle, or embryo. Upon recognizing its corresponding PAM sequence, the RGN, if active, may cleave one or both strands of a target sequence at a specific cleavage site. As used herein, a cleavage site comprises particular nucleotides within a target sequence at which the target strand, non-target strand, or both strands of a target sequence are cleaved by an RGN. The cleavage site can comprise the 1stand 2nd, 2ndand 3rd, 3rdand 4th, 4thand 5th, 5thand 6th, 7thand 8th, or 8thand 9thnucleotides from the PAM in either the 5' or 3' direction. In some embodiments, the cleavage site may be over 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides from the PAM in either the 5' or 3' direction. As RGNs can cleave a target sequence resulting in staggered ends, in some embodiments, the cleavage site is defined based on the distance of the two nucleotides from the PAM on the non-target strand of the target sequence and for the target strand, the distance of the two nucleotides from the complement of the PAM. 1. PEgRNA In those embodiments involving a polymerase editor (PE), the PE system utilizes a polymerase editing guide RNA (“PEgRNA”). The PEgRNA is a guide RNA that both specifies the target sequence and provides the template for polymerization of the replacement strand containing a 35 Atty Dkt No: L1034381390WO (0330.1) desired edit by way of an extension engineered onto the RGN guide RNA or a part thereof, referred to herein as an extension arm. The PEgRNA can be a single guide RNA, wherein the extension arm can be at the 5' or 3' end, or at an internal portion of the guide RNA, or multiple polynucleotides (e.g., a dual guide RNA). In embodiments wherein the PEgRNA is a dual guide RNA, the extension arm can be at the 5' or 3' end, or at an internal portion of the crRNA or tracrRNA molecule. The template for polymerization within an extension arm is referred to herein as the DNA synthesis template. In those embodiments wherein the polymerase of the PE is a reverse transcriptase, the DNA synthesis template can be referred to as the reverse transcriptase template (RTT). The RGN is guided to the target sequence by the PEgRNA and in those embodiments wherein the RGN is a nickase with an inactivated HNH domain and active RuvC domain, the RGN nickase nicks the non-target strand upstream of the sequence to be edited and upstream of the PAM, creating a 3' flap on the non-target strand. The PEgRNA includes a primer binding site (PBS) that is complementary to the 3' flap of the non-target strand. The PBS can be at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides in length. In certain embodiments, the PEgRNA comprises a PBS that is at least 5 (e.g., 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) nucleotides in length. In some embodiments, the PEgRNA may comprise a PBS that is 9, 11, 12, 13, or 15 nucleotides in length. Hybridization of the PBS and 3′ flap of the non-target strand allows polymerization of the replacement strand containing the edit using the DNA synthesis template in the extension of the PEgRNA. The DNA synthesis template can be at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more nucleotides in length. In certain embodiments, the PEgRNA comprises a DNA synthesis template that is at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, or at least 50 nucleotides in length. In some embodiments, the PEgRNA comprises a DNA synthesis template that is 19, 22, 23, 24, 25, 26, 29, 30, 32, 34, 37, 38, 39, 40, 42, or 46 nucleotides in length. The DNA synthesis template comprises the desired edit, which can be a substitution of one or more nucleotides, a deletion of one or more nucleotides, or an addition of one or more nucleotides. The extension arm of the PEgRNA can be formed from RNA or DNA. In the case of an RNA extension, the polymerase of the polymerase editor can be an RNA-dependent DNA polymerase (such as a reverse transcriptase). In the case of a DNA extension, the polymerase of the polymerase editor may be a DNA-dependent DNA polymerase. The replacement strand containing the desired edit (e.g., substitution, deletion, or addition) shares the same sequence as the non-target strand of the target sequence to be edited (with the exception that it includes the desired edit). Through DNA repair and / or replication machinery, the 36 Atty Dkt No: L1034381390WO (0330.1) non-target strand of the target sequence is replaced by the newly synthesized replacement strand containing the desired edit. In some cases, polymerase editing may be thought of as a “search-and- replace” genome editing technology since the polymerase editors not only search and locate the desired target sequence to be edited, but at the same time, encode a replacement strand containing a desired edit which is installed in place of the corresponding non-target strand of the target sequence. Thus, in some embodiments, a guide RNA of the disclosure comprises an extension comprising an edit template for polymerase editing. 2. Nicking guide RNA In order to reduce the possibility that the edit introduced by a polymerase editor is removed due to mismatch repair of the edited strand, a nicking guide RNA can be used. A “nicking guide RNA” is a guide RNA that targets a sequence within the unedited strand at a site nearby and opposite to the original nick and guides the RGN nickase of the PE system to this unedited strand to introduce a single-stranded nick. The nicking guide RNA can be designed to match the edited sequence introduced by the PEgRNA, but not the original unedited sequence, to ensure that the nicking occurs after the editing event on the non-target strand takes place. III. APG07433.1 RGN variants Provided herein are variants of the RGN APG07433.1 that recognize an alternative PAM (e.g., NNNNCY, NNNNC, NNNNCT, and NNNNCM vs NNNNCC for APG07433.1). Such RGNs can have at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence set forth as SEQ ID NO: 1 and comprise: a) a S at a position corresponding to amino acid position 1020 in SEQ ID NO: 1; b) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1; c) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1; d) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1; and e) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1. Such RGNs can have at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence set forth as SEQ ID NO: 1 and comprise: a) a S at a position corresponding to amino acid position 1020 in SEQ ID NO: 1; b) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1; c) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1; d) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1; or e) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1. 37 Atty Dkt No: L1034381390WO (0330.1) In some embodiments, the APG07433.1 variant has at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence set forth as SEQ ID NO: 579 and comprise a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 579. In some embodiments, the APG07433.1 variant has at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence set forth as SEQ ID NO: 584 and comprise a T at a position corresponding to amino acid position 1021 in SEQ ID NO: 584 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 584. In some embodiments, the APG07433.1 variant has at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence set forth as SEQ ID NO: 583 and comprise an N at a position corresponding to amino acid position 1021 in SEQ ID NO: 583 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 583. In some embodiments, the APG07433.1 variant has at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence set forth as SEQ ID NO: 591 and comprise: a) a Q at a position corresponding to amino acid position 975 in SEQ ID NO: 591; b) an A at a position corresponding to amino acid position 1020 in SEQ ID NO: 591; c) a G at a position corresponding to amino acid position 1022 in SEQ ID NO: 591; and d) a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 591. In some embodiments, the presently disclosed RGN, or an active variant or fragment thereof, recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNNNCC 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 7 (APG07433.1), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNCC 3' of the target sequence on its non-target strand. In some embodiments, the presently disclosed RGN, or an active variant or fragment thereof, recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNNNCY 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G and wherein Y is C or T / U). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 1 (LPG10221), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNCY 3' of the target sequence on its non-target strand. In some embodiments, the presently disclosed RGN, or an active variant or fragment thereof, recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNNNC 38 Atty Dkt No: L1034381390WO (0330.1) 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 579 (LPG10209), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNC 3' of the target sequence on its non-target strand. In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 583 (LPG10212), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNC 3' of the target sequence on its non-target strand. In some embodiments, the presently disclosed RGN, or an active variant or fragment thereof, recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNNNCM 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G and wherein M is C or A). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 584 (LPG10210), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNCM 3' of the target sequence on its non-target strand. In some embodiments, the presently disclosed RGN, or an active variant or fragment thereof, recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNNNCT 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 591 (LPG10213), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNNNCT 3' of the target sequence on its non-target strand. In some embodiments, the presently disclosed RGN, or an active variant or fragment thereof, recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNGRR 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G and wherein R is A or G). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 565 (APG01604), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNGRR 3' of the target sequence on its non-target strand. In some embodiments, the presently disclosed RGN, or an active variant or fragment thereof, recognizes a protospacer adjacent motif (PAM) having a consensus nucleotide sequence of NNGG 3' of the target sequence on its non-target strand (wherein N is A, C, T / U, or G). In some embodiments, the PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 566 (LPG10145), or an active variant or fragment thereof, that recognizes a PAM having a consensus nucleotide sequence of NNGG 3' of the target sequence on its non-target strand. The presently disclosed RGN, or an active variant or fragment thereof, can have a PAM- interacting (PI) domain that contributes to recognition of a PAM site in a target polynucleotide. The 39 Atty Dkt No: L1034381390WO (0330.1) PI domain can comprise 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150 or more amino acid residues. In some embodiments, the PI domain of an RGN, or an active variant or fragment thereof, of the disclosure is located within the carboxy (C)-terminal region of the RGN. The C-terminal region comprising the PI domain of an RGN, or an active variant or fragment thereof, of the disclosure can include the C-terminal 151 amino acid residues, the C-terminal 150 amino acid residues, the C-terminal 140 amino acid residues, the C- terminal 135 amino acid residues, the C-terminal 132 amino acid residues, the C-terminal 130 amino acid residues, the C-terminal 125 amino acid residues, the C-terminal 120 amino acid residues, the C- terminal 110 amino acid residues, the C-terminal 100 amino acid residues, the C-terminal 90 amino acid residues, the C-terminal 80 amino acid residues, the C-terminal 70 amino acid residues, the C- terminal 60 amino acid residues, the C-terminal 50 amino acid residues, the C-terminal 40 amino acid residues, the C-terminal 30 amino acid residues, the C-terminal 20 amino acid residues, or the C- terminal 10 amino acid residues of the RGN. In some embodiments, the PI domain of an RGN, or an active variant or fragment thereof, of the disclosure is within or includes amino acid residues 939- 1071 of the RGN. In some embodiments, the PI domain of an RGN having the amino acid sequence set forth as SEQ ID NO: 1, 7, 579, 583, 584, or 591, or an active variant or fragment thereof, is within or includes amino acid residues 939-1071 of the RGN. In certain embodiments, the RGN variant described herein comprises a PI domain that has at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid residues 939-1071 of SEQ ID NO: 1, 7, 579, 583, 584, or 591. In other embodiments, the RGN variant described herein comprises a PI domain that has at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid residues 939-1071 of SEQ ID NO: 1, and recognizes a PAM having a consensus nucleotide sequence of NNNNCY 3' of the target sequence on its non-target strand. In other embodiments, the RGN variant described herein comprises a PI domain that has at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid residues 939-1071 of SEQ ID NO: 579 or 583, and recognizes a PAM having a consensus nucleotide sequence of NNNNC 3' of the target sequence on its non-target strand. In other embodiments, the RGN variant described herein comprises a PI domain that has at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid residues 939-1071 of SEQ ID NO: 584, and recognizes a PAM having a consensus nucleotide sequence of NNNNCM 3' of the target sequence on its non-target strand. 40 Atty Dkt No: L1034381390WO (0330.1) In other embodiments, the RGN variant described herein comprises a PI domain that has at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid residues 939-1071 of SEQ ID NO: 591, and recognizes a PAM having a consensus nucleotide sequence of NNNNCT 3' of the target sequence on its non-target strand. The presently disclosed RGNs can comprise at least one nuclease domain (e.g., DNase, RNase domain) and at least one RNA recognition and / or RNA binding domain to interact with guide RNAs. In some embodiments, the RGN comprises only one active nuclease domain and thus functions as a nickase. In some embodiments, the RGN nuclease domain that is active is a RuvC domain. In some embodiments, the RGN comprises an inactivated HNH nuclease domain. Further domains that can be found in RGNs include, but are not limited to: DNA binding domains, helicase domains, protein- protein interaction domains, and dimerization domains. In some embodiments, the RGNs can comprise at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to one or more of a DNA binding domain, helicase domain, protein-protein interaction domain, and dimerization domain. In various embodiments, a target sequence is bound by a presently disclosed RGN. In those instances wherein the target sequence is double-stranded (e.g., double-stranded DNA), the target strand of the target sequence hybridizes with the guide RNA associated with the RGN. The target strand and / or the non-target strand of the target sequence (e.g., target DNA sequence) can then be subsequently cleaved by the RGN if the polypeptide possesses nuclease activity. The presently disclosed RGN can cleave nucleotides within a polynucleotide, functioning as an endonuclease or can be an exonuclease, removing successive nucleotides from the end (the 5' and / or the 3' end) of a polynucleotide. In some embodiments, the presently disclosed RGNs can cleave nucleotides of a target polynucleotide within any position of a polynucleotide and thus function as both an endonuclease and exonuclease. The cleavage of a target polynucleotide by the presently disclosed RGNs can result in staggered breaks or blunt ends. The presently disclosed RGNs can be wild-type sequences derived from bacterial or archaeal species. Alternatively, the RGNs can be variants or fragments of wild-type polypeptides. The wild- type RGN can be modified to alter nuclease activity or alter PAM specificity, for example. In some embodiments, the RGN is not naturally-occurring. In some embodiments, a presently disclosed RGN can function as a nickase, only cleaving a single strand of a double-stranded target sequence (e.g., target DNA sequence). Such RGNs have a single functioning nuclease domain. In particular embodiments, the nickase is capable of cleaving the target strand (has an active HNH domain) or the non-target strand (has an active RuvC domain) of the double-stranded target sequence (e.g., target DNA sequence). In order to effect the nicking of a single strand of a double-stranded target polynucleotide (e.g., target DNA), at least one inactivating mutation (also referred to herein as a mutation that reduces nuclease activity) can be introduced into a nuclease 41 Atty Dkt No: L1034381390WO (0330.1) domain of an RGN. For example, in order to inactivate the HNH domain of LPG10221, the following catalytic amino acid residues can be mutated to an alanine, for example, or another non-conserved amino acid residue: D603, H604, N618, N627. More than one mutation that reduces nuclease activity can be introduced into a nuclease domain of an RGN in order to further reduce its activity. Thus, in some embodiments, the HNH nuclease domain of a presently disclosed RGN comprises an alanine (or another non-conserved amino acid residue) at a position corresponding to 604 and an alanine (or another non-conserved amino acid residue) at a position corresponding to 627 of SEQ ID NO: 1. In some embodiments, the RGN nickase comprises the sequence set forth as SEQ ID NO: 8, or an active fragment or variant thereof, such as one having at least at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 8. RGN nickases with inactivated HNH domains can be used for polymerase editing and can be fused to a polymerase as described herein. Alternatively, RGN nickases with inactivated RuvC domains are often used for base editing and fused with a base editing polypeptide, such as a deaminase that directly chemically modifies (e.g., deaminates) a nucleobase, resulting in conversion from one nucleobase to another. The base-editing polypeptide can be fused to the RGN at its N-terminal or C-terminal end. Additionally, the base- editing polypeptide may be fused to the RGN via a peptide linker. A non-limiting example of a deaminase polypeptide that is useful for such compositions and methods includes a cytosine deaminase or an adenine deaminase (such as the adenine deaminase base editor described in Gaudelli et al. (2017) Nature 551:464-471, U.S. Publ. Nos.2017 / 0121693 and 2018 / 0073012, and International Publ. No. WO 2018 / 027078, or any of the deaminases disclosed in International Publ. Nos. WO 2020 / 139783, WO 2022 / 056254, WO 2022 / 204093, and PCT International Appl. No. PCT / IB2023 / 061192, filed November 6, 2023, each of which is herein incorporated by reference in its entirety). In embodiments wherein a nickase is used and a double-stranded cleavage is desired, two nickases can be used, each of which nicks a single strand within the double-stranded target sequence. Alternatively, the same RGN nickase can be used, along with two guide RNAs that each target one of the strands of the double-stranded target sequence. In other embodiments, the RGN lacks nuclease activity altogether and is referred to herein as nuclease-dead or nuclease inactive. In some embodiments, nuclease-dead or nuclease inactive versions of the enzymes are used for modifying a nucleic acid, such as in base editing as described herein. Any method known in the art for introducing mutations into an amino acid sequence, such as PCR-mediated mutagenesis and site-directed mutagenesis, can be used for generating nickases or nuclease-dead RGNs. See, e.g., U.S. Publ. No.2014 / 0068797 and U.S. Pat. No.9,790,490; each of which is incorporated by reference in its entirety. RGNs including those that comprise nuclease activity or that lack nuclease activity can be used to deliver a fused polypeptide, polynucleotide, or small molecule payload to a particular genomic 42 Atty Dkt No: L1034381390WO (0330.1) location. In some of these embodiments, the RGN polypeptide or guide RNA can be fused to a detectable label or purification tag to allow for detection of a particular sequence. As a non-limiting example, a nuclease-dead RGN can be fused to a detectable label (e.g., fluorescent protein) and targeted to a particular sequence associated with a disease to allow for detection of the disease- associated sequence. As another non-limiting example, a nuclease active RGN can be fused to a detectable label (e.g., fluorescent protein) and targeted to a particular sequence associated with a disease to allow for detection of the disease-associated sequence. The detectable label or purification tag can be located at the N-terminus, the C-terminus, or an internal location of the RGN, either directly or indirectly via a linker peptide. In some embodiments, the RGN component of the fusion protein is a nuclease-dead RGN. In some embodiments, the RGN component of the fusion protein is an RGN with nickase activity. A detectable label is a molecule that can be visualized or otherwise observed. The detectable label may be fused to the RGN as a fusion protein (e.g., fluorescent protein) or may be a small molecule conjugated to the RGN polypeptide that can be detected visually or by other means. Detectable labels that can be fused to the presently disclosed RGNs as a fusion protein include any detectable protein domain, including but not limited to, a fluorescent protein or a protein domain that can be detected with a specific antibody. Non-limiting examples of fluorescent proteins include green fluorescent proteins (e.g., GFP, EGFP, ZsGreen1) and yellow fluorescent proteins (e.g., YFP, EYFP, ZsYellow1). Non-limiting examples of small molecule detectable labels include radioactive labels, such as3H and35S. RGN polypeptides can also comprise a purification tag, which is any molecule that can be utilized to isolate a protein or fused protein from a mixture (e.g., biological sample, culture medium). Non-limiting examples of purification tags include biotin, myc, maltose binding protein (MBP), glutathione-S-transferase (GST), and 3X FLAG tag. Alternatively, nuclease-dead RGNs can be targeted to particular genomic locations to alter the expression of a desired gene (i.e., target gene). In some embodiments, the binding of a nuclease-dead RGN to a target sequence results in the reduction in expression of the target gene by interfering with the binding of RNA polymerase or transcription factors within the targeted genomic region. In some embodiments, the RGN (e.g., a nuclease-dead RGN) or its complexed guide RNA further comprises an expression modulator that, upon binding to a target sequence within a target gene, serves to either repress or activate the expression of the target gene. In some embodiments, the expression modulator of the fusion protein comprises a transcriptional repressor domain, which interacts with transcriptional control elements and / or transcriptional regulatory proteins, such as RNA polymerases and transcription factors, to reduce or terminate transcription of at least one gene. Transcriptional repressor domains are known in the art and include, but are not limited to, Sp1-like repressors, IκB, and Krüppel associated box (KRAB) domains. 43 Atty Dkt No: L1034381390WO (0330.1) In some embodiments, the expression modulator of the fusion protein comprises a transcriptional activation domain, which interacts with transcriptional control elements and / or transcriptional regulatory proteins, such as RNA polymerases and transcription factors, to increase or activate transcription of at least one gene. Transcriptional activation domains are known in the art and include, but are not limited to, a herpes simplex virus VP16 activation domain and an NFAT activation domain. In some embodiments, the expression modulator modulates the expression of the target sequence or regulated gene through epigenetic mechanisms. In some embodiments, an epigenetic modulator covalently modifies DNA or histone proteins to alter histone structure and / or chromosomal structure without altering the DNA sequence, leading to changes in gene expression (e.g., upregulation or downregulation). Non-limiting examples of epigenetic modifications include acetylation or methylation of lysine residues, arginine methylation, serine and threonine phosphorylation, and lysine ubiquitination and sumoylation of histone proteins, and methylation and hydroxymethylation of cytosine residues in DNA. Non-limiting examples of epigenetic modulators include histone acetyltransferases, histone deacetylases, histone methyltransferases, histone demethylases, DNA methyltransferases, and DNA demethylases. In some embodiments, the nuclease-dead RGNs or an RGN with nickase activity can be targeted to particular genomic locations to modify the sequence of a target polynucleotide through fusion to a base-editing polypeptide, for example a deaminase polypeptide or active variant or fragment thereof, that directly chemically modifies (e.g., deaminates) a nucleobase, resulting in conversion from one nucleobase to another. The base-editing polypeptide can be fused to the RGN at its amino-terminal (N-terminal) or carboxy-terminal (C-terminal) end. The base-editing polypeptide can be operably fused to the RGN at an internal location of the RGN. Insertion of a polypeptide (e.g., a base-editing polypeptide or a DNA polymerase) at an internal location of an RGN polypeptide is described elsewhere herein. Additionally, the base-editing polypeptide may be fused to the RGN via a peptide linker. “Base editors” are fusion proteins comprising a DNA-targeting polypeptide, such as an RGN, and a base-editing polypeptide, such as a deaminase. Non-limiting examples of deaminases or base editors that are useful for such compositions and methods includes a cytosine deaminase, an adenine deaminase, or their corresponding cytosine base editor or adenine base editor (such as the adenine deaminase or base editor described in Gaudelli et al. (2017) Nature 551:464-471, U.S. Publ. Nos.2017 / 0121693 and 2018 / 0073012, and International Publ. No. WO 2018 / 027078, or any of the deaminases or base editors disclosed in International Publ. Nos. WO 2020 / 139783, WO 2022 / 056254, WO 2022 / 204093, PCT / IB2023 / 061192 filed November 6, 2023, each of which is herein incorporated by reference in its entirety). In some embodiments, the deaminase polypeptide that is useful for such compositions and methods is a cytosine deaminase or an adenine deaminase comprising an amino acid sequence selected from any one of SEQ ID NOs: 484-555. In one embodiment, the deaminase polypeptide that is useful for such compositions and methods is a cytosine deaminase or an adenine 44 Atty Dkt No: L1034381390WO (0330.1) deaminase having a sequence that is at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater identity to any one of the amino acid sequences set forth as SEQ ID NOs: 484-555. In some embodiments, the deaminase that is useful for such presently disclosed compositions and methods is a deaminase disclosed in Table 17 of International Publ. No. WO 2020 / 139783, which is incorporated herein by reference in its entirety. Further, it is known in the art that certain fusion proteins between an RGN and a base-editing enzyme (e.g., cytosine deaminase) may also comprise at least one uracil stabilizing polypeptide that increases the mutation rate of a cytidine, deoxycytidine, or cytosine to a thymidine, deoxythymidine, or thymine in a polynucleotide by a deaminase. Non- limiting examples of uracil stabilizing polypeptides include those disclosed in PCT Publication No. WO 2021 / 217002 and PCT Publication No. WO 2022 / 015969, each of which is herein incorporated by reference in its entirety. The disclosed uracil stabilizing polypeptides include USP2 (SEQ ID NO: 556), and a uracil glycosylase inhibitor (UGI) domain (SEQ ID NO: 557), which may increase base editing efficiency. Therefore, a base editor may comprise an RGN described herein or variant thereof, a deaminase, and optionally at least one uracil stabilizing polypeptide, such as UGI or USP2. In some embodiments, the RGN fusion protein comprises a cleavage domain, which is any domain that is capable of cleaving a polynucleotide (i.e., RNA, DNA, or RNA / DNA hybrid) and includes, but is not limited to, restriction endonucleases and homing endonucleases, such as Type IIS endonucleases (e.g., FokI) (see, e.g., Belfort et al. (1997) Nucleic Acids Res.25:3379-3388; Linn et al. (eds.) Nucleases, Cold Spring Harbor Laboratory Press, 1993). RGNs that are fused to a polypeptide or domain can be connected a linker as described elsewhere herein. The presently disclosed RGNs can comprise at least one nuclear localization signal (NLS) to enhance transport of the protein to the nucleus of a cell, as described elsewhere herein. Other localization signal sequences known in the art that localize polypeptides to particular subcellular location(s) can also be used to target the RGNs, including, but not limited to, plastid localization sequences, mitochondrial localization sequences, and dual-targeting signal sequences that target to both the plastid and mitochondria. The presently disclosed RGNs can comprise at least one cell-penetrating domain that facilitates cellular uptake of the RGN, as described elsewhere herein. The nuclear localization signal, plastid localization signal, mitochondrial localization signal, dual-targeting localization signal, and / or cell-penetrating domain can be located at the amino-terminus (N-terminus), the carboxyl-terminus (C-terminus), and / or in an internal location of the RGN. IV. Polynucleotides encoding polymerase editors, polymerase editor systems, RGNs, and guide RNAs The present disclosure provides polynucleotides comprising or encoding the presently disclosed guide RNAs or PEgRNAs and polynucleotides comprising a nucleotide sequence encoding 45 Atty Dkt No: L1034381390WO (0330.1) the presently disclosed RNA-guided nucleases (RGNs), PEs, or polymerases. Presently disclosed polynucleotides include those that encode an RGN having the amino acid sequence set forth as SEQ ID NO: 1, and active fragments or variants thereof, that retain the ability to bind to a target sequence in an RNA-guided sequence-specific manner and comprise: a) a S at a position corresponding to amino acid position 1020 in SEQ ID NO: 1, b) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1, c) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1, d) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1, and e) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1. Presently disclosed polynucleotides also include those that encode an RGN having the amino acid sequence set forth as SEQ ID NO: 579, and active fragments or variants thereof, that retain the ability to bind to a target sequence in an RNA-guided sequence-specific manner and comprise a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 579. Presently disclosed polynucleotides also include those that encode an RGN having the amino acid sequence set forth as SEQ ID NO: 584, and active fragments or variants thereof, that retain the ability to bind to a target sequence in an RNA-guided sequence-specific manner and comprise a T at a position corresponding to amino acid position 1021 in SEQ ID NO: 584 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 584. Presently disclosed polynucleotides also include those that encode an RGN having the amino acid sequence set forth as SEQ ID NO: 583, and active fragments or variants thereof, that retain the ability to bind to a target sequence in an RNA-guided sequence-specific manner and comprise an N at a position corresponding to amino acid position 1021 in SEQ ID NO: 583 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 583. Presently disclosed polynucleotides also include those that encode an RGN having the amino acid sequence set forth as SEQ ID NO: 591, and active fragments or variants thereof, that retain the ability to bind to a target sequence in an RNA-guided sequence-specific manner and comprise: a) a Q at a position corresponding to amino acid position 975 in SEQ ID NO: 591, b) an A at a position corresponding to amino acid position 1020 in SEQ ID NO: 591, c) a G at a position corresponding to amino acid position 1022 in SEQ ID NO: 591, and d) a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 591. Also provided herein are polynucleotides encoding a PE comprising a polymerase operably linked to an RGN, wherein the RGN is LG10221, LPG10209, LPG10210, LPG10212, LPG10213, APG07433.1, APG05586, APG01604, or LPG10145, or an active variant or fragment thereof. The presently disclosed compositions and methods can also comprise a polynucleotide encoding a polymerase (e.g., reverse transcriptase), wherein it is provided in trans with a polynucleotide encoding a RGN polypeptide. The use of the term "polynucleotide" or “nucleic acid molecule” is not intended to limit the present disclosure to polynucleotides comprising DNA. Those of ordinary skill in the art will 46 Atty Dkt No: L1034381390WO (0330.1) recognize that polynucleotides can comprise ribonucleotides (RNA) and combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues. These include peptide nucleic acids (PNAs), PNA-DNA chimers, locked nucleic acids (LNAs), and phosphothiorate linked sequences. The polynucleotides disclosed herein also encompass all forms of sequences including, but not limited to, single-stranded forms, double-stranded forms, DNA-RNA hybrids, triplex structures, stem-and- loop structures, circular RNA (circRNA), and the like. In some of those embodiments wherein the presently disclosed compositions and methods comprise a polynucleotide encoding an RGN, a polymerase, or a PE, the polynucleotide is an RNA polynucleotide (e.g., an mRNA (messenger RNA) molecule). An mRNA refers to any polynucleotide which encodes a polypeptide of interest and which is capable of being translated to produce the encoded polypeptide of interest in vitro, in vivo, in situ, or ex vivo. In some embodiments, the basic components of an mRNA molecule include at least a coding region, a 5′ untranslated region (UTR), a 3′ UTR, a 5′ cap and a poly-A tail. A 5′ UTR, situated 5′ of a coding sequence and transcribed as part of an mRNA, may comprise various regulatory elements, including, e.g., 5′ cap structure, G- quadruplex structure (G4), stem-loop structure, and internal ribosome entry sites (IRES), which can control translation initiation of the mRNA. A 3′ UTR, situated 3′ of a coding sequence and transcribed as part of an mRNA, can be involved in numerous regulatory processes including transcript cleavage, stability and polyadenylation, translation, and mRNA localization. The 3′ UTR can serve as a binding site for numerous regulatory proteins and small non-coding RNAs, e.g., microRNAs. A 5′ UTR and / or a 3′ UTR heterologous to an mRNA originates from an organism or species that is different from that of the mRNA, or if from the same organism or species as the mRNA, is substantially modified from its native form in composition and / or genomic locus by deliberate human intervention. In some embodiments, inclusion of a 5′ UTR and / or a 3′ UTR heterologous to an mRNA encoding an RGN polypeptide, polymerase or PE of the disclosure improves polypeptide synthesis from the mRNA in a tissue (e.g., liver, or cells in vitro, such as stem cells, hepatocytes or lymphocytes). Heterologous 5′ UTRs and / or 3′ UTRs may, for example, increase protein synthesis by increasing the time that the mRNA remains in translating polysomes (message stability) and / or the rate at which ribosomes initiate translation on the mRNA (message translation efficiency). Thus, inclusion of a 5′ UTR and / or a 3′ UTR heterologous to an mRNA encoding an RGN polypeptide, polymerase, or PE of the disclosure can lead to prolonged and / or increased polypeptide synthesis, enabling improved cleavage or modification of a target polynucleotide by the RGN polypeptide or PE or PE system. In some embodiments, the enhanced polypeptide synthesis from an mRNA occurs in a tissue-specific manner. Heterologous UTR sequences are described, for example, in US 2023 / 0050143 and US 2017 / 0252461. In some embodiments, an mRNA encoding an RGN, polymerase, or PE useful in the presently disclosed methods and compositions can include one or more structural and / or chemical 47 Atty Dkt No: L1034381390WO (0330.1) modifications or alterations which impart useful properties to the polynucleotide. For instance, a useful property of an mRNA includes the lack of a substantial induction of the innate immune response of a cell into which the mRNA is introduced. A “structural” feature or modification is one in which two or more linked nucleotides are inserted, deleted, duplicated, inverted or randomized in an mRNA without significant chemical modification to the nucleotides themselves. Because chemical bonds will necessarily be broken and reformed to effect a structural modification, structural modifications are of a chemical nature and hence are chemical modifications. However, structural modifications will result in a different sequence of nucleotides. Chemical modifications to mRNA can involve inclusion of 5-methylcytosine, N1-methyl-pseudouridine, pseudouridine, 2-thiouridine, 4- thiouridine, 5-methoxyuridine, 2′Fluoroguanosine, 2′Fluorouridine, 5-bromouridine, 5-(2- carbomethoxyvinyl) uridine, 5-[3(1-E-propenylamino)] uridine, α-thiocytidine, N6-methyladenosine, 5-methylcytidine, N4-acetylcytidine, 5-formylcytidine, or combinations thereof, in an mRNA. The polynucleotides encoding RGNs, polymerases, PEs, and / or guide RNAs can be codon optimized for expression in an organism of interest. A "codon-optimized” coding sequence is a polynucleotide coding sequence having its frequency of codon usage designed to mimic the frequency of preferred codon usage or transcription conditions of a particular host cell. Expression in the particular host cell or organism is enhanced as a result of the alteration of one or more codons at the nucleic acid level such that the translated amino acid sequence is not changed. Polynucleotides can be codon optimized, either wholly or in part. Codon tables and other references providing preference information for a wide range of organisms are available in the art (see, e.g., Campbell and Gowri (1990) Plant Physiol.92:1-11 for a discussion of plant-preferred codon usage). Methods are available in the art for synthesizing plant-preferred genes or mammalian (for example human) codon-optimized coding sequences. See, for example, U.S. Patent Nos.5,380,831, and 5,436,391, and Murray et al. (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference. Polynucleotides encoding the RGNs, polymerases, PEs and / or gRNAs provided herein can be provided in expression cassettes for in vitro expression or expression in a cell, organelle, embryo, or organism of interest. The cassette will include 5' and 3' regulatory sequences operably linked to a polynucleotide encoding an RGN, polymerase, PE, and / or gRNA provided herein that allows for expression of the polynucleotide. The cassette may additionally contain at least one additional gene or genetic element to be cotransformed into the organism. Where additional genes or elements are included, the components are operably linked. The term “operably linked” is intended to mean a functional linkage between two or more elements. For example, an operable linkage between a promoter and a coding region of interest (e.g., region coding for an RGN and / or gRNA) is a functional link that allows for expression of the coding region of interest. Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions (either by fusion or insertion), by “operably linked” or “operably fused” is intended that the coding regions are in the same reading frame, even if one is inserted into another. In some embodiments, 48 Atty Dkt No: L1034381390WO (0330.1) polypeptides that are “operably fused” or “operably linked” means that the structure and / or biological activity of each individual peptide is also present in the fusion. Alternatively, the additional gene(s) or element(s) can be provided on multiple expression cassettes. For example, the nucleotide sequence encoding a presently disclosed RGN, polymerase, or PE can be present on one expression cassette, whereas the nucleotide sequence encoding a guide RNA can be on a separate expression cassette. Such an expression cassette is provided with a plurality of restriction sites and / or recombination sites for insertion of the polynucleotides to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain a selectable marker gene. The expression cassette will include in the 5'-3' direction of transcription, a transcriptional (and, in some embodiments, translational) initiation region (i.e., a promoter), an RGN-, polymerase-, PE-, and / or gRNA-encoding polynucleotide of the invention, and a transcriptional (and in some embodiments, translational) termination region (i.e., termination region) functional in the cell or organism of interest. The promoters of the disclosure are capable of directing or driving expression of a coding sequence in a host cell. The regulatory regions (e.g., promoters, transcriptional regulatory regions, and translational termination regions) may be endogenous or heterologous to the host cell or to each other. As used herein, “heterologous” in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and / or genomic locus by deliberate human intervention. As used herein, a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence. Convenient termination regions include ones from simian virus (SV40), human growth hormone (hGH), bovine growth hormone (BGH), and rabbit beta-globin (rbGlob). See also Proudfoot (1991) Cell 64:671-674; Munroe et al. (1990) Gene 91:151-158; Schek et al. (1992) Molecular and Cellular Biology 12(12):5386-5393; Gil and Proudfoot (1987) Cell 49(3):399-406; Goodwin and Rottman (1992) The Journal of Biological Chemistry 267(23):16330-16334; and Lanoix and Acheson (1988) EMBO J.7(8): 2515-2522. Additional termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet.262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev.5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Nucleic Acids Res.17:7891-7903; and Joshi et al. (1987) Nucleic Acids Res.15:9627-9639. Additional regulatory signals include, but are not limited to, transcriptional initiation start sites, operators, activators, enhancers, other regulatory elements, ribosomal binding sites, an initiation codon, termination signals, and the like. See, for example, U.S. Pat. Nos.5,039,523 and 4,853,331; EPO 0480762A2; Sambrook et al. (1992) Molecular Cloning: A Laboratory Manual, ed. Maniatis et al. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.), hereinafter "Sambrook 11"; 49 Atty Dkt No: L1034381390WO (0330.1) Davis et al., eds. (1980) Advanced Bacterial Genetics (Cold Spring Harbor Laboratory Press), Cold Spring Harbor, N.Y., and the references cited therein. In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved. A number of promoters can be used in the practice of the disclosure. The promoters can be selected based on the desired outcome. The nucleic acids can be combined with constitutive, inducible, growth stage-specific, cell type-specific, tissue-preferred, tissue-specific, or other promoters for expression in the organism of interest. See, for example, promoters set forth in WO 99 / 43838 and in US Patent Nos: 8,575,425; 7,790,846; 8,147,856; 8,586832; 7,772,369; 7,534,939; 6,072,050; 5,659,026; 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611; herein incorporated by reference. Exemplary constitutive promoters for expression in cells of the present disclosure include: an SV40 early promoter; a mouse mammary tumor virus long terminal repeat (LTR) promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (HSV) promoter; a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE); a rous sarcoma virus (RSV) promoter; a human ubiquitin C promoter (UBC); a human U6 small nuclear promoter (U6); an enhanced U6 promoter; a human H1 promoter from RNA polymerase III (H1); a human elongation factor 1α promoter (EF1A); a human beta-actin promoter (ACTB); a human or mouse phosphoglycerate kinase 1 promoter (PGK); a chicken β-Actin promoter coupled with CMV early enhancer (CAGG); a yeast transcription elongation factor promoter (TEF1); and the like. See, for example, Miyagishi et al. (2002) Nature Biotechnology 20:497-500; Xia et al. (2003) Nucleic Acids Res.31(17):e100-e100; Pasleau et al. (1985) Gene 38:227–232; Martin-Gallardo et al. (1988) Gene 70: 51–56; Oellig and Seliger (1990) J Neurosci Res 26: 390–396; Manthorpe et al. (1993) Hum Gene Ther 4: 419–431; Yew et al. (1997) Hum Gene Ther 8: 575–584; Xu et al. (2001) Gene 272: 149–156; Nguyen et al. (2008) J Surg Res 148: 60–66; Costa et al. (2005) Nat Meth.2:259–260; Lam and Truong (2020) ACS Synth. Biol. 9(10):2625–2631. For expression in plants, constitutive promoters also include CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol.12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet.81:581-588); and MAS (Velten et al. (1984) EMBO J.3:2723-2730). Examples of inducible promoters include: stress-regulated promoters such as Adh1 promoter, Hsp70 promoter, and Hsp90 promoter (Wurm et al. (1986) Proc. Natl. Acad. Sci. USA.83:5414– 50 Atty Dkt No: L1034381390WO (0330.1) 5418; Nover L. Heat Shock Response. CRC Press; Boca Raton, FL, USA: 1991); light-inducible promoters such as PPDK promoter and pepcarboxylase promoter; metal-regulated promoters (Mayo et al. (1982) Cell.29:99–108; Searle et al. (1985) Mol. Cell. Biol.5:1480–1489); hormone-responsive promoters including a glucocorticoid-responsive promoter (Hynes et al. (1981) Proc. Natl. Acad. Sci. USA.78:2038–2042; Klock et al. (1987) Nature.329:734–736). Chemically regulated promoters include: In2-2 promoter which is safener induced (U.S. Pat. No.5,364,780); the Axig1 promoter which is auxin induced and tapetum specific but also active in callus (PCT US01 / 22169); the steroid- responsive promoters (see, for example, the ERE promoter which is estrogen induced, and the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998) Plant J.14(2):247-257); tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet.227:229-237; Gossen et al. (1993) Trends Biochem Sci.18:471–475; Gossen and Bujard (1992) Proc. Natl Acad. Sci. USA 89:5547– 5551; Zhou et al. (2006) Gene Ther.13:1382–1390; and U.S. Pat. Nos.5,814,618 and 5,789,156); isopropyl-beta-D-thiogalactopyranoside (IPTG)-regulated promoters; and lactose-regulated promoters. Inducible expression can be obtained using operator systems including AlcR / acetaldehyde, ArgR / L-arginine, BirA / biotinyl-AMP, CymR / cumate, EthR / 2-phenylethylbutyrate, HdnoR / 6- hydroxynicotine, HucR / uric acid, MphR(A) / macrolides, PIP / Streptogramins, Rex / NADH, RheA / heat, ScbR / SCB1, TraR / 3-oxo-C8-HSL, and TtgR / phloretin; see, for example, U.S. Patent No. 8,728,759B2; U.S. Patent No.7,745,592B2; Weber and Fussenegger (2004) Methods Mol. Biol. 267:451–466; Hartenbach et al. (2007) Nucleic Acids Res.35:e136; Weber et al. (2009) Metab. Eng. 11:117–124; Weber et al. (2008) Proc. Natl. Acad. Sci. USA.105:9994–9998; Malphettes et al. (2005) Nucleic Acids Res. 33:e107; Kemmer et al. (2010) Nat. Biotechnol.28:355–360; Weber et al. (2002) Nat. Biotechnol.20:901–907; Fussenegger et al. (2000) Nat. Biotechnol.18:1203–1208; Weber et al. (2006) Metab. Eng.8:273–280; Weber et al. (2003) Nucleic Acids Res.31:e69; Weber et al. (2003) Nucleic Acids Res.31:e71; Neddermann et al. (2003) EMBO Rep.4:159–165; and Gitzinger et al. (2009) Proc. Natl. Acad. Sci. USA.106:10638–10643. Inducible expression can be obtained using protein-protein interaction systems including: rapamycin-induced interaction between FKBP12 (FK506 binding protein 12) and mTOR (Rivera et al. (1996) Nat. Med.2:1028–1032; Belshaw et al. (1996) Proc. Natl. Acad. Sci. USA.93:4604–46077); abscisic acid (ABA)-regulated interaction between PYL1 (abscisic acid receptor) and ABI1 (protein phosphatase 2C56) (Liang et al. (2011) Sci. Signal.4(164):rs2-rs2); and light-induced protein–protein interaction systems (Wang et al. (2012) Nat. Methods. 9:266–269; Yamada et al. (2018) Cell. Rep.25:487–500). Tissue-specific or tissue-preferred promoters can be utilized to target expression of an expression construct within a particular tissue. In some embodiments, the tissue-specific or tissue- preferred promoters are active in mammalian tissue. Examples of tissue-specific or tissue-preferred promoters include promoters that initiate transcription preferentially in certain tissues, such as white blood cells (e.g., CD4 T cell), heart, kidney, liver, CNS, eye, pancreas, skeletal muscle, and testis. In 51 Atty Dkt No: L1034381390WO (0330.1) some embodiments, the tissue-specific or tissue-preferred promoters are active in plant tissue. Examples of promoters under developmental control in plants include promoters that initiate transcription preferentially in certain tissues, such as leaves, roots, fruit, seeds, or flowers. A "tissue specific" promoter is a promoter that initiates transcription only in certain tissues. Unlike constitutive expression of genes, tissue-specific expression is the result of several interacting levels of gene regulation. As such, promoters from homologous or closely related plant species can be preferable to use to achieve efficient and reliable expression of transgenes in particular tissues. In some embodiments, the expression comprises a tissue-preferred promoter. A "tissue preferred" promoter is a promoter that initiates transcription preferentially, but not necessarily entirely or solely in certain tissues. In some embodiments, the polynucleotides encoding an RGN, polymerase, PE, and / or gRNA comprise a cell type-specific promoter. A "cell type specific" promoter is a promoter that primarily drives expression in certain cell types in one or more organs. Some examples of cells in which cell type specific promoters may be primarily active include, for example, a primary cell, a neuronal cell, a glial cell, an adipocyte, a cardiomyocyte, a smooth muscle cell, a photoreceptor cell, and a retinal ganglia cell. Some examples of plant cells in which cell type specific promoters functional in plants may be primarily active include, for example, BETL cells, vascular cells in roots, leaves, stalk cells, and stem cells. The polynucleotides can also include cell type preferred promoters. A "cell type preferred" promoter is a promoter that primarily drives expression mostly, but not necessarily entirely or solely in certain cell types in one or more organs. Some examples of cells in which cell type preferred promoters may be preferentially active include, for example, a primary cell, a neuron, an adipocyte, a cardiomyocyte, a smooth muscle cell, and a photoreceptor cell. Some examples of plant cells in which cell type preferred promoters functional in plants may be preferentially active include, for example, BETL cells, vascular cells in roots, leaves, stalk cells, and stem cells. The nucleic acid sequences encoding the RGNs, polymerases, PEs, and / or gRNAs can be operably linked to a promoter sequence that is recognized by a phage RNA polymerase for example, for in vitro mRNA synthesis. In such embodiments, the in vitro-transcribed RNA can be purified for use in the methods described herein. For example, the promoter sequence can be a T7, T3, or SP6 promoter sequence or a variation of a T7, T3, or SP6 promoter sequence. In such embodiments, the expressed protein and / or RNAs can be purified for use in the methods of genome modification described herein. In some embodiments, the polynucleotide encoding the RGN, polymerase, PEs, and / or gRNA can be linked to a polyadenylation signal (e.g., SV40 polyA signal and other signals functional in plants) and / or at least one transcriptional termination sequence. Additionally, the sequence encoding the RGN, polymerase, or PE also can be linked to sequence(s) encoding at least one nuclear localization signal, at least one cell-penetrating domain, and / or at least one signal peptide capable of trafficking proteins to particular subcellular locations, as described elsewhere herein. 52 Atty Dkt No: L1034381390WO (0330.1) The polynucleotide encoding the RGN, polymerase, PE, and / or gRNA can be present in a vector or multiple vectors. A “vector” refers to a polynucleotide composition for transferring, delivering, or introducing a nucleic acid into a host cell. Suitable vectors include plasmid vectors, phagemids, cosmids, artificial / mini-chromosomes, transposons, and viral vectors (e.g., lentiviral vectors, adeno-associated viral vectors, baculoviral vector). The vector can comprise additional expression control sequences (e.g., enhancer sequences, Kozak sequences, polyadenylation sequences, transcriptional termination sequences), selectable marker sequences (e.g., antibiotic resistance genes), origins of replication, and the like. Additional information can be found in "Current Protocols in Molecular Biology" Ausubel et al., John Wiley & Sons, New York, 2003 or "Molecular Cloning: A Laboratory Manual" Sambrook & Russell, Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 3rd edition, 2001. The vector can also comprise a selectable marker gene for the selection of transformed cells. Selectable marker genes are utilized for the selection of transformed cells or tissues. Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4- dichlorophenoxyacetate (2,4-D). Marker genes can include genes that allow selection for growth on a particular nutrient or substance, such as dihydrofolate reductase (DHFR; Simonsen and Levinson (1983) Proc. Natl. Acad. Sci. U.S.A.80:2495-2499), histidinol dehydrogenase (hisD; Hartman and Mulligan (1988) Proc. Natl. Acad. Sci. U.S.A.85:8047-8051), puromycin-N-acetyl transferase (PAC or puro; de la Luna et al. (1988) Gene 62:121- 126), thymidine kinase (TK; Littlefield (1964) Science 145:709-710), and xanthine-guanine phosphoribosyltransferase (XGPRT or gpt; Mulligan and Berg (1981) Proc. Natl. Acad. Sci. U.S.A.78:2072- 2076).   The expression cassette or vector comprising the polynucleotide encoding an RGN polypeptide, polymerase, and / or PE can further comprise a polynucleotide encoding a gRNA. The polynucleotide sequence encoding the gRNA can be operably linked to at least one transcriptional control sequence for expression of the gRNA in the organism or host cell of interest. For example, the polynucleotide encoding the gRNA can be operably linked to a promoter sequence that is recognized by RNA polymerase III (Pol III). Examples of suitable Pol III promoters include, but are not limited to, mammalian U6, U3, H1, and 7SL RNA promoters and rice U6 and U3 promoters, such as the promoter set forth as SEQ ID NO: 609 and those disclosed in International Appl. Publ. No. WO 2022 / 261394, which is herein incorporated by reference in its entirety. As indicated, expression constructs comprising nucleotide sequences encoding the RGNs, polymerases, PEs, and / or gRNAs can be used to transform organisms of interest. Methods for transformation involve introducing a nucleotide construct into an organism of interest. By "introducing" is intended to introduce the nucleotide construct to the host cell in such a manner that the construct gains access to the interior of the host cell. The methods of the invention do not require a 53 Atty Dkt No: L1034381390WO (0330.1) particular method for introducing a nucleotide construct to a host organism, only that the nucleotide construct gains access to the interior of at least one cell of the host organism. The host cell can be a eukaryotic or prokaryotic cell. In some embodiments, the eukaryotic host cell is a plant cell, a mammalian cell, an avian cell, or an insect cell. In some embodiments, the eukaryotic cell that comprises or expresses a presently disclosed RGN, polymerase, PE, and / or gRNA is a human cell. In some embodiments, the eukaryotic cell that comprises or expresses a presently disclosed RGN, polymerase, PE, and / or gRNA is a primary cell. The term "primary cell" refers to a cell isolated directly from a multicellular organism. Primary cells typically have undergone very few population doublings and are therefore more representative of the main functional component of the tissue from which they are derived in comparison to continuous (tumor or artificially immortalized) cell lines. In some cases, primary cells are cells that have been isolated and then used immediately. In other cases, primary cells cannot divide indefinitely and thus cannot be cultured for long periods of time in vitro. In some embodiments, a primary cell is a primary T cell. In some embodiments, the eukaryotic cell that comprises or expresses a presently disclosed RGN, polymerase, PE, and / or gRNA is a cell of hematopoietic origin, such as an immune cell (i.e., a cell of the innate or adaptive immune system) including but not limited to a B cell, a T cell, a natural killer (NK) cell, a chimeric antigen receptor T (CAR-T) cell, a monocyte, a macrophage, and a dendritic cell. In some embodiments, the eukaryotic cell is a pluripotent stem cell or an induced pluripotent stem cell. In some embodiments, the eukaryotic cell that comprises or expresses a presently disclosed RGN, polymerase, PE, and / or gRNA is an ocular cell, muscle cell (e.g., skeletal muscle cell), epithelial cell (e.g., lung epithelial cell), or a diseased cell (e.g., tumor cell). Methods for introducing nucleotide constructs into plants and other host cells are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods. The methods result in a transformed organism, such as a plant, including whole plants, as well as plant organs (e.g., leaves, stems, roots, etc.), seeds, plant cells, propagules, embryos and progeny of the same. Plant cells can be differentiated or undifferentiated (e.g., callus, suspension culture cells, protoplasts, leaf cells, root cells, phloem cells, pollen). In some embodiments, the presently disclosed methods can result in a transformed organism or cell line derived from these transformed cells. "Transgenic organisms" or "transformed organisms" or "stably transformed" organisms or cells or tissues refers to organisms that have incorporated or integrated a polynucleotide encoding an RGN, polymerase, PE, and / or gRNA of the disclosure. It is recognized that other exogenous or endogenous nucleic acid sequences or DNA fragments may also be incorporated into the host cell. Agrobacterium-and biolistic-mediated transformation remain the two predominantly employed approaches for transformation of plant cells. However, transformation of a host cell may be performed by infection, transfection, microinjection, electroporation, microprojection, biolistics or particle bombardment, electroporation, silica / carbon fibers, ultrasound mediated, PEG mediated, calcium 54 Atty Dkt No: L1034381390WO (0330.1) phosphate co-precipitation, polycation DMSO technique, DEAE dextran procedure, and viral mediated, liposome mediated and the like. Viral-mediated introduction of a polynucleotide encoding an RGN, polymerase, PE, and / or gRNA includes retroviral, lentiviral, adenoviral, and adeno- associated viral mediated introduction and expression, as well as the use of Caulimoviruses (e.g., cauliflower mosaic virus), Geminiviruses (e.g., bean golden yellow mosaic virus or maize streak virus), and RNA plant viruses (e.g., tobacco mosaic virus). Transformation protocols as well as protocols for introducing polypeptides or polynucleotide sequences into plants may vary depending on the type of host cell (e.g., monocot or dicot plant cell) targeted for transformation. Methods for transformation are known in the art and include those set forth in US Patent Nos: 8,575,425; 7,692,068; 8,802,934; 7,541,517; each of which is herein incorporated by reference. See, also, Rakoczy-Trojanowska, M. (2002) Cell Mol Biol Lett.7:849- 858; Jones et al. (2005) Plant Methods 1:5; Rivera et al. (2012) Physics of Life Reviews 9:308-345; Bartlett et al. (2008) Plant Methods 4:1-12; Bates, G.W. (1999) Methods in Molecular Biology 111:359-366; Binns and Thomashow (1988) Annual Reviews in Microbiology 42:575-606; Christou, P. (1992) The Plant Journal 2:275-281; Christou, P. (1995) Euphytica 85:13-27; Tzfira et al. (2004) TRENDS in Genetics 20:375-383; Yao et al. (2006) Journal of Experimental Botany 57:3737-3746; Zupan and Zambryski (1995) Plant Physiology 107:1041-1047; Jones et al. (2005) Plant Methods 1:5. Transformation may result in stable or transient incorporation of the nucleic acid into the cell. "Stable transformation" is intended to mean that the nucleotide construct introduced into a host cell integrates into the genome of the host cell and is capable of being inherited by the progeny thereof. "Transient transformation" is intended to mean that a polynucleotide is introduced into the host cell and does not integrate into the genome of the host cell. Methods for transformation of chloroplasts are known in the art. See, for example, Svab et al. (1990) Proc. Nail. Acad. Sci. USA 87:8526-8530; Svab and Maliga (1993) Proc. Natl. Acad. Sci. USA 90:913-917; Svab and Maliga (1993) EMBO J.12:601-606. The method relies on particle gun delivery of DNA containing a selectable marker and targeting of the DNA to the plastid genome through homologous recombination. Additionally, plastid transformation can be accomplished by transactivation of a silent plastid-borne transgene by tissue-preferred expression of a nuclear-encoded and plastid-directed RNA polymerase. Such a system has been reported in McBride et al. (1994) Proc. Natl. Acad. Sci. USA 91:7301-7305. The cells that have been transformed may be grown into a transgenic organism, such as a plant, in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that the polynucleotide encoding an RGN, polymerase, PE, and / or gRNA is stably maintained and inherited and then seeds harvested to ensure the presence of the polynucleotide encoding an RGN, polymerase, 55 Atty Dkt No: L1034381390WO (0330.1) PE, and / or gRNA. In this manner, the present disclosure provides a transformed plant or plant part having a nucleotide construct of the disclosure, for example, an expression cassette of the disclosure, stably incorporated into their genome. Seed having an expression cassette of the disclosure stably incorporated into their genome can be referred to as "transgenic seed". Alternatively, cells that have been transformed may be introduced into an organism. These cells could have originated from the organism, wherein the cells are transformed in an ex vivo approach. These cells can be autologous (originated and returned to the same subject), allogeneic (the donor and recipient subjects are of the same species). The sequences provided herein may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Examples of plants of interest include, but are not limited to, corn (maize), sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, and oilseed rape, Brassica sp., alfalfa, rye, millet, safflower, peanuts, sweet potato, cassava, coffee, coconut, pineapple, citrus trees, cocoa, tea, banana, avocado, fig, guava, mango, olive, papaya, cashew, macadamia, almond, oats, vegetables, ornamentals, and conifers. Vegetables include, but are not limited to, tomatoes, lettuce, green beans, lima beans, peas, and members of the genus Curcumis such as cucumber, cantaloupe, and musk melon. Ornamentals include, but are not limited to, azalea, hydrangea, hibiscus, roses, tulips, daffodils, petunias, carnation, poinsettia, and chrysanthemum. In specific embodiments, plants of the present invention are crop plants (for example, maize, sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, oilseed rape, etc.). As used herein, the term plant includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like. Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides. Further provided is a processed plant product or byproduct that retains the sequences disclosed herein, including for example, soymeal. The polynucleotides encoding the RGNs, polymerase, PE, and / or gRNA or comprising the gRNAs can be used to transform any eukaryotic species, including but not limited to animals (e.g., mammals, humans, insects, fish, birds, and reptiles), plants, fungi, amoeba, algae, and yeast. In some embodiments, the polynucleotides encoding the RGNs, polymerase, PE, and / or gRNAs or comprising the gRNAs can be used to transform any prokaryotic species, including but not limited to, archaea and bacteria (e.g., Bacillus sp., Klebsiella sp. Streptomyces sp., Rhizobium sp., Escherichia sp., Pseudomonas sp., Salmonella sp., Shigella sp., Vibrio sp., Yersinia sp., Mycoplasma sp., 56 Atty Dkt No: L1034381390WO (0330.1) Agrobacterium, Lactobacillus sp.). Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids in mammalian, insect, or avian cells or target tissues. Such methods can be used to administer nucleic acids encoding components of an RGN system to cells in culture, or in a host organism. Non-viral vector delivery systems include DNA plasmids, RNA (e.g., a transcript of a vector described herein), naked nucleic acid, and nucleic acid complexed with a delivery vehicle, such as a liposome. Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell. Non-limiting examples include vectors utilizing Caulimoviruses (e.g., cauliflower mosaic virus), Geminiviruses (e.g., bean golden yellow mosaic virus or maize steak virus), and RNA plant viruses (e.g., tobacco mosaic virus). For a review of gene therapy procedures, see Anderson, Science 256: 808- 813 (1992); Nabel & Feigner, TIBTECH 11:211-217 (1993); Mitani & Caskey, TIBTECH 11:162-166 (1993); Dillon, TIBTECH 11:167-175 (1993); Miller, Nature 357:455-460 (1992); Van Brunt, Biotechnology 6(10): 1149-1154 (1988); Vigne, Restorative Neurology and Neuroscience 8:35-36 (1995); Kremer & Perricaudet, British Medical Bulletin 51(1):31-44 (1995); Haddada et al., in Current Topics in Microbiology and Immunology, Doerfler and Bohm (eds) (1995); and Yu et al., Gene Therapy 1:13-26 (1994). Methods of non-viral delivery of nucleic acids include lipofection, nucleofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid: nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Lipofection is described in e.g., U.S. Pat. Nos. 5,049,386, 4,946,787; and 4,897,355) and lipofection reagents are sold commercially (e.g., Transfectam ™ and Lipofectin™). Cationic and neutral lipids that are suitable for efficient receptor-recognition lipofection of polynucleotides include those of Feigner, WO 91 / 17424; WO 91 / 16024. Delivery can be to cells (e.g. in vitro or ex vivo administration) or target tissues (e.g. in vivo administration). The preparation of lipid:nucleic acid complexes, including targeted liposomes such as immunolipid complexes, is well known to one of skill in the art (see, e.g., Crystal, Science 270:404-410 (1995); Blaese et al., Cancer Gene Ther. 2:291- 297 (1995); Behr et al., Bioconjugate Chem. 5:382-389 (1994); Remy et al., Bioconjugate Chem. 5:647-654 (1994); Gao et al., Gene Therapy 2:710-722 (1995); Ahmad et al., Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787). The use of RNA or DNA viral based systems for the delivery of nucleic acids takes advantage of highly evolved processes for targeting a virus to specific cells in the body and trafficking the viral payload to the nucleus. Viral vectors can be administered directly to patients (in vivo) or they can be used to treat cells in vitro, and the modified cells may optionally be administered to patients (ex vivo). Conventional viral based systems could include retroviral, lentivirus, adenoviral, adeno-associated and herpes simplex virus vectors for gene transfer. Integration in the host genome is possible with the retrovirus, lentivirus, and adeno-associated virus gene transfer methods, often resulting in long term 57 Atty Dkt No: L1034381390WO (0330.1) expression of the inserted transgene. Additionally, high transduction efficiencies have been observed in many different cell types and target tissues. The tropism of a retrovirus can be altered by incorporating foreign envelope proteins, expanding the potential target population of target cells. Lentiviral vectors are retroviral vectors that are able to transduce or infect non-dividing cells and typically produce high viral titers. Selection of a retroviral gene transfer system would therefore depend on the target tissue. Retroviral vectors are comprised of cis-acting long terminal repeats with packaging capacity for up to 6-10 kb of foreign sequence. The minimum cis-acting LTRs are sufficient for replication and packaging of the vectors, which are then used to integrate the therapeutic gene into the target cell to provide permanent transgene expression. Widely used retroviral vectors include those based upon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), Simian Immuno deficiency virus (SIV), human immuno deficiency virus (HIV), and combinations thereof (see, e.g., Buchscher et al., J. Viral. 66:2731-2739 (1992); Johann et al., J. Viral. 66:1635-1640 (1992); Sommnerfelt et al., J. Viral. 176:58-59 (1990); Wilson et al., J. Viral. 63:2374-2378 (1989); Miller et al., J. Viral. 65:2220-2224 (1991); PCT / US94 / 05700). In applications where transient expression is preferred, adenoviral based systems may be used. Adenoviral based vectors are capable of very high transduction efficiency in many cell types and do not require cell division. With such vectors, high titer and levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system. Adeno- associated virus ("AAV") vectors may also be used to transduce cells with target nucleic acids, e.g., in the in vitro production of nucleic acids and peptides, and for in vivo and ex vivo gene therapy procedures (see, e.g., West et al., Virology 160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93 / 24641; Katin, Human Gene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest. 94:1351 (1994). The term "adeno-associated virus" or "AAV" as used herein refers to a member of the class of viruses associated with this name and belonging to the genus dependoparvovirus, family Parvoviridae. Multiple serotypes of this virus are known to be suitable for gene delivery; all known serotypes can infect cells from various tissue types. At least 11, sequentially numbered, have been described. Non- limiting exemplary serotypes useful in the compositions and methods disclosed herein include any of the 11 serotypes (e.g., AAV2, AAV5, AAV6, AAV8), or variant serotypes, e.g., AAV-DJ. AAV is advantageous over other viral vectors for in vivo delivery of genes (e.g., encoding gene editing components) due to their low toxicity and low probability of causing insertional mutagenesis because it typically does not integrate into the host genome. AAV has a packaging limit of about 4.5 to 4.75 Kb. Construction of recombinant AAV vectors is described in a number of publications, including U.S. Pat. No. 5,173,414; Tratschin et al., Mol. Cell. Biol. 5:3251-3260 (1985); Tratschin, et al., Mol. Cell. Biol. 4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470 (1984); and 58 Atty Dkt No: L1034381390WO (0330.1) Samulski et al., 1. Viral. 63:03822-3828 (1989). Packaging cells are typically used to form virus particles that are capable of infecting a host cell. Such cells include 293 cells, which package adenovirus, and ψJ2 cells or PA317 cells, which package retrovirus. Viral vectors used in gene therapy are usually generated by producing a cell line that packages a nucleic acid vector into a viral particle. The vectors typically contain the minimal viral sequences required for packaging and subsequent integration into a host, other viral sequences being replaced by an expression cassette for the polynucleotide(s) to be expressed. The missing viral functions are typically supplied in trans by the packaging cell line. For example, AAV vectors used in gene therapy typically only possess ITR sequences from the AAV genome which are required for packaging and integration into the host genome. Viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences. The cell line may also be infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV. Additional methods for the delivery of nucleic acids to cells are known to those skilled in the art. See, for example, US20030087817, incorporated herein by reference. In some embodiments, a host cell is transiently or non-transiently transfected with one or more vectors described herein. In some embodiments, a cell is transfected as it naturally occurs in a subject. In some embodiments, a cell that is transfected is taken from a subject. In some embodiments, a cell that is transfected is a eukaryotic cell. In some embodiments, the eukaryotic cell is an animal cell (e.g., mammals, humans, insects, fish, birds, and reptiles). In some embodiments, a cell that is transfected is a human cell. In some embodiments, a cell that is transfected is a cell of hematopoietic origin, such as an immune cell (i.e., a cell of the innate or adaptive immune system) including but not limited to a B cell, a T cell, a natural killer (NK) cell, a pluripotent stem cell, an induced pluripotent stem cell, a chimeric antigen receptor T (CAR-T) cell, a monocyte, a macrophage, and a dendritic cell. In some embodiments, the cell is derived from cells taken from a subject, such as a cell line. In some embodiments, the cell or cell line is prokaryotic. In some embodiments, the cell or cell line is eukaryotic. In further embodiments, the cell or cell line is derived from insect, avian, plant, or fungal species. In some embodiments, the cell or cell line may be mammalian, such as for example human, monkey, mouse, cow, swine, goat, hamster, rat, cat, or dog. A wide variety of cell lines for tissue culture are known in the art. Examples of cell lines include, but are not limited to, C8161, CCRF- CEM, MOLT, mIMCD-3, NHDF, HeLaS3, Huhl, Huh4, Huh7, HUVEC, HASMC, HEKn, HEKa, MiaPaCell, Panel, PC-3, TFl, CTLL-2, CIR, Rat6, CVI, RPTE, AlO, T24, 182, A375, ARH-77, Calul, SW480, SW620, SKOV3, SK-UT, CaCo2, P388Dl, SEM-K2, WEHI- 231, HB56, TIB55, lurkat, 145.01, LRMB, Bcl-1, BC-3, IC21, DLD2, Raw264.7, NRK, NRK-52E, MRC5, MEF, Hep G2, HeLa 59 Atty Dkt No: L1034381390WO (0330.1) B, HeLa T4. COS, COS-1, COS-6, COS-M6A, BS-C-1 monkey kidney epithelial, BALB / 3T3 mouse embryo fibroblast, 3T3 Swiss, 3T3-Ll, 132-d5 human fetal fibroblasts; 10.1 mouse fibroblasts, 293-T, 3T3, 721, 9L, A2780, A2780ADR, A2780cis, A172, A20, A253, A431, A-549, ALC, B16, B35, BCP-I cells, BEAS-2B, bEnd.3, BHK-21, BR 293, BxPC3, C3H-10Tl / 2, C6 / 36, Cal-27, CHO, CHO- 7, CHO-IR, CHO-Kl, CHO-K2, CHO-T, CHO Dhfr- / -, COR-L23, COR-L23 / CPR, COR-L235010, CORL23 / R23, COS-7, COV-434, CML Tl, CMT, CT26, D17, DH82, DU145, DuCaP, EL4, EM2, EM3, EMT6 / AR1, EMT6 / AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, HEK-293, HeLa, Hepalclc7, HL-60, HMEC, HT-29, lurkat, lY cells, K562 cells, Ku812, KCL22, KGl, KYOl, LNCap, Ma-Mel 1-48, MC-38, MCF-7, MCF-l0A, MDA-MB-231, MDA-MB-468, MDA-MB-435, MDCKII, MDCKII, MOR / 0.2R, MONO-MAC 6, MTD-lA, MyEnd, NCI-H69 / CPR, NCI-H69 / LX10, NCI- H69 / LX20, NCI-H69 / LX4, NIH-3T3, NALM-1, NW-145, OPCN / OPCT cell lines, Peer, PNT-lA / PNT 2, RenCa, RIN-5F, RMA / RMAS, Saos-2 cells, Sf-9, SkBr3, T2, T-47D, T84, THPl cell line, U373, U87, U937, VCaP, Vero cells, WM39, WT-49, X63, YAC-1, YAR, and transgenic varieties thereof. Cell lines are available from a variety of sources known to those with skill in the art (see, e.g., the American Type Culture Collection (ATCC) (Manassas, Va.)). In some embodiments, a cell transfected with one or more polynucleotides or vectors described herein is used to establish a new cell line comprising one or more vector-derived sequences. In some embodiments, a cell transiently transfected with the components of an RGN or PE system as described herein (such as by transient transfection of one or more vectors, or transfection with RNA), and modified through the activity of an RGN or PE system, is used to establish a new cell line comprising cells containing the modification but lacking any other exogenous sequence. In some embodiments, cells transiently or non-transiently transfected with one or more vectors described herein, or cell lines derived from such cells are used in assessing one or more test compounds. In some embodiments, one or more vectors described herein are used to produce a non-human transgenic animal or transgenic plant. In some embodiments, the transgenic animal is an insect. In further embodiments, the insect is an insect pest, such as a mosquito or tick. In some embodiments, the insect is a plant pest, such as a corn rootworm or a fall armyworm. In some embodiments, the transgenic animal is a bird, such as a chicken, turkey, goose, or duck. In some embodiments, the transgenic animal is a mammal, such as a human, mouse, rat, hamster, monkey, ape, rabbit, swine, cow, horse, goat, sheep, cat, or dog. V. Variants and Fragments of Polypeptides and Polynucleotides The present disclosure provides active variants and fragments of an RNA-guided nuclease (RGN), a polymerase, or a PE comprising the same. The RGN can have the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179, and the corresponding gRNAs, or be an active variant or fragment thereof. In some embodiments, the disclosure provides: 60 Atty Dkt No: L1034381390WO (0330.1) active variants and fragments of an RGN having the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179; active variants and fragments of naturally-occurring CRISPR repeats, including the nucleotide sequence set forth as SEQ ID NOs: 3, 5, 470, 471, 475, 476, 571, 573, and 1180; active variants and fragments of tracrRNAs, including a sequence set forth as SEQ ID NOs: 4, 6, 472, 473, 474, 477, 478, 479, 480, 572, 574, and 1181; active variants and fragments of a PE having the sequence of any one of SEQ ID NOs: 9-11, 111-130, 137-173, 364, 774- 787, 790-814, 817-901, 926, 1143-1155, 1164, 1182-1185, 1189-2085, and 2121-2125; active variants and fragments of a PE having the sequence of any one of SEQ ID NOs: 364, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 1432, 1443, 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718; active variants and fragments of a polymerase having the sequence set forth as any one of SEQ ID NOs: 174, 175, and 2127-2131; and polynucleotides encoding the same. While the activity of a variant or fragment may be altered compared to the polynucleotide or polypeptide of interest, the variant and fragment should retain the functionality of the polynucleotide or polypeptide of interest. For example, a variant or fragment may have increased activity, decreased activity, different spectrum of activity or any other alteration in activity when compared to the polynucleotide or polypeptide of interest. Fragments and variants of RGN polypeptides (or PEs comprising the same) having any one of the amino acid sequences set forth as SEQ ID NOs: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165- 1179, such as those disclosed herein, will retain sequence-specific, RNA-guided DNA-binding activity. In some embodiments, fragments and variants of RGN polypeptides disclosed herein, will retain nuclease (e.g., nickase) activity. Fragments and variants of CRISPR RNA (crRNA) repeats or tracrRNAs disclosed herein, will retain the ability, when part of a guide RNA, to bind to and guide an RGN (or a PE comprising the same) to a target sequence (e.g., target DNA sequence) in a sequence-specific manner. Fragments and variants of polymerases disclosed herein will retain the ability, when part of a PE, to catalyze the addition of nucleotides to a nicked polynucleotide strand, using a template. Fragments and variants of PEs disclosed herein, will retain the ability to, when associated with a PEgRNA, edit a double-stranded polynucleotide through the replacement of a target sequence using the template sequence of the PEgRNA. The term “fragment” refers to a portion of a polynucleotide or polypeptide sequence of the disclosure. "Fragments" or "biologically active portions" include polynucleotides comprising a sufficient number of contiguous nucleotides to retain the biological activity (i.e., binding to and directing an RGN in a sequence-specific manner to a target nucleotide sequence when comprised within a guide RNA). "Fragments" or "biologically active portions" include polypeptides comprising a sufficient number of contiguous amino acid residues to retain the biological activity (i.e., binding to a target sequence in a sequence-specific manner when complexed with a guide RNA). Fragments of 61 Atty Dkt No: L1034381390WO (0330.1) the RGN proteins (or PEs comprising the same) include those that are shorter than the full-length sequences due to the use of an alternate downstream start site. A biologically active portion of an RGN protein can be a polypeptide that comprises, for example, 10, 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 1000, or more contiguous amino acid residues of any one of SEQ ID NOs: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179. A biologically active portion of a PE can be a polypeptide that comprises, for example, 10, 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 1000, or more contiguous amino acid residues of any one of SEQ ID NOs: 9-11, 111-130, 137-173, 364, 774-787, 790-814, 817-901, 926, 1143-1155, 1164, 1182-1185, 1189-2085, and 2121-2125. In some embodiments, a biologically active portion of a PE can be a polypeptide that comprises, for example, 10, 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 1000, or more contiguous amino acid residues of any one of SEQ ID NOs: 364, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 1432, 1443, 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718. A biologically active portion of a polymerase can be a polypeptide that comprises, for example, 10, 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, or more contiguous amino acid residues of any one of SEQ ID NOs: 174, 175, and 2127-2131. A biologically active fragment of a crRNA repeat sequence can comprise at least 8 contiguous amino acids of SEQ ID NO: 3, 5, 470, 471, 475, 476, 571, 573, or 1180. A biologically active portion of a CRISPR repeat sequence can be a polynucleotide that comprises, for example, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides of SEQ ID NO: 3, 5, 470, 471, 475, 476, 571, 573, or 1180. A biologically active fragment of a tracrRNA sequence can comprise at least 10 contiguous amino acids of SEQ ID NO: 4, 6, 472, 473, 474, 477, 478, 479, 480, 572, 574, or 1181. A biologically active portion of a tracrRNA sequence can be a polynucleotide that comprises, for example, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, or more contiguous nucleotides of SEQ ID NO: 4, 6, 472, 473, 474, 477, 478, 479, 480, 572, 574, or 1181. Such biologically active portions can be prepared by recombinant techniques and evaluated for activity. In general, "variants" is intended to mean substantially similar sequences. For polynucleotides, a variant comprises a deletion and / or addition of one or more nucleotides at one or more internal sites within the native polynucleotide and / or a substitution of one or more nucleotides at one or more sites in the native polynucleotide. As used herein, a "native" or “wild type” polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively. For polynucleotides, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the native amino acid sequence of the gene of interest. Naturally occurring allelic variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR) and hybridization techniques as outlined below. Variant polynucleotides also include synthetically derived 62 Atty Dkt No: L1034381390WO (0330.1) polynucleotides, such as those generated, for example, by using site-directed mutagenesis but which still encode the polypeptide or the polynucleotide of interest. Generally, variants of a particular polynucleotide disclosed herein will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters described elsewhere herein. Variants of a particular polynucleotide disclosed herein (i.e., the reference polynucleotide) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein. Where any given pair of polynucleotides disclosed herein is evaluated by comparison of the percent sequence identity shared by the two polypeptides they encode, the percent sequence identity between the two encoded polypeptides is at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity. The presently disclosed polynucleotides encode a polymerase, an RGN polypeptide (or a PE comprising the same). In some embodiments, the presently disclosed polynucleotides encode an RGN polypeptide (or a PE comprising the same) comprising an amino acid sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater identity to any one of the amino acid sequences set forth as SEQ ID NOs: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179. In some embodiments, the presently disclosed polynucleotides encode a polymerase comprising an amino acid sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater identity to the amino acid sequence set forth as any one of SEQ ID NOs: 174 ,175, and 2127-2131. In some embodiments, the presently disclosed polynucleotides encode a PE comprising an amino acid sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater identity to any one of the amino acid sequences set forth as SEQ ID NOs: 9-11, 111-130, 137-173, 364, 774-787, 790-814, 817-901, 926, 1143-1155, 1164, 1182-1185, 1189-2085, and 2121-2125. In some embodiments, the presently disclosed polynucleotides encode a PE comprising an amino acid sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater identity to any one of the amino acid sequences set forth as SEQ ID NOs: 364, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 1432, 1443, 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718. A biologically active variant of an RGN polypeptide of the disclosure may differ by as few as 63 Atty Dkt No: L1034381390WO (0330.1) about 1-15 amino acid residues, as few as about 1-10, such as about 6-10, as few as 5, as few as 4, as few as 3, as few as 2, or as few as 1 amino acid residue. In some embodiments, the polypeptides can comprise an N-terminal or a C-terminal truncation, which can comprise at least a deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300 amino acids or more from either the N- or C-terminus of the polypeptide. In some embodiments, the presently disclosed polynucleotides comprise or encode a crRNA repeat comprising a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater sequence identity to the nucleotide sequences set forth as SEQ ID NO: 3, 5, 470, 471, 475, 476, 571, 573, or 1180. In some embodiments, the presently disclosed polynucleotides comprise or encode a tracrRNA comprising a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater sequence identity to the nucleotide sequences set forth as SEQ ID NO: 4, 6, 472, 473, 474, 477, 478, 479, 480, 572, 574, or 1181. Variants of guide RNAs disclosed herein include guide RNAs that have modified nucleotides, sugars, phosphate backbone, and / or nucleobases. Variant guide RNAs can include modifications including: 2'-O-methyl (2'-O-Me) modification; 2'-fluoro (2'-F) modification; 2'F-4'Cα-OMe modification; 2',4'-di-Cα-OMe modification; 2'-O-methyl 3'-phosphorothioate (MS) modification; 2'- O-methyl 3'thiophosphonoacetate (MSP; 2'-O-methyl 3'thioPACE) modification; 2'-O-methyl 3'phosphonoacetate (MP) modification; phosphorothioate (PS) modification; bridged nucleic acid (BNA) modification (e.g., 2',4' BNA, locked nucleic acid (LNA), N-methyl substituted bridged nucleic acid BNANC[N-Me], 2'-O,4'-C-ethylene bridged nucleic acid (2',4'-ENA), and S-constrained ethyl (cEt)); or a combination thereof. Chemical modifications of spacers, crRNA repeats, crRNAs, tracrRNAs, and guide RNAs are described in International application no. PCT / IB2023 / 058418, filed August 25, 2023, which is hereby incorporated by reference in its entirety herein. Biologically active variants of a guide RNA of the disclosure may differ by as few as about 1- 15 nucleotides, as few as about 1-10, such as about 6-10, as few as 5, as few as 4, as few as 3, as few as 2, or as few as 1 nucleotide. In some embodiments, the polynucleotides can comprise a 5' or 3' truncation, which can comprise at least a deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 nucleotides or more from either the 5' or 3' end of the polynucleotide. It is recognized that modifications may be made to the polymerases, RGN polypeptides (or PEs comprising the same), crRNA repeats, or tracrRNAs provided herein creating variant proteins and polynucleotides. Changes designed by man may be introduced through the application of site-directed mutagenesis techniques. Alternatively, native, as yet unknown or as yet unidentified polynucleotides and / or polypeptides structurally and / or functionally related to the sequences disclosed herein may also 64 Atty Dkt No: L1034381390WO (0330.1) be identified that fall within the scope of the present invention. Conservative amino acid substitutions may be made in nonconserved regions that do not alter the function of the polymerases, RGN proteins, or PEs. Alternatively, modifications may be made that improve the activity of the RGN or PEs. Variant polynucleotides and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling. With such a procedure, one or more different polymerases, RGN proteins or PEs disclosed herein is manipulated to create a new polymerase, RGN protein or PE possessing the desired properties. In this manner, libraries of recombinant polynucleotides are generated from a population of related sequence polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo. For example, using this approach, sequence motifs encoding a domain of interest may be shuffled between the polymerase, RGN, or PE sequences provided herein and other known polymerase, RGN, or PE genes to obtain a new gene coding for a protein with an improved property of interest, such as an increased Kmin the case of an enzyme. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech.15:436- 438; Moore et al. (1997) J. Mol. Biol.272:336-347; Zhang et al. (1997) Proc. Natl. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Patent Nos.5,605,793 and 5,837,458. A "shuffled" nucleic acid is a nucleic acid produced by a shuffling procedure such as any shuffling procedure set forth herein. Shuffled nucleic acids are produced by recombining (physically or virtually) two or more nucleic acids (or character strings), for example in an artificial, and optionally recursive, fashion. Generally, one or more screening steps are used in shuffling processes to identify nucleic acids of interest; this screening step can be performed before or after any recombination step. In some (but not all) shuffling embodiments, it is desirable to perform multiple rounds of recombination prior to selection to increase the diversity of the pool to be screened. The overall process of recombination and selection are optionally repeated recursively. Depending on context, shuffling can refer to an overall process of recombination and selection, or, alternately, can simply refer to the recombinational portions of the overall process. As used herein, "sequence identity" or "identity" in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. It is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Protein sequences that differ by such conservative substitutions are said to have "sequence similarity" or "similarity". Means for measuring sequence similarity are well known to those of skill in the art. Typically, this involves scoring a conservative substitution as a partial rather than a full mismatch. 65 Atty Dkt No: L1034381390WO (0330.1) Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC / GENE (Intelligenetics, Mountain View, California). As used herein, "percentage of sequence identity" means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity. Unless otherwise stated, sequence identity / similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof. By "equivalent program" is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10. Two sequences are "optimally aligned" when they are aligned for similarity scoring using a defined amino acid substitution matrix (e.g., BLOSUM62), gap existence penalty and gap extension penalty so as to arrive at the highest score possible for that pair of sequences. Amino acid substitution matrices and their use in quantifying the similarity between two sequences are well-known in the art and described, e.g., in Dayhoff et al. (1978) "A model of evolutionary change in proteins." In "Atlas of Protein Sequence and Structure," Vol.5, Suppl.3 (ed. M. O. Dayhoff), pp.345-352. Natl. Biomed. Res. Found., Washington, D.C. and Henikoff et al. (1992) Proc. Natl. Acad. Sci. USA 89:10915- 10919. The BLOSUM62 matrix is often used as a default scoring substitution matrix in sequence alignment protocols. The gap existence penalty is imposed for the introduction of a single amino acid gap in one of the aligned sequences, and the gap extension penalty is imposed for each additional empty amino acid position inserted into an already opened gap. The alignment is defined by the amino acid positions of each sequence at which the alignment begins and ends, and optionally by the insertion of a gap or multiple gaps in one or both sequences, so as to arrive at the highest possible score. While optimal alignment and scoring can be accomplished manually, the process is facilitated by the use of a computer-implemented alignment algorithm, e.g., gapped BLAST 2.0, described in 66 Atty Dkt No: L1034381390WO (0330.1) Altschul et al. (1997) Nucleic Acids Res.25:3389-3402, and made available to the public at the National Center for Biotechnology Information Website (World Wide Web at ncbi.nlm.nih.gov). Optimal alignments, including multiple alignments, can be prepared using, e.g., PSI-BLAST, available through World Wide Web at ncbi.nlm.nih.gov and described by Altschul et al. (1997) Nucleic Acids Res.25:3389-3402. With respect to an amino acid sequence that is optimally aligned with a reference sequence, an amino acid residue "corresponds to" the position in the reference sequence with which the residue is paired in the alignment. The "position" is denoted by a number that sequentially identifies each amino acid in the reference sequence based on its position relative to the N-terminus. Owing to deletions, insertion, truncations, fusions, etc., that must be taken into account when determining an optimal alignment, in general the amino acid residue number in a test sequence as determined by simply counting from the N-terminal will not necessarily be the same as the number of its corresponding position in the reference sequence. For example, in a case where there is a deletion in an aligned test sequence, there will be no amino acid that corresponds to a position in the reference sequence at the site of deletion. Where there is an insertion in an aligned reference sequence, that insertion will not correspond to any amino acid position in the reference sequence. In the case of truncations or fusions there can be stretches of amino acids in either the reference or aligned sequence that do not correspond to any amino acid in the corresponding sequence. VI. Antibodies Antibodies to the polymerases, RGN polypeptides, PEs, or ribonucleoprotein complexes comprising the polymerases, RGN polypeptides or PEs of the present disclosure, including those RGN polypeptides (or PEs comprising the same) having the amino acid sequence set forth as any one of SEQ ID NOs: 1, 2, 7, 579, 583, 584, or 591, or active variants or fragments thereof, are also encompassed. Methods for producing antibodies are well known in the art (see, for example, Harlow and Lane (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.; and U.S. Pat. No.4,196,265). These antibodies can be used in kits for the detection and isolation of polymerases, RGN polypeptides, PEs or ribonucleoprotein complexes. Thus, this disclosure provides kits comprising antibodies that specifically bind to the polypeptides or ribonucleoprotein complexes described herein, including, for example, RGN polypeptides (or PEs comprising the same) having the amino acid sequence set forth as any one of SEQ ID NOs: 1, 2, 7, 579, 583, 584, or 591. VII. RGN or PE Systems and Ribonucleoprotein Complexes for Binding and Modifying a Target Sequence and Methods of Making the Same 67 Atty Dkt No: L1034381390WO (0330.1) The present disclosure provides an RNA-guided nuclease (RGN) system for binding a target sequence (e.g., target DNA sequence) of interest, wherein the RGN system comprises at least one RGN polypeptide (or a polynucleotide sequence encoding the same) and one or more guide RNAs (or one or more polynucleotide sequences encoding the same) capable of forming a complex with the RGN polypeptide (ribonucleoprotein complex). The guide RNA hybridizes to the target strand of a target sequence of interest and also forms a complex with the RGN polypeptide, thereby directing the RGN polypeptide to bind to the target sequence. Also provided herein are PE systems for binding and modifying a target sequence of interest, wherein the PE system comprises a polymerase (or a polynucleotide encoding the same) and an RGN (or a polynucleotide encoding the same), along with one or more PEgRNAs (or one or more polynucleotide sequences encoding the same). The PE system may comprise a PE wherein the polymerase is operably linked to the RGN or the polymerase and RGN can be two separate polypeptides. In some embodiments, an RGN (in an RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 1, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCY. In some embodiments, an RGN (in a RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 1, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCY, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof. In some embodiments, an RGN (in a RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 2, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNRYA. In some embodiments, an RGN (in a RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 2, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNRYA, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 5, 475, and 476, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 6, 477, 478, 479, and 480, or an active variant or fragment thereof. In some embodiments, an RGN (in an RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 7, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCC. In some embodiments, a PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 7, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCC, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or 68 Atty Dkt No: L1034381390WO (0330.1) fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof.In some embodiments, the RGN system comprises an RGN polypeptide that is heterologous to the guide RNA, wherein the RGN polypeptide and guide RNA are not found complexed to one another (i.e., bound to one another) in nature. In some embodiments, an RGN (in an RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 579, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNC. In some embodiments, a PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 579, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNC, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof.In some embodiments, the RGN system comprises an RGN polypeptide that is heterologous to the guide RNA, wherein the RGN polypeptide and guide RNA are not found complexed to one another (i.e., bound to one another) in nature. In some embodiments, an RGN (in an RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 583, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNC. In some embodiments, a PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 583, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNC, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof.In some embodiments, the RGN system comprises an RGN polypeptide that is heterologous to the guide RNA, wherein the RGN polypeptide and guide RNA are not found complexed to one another (i.e., bound to one another) in nature. In some embodiments, an RGN (in an RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 584, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCM. In some embodiments, a PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 584, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCM, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof.In some embodiments, the RGN system comprises an RGN polypeptide that is heterologous to the guide RNA, wherein the RGN polypeptide and guide RNA are not found complexed to one another (i.e., bound to one another) in nature. 69 Atty Dkt No: L1034381390WO (0330.1) In some embodiments, an RGN (in an RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 591, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCT. In some embodiments, a PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 591, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNNNCT, when bound to a guide RNA comprising a crRNA repeat sequence of any one of SEQ ID NOs: 3, 470, and 471, or an active variant or fragment thereof, and a tracrRNA sequence of any one of SEQ ID NOs: 4, 472, 473, and 474, or an active variant or fragment thereof.In some embodiments, the RGN system comprises an RGN polypeptide that is heterologous to the guide RNA, wherein the RGN polypeptide and guide RNA are not found complexed to one another (i.e., bound to one another) in nature. In some embodiments, an RGN (in an RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 565, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNGRR. In some embodiments, a PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 565, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNGRR, when bound to a guide RNA comprising a crRNA repeat sequence of SEQ ID NO: 571, or an active variant or fragment thereof, and a tracrRNA sequence of SEQ ID NO: 572, or an active variant or fragment thereof.In some embodiments, the RGN system comprises an RGN polypeptide that is heterologous to the guide RNA, wherein the RGN polypeptide and guide RNA are not found complexed to one another (i.e., bound to one another) in nature. In some embodiments, an RGN (in an RGN system or a PE system comprising the same) has the amino acid sequence set forth as SEQ ID NO: 566, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNGG. In some embodiments, a PE or PE system comprises an RGN having the amino acid sequence set forth as SEQ ID NO: 566, or an active variant or fragment thereof, and binds a target nucleotide sequence adjacent to and 5′ of a PAM sequence set forth as NNGG, when bound to a guide RNA comprising a crRNA repeat sequence of SEQ ID NO: 573 or 1180, or an active variant or fragment thereof, and a tracrRNA sequence of SEQ ID NO: 574 or 1181, or an active variant or fragment thereof. In some embodiments, the RGN system comprises an RGN polypeptide that is heterologous to the guide RNA, wherein the RGN polypeptide and guide RNA are not found complexed to one another (i.e., bound to one another) in nature. In some embodiments, a dual PE (DPE) system for dual polymerase editing is provided, wherein the system comprises a first PE system comprising a first PE (or a polynucleotide encoding the same) and a first PEgRNA (or a polynucleotide encoding the same) and a second PE system comprising a second PE (or a polynucleotide encoding the same) and a second PEgRNA (or a 70 Atty Dkt No: L1034381390WO (0330.1) polynucleotide encoding the same). The first and second PE can be the same or different and can be any one of the PEs described herein. The DPE system can also comprise a PE (or a polynucleotide encoding the same) and a first PEgRNA (or a polynucleotide encoding the same) and a second PEgRNA (or a polynucleotide encoding the same). The first and second PEgRNAs bind to opposite strands of a target DNA so that the intended repair event is installed on both strands of the target DNA. The DNA synthesis template of the first PEgRNA and the DNA synthesis template of the second PEgRNA each encode a single-stranded DNA sequence that is complementary (full or partial) to each other so that the region of the DNA between the two nicked sites is replaced. For large insertions, the DPE system comprises PEgRNAs wherein the DNA synthesis templates are designed such that the replacement sequence (comprising the complementary single- stranded DNA sequences encoded by the first and second DNA synthesis templates) comprises a first recombinase site, as well as a donor DNA comprising a second recombinase site and the corresponding site-specific recombinase that recognizes the first and second recombinase site. The recombination of the replacement sequence and donor DNA results in an insertion of exogenous DNA. As used herein, the term “recombinase” refers to a site-specific enzyme that catalyzes the recombination of DNA between recombinase sites that results in the excision, integration, inversion, or exchange of DNA fragments between the recombinase sites. Non-limiting examples of recombinases are serine recombinases (e.g., Hin, Gin, Tn3, β-six, CinH, ParA, γδ, Bxb1, ϕC31, TP901, TG1, φBT1, R4, φRV1, φFC1, MR11, A118, U153, and gp29) and tyrosine recombinases (e.g., Cre, FLP, R, Lambda, HK101, HK022, and pSAM2). See, e.g., Brown et al., “Serine recombinases as tools for genome engineering.” Methods.2011;53(4):372-9; Hirano et al., “Site- specific recombinases as tools for heterologous gene integration.” Appl. Microbiol. Biotechnol.2011; 92(2):227-39; Chavez and Calos, “Therapeutic applications of the ΦC31 integrase system.” Curr. Gene Ther.2011;11(5):375-81; Turan and Bode, “Site-specific recombinases: from tag-and-target- to tag-and-exchange-based genomic modifications.” FASEB J.2011; 25(12):4088-107; Venken and Bellen, “Genome-wide manipulations of Drosophila melanogaster with transposons, Flp recombinase, and ΦC31 integrase.” Methods Mol. Biol.2012; 859:203-28; Murphy, “Phage recombinases and their applications.” Adv. Virus Res.2012; 83:367-414; Zhang et al., “Conditional gene manipulation: Cre- ating a new biological era.” J. Zhejiang Univ. Sci. B.2012; 13(7):511-24; Karpenshif and Bernstein, “From yeast to mammals: recent advances in genetic control of homologous recombination.” DNA Repair (Amst).2012; 1;11(10):781-8; each of which are hereby incorporated by reference in its entirety. Serine and tyrosine recombinases derive their name from the conserved nucleophilic amino acid residue that it uses to attack the DNA and is covalently linked to the DNA during strand exchange. As used herein, the term “recombinase site” refers to a target nucleotide sequence recognized by a recombinase that undergoes strand exchange with another nucleotide sequence having a similar 71 Atty Dkt No: L1034381390WO (0330.1) recombinase site. Non-limiting examples of recombinase sites are the attB / attP sites recognized by the HK022 and ϕC31 recombinases. The RGN system or PE system for binding a target sequence of interest provided herein can include a ribonucleoprotein (RNP) complex, which is at least one molecule of an RNA bound to at least one protein. The RNP complexes provided herein comprise at least one guide RNA as the RNA component and an RGN polypeptide or PE as the protein component. The guide RNA of an RNP complex of the disclosure can comprise a spacer that hybridizes to a eukaryotic target sequence. In some embodiments, the eukaryotic target sequence comprises a mammalian target sequence. Such RNP complexes can be purified from a cell or organism that naturally expresses an RGN polypeptide and has been engineered to express a particular guide RNA that is specific for a target sequence of interest. In some embodiments, the RNP complex can be purified from a cell or organism that has been transformed with one or more polynucleotides that encode an RGN polypeptide (e.g., an mRNA encoding an RGN polypeptide) or a PE comprising the same, and a guide RNA (or a polynucleotide that comprises a guide RNA) and cultured under conditions to allow for the expression of the RGN polypeptide (or PE) and guide RNA. Methods are provided for making a polymerase, an RGN polypeptide, a PE, or an RNP complex. Such methods comprise culturing a cell comprising a polynucleotide sequence encoding a polymerase, an RGN polypeptide or a PE, and in some embodiments a polynucleotide sequence encoding or comprising a guide RNA, under conditions in which the polymerase, RGN polypeptide or PE (and in some embodiments, the guide RNA) is expressed. The polymerase, RGN polypeptide, PE, or RNP complex can then be purified from a lysate of the cultured cells. In some embodiments, the polynucleotide sequence encoding a polymerase, an RGN polypeptide or PE includes a mRNA (messenger RNA). In some embodiments, methods for assembling an RNP complex comprise combining one or more of the presently disclosed guide RNAs and one or more of the presently disclosed polymerases, RGN polypeptides or PEs under conditions suitable for formation of the RNP complex. Methods for purifying a polymerase, an RGN polypeptide, PE, or RNP complex from a lysate of a biological sample are known in the art (e.g., size exclusion and / or affinity chromatography, 2D- PAGE, HPLC, reversed-phase chromatography, immunoprecipitation). In particular methods, the polymerase, RGN polypeptide or PE is recombinantly produced and comprises a purification tag to aid in its purification, including but not limited to, glutathione-S-transferase (GST), chitin binding protein (CBP), maltose binding protein, thioredoxin (TRX), poly(NANP), tandem affinity purification (TAP) tag, myc, AcV5, AU1, AU5, E, ECS, E2, FLAG (e.g., 3X FLAG tag), HA, nus, Softag 1, Softag 3, Strep, SBP, Glu-Glu, HSV, KT3, S, S1, T7, V5, VSV-G, 6xHis, 10xHis, biotin carboxyl carrier protein (BCCP), and calmodulin. Generally, the tagged polymerase, RGN polypeptide, PE, or RNP complex is purified using immobilized metal affinity chromatography. It will be appreciated that 72 Atty Dkt No: L1034381390WO (0330.1) other similar methods known in the art may be used, including other forms of chromatography or for example immunoprecipitation, either alone or in combination. An "isolated" or "purified" polypeptide, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polypeptide as found in its naturally occurring environment. Thus, an isolated or purified polypeptide is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. A protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein. When the protein of the invention or biologically active portion thereof is recombinantly produced, optimally culture medium represents less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of chemical precursors or non- protein-of-interest chemicals. Similarly, an “isolated” polynucleotide or nucleic acid molecule is removed from its naturally occurring environment. An isolated polynucleotide is substantially free of chemical precursors or other chemicals when chemically synthesized or has been removed from a genomic locus via the breaking of phosphodiester bonds. An isolated polynucleotide can be part of a vector, a composition of matter or can be contained within a cell so long as the cell is not the original environment of the polynucleotide. Particular methods provided herein for binding and / or cleaving a target polynucleotide comprising a target sequence of interest involve the use of an in vitro assembled RNP complex. In vitro assembly of an RNP complex can be performed using any method known in the art in which an RGN polypeptide or PE is contacted with a guide RNA under conditions that allow for binding of the RGN polypeptide or PE to the guide RNA. As used herein, “contact”, contacting”, “contacted,” refer to placing the components of a desired reaction together under conditions suitable for carrying out the desired reaction. The RGN polypeptide or PE can be purified from a biological sample, cell lysate, or culture medium, produced via in vitro translation, or chemically synthesized. The guide RNA can be purified from a biological sample, cell lysate, or culture medium, transcribed in vitro, or chemically synthesized. The RGN polypeptide or PE and guide RNA can be brought into contact in solution (e.g., buffered saline solution) to allow for in vitro assembly of the RNP complex. Some aspects of this disclosure provide kits comprising one or more elements of an RGN system or PE system described herein, including: guide RNAs, polymerases, RGN polypeptides or PEs or polynucleotides encoding the same; cells; and complete RGN or PE systems. In some embodiments, the kit includes suitable reagents, buffers, and / or instructions for using one or more elements of an RGN or PE system, e.g., for in vitro or in vivo nucleic acid editing. Reagents may be provided in any suitable container, such as a vial, a bottle, or a tube. Reagents may be used in a process utilizing one or more of the elements of an RGN or PE system. For example, restriction enzymes may be included for cloning of a polynucleotide encoding a polymerase, an RGN or PE into a vector. In some embodiments, the kit includes instructions regarding the design and use of suitable 73 Atty Dkt No: L1034381390WO (0330.1) guide RNAs for targeted editing of a target sequence. Reagents may be provided in a form that is usable in a particular assay, or in a form that requires addition of one or more other components before use (e.g. in concentrate or lyophilized form). A buffer can be any buffer, including but not limited to a sodium carbonate buffer, a sodium bicarbonate buffer, a borate buffer, a Tris buffer, a MOPS buffer, a HEPES buffer, and combinations thereof. In some embodiments, the buffer is alkaline. In some embodiments, the buffer has a pH from about 7 to about 10. A kit including one or more elements of an RGN or PE system of the disclosure has utility in a wide variety of applications including modifying (e.g., deleting, inserting a donor polynucleotide, translocating, inactivating, activating, base editing, polymerase editing) a target sequence in a multiplicity of cell types. As such, kits including one or more elements of an RGN or PE system of the disclosure may be useful in, for example, gene therapy, drug screening, disease diagnosis, and prognosis. In some embodiments, a kit of the disclosure includes a pharmaceutical kit including a pharmaceutical composition described herein. In some embodiments, a pharmaceutical kit may include: (a) a container containing a composition of the disclosure in lyophilized form and (b) a second container containing a pharmaceutically acceptable diluent (e.g., sterile water) for injection. The pharmaceutically acceptable diluent can be used for reconstitution or dilution of the lyophilized compound of the disclosure. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration. VIII. Methods of Binding, Cleaving, or Modifying a Target Polynucleotide The present disclosure provides methods for binding, cleaving, and / or modifying a target polynucleotide (e.g., target DNA) of interest comprising a target sequence. The methods include delivering an RGN or PE system comprising at least one guide RNA or a polynucleotide encoding the same, and at least one RGN polypeptide (or a PE, or a polymerase and RGN polypeptide provided in trans) or a polynucleotide encoding the same, to the target sequence or a cell, organelle, or embryo comprising the target sequence. The PE system used in methods for binding, cleaving, and / or modifying a target polynucleotide (e.g., target DNA) of interest can comprise a PE comprising a DNA polymerase and an RNA-guided nuclease (RGN) polypeptide, wherein the RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179. In some embodiments, the RGN polypeptide comprises an amino acid sequence having: a) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1 and comprises: i) a S at a position corresponding to amino acid 74 Atty Dkt No: L1034381390WO (0330.1) position 1020 in SEQ ID NO: 1; ii) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1; iii) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1; iv) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1; and v) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1; b) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 579, wherein said RGN polypeptide comprises a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 579; c) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 584, wherein said RGN polypeptide comprises a T at a position corresponding to amino acid position 1021 in SEQ ID NO: 584 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 584; d) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 583, wherein said RGN polypeptide comprises an N at a position corresponding to amino acid position 1021 in SEQ ID NO: 583 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 583; or e) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 591, wherein said RGN polypeptide comprises: i) a Q at a position corresponding to amino acid position 975 in SEQ ID NO: 591; ii) an A at a position corresponding to amino acid position 1020 in SEQ ID NO: 591; iii) a G at a position corresponding to amino acid position 1022 in SEQ ID NO: 591; and iv) a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 591. In some embodiments, the RGN polypeptide comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179. In some embodiments, the RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179. The PE system used in methods for binding, cleaving, and / or modifying a target polynucleotide (e.g., target DNA) of interest can comprise one or more PEgRNAs, or one or more polynucleotides comprising one or more nucleotide sequences encoding the one or more PEgRNAs. The modification of a target polynucleotide comprising a target sequence can comprise insertion of heterologous DNA into the target polynucleotide, deletion of at least one nucleotide from the target polynucleotide, and / or mutation of at least one nucleotide in the target polynucleotide using the one or more PEgRNAs. The PE system used in methods for binding, cleaving, and / or modifying a target polynucleotide (e.g., target DNA) of interest can comprise a PE having an amino acid sequence having at least 90% sequence identity or at least 95% sequence identity to any one of SEQ ID NOs: 9- 11, 111-130, 137-173, 364, 774-787, 790-814, 817-901, 926, 1143-1155, 1164, 1182-1185, 1189- 2085, and 2121-2125. In some embodiments, the PE has the amino acid sequence set forth as any one of SEQ ID NOs: 9-11, 111-130, 137-173, 364, 774-787, 790-814, 817-901, 926, 1143-1155, 1164, 1182-1185, 1189-2085, and 2121-2125. The PE system used in methods for binding, cleaving, and / or modifying a target polynucleotide (e.g., target DNA) of interest can comprise a PE having an amino acid sequence having at least 90% sequence identity or at least 95% sequence identity to any one of SEQ ID NOs: 364, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 1432, 1443, 75 Atty Dkt No: L1034381390WO (0330.1) 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718. In some embodiments, the PE has the amino acid sequence set forth as any one of SEQ ID NOs: 364, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 1432, 1443, 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718. The methods for binding, cleaving, and / or modifying a target polynucleotide (e.g., target DNA) of interest comprising a target sequence can be performed ex vivo or in vitro. In some embodiments, the methods for binding, cleaving, and / or modifying a target polynucleotide (e.g., target DNA) of interest are not methods for treatment of the human or animal body by therapy or are not processes for modifying the germ line genetic identity of a human being. In particular embodiments, the polymerase, RGN, PE, and / or guide RNA is heterologous to the cell, organelle, or embryo to which the polymerase, RGN, PE and / or guide RNA (or polynucleotide(s) encoding at least one of the polymerase, RGN, PE, and guide RNA) are introduced. Delivery of a polynucleotide encoding a guide RNA, a polymerase, a PE, and / or an RGN polypeptide to a cell or embryo can be delivered to a cell or embryo ex vivo, in vitro, or in vivo. The cell or embryo can be cultured under conditions in which the guide RNA, polymerase, PE, and / or RGN polypeptide are expressed. In some embodiments, the method comprises contacting a target polynucleotide with an RNP complex. The contacting can be ex vivo, in vitro, or in vivo. In some embodiments, the method comprises introducing into a cell, organelle, or embryo comprising a target polynucleotide an RNP complex. The RNP complex can be one that has been purified from a biological sample, recombinantly produced and subsequently purified, or in vitro-assembled as described herein. In those embodiments wherein the RGN or PE ribonucleoprotein complex that is contacted with the target polynucleotide, cell, organelle, or embryo, has been assembled in vitro, the method can further comprise the in vitro assembly of the complex prior to contact with the target polynucleotide, cell, organelle, or embryo. A purified or in vitro assembled RGN or PE ribonucleoprotein complex can be introduced into a cell, organelle, or embryo using any method known in the art (e.g., electroporation). In some embodiments, delivery of a polynucleotide encoding a guide RNA, polymerase, a PE, and / or an RGN polypeptide to a cell or embryo is not a method for treatment of the human or animal body by therapy or is not a process for modifying the germ line genetic identity of a human being. In some embodiments, a method comprising contacting a target polynucleotide with an RNP complex is not a method for treatment of the human or animal body by therapy or is not a process for modifying the germ line genetic identity of a human being. In some embodiments, the embryo is a non-human embryo. Upon delivery to or contact with the target polynucleotide or cell, organelle, or embryo comprising the target polynucleotide, the guide RNA directs the RGN polypeptide or PE to bind to the target sequence within the target polynucleotide in a sequence-specific manner. In those embodiments wherein the RGN has nuclease activity, the RGN polypeptide cleaves the target 76 Atty Dkt No: L1034381390WO (0330.1) sequence of interest upon binding. The target sequence (e.g, target DNA sequence) can subsequently be modified via endogenous repair mechanisms, such as non-homologous end joining, or homology- directed repair with a provided donor polynucleotide. In those embodiments wherein the PE comprises an RGN nickase, a single strand of a double-stranded DNA target sequence is nicked and the DNA synthesis template within the extension arm of the associated PEgRNA is used as a template to introduce a desired edit into the target sequence. Methods to measure binding of an RGN polypeptide (or a PE comprising the same) to a target sequence are known in the art and include chromatin immunoprecipitation assays, gel mobility shift assays, DNA pull-down assays, reporter assays, microplate capture and detection assays. Likewise, methods to measure cleavage or modification of a target polynucleotide comprising a target sequence are known in the art and include in vitro or in vivo cleavage assays wherein cleavage is confirmed using PCR, sequencing, or gel electrophoresis, with or without the attachment of an appropriate label (e.g., radioisotope, fluorescent substance) to the target sequence to facilitate detection of degradation products. Alternatively, the nicking triggered exponential amplification reaction (NTEXPAR) assay can be used (see, e.g., Zhang et al. (2016) Chem. Sci.7:4951-4957). In vivo cleavage can be evaluated using the Surveyor assay (Guschin et al. (2010) Methods Mol Biol 649:247-256). In some embodiments, the methods involve the use of a single type of RGN or PE complexed with more than one guide RNA. The more than one guide RNA can target different regions of a single gene or can target multiple genes. In some embodiments, the methods comprise dual polymerase editing wherein a single PE (or a polynucleotide encoding the same) and two PEgRNAs (or polynucleotides encoding the same) that associate with the PE are contacted with a target DNA molecule for the programmable replacement or excision of DNA sequences. Alternatively, a first PE (or a polynucleotide encoding the same) and its associated first PEgRNA (or a polynucleotide encoding the same) and a second PE (or a polynucleotide encoding the same) and its associated second PEgRNA (or a polynucleotide encoding the same) are contacted with a target DNA molecule, wherein the first and second PEs are different from each other. In both scenarios, the two PEgRNAs bind to opposite strands of a target DNA so that the intended repair event is installed on both strands of the target DNA. The DNA synthesis template of the first PEgRNA and the DNA synthesis template of the second PEgRNA each encode a single-stranded DNA sequence that is complementary (full or partial) to each other so that the region of the DNA between the two nicked sites is replaced. For large insertions, the DPE DNA synthesis templates are designed such that the replacement sequence comprises a first recombinase site, and a donor DNA comprising a second recombinase site is introduced, as well as the corresponding site-specific recombinase that recognizes the first and second recombinase site, which results in site-specific integration of exogenous DNA into the target DNA molecule.In those embodiments wherein a donor polynucleotide is not provided, a double- stranded break introduced by an RGN polypeptide can be repaired by a non-homologous end-joining 77 Atty Dkt No: L1034381390WO (0330.1) (NHEJ) repair process. Due to the error-prone nature of NHEJ, repair of the double-stranded break can result in a modification to the target sequence. As used herein, a “modification” in reference to a polynucleotide refers to a change in the nucleotide sequence of the polynucleotide, which can be a deletion, insertion, or substitution of one or more nucleotides, or a combination thereof. Modification of the target polynucleotide comprising a target sequence can result in the expression of an altered protein product or inactivation of a coding sequence. In those embodiments wherein a donor polynucleotide is present, the donor sequence in the donor polynucleotide can be integrated into or exchanged with the target nucleotide sequence during the course of repair of the introduced double-stranded break, resulting in the introduction of the exogenous donor sequence. A donor polynucleotide thus comprises a donor sequence that is desired to be introduced into a target sequence of interest. In some embodiments, the donor sequence alters the original target nucleotide sequence such that the newly integrated donor sequence will not be recognized and cleaved by the RGN. In some embodiments, the donor polynucleotide is a single- stranded DNA. Integration of the donor sequence can be enhanced by the inclusion within the donor polynucleotide of flanking sequences, referred to herein as “homology arms” that have substantial sequence identity with the sequences flanking the target nucleotide sequence, allowing for a homology-directed repair process. In some embodiments, homology arms have a length of at least 30 base pairs, at least 35 base pairs, at least 40 base pairs, at least 45 base pairs, at least 50 base pairs, at least 55 base pairs, at least 60 base pairs, at least 65 base pairs, at least 70 base pairs, at least 75 base pairs, at least 80 base pairs, at least 85 base pairs, at least 90 base pairs, at least 95 base pairs, at least 100 base pairs, and up to 2000 base pairs or more, and have at least 90%, at least 95%, or more, sequence homology to their corresponding sequence within the target nucleotide sequence. In those embodiments wherein the RGN polypeptide introduces double-stranded staggered breaks, the donor polynucleotide can comprise a donor sequence flanked by compatible overhangs, allowing for direct ligation of the donor sequence to the cleaved target nucleotide sequence comprising overhangs by a non-homologous repair process during repair of the double-stranded break. In those embodiments wherein the method involves the use of an RGN that is a nickase (i.e., is only able to cleave a single strand of a double-stranded polynucleotide), the method can comprise introducing two RGN nickases that target identical or overlapping target sequences and cleave different strands of the polynucleotide. For example, an RGN nickase that only cleaves the positive (+) strand of a double-stranded polynucleotide can be introduced along with a second RGN nickase that only cleaves the negative (-) strand of a double-stranded polynucleotide. In some embodiments, a method is provided for binding a target nucleotide sequence and detecting the target sequence, wherein the method comprises introducing into a cell, organelle, or embryo at least one guide RNA or a polynucleotide encoding the same, and at least one RGN polypeptide or a polynucleotide encoding the same, expressing the guide RNA and / or RGN 78 Atty Dkt No: L1034381390WO (0330.1) polypeptide (if coding sequences are introduced), wherein the RGN polypeptide is a nuclease-dead RGN and further comprises a detectable label, and the method further comprises detecting the detectable label. The detectable label may be fused to the RGN as a fusion protein (e.g., fluorescent protein) or may be a small molecule conjugated to or incorporated within the RGN polypeptide that can be detected visually or by other means. Also provided herein are methods for modulating the expression of a target gene of interest comprising a target sequence or a gene under the regulation of a target sequence. The methods comprise introducing into a cell, organelle, or embryo at least one guide RNA or a polynucleotide encoding the same, and at least one RGN polypeptide or a polynucleotide encoding the same, expressing the guide RNA and / or RGN polypeptide (if coding sequences are introduced), wherein the RGN polypeptide is a nuclease-dead RGN. In some of these embodiments, the nuclease-dead RGN is a fusion protein comprising an expression modulator domain (i.e., epigenetic modification domain, transcriptional activation domain or a transcriptional repressor domain) as described herein. The present disclosure also provides methods for binding and / or modifying a target polynucleotide of interest comprising a target sequence. The methods include delivering a system comprising at least one guide RNA or a polynucleotide encoding the same, and at least one fusion polypeptide comprising an RGN of the disclosure and a base-editing polypeptide, for example a cytosine deaminase or an adenine deaminase, or a polynucleotide encoding the fusion polypeptide, to the target sequence or to a cell, organelle, or embryo comprising the target sequence. In some embodiments wherein a fusion polypeptide comprising an RGN and a base-editing polypeptide is utilized, the binding of the fusion polypeptide to a target sequence results in the modification of nucleotide(s) adjacent to the target sequence. The nucleobase adjacent to the target sequence that is modified by the deaminase may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 base pairs from the 5’ or 3’ end of the target sequence. In some embodiments wherein a PE or a PE system disclosed herein is utilized, the binding of the PE or PE system results in the modification of nucleotide(s) within or adjacent to the target sequence through the use of a DNA synthesis template of varying lengths such that the editing window using a polymerase editor can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 base pairs from the 5’ or 3’ end of the target sequence In order to minimize removal of the edit inserted by the polymerase editor by the DNA mismatch repair machinery, one or more components of the mismatch repair system can be inactivated using, for example, a dominant negative version thereof. A non-limiting example of a component of the mismatch repair system that can be inactivated or have its activity reduced is MLH1. A dominant negative MLH1 or a polynucleotide encoding the same can be introduced into the cell, along with, preceding or subsequent to the introduction of the PE system. A non-limiting 79 Atty Dkt No: L1034381390WO (0330.1) example of a dominant-negative MLH1 is the sequence set forth as SEQ ID NO: 334. In some embodiments, the DNA construct encoding the PE comprises the dominant-negative MLH1-encoding sequence on its N-terminus or its C-terminus and the dominant-negative MLH1-encoding sequence can connect to the PE-encoding sequence through a peptide linker and / or a NLS. Non-limiting examples of DNA constructs encoding a PE comprising the APG07433.1 nickase and a dominant- negative MLH1 are SEQ ID NOs: 1146-1153. One of ordinary skill in the art will appreciate that any of the presently disclosed methods can be used to target a single target sequence or multiple target sequences. Thus, methods comprise the use of a single RGN polypeptide or PE in combination with multiple, distinct guide RNAs, which can target multiple, distinct sequences within a single gene and / or multiple genes. Also encompassed herein are methods wherein multiple, distinct guide RNAs are introduced in combination with multiple, distinct RGN polypeptides or PEs. These guide RNAs and guide RNA / RGN or guide RNA / PE systems can target multiple, distinct sequences within a single gene and / or multiple genes. IX. Target Polynucleotides The disclosure provides for methods of modifying a target polynucleotide comprising a target sequence or modifying the expression of a target polynucleotide in a eukaryotic cell, which may be in vivo, ex vivo, or in vitro. In some embodiments, the method comprises sampling a cell or population of cells from a human or non-human animal or plant (including microalgae) and modifying the cell or cells. Culturing may occur at any stage ex vivo. The cell or cells may even be re-introduced into the non-human animal or plant (including micro-algae). Using natural variability, plant breeders combine most useful genes for desirable qualities, such as yield, quality, uniformity, hardiness, and resistance against pests. These desirable qualities also include growth, day length preferences, temperature requirements, initiation date of floral or reproductive development, fatty acid content, insect resistance, disease resistance, nematode resistance, fungal resistance, herbicide resistance, tolerance to various environmental factors including drought, heat, wet, cold, wind, and adverse soil conditions including high salinity. The sources of these useful genes include native or foreign varieties, heirloom varieties, wild plant relatives, and induced mutations, e.g., treating plant material with mutagenic agents. Using the present invention, plant breeders are provided with a new tool to induce mutations. Accordingly, one skilled in the art can analyze the genome for sources of useful genes, and in varieties having desired characteristics or traits employ the present invention to induce the rise of useful genes, with more precision than previous mutagenic agents and hence accelerate and improve plant breeding programs. The target polynucleotide of an RGN or PE system can be any polynucleotide endogenous or exogenous to the eukaryotic cell. For example, the target polynucleotide can be a polynucleotide residing in the nucleus of the eukaryotic cell. The target polynucleotide can be a sequence encoding a 80 Atty Dkt No: L1034381390WO (0330.1) gene product (e.g., a protein) or can be a non-coding sequence (e.g., a regulatory polynucleotide or a junk DNA). The target polynucleotide of an RGN or PE system of the disclosure may include a number of disease-associated genes and polynucleotides as well as signaling biochemical pathway-associated genes and polynucleotides. Examples of target polynucleotides include a sequence associated with a signaling biochemical pathway, e.g., a signaling biochemical pathway-associated gene or polynucleotide. Examples of target polynucleotides include a disease associated gene or polynucleotide. A “disease-associated” gene or polynucleotide refers to any gene or polynucleotide which is yielding transcription or translation products at an abnormal level or in an abnormal form in cells derived from a disease-affected tissues compared with tissues or cells of a non-disease control. It may be a gene that becomes expressed at an abnormally high level; it may be a gene that becomes expressed at an abnormally low level, where the altered expression correlates with the occurrence and / or progression of the disease. A disease-associated gene also refers to a gene possessing mutation(s) or genetic variation that is directly responsible or is in linkage disequilibrium with a gene(s) that is responsible for the etiology of a disease (e.g., a mutation). The transcribed or translated products may be known or unknown, and further may be at a normal or abnormal level. In some embodiments, the disease may be an animal disease. In some embodiments, the disease may be an avian disease. In some embodiments, the disease may be a mammalian disease. In some embodiments, the disease may be a human disease. Non-limiting examples of disease-associated genes and polynucleotides in humans are available from McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, Md.) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, Md.), available on the World Wide Web. The methods comprise contacting a target polynucleotide comprising a target sequence with an RGN, PE, or PE system of the disclosure, wherein the target polynucleotide is contacted with the RGN, PE, or PE system in an amount effective and under conditions suitable for editing of the target sequence (e.g., cleaving, insertion of a donor polynucleotide, modifying expression, base editing, polymerase editing). In some embodiments, the target sequence comprises a sequence associated with a disease or disorder, and the editing of the target sequence results in a sequence that is not associated with a disease or disorder. In some embodiments, the target sequence resides in an allele of a crop plant, wherein the particular allele is associated with a trait that results in a plant of lesser agronomic value. The editing of the target sequence results in an allele that is associated with a trait that increases the agronomic value of the plant. In some embodiments, the target DNA sequence comprises a T^C or A^G point mutation associated with a disease or disorder, and wherein the deamination of the mutant C or G base results in a sequence that is not associated with a disease or disorder. In some embodiments, the deamination corrects a point mutation in the sequence associated with the disease or disorder. 81 Atty Dkt No: L1034381390WO (0330.1) In some embodiments, the sequence associated with the disease or disorder encodes a protein, and the editing of the target sequence introduces a stop codon into the sequence associated with the disease or disorder, resulting in a truncation of the encoded protein. In some embodiments, the contacting is performed in vivo in a subject susceptible to having or diagnosed with the disease or disorder. In some embodiments, the disease or disorder is a disease associated with a point mutation, or a single-base mutation, in the genome. In some embodiments, the disease is a genetic disease, a cancer, a metabolic disease, or a lysosomal storage disease. X. Cells Comprising a Polynucleotide Genetic Modification Provided herein are cells and organisms comprising a target polynucleotide that has been modified using a process mediated by an RGN or PE system, as described herein. The modified cells can be eukaryotic (e.g., mammalian, plant, insect, avian cell) or prokaryotic. Prokaryotic cells can be from species, including but not limited to, archaea and bacteria (e.g., Bacillus sp., Klebsiella sp. Streptomyces sp., Rhizobium sp., Escherichia sp., Pseudomonas sp., Salmonella sp., Shigella sp., Vibrio sp., Yersinia sp., Mycoplasma sp., Agrobacterium, Lactobacillus sp.). Eukaryotic cells can include cells from animals (e.g., mammals, humans, insects, fish, birds, and reptiles), plants, fungi, amoeba, algae, and yeast. In some embodiments, the cell that is modified by the presently disclosed methods include cells of hematopoietic origin, such as cells of the immune system including but not limited to B cells, T cells, natural killer (NK) cells, chimeric antigen receptor T (CAR-T) cells, monocytes, macrophages, and dendritic cells. In some embodiments, the cell is a pluripotent stem cell or induced pluripotent stem cell. In some embodiments, the cell that is modified by the presently disclosed methods include primary cells. In certain embodiments, the primary cells include primary T cells. The methods provided herein may be used for modification of any plant species, including, but not limited to, monocots and dicots. Examples of plants of interest include, but are not limited to, corn (maize), sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, and oilseed rape, Brassica sp., alfalfa, rye, millet, safflower, peanuts, sweet potato, cassava, coffee, coconut, pineapple, citrus trees, cocoa, tea, banana, avocado, fig, guava, mango, olive, papaya, cashew, macadamia, almond, oats, vegetables, ornamentals, and conifers. Vegetables include, but are not limited to, tomatoes, lettuce, green beans, lima beans, peas, and members of the genus Curcumis such as cucumber, cantaloupe, and musk melon. Ornamentals include, but are not limited to, azalea, hydrangea, hibiscus, roses, tulips, daffodils, petunias, carnation, poinsettia, and chrysanthemum. In specific embodiments, plants of the present invention are crop plants (for example, maize, sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, oilseed rape, etc.). 82 Atty Dkt No: L1034381390WO (0330.1) Also provided are organelles and embryos comprising at least one target sequence that has been modified by a process utilizing an RGN or PE system as described herein. The genetically modified cells, organisms, organelles, and embryos can be heterozygous or homozygous for the modified target sequence. The chromosomal modification of the cell, organism, organelle, or embryo can result in altered expression (up-regulation or down-regulation), inactivation, or the expression of an altered protein product or an integrated sequence. In those embodiments wherein the chromosomal modification results in either the inactivation of a gene or the expression of a non-functional protein product, the genetically modified cell, organism, organelle, or embryo is referred to as a “knock out”. The knock out phenotype can be the result of a deletion mutation (i.e., deletion of at least one nucleotide), an insertion mutation (i.e., insertion of at least one nucleotide), or a nonsense mutation (i.e., substitution of at least one nucleotide such that a stop codon is introduced). In some embodiments, chromosomal modification results in upregulation of expression of a protein product that had been lacking or reduced due to mutation(s) in a target sequence. Alternatively, the chromosomal modification of a cell, organism, organelle, or embryo can produce a “knock in”, which results from the chromosomal integration of a nucleotide sequence that encodes a protein. In some of these embodiments, the coding sequence is integrated into the chromosome such that the chromosomal sequence encoding the wild-type protein is inactivated, but the exogenously introduced protein is expressed. In some embodiments, the mutation(s) introduced using the presently disclosed RGN or PE systems yields production of a variant protein product. The expressed variant protein product can have at least one amino acid substitution and / or the addition or deletion of at least one amino acid. The variant protein product encoded by the altered chromosomal sequence can exhibit modified characteristics or activities when compared to the wild-type protein, including but not limited to altered enzymatic activity or substrate specificity. In some embodiments, the chromosomal modification can result in an altered expression pattern of a protein. As a non-limiting example, chromosomal alterations in the regulatory regions controlling the expression of a protein product can result in the overexpression or downregulation of the protein product or an altered tissue or temporal expression pattern. In some embodiments, the mutation(s) introduced as a result of these RGN or PE systems yields a reduction or elimination in expression of a gene. Cells that have been modified may be introduced into an organism. These cells could have originated from the same organism (e.g., person) in the case of autologous cellular transplants, wherein the cells are modified in an ex vivo approach. Alternatively, the cells originated from another organism within the same species (e.g., another person) in the case of allogeneic cellular transplants. The cells that have been modified can be grown into an organism, such as a plant, in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same modified strain or different strains, and 83 Atty Dkt No: L1034381390WO (0330.1) the resulting hybrid having the genetic modification. The present disclosure provides genetically modified seed. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the disclosure, provided that these parts comprise the genetic modification. Further provided is a processed plant product or byproduct that retains the genetic modification, including for example, soymeal. XI. Pharmaceutical Compositions Pharmaceutical compositions of the present disclosure can comprise: RGN polypeptides (or PEs comprising the same), or active variants and fragments thereof, described herein, as well as polynucleotides encoding the same; gRNAs, or active variants and fragments thereof, described herein, or polynucleotides encoding the same; RGN systems described herein comprising RGN polypeptides and / or gRNAs; polymerases; PE systems (including DPE systems); or cells described herein comprising any of the RGN polypeptides (or PEs comprising the same) or polymerase-, RGN- or PE-encoding polynucleotides, gRNA or gRNA-encoding polynucleotides, or the polymerases or RGN or PE systems (including DPE systems); and a pharmaceutically acceptable carrier are provided. A pharmaceutical composition is a composition that is employed to prevent, reduce in intensity, cure or otherwise treat a target condition or disease that comprises an active ingredient (i.e. RGN polypeptides, RGN-encoding polynucleotides, polymerases, polymerase-encoding polynucleotides, PEs, PE-encoding polynucleotides, gRNA, gRNA-encoding polynucleotides, RGN systems, PE systems (including DPE systems), or cells comprising any one of these) and a pharmaceutically acceptable carrier. As used herein, a “pharmaceutically acceptable carrier” refers to a material that does not cause significant irritation to an organism and does not abrogate the activity and properties of the active ingredient (i.e. RGN polypeptides, RGN-encoding polynucleotides, polymerases, polymerase- encoding polynucleotides, PEs, PE-encoding polynucleotides, gRNA, gRNA-encoding polynucleotides, RGN systems, PE systems (including DPE systems), or cells comprising any one of these). Carriers must be of sufficiently high purity and of sufficiently low toxicity to render them suitable for administration to a subject being treated. The carrier can be inert, or it can possess pharmaceutical benefits. In some embodiments, a pharmaceutically acceptable carrier comprises one or more compatible solid or liquid filler, diluents or encapsulating substances which are suitable for administration to a human or other vertebrate animal. In some embodiments, the pharmaceutically acceptable carrier is not naturally-occurring. In some embodiments, the pharmaceutically acceptable carrier and the active ingredient are not found together in nature. Pharmaceutical compositions used in the presently disclosed methods can be formulated with suitable carriers, excipients, and other agents that provide suitable transfer, delivery, tolerance, and the like. A multitude of appropriate formulations are known to those skilled in the art. See, e.g., Remington, The Science and Practice of Pharmacy (21sted.2005). Suitable formulations include, for 84 Atty Dkt No: L1034381390WO (0330.1) example, powders, pastes, ointments, jellies, waxes, oils, lipids, lipid (cationic or anionic) containing vesicles (such as LIPOFECTIN vesicles), lipid nanoparticles, DNA conjugates, anhydrous absorption pastes, oil-in-water and water-in-oil emulsions, emulsions carbowax (polyethylene glycols of various molecular weights), semi-solid gels, and semi-solid mixtures containing carbowax. Pharmaceutical compositions for oral or parenteral use may be prepared into dosage forms in a unit dose suited to fit a dose of the active ingredients. Such dosage forms in a unit dose include, for example, tablets, pills, capsules, injections (ampoules), suppositories, etc. The disclosure provides for pharmaceutical compositions comprising lipid-based formulations including an active ingredient (i.e. RGN polypeptides, RGN-encoding polynucleotides, polymerases, polymerase-encoding polynucleotides, PEs, PE-encoding polynucleotides, gRNA, gRNA-encoding polynucleotides, RGN systems, PE systems (including DPE systems), or cells comprising any one of these). The lipid-based formulations can include liposomes. The lipid-based formulations can include lipid nanoparticles (LNPs). In some embodiments, an active ingredient is encapsulated in the lipid particle and / or disposed on the surface of the lipid particle. In some embodiments, an active ingredient is covalently attached to the lipid particle. In some embodiments, an active ingredient is non-covalently associated with the lipid particle. A covalent attachment includes the sharing of electrons in a chemical bond. Non-covalent interactions include dispersed electromagnetic interactions such as hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic bonds. In some embodiments, an active ingredient is encapsulated in the lipid particle. The term “encapsulate” means to enclose, surround or encase. As it relates to the formulation of the compounds of the disclosure, encapsulation may be substantial, complete or partial. The term “substantially encapsulated” or “substantial encapsulation” means that greater than 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or greater of the pharmaceutical composition or active ingredient of the disclosure may be enclosed, surrounded, or encased within a delivery agent (e.g., liposome or LNP). The term “partially encapsulated” or “partial encapsulation” means that less than 50%, 40%, 30%, 20%, 10%, or less of the pharmaceutical composition or active ingredient of the disclosure may be enclosed, surrounded, or encased within the delivery agent. Encapsulation may be determined by measuring the escape or the activity of the pharmaceutical composition or active ingredient of the disclosure using fluorescence and / or electron microscopy. For example, at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or greater of the pharmaceutical composition or active ingredient of the disclosure is encapsulated in a delivery agent (e.g., liposome or LNP). Liposomes are spherical vesicle structures composed of a uni- or multilamellar lipid bilayer surrounding internal aqueous compartments and a relatively impermeable outer lipophilic phospholipid bilayer. Liposomes have gained considerable attention as drug delivery carriers because they are biocompatible, nontoxic, can deliver both hydrophilic and lipophilic drug molecules, protect their cargo from degradation by plasma enzymes, and transport their load across biological 85 Atty Dkt No: L1034381390WO (0330.1) membranes and the blood brain barrier (BBB) (see, e.g., Spuch and Navarro (2011) Journal of drug delivery 2011). Liposomes can be made from several different types of lipids (e.g. ionizable lipids, structural lipids, helper lipids, and pegylated lipids); however, phospholipids are most commonly used to generate liposomes as drug carriers. Although liposome formation is spontaneous when a lipid film is mixed with an aqueous solution, it can also be expedited by applying force in the form of shaking by using a homogenizer, sonicator, or an extrusion apparatus (see, e.g., Spuch and Navarro (2011) Journal of drug delivery 2011). A conventional liposome formulation is mainly comprised of natural phospholipids and phospholipids such as 1,2-distearoryl-sn-glycero-3-phosphatidyl choline (DSPC), sphingomyelin, egg phosphatidylcholines, and monosialoganglioside. In some embodiments, 1,2-dioleoyl-sn-glycero-3- phosphoethanolamine (DOPE) increases stability of a liposome. Additives may be added to liposomes in order to modify their structure and properties. In some embodiments, cholesterol and / or sphingomyelin may be added to a liposomal mixture to help stabilize the liposomal structure and to prevent leakage of the liposomal inner cargo. In some embodiments, addition of cholesterol to a conventional liposome formulation reduces rapid release of the encapsulated active ingredient (i.e. RGN polypeptides, RGN-encoding polynucleotides, polymerases, polymerase-encoding polynucleotides, PEs, PE-encoding polynucleotides, gRNA, gRNA-encoding polynucleotides, RGN systems, PE systems (including DPE systems), or cells comprising any one of these) into the plasma. In some embodiments, liposomes are prepared from hydrogenated egg phosphatidylcholine or egg phosphatidylcholine, cholesterol, and dicetyl phosphate. In some embodiments, mean liposome vesicle size is adjusted to about 50 or 100 nm. In some embodiments, Trojan Horse liposomes (also known as Molecular Trojan Horses or PEGylated immunoliposomes) may be used in pharmaceutical compositions for delivery of an active ingredient across the BBB (described on World Wide Web at cshprotocols.cshlp.org / content / 2010 / 4 / pdb.prot5407.long). Without being bound by any theory, it is believed that neutral lipid particles with specific antibodies conjugated to the surface allows crossing of the BBB via endocytosis. In some embodiments, pharmaceutical compositions comprising Trojan Horse liposomes may be used to deliver an active ingredient (i.e. RGN polypeptides, RGN-encoding polynucleotides, polymerases, polymerase-encoding polynucleotides, PEs, PE-encoding polynucleotides, gRNA, gRNA-encoding polynucleotides, RGN systems, PE systems (including DPE systems), or cells comprising any one of these) to the brain via an intravascular injection. In some embodiments, liposomes include stable nucleic-acid-lipid particles (SNALP) (see, e.g., Morrissey et al. (2005) Nature Biotechnology 23(8):1002-1007; Zimmerman et al. (2006) Nature 441: 111-114). SNALPs include a mixture of cationic and fusogenic lipids and coated with polyethylene glycol (PEG) that allow cellular uptake and endosomal release of an active ingredient cargo. In some embodiments, a SNALP is a class of LNP and includes an ionizable lipid that is 86 Atty Dkt No: L1034381390WO (0330.1) cationic at low pH (e.g., DLinDMA, COATSOME® SS-OC), a neutral helper lipid (e.g. DSPC), cholesterol, and a diffusible polyethylene glycol (PEG)-lipid (e.g. Brij S100). In some embodiments, a SNALP formulation includes the following lipids: 3-N-(-methoxy poly(ethylene glycol)2000) carbamoyl-1,2-dimyrestyloxy-propylamine (PEG-cDMA); 1,2-dilinoleyloxy-N,N-dimethyl-3- aminopropane (DLinDMA); 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC); and cholesterol. In some embodiments, a SNALP includes synthetic cholesterol, dipalmitoylphosphatidylcholine (DOPC), PEG-cDMA, and DLinDMA (see, e.g., Geisbert et al. (2010) Lancet 375:1896-1905). In some embodiments, a SNALP includes synthetic cholesterol, DSPC, PEG-cDMA, and DLinDMA (see, e.g., Judge et al. (2009) J. Clin. Invest.119:661-673). In some embodiments, a SNALP formulation includes COATSOME® SS-OC, DSPC, Brij S100, and cholesterol. In some embodiments, a SNALP formulation includes an ionizable lipid, DSPC, cholesterol, and a PEG lipid. In some embodiments, a SNALP formulation includes the ionizable lipids and / or PEG lipids disclosed in WO2022173531 or WO2022173531 each of which is herein incorporated by reference in its entirety. In some embodiments, SNALP liposomes are about 80-100 nm in size. SNALPs have been used as effective delivery molecules to highly vascularized HepG2-derived liver tumors (see, e.g., Li et al. (2012) Gene Therapy 19:775- 780). Without being bound by any one theory, during formulation of SNALPs, the ionizable lipid serves to condense lipid with an active ingredient (e.g., a polynucleotide) during particle formation. When positively charged under increasingly acidic endosomal conditions, the ionizable lipid may mediate the fusion of a SNALP with the endosomal membrane, enabling release of the active ingredient into the cytoplasm. The PEG-lipid may stabilize the particle and reduce aggregation during formulation, and subsequently may provide a neutral hydrophilic exterior that improves pharmacokinetic properties. In some embodiments, SNALP liposomes are prepared by formulating DLinDMA and PEG-cDMA with DSPC, cholesterol and an active ingredient using a 25:1 lipid: active ingredient ratio and a 48:40:10:2 molar ratio of cholesterol: DLinDMA: DSPC: PEG-cDMA. In some embodiments, a pharmaceutical composition of the disclosure includes LNPs. In some embodiments, lipids may be formulated with an active ingredient of the present disclosure to form LNPs. An LNP comprises a plurality of lipid molecules physically associated with each other by intermolecular forces. In some embodiments, LNPs include liposomes. In some embodiments, LNPs differ from liposomes in not having a continuous lipid bilayer. In some embodiments, LNPs comprise solid particles having a mixture of solid and liquid lipids. In some embodiments, LNPs include dendrimer lipid nanoparticles (DLNPs), SNALPs, and lipid-like nanoparticles (LLNPs). In general, a “nanoparticle” refers to any particle having a diameter of less than 1000 nanometers (nm). In some embodiments, nanoparticles have a diameter of 500 nm or less. In some embodiments, nanoparticles have a diameter ranging between 25 nm and 200 nm, or 100 nm or less. In some embodiments, 87 Atty Dkt No: L1034381390WO (0330.1) nanoparticles have a diameter ranging between 35 nm and 60 nm. In some embodiments, an LNP includes a lipid particle between about 1 and about 100 nm in size. LNPs include four components: ionizable cationic lipids, fusogenic zwitterionic phospholipids, cholesterol, and PEGylated (PEG) lipids. In some embodiments, the ionizable cationic lipid component complexes a negatively charged polynucleotide and enhances endosomal escape). In some embodiments, the phospholipid component functions in modifying lipid bilayer structure. In some embodiments, the cholesterol component helps to stabilize an LNP. In some embodiments, the PEG lipid component decreases LNP aggregation and non-specific uptake. In some embodiments, the LNP includes an ionizable lipid that is cationic at low pH (e.g., DLinDMA, COATSOME® SS-OC), a neutral helper lipid (e.g. DSPC), cholesterol, and a diffusible polyethylene glycol (PEG)-lipid (e.g. Brij S100). In some embodiments, the LNP includes the following lipids: 3-N-(-methoxy poly(ethylene glycol)2000) carbamoyl-1,2-dimyrestyloxy- propylamine (PEG-cDMA); 1,2-dilinoleyloxy-N,N-dimethyl-3-aminopropane (DLinDMA); 1,2- distearoyl-sn-glycero-3-phosphocholine (DSPC); and cholesterol. In some embodiments, the LNP includes synthetic cholesterol, dipalmitoylphosphatidylcholine (DOPC), PEG-cDMA, and DLinDMA (see, e.g., Geisbert et al. (2010) Lancet 375:1896-1905). In some embodiments, the LNP includes synthetic cholesterol, DSPC, PEG-cDMA, and DLinDMA (see, e.g., Judge et al. (2009) J. Clin. Invest.119:661-673). Ionizable cationic lipids useful in LNPs include: COATSOME® SS-OC, 1,2-dilineoyl-3- dimethylammonium-propane (DLinDAP); DLinDMA; l,2-dilinoleyloxy-keto-N,N-dimethyl-3- aminopropane (DlinK-DMA); 1,2-dilinoleyl-4-(2-dimethylaminoethyl)-[1,3]-dioxolane (DlinKC2- DMA); 5A2-SC8 (Zhou et al. (2016) Proc. Natl Acad. Sci. USA 113:520–525); C12-200 (Love et al. (2010) Proc. Natl Acad. Sci. USA 107:1864–1869); 246C10 (Kim et al. (2021) Sci Adv 7(9): eabf4398); cKK-E12 (Fenton et al. (2016) Advanced Materials 28(15):2939-2943); 1,2-distearyloxy- N,N-dimethyl-3-aminopropane (DSDMA); 1,2-dioleyloxy-N,N -dimethyl-3-aminopropane (DODMA); 1,2-dilinolenyloxy-N,N -dimethyl-3-aminopropane (DLenDMA); and dilinoleylmethyl-4- dimethylaminobutyrate (Dlin-MC3-DMA; Jayaraman et al. (2012) Angew Chem Int Ed Engl.51(34): 8529–8533). Cationic lipids are further described in International Publication Nos. WO2012040184, WO2011153120, WO2011149733, WO2011090965, WO2011043913, WO2011022460, WO2012061259, WO2012054365, WO2012044638, WO2010080724, WO201021865, WO2022173531, WO2022150485 and WO2008103276, US Patent Nos.7,893,302 and 7,404,969 and US Patent Publication No. US20100036115, each of which is herein incorporated by reference in its entirety. Zwitterionic phospholipids useful for LNPs include DSPC, DOPE, and DOPC. PEG lipids useful for LNPs include: 1,2-dimyristoyl-rac-glycero-3-methoxypolyethylene glycol (PEG-DMG); (3- o-[2’’-(methoxypolyethyleneglycol 2000) succinoyl]-l,2-dimyristoyl-sn-glycol (PEG-S-DMG); R-3- [(ω-methoxy-poly(ethylene glycol)2000) carbamoyl]-1,2-dimyristyloxlpropyl-3-amine (PEG-C- 88 Atty Dkt No: L1034381390WO (0330.1) DOMG); and C16 PEG-ceramide. In some embodiments, an LNP includes 50: 10: 38.5: 1.5 molar ratio of DlinKC2-DMA or C12-200: DSPC: cholesterol: PEG-DMG (see, e.g., Basha et al. (2011) Molecular Therapy 19(12):2186-2200). In some embodiments, an LNP includes 26.5: 20: 52: 1.5 ionizable lipid: DOPE: cholesterol: PEG lipid (see, e.g., Han et al. (2022) Sci Adv 8(3): eabj6901; Kim et al. (2021) Sci Adv 7(9): eabf4398). PEG lipids are further described in WO2012099755, WO2022173531 and WO2022150485 each of which is herein incorporated by reference in its entirety. In some embodiments, the ratio of PEG in the LNP formulations may be increased or decreased and / or the carbon chain length of the PEG lipid may be modified from C14 to C18 to alter the pharmacokinetics and / or biodistribution of the LNP formulations. In some embodiments, a LNP formulation includes COATSOME® SS-OC, DSPC, Brij S100, and cholesterol. In some embodiments, a LNP formulation includes an ionizable lipid, DSPC, cholesterol, and a PEG lipid. In some embodiments, a LNP formulation includes the ionizable lipids and / or PEG lipids disclosed in WO2022173531 or WO2022150485 each of which is herein incorporated by reference in its entirety. In some embodiments, a LNP formulation includes the ionizable lipids and / or PEG lipids disclosed in WO2022173531 or WO2022150485 (each of which is herein incorporated by reference in its entirety), DSPC, and cholesterol. In some embodiments, a LNP formulation includes any one of CAT1-CAT35 and any one of CHM-001 to CHM-016 disclosed in WO2022173531 or WO2022150485 each of which is herein incorporated by reference in its entirety. In some embodiments, a LNP formulation includes any one of CAT1-CAT35 and any one of CHM-001 to CHM-016 disclosed in WO2022173531 or WO2022150485 (each of which is herein incorporated by reference in its entirety), DSPC, and cholesterol. In some embodiments, the LNP of the disclosure comprises 44-60 mol % of the cationic lipid, 19-25 mol % of the helper lipid, 25-33 mol % of the structural lipid, and 0.2-0.8 mol % of the PEG- lipid, inclusive of the endpoints. In some embodiments, the LNP of the disclosure comprises 44-54 mol % of the cationic lipid, 19-25 mol % of the helper lipid, 24-32 mol % of the structural lipid, and 1.2-1.8 mol % of the PEG-lipid, inclusive of the endpoints. In some embodiments, the LNP of the disclosure comprises 44-54 mol % of the cationic lipid, 8-14 mol % of the helper lipid, 35-43 mol % of the structural lipid, and 1.2-1.8 mol % of the PEG-lipid, inclusive of the endpoints. In some embodiments, the LNP of the disclosure comprises 45-55 mol % of the cationic lipid, 5-9 mol % of the helper lipid, 36-44 mol % of the structural lipid, and 2.5-3.5 mol % of the PEG-lipid, inclusive of the endpoints. In some embodiments, the LNP of the disclosure comprises 49 mol % of the cationic lipid, 22 mol % of the helper lipid, 28.5 % of the structural lipid, and .05 mol % of the PEG-lipid. In some embodiments, the LNP of the disclosure comprises 49 mol % of SS-OC, 22 mol % DSPC, 28.5 mol % cholesterol, and .05 mol % Brij S100. In some embodiments, the LNP of the disclosure comprises 50 mol % of the cationic lipid, 7 mol % of the helper lipid, 40 % of the structural lipid, and 3 mol % of the PEG-lipid. In some 89 Atty Dkt No: L1034381390WO (0330.1) embodiments, the LNP of the disclosure comprises 50 mol % of the ionizable lipid, 7 mol % DSPC, 40 mol % cholesterol, and .05 mol % the PEG-lipid. In some embodiments, the LNP of the disclosure comprises 50 mol % any one of CAT1-CAT35 disclosed in WO2022173531 or WO2022150485 (each of which is herein incorporated by reference in its entirety), 7 mol % DSPC, 40 mol % cholesterol, and .05 mol % any one of CHM-001 – CHM-016 disclosed in WO2022173531 or WO2022150485 (each of which is herein incorporated by reference in its entirety). In some embodiments, the LNP of the disclosure comprises 50 mol % CAT7 disclosed in disclosed in WO2022173531 or WO2022150485 (each of which is herein incorporated by reference in its entirety), 7 mol % DSPC, 40 mol % cholesterol, and .05 mol % CHM-006 disclosed in WO2022173531 or WO2022150485 (each of which is herein incorporated by reference in its entirety). In some embodiments, LNPs are about 80-100 nm in size. In some embodiments, the LNPs are about 80 nm, about 81 nm, about 82 nm, about 83 nm, about 84 nm, about 85 nm, about 86 nm, about 87 nm, about 88 nm, about 89 nm, about 90 nm, about 91 nm, about 92 nm, about 93 nm, about 94 nm, about 95 nm, about 96 nm, about 97 nm, about 98 nm, about 99 nm, or about 100 nm in size. The individual LNPs in a population of LNPs may vary in size by about +5 nm. In some embodiments, the charge of an LNP is taken into consideration. Cationic lipids may combine with negatively charged lipids to induce non-bilayer structures that facilitate intracellular delivery. Because charged LNPs are rapidly cleared from circulation following intravenous injection, ionizable cationic lipids with pKa values below 7 were developed (see, e.g., Basha et al. (2011) Molecular Therapy 19(12):2186-2200). Negatively charged polymers such as polynucleotides may be loaded into LNPs at low pH values (e.g., pH 4) where the ionizable lipids display a positive charge. However, at physiological pH values, the LNPs exhibit a low surface charge compatible with longer circulation times. Preparation of LNPs and encapsulation of an active ingredient are described in e.g., Basha et al. (2011) Molecular Therapy 19(12):1286-2200; Han et al. (2022) Sci Adv 8(3): eabj6901; Kim et al. (2021) Sci Adv 7(9): eabf4398; Finn et al. (2018) Cell Reports 22:2227–2235; Wei et al. (2020) Nature Communications 11:3232; WO2011127255; and WO2008103276. Lipids are commercially available (e.g., from Tekmira Pharmaceuticals, Vancouver, Canada; Avanti Polar Lipids, Inc., Alabaster, AL) or may be synthesized (e.g., Kim et al. (2021) Sci Adv 7(9): eabf4398). Synthesis of cationic lipids are also described in International Publication Nos. WO2012040184, WO2011153120, WO2011149733, WO2011090965, WO2011043913, WO2011022460, WO2012061259, WO2012054365, WO2012044638, WO2010080724 and WO201021865. Cholesterol is commercially available (e.g., from Sigma-Aldrich, St Louis, MO). In some em...

Claims

THAT WHICH IS CLAIMED:

1. One or more polynucleotides encoding a polymerase editor (PE) comprising a DNA polymerase and an RNA-guided nuclease (RGN) polypeptide, wherein said RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179.

2. The one or more polynucleotides of claim 1, wherein said RGN polypeptide comprises an amino acid sequence having: a) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1 and comprises: i) a S at a position corresponding to amino acid position 1020 in SEQ ID NO: 1; ii) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1; iii) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1; iv) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1; and v) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1; b) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 579, wherein said RGN polypeptide comprises a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 579; c) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 584, wherein said RGN polypeptide comprises a T at a position corresponding to amino acid position 1021 in SEQ ID NO: 584 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 584; d) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 583, wherein said RGN polypeptide comprises an N at a position corresponding to amino acid position 1021 in SEQ ID NO: 583 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 583; or e) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 591, wherein said RGN polypeptide comprises: i) a Q at a position corresponding to amino acid position 975 in SEQ ID NO: 591; ii) an A at a position corresponding to amino acid position 1020 in SEQ ID NO: 591; 1019 Atty Dkt No: L1034381390WO (0330.1)iii) a G at a position corresponding to amino acid position 1022 in SEQ ID NO: 591; and iv) a Q at a position corresponding to amino acid position 1023 in SEQ ID NO:

591.

3. The one or more polynucleotides of claim 1, wherein said RGN polypeptide comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179.

4. The one or more polynucleotides of any one of claims 1 or 3, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179.

5. The one or more polynucleotides of any one of claims 1-4, comprising at least a first and a second polynucleotide, wherein the first polynucleotide comprises a nucleotide sequence encoding said DNA polymerase and the second polynucleotide comprises a nucleotide sequence encoding said RGN polypeptide.

6. The one or more polynucleotides of any one of claims 1-4, wherein a nucleotide sequence encoding said DNA polymerase and a nucleotide sequence encoding said RGN polypeptide are comprised within a single polynucleotide.

7. The one or more polynucleotides of claim 6, wherein a single promoter is operably linked to said nucleotide sequence encoding said DNA polymerase and said nucleotide sequence encoding said RGN polypeptide.

8. The one or more polynucleotides of claim 7, wherein said single polynucleotide further comprises a nucleotide sequence encoding a self-cleaving peptide in between said nucleotide sequence encoding said DNA polymerase and said nucleotide sequence encoding said RGN polypeptide.

9. The one or more polynucleotides of any one of claims 1-7, wherein said nucleotide sequence encoding said DNA polymerase and said nucleotide sequence encoding said RGN polypeptide are translated as two separate polypeptides.

10. The one or more polynucleotides of claim 8 or 9, wherein said DNA polymerase, said RGN polypeptide, or both said DNA polymerase and said RGN polypeptide are operably fused to one or more nuclear localization signals (NLSs).

11. The one or more polynucleotides of claim 10, wherein said NLS is selected from the group consisting of SEQ ID NOs: 107-109, 2086-2101, 2118, and 2119.

12. The one or more polynucleotides of claim 10, wherein said DNA polymerase, said RGN polypeptide, or both said DNA polymerase and said RGN polypeptide are operably fused to said NLS at its N-terminus, C-terminus, or both its N-terminus and C-terminus.

13. The one or more polynucleotides of any one of claims 10-12, wherein said DNA polymerase, said RGN polypeptide, or both said DNA polymerase and said RGN polypeptide are 1020 Atty Dkt No: L1034381390WO (0330.1)further operably fused to one or more linker sequences between said one or more NLSs and said DNA polymerase, said RGN polypeptide, or both said DNA polymerase and said RGN polypeptide.

14. The one or more polynucleotides of claim 7, wherein said DNA polymerase is operably fused to said RGN polypeptide.

15. The one or more polynucleotides of claim 14, wherein said PE comprises said DNA polymerase fused at the amino terminus of said RGN polypeptide.

16. The one or more polynucleotides of claim 14, wherein said PE comprises said DNA polymerase fused at the carboxy terminus of said RGN polypeptide.

17. The one or more polynucleotides of any one of claims 14-16, wherein said PE is operably fused to one or more NLSs.

18. The one or more polynucleotides of claim 17, wherein said NLS is selected from the group consisting of SEQ ID NOs: 107-109, 2086-2101, 2118, and 2119.

19. The one or more polynucleotides of claim 17 or 18, wherein said PE is operably fused to said NLS at its N-terminus, C-terminus, within said PE, or a combination thereof.

20. The one or more polynucleotides of any one of claims 14-19, wherein said PE is further operably fused to one or more linker sequences.

21. The one or more polynucleotides of claim 20, wherein at least one of said one or more linker sequences is between said DNA polymerase and said RGN polypeptide.

22. The one or more polynucleotides of claim 21, wherein said one or more linker sequences has a formula of –(SGGS)x-NLSm-(SGGS)y-NLSn-(SGGS)z-, wherein each of x, y, or z is 0, 1, 2, 3, or 4; and wherein each of m or n is 0 or 1.

23. The one or more polynucleotides of claim 21, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide comprises one or more copies of amino acid sequence SGGS.

24. The one or more polynucleotides of any one of claims 21-23, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide has a length of 42 amino acids.

25. The one or more polynucleotides of any one of claims 21-24, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide comprises at least one NLS.

26. The one or more polynucleotides of claim 25, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide comprises two NLSs.

27. The one or more polynucleotides of any one of claims 21-26, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide comprises the sequence set forth as SEQ ID NO: 110, 366, 603, 605, 2120, or 2126.

28. The one or more polynucleotides of claim 14, wherein said PE comprises said DNA polymerase inserted within said RGN polypeptide. 1021 Atty Dkt No: L1034381390WO (0330.1)29. The one or more polynucleotides of claim 28, wherein said DNA polymerase is inserted within a linker domain 2, a wedge domain, a RuvC domain, an HNH domain, a Rec-2 domain, or a PAM-interacting domain of said RGN polypeptide or wherein said DNA polymerase is inserted between a linker domain 2, a wedge domain, a RuvC domain, an HNH domain, a Rec-2 domain, or a PAM-interacting domain of said RGN polypeptide and another domain 5’ or 3’ to said linker domain 2, wedge domain, RuvC domain, HNH domain, Rec-2 domain, or PAM-interacting domain.

30. The one or more polynucleotides of claim 29, wherein said RuvC domain is a RuvCIII domain.

31. The one or more polynucleotides of claim 28, wherein said DNA polymerase is inserted within a linker domain 2, a wedge domain, or a RuvCIII domain of said RGN polypeptide.

32. The one or more polynucleotides of claim 28, wherein said DNA polymerase is inserted within said RGN polypeptide immediately after an amino acid at a position selected from the group consisting of: a) an amino acid position corresponding to position 678 of SEQ ID NO: 2; b) an amino acid position corresponding to position 736 of SEQ ID NO: 2; c) an amino acid position corresponding to position 922 of SEQ ID NO: 2; d) an amino acid position corresponding to position 642 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; e) an amino acid position corresponding to position 772 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; f) an amino acid position corresponding to position 739 of SEQ ID NO: 565; g) an amino acid position corresponding to position 744 of SEQ ID NO: 565; h) an amino acid position corresponding to position 680 of SEQ ID NO: 566; i) an amino acid position corresponding to position 785 of SEQ ID NO: 566; and j) an amino acid position corresponding to position 910 of SEQ ID NO:

566.

33. The one or more polynucleotides of any one of claims 28-32, wherein said PE is operably fused to one or more NLSs.

34. The one or more polynucleotides of claim 33, wherein said NLS is selected from the group consisting of SEQ ID NOs: 107-109, 2086-2101, 2118, and 2119.

35. The one or more polynucleotides of claim 33 or 34, wherein said PE is operably fused to said NLS at its N-terminus, C-terminus, within said PE, or a combination thereof.

36. The one or more polynucleotides of any one of claims 33-35, wherein said PE is operably fused to one or more linker sequences.

37. The one or more polynucleotides of claim 36, wherein said one or more linker sequences comprises one or more copies of amino acid sequence SGGS. 1022 Atty Dkt No: L1034381390WO (0330.1)38. The one or more nucleic molecules of claim 36 or 37, wherein at least one of said one or more linker sequences is between said DNA polymerase and a fragment of said RGN polypeptide.

39. The one or more polynucleotides of any one of claims 1-38, wherein said RGN polypeptide is capable of binding a target sequence in a target polynucleotide in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA), wherein said target sequence comprises a target strand and a non-target strand, and wherein said gRNA is capable of hybridizing to the target strand of the target sequence.

40. The one or more polynucleotides of claim 39, wherein said RGN polypeptide recognizes a protospacer adjacent motif (PAM) that is 3′ of said target sequence.

41. The one or more polynucleotides of claim 40, wherein: a) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCY; b) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 7 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCC; c) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 2 recognizes a PAM having a consensus nucleotide sequence set forth as NNRYA; d) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 565 recognizes a PAM having a consensus nucleotide sequence set forth as NNGRR; e) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 566 recognizes a PAM having a consensus nucleotide sequence set forth as NNGG; f) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 579 or 583 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNC; g) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 584 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCM; or h) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 591 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCT.

42. The one or more polynucleotides of any one of claims 39-41, wherein said RGN polypeptide is capable of cleaving said target polynucleotide upon binding. 1023 Atty Dkt No: L1034381390WO (0330.1)43. The one or more polynucleotides of claim 42, wherein said RGN polypeptide is capable of generating a double-stranded break.

44. The one or more polynucleotides of claim 42, wherein said RGN polypeptide is capable of generating a single-stranded break.

45. The one or more polynucleotides of claim 44, wherein said RGN polypeptide comprises an RGN nickase comprising an HNH domain with at least one mutation that reduces or eliminates its nuclease activity.

46. The one or more polynucleotides of claim 44, wherein said RGN polypeptide does not comprise an HNH domain.

47. The one or more polynucleotides of claim 46, wherein said HNH domain of an RGN polypeptide has been replaced with said DNA polymerase.

48. The one or more polynucleotides of claim 47, wherein said DNA polymerase is operably fused to one or more linker sequences.

49. The one or more polynucleotides of claim 48, wherein at least one of said one or more linker sequences is between said DNA polymerase and said RGN polypeptide.

50. The one or more polynucleotides of claim 45, wherein said RGN nickase comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 8, 106, 365, 567, or 568.

51. The one or more polynucleotides of claim 45 or 50, wherein said RGN nickase comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 8, 106, 365, 567, or 568.

52. The one or more polynucleotides of any one of claims 45, 50, and 51, wherein said RGN nickase comprises the amino acid sequence set forth as SEQ ID NO: 8, 106, 365, 567, or 568.

53. The one or more polynucleotides of claim 45, wherein said HNH domain comprises at least two mutations that reduces or eliminates its nuclease activity.

54. The one or more polynucleotides of claim 53, wherein said RGN nickase comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 367, 368, 369, 569, or 570.

55. The one or more polynucleotides of claim 53 or 54, wherein said RGN nickase comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 367, 368, 369, 569, or 570.

56. The one or more polynucleotides of any one of claims 53-55, wherein said RGN nickase comprises the amino acid sequence set forth as SEQ ID NO: 367, 368, 369, 569, or 570.

57. The one or more polynucleotides of any one of claims 39-41, wherein said RGN polypeptide is nuclease inactive.

58. The one or more polynucleotides of any one of claims 1-57, wherein one or more nucleotide sequences encoding the PE are codon optimized for expression in a eukaryotic cell. 1024 Atty Dkt No: L1034381390WO (0330.1)59. The one or more polynucleotides of claim 58, wherein the eukaryotic cell is a mammalian cell.

60. The one or more polynucleotides of any one of claims 1-59, wherein said DNA polymerase is a reverse transcriptase (RT).

61. The one or more polynucleotides of claim 60, wherein said RT is a Moloney murine leukemia virus RT (MMLV RT).

62. The one or more polynucleotides of claim 60, wherein said RT has an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 174, and 2127-2131.

63. The one or more polynucleotides of claim 60 or 62, wherein said RT has an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 174, and 2127-2131.

64. The one or more polynucleotides of any one of claims 60, 62, and 63, wherein said RT has the amino acid sequence set forth as any one of SEQ ID NOs: 174, and 2127-2131.

65. The one or more polynucleotides of claim 60, wherein said RT lacks an Rnase H domain.

66. The one or more polynucleotides of claim 65, wherein said RT is truncated after an amino acid at a position corresponding to D497 in SEQ ID NO:

174.

67. The one or more polynucleotides of claim 65 or 66, wherein said RT has an amino acid sequence having at least 90% sequence identity to SEQ ID NO:

175.

68. The one or more polynucleotides of any one of claims 65-67, wherein said RT has an amino acid sequence having at least 95% sequence identity to SEQ ID NO:

175.

69. The one or more polynucleotides of any one of claims 65-68, wherein said RT has the amino acid sequence set forth as SEQ ID NO:

175.

70. The one or more polynucleotides of any one of claims 1-69, wherein said PE has an amino acid sequence having at least 90% sequence identity or at least 95% sequence identity to any one of SEQ ID NOs: 9-11, 111-130, 137-173, 364, 774-787, 790-814, 817-901, 926, 1143-1155, 1164, 1182-1185, 1189-2085, and 2121-2125.

71. The one or more polynucleotides of any one of claims 1-70, wherein said PE has an amino acid sequence having at least 90% sequence identity or at least 95% sequence identity to any one of SEQ ID NOs: 364, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 1432, 1443, 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718.

72. The one or more polynucleotides of any one of claims 1-71, wherein said PE has the amino acid sequence set forth as any one of SEQ ID NOs: 9-11, 111-130, 137-173, 364, 774-787, 790-814, 817-901, 926, 1143-1155, 1164, 1182-1185, 1189-2085, 2121-2125, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 1432, 1443, 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718. 1025 Atty Dkt No: L1034381390WO (0330.1)73. The one or more polynucleotides of any one of claims 1-72, wherein at least one of said one or more polynucleotides is an RNA polynucleotide.

74. The one or more polynucleotides of claim 73, wherein said RNA polynucleotide is an mRNA.

75. The one or more polynucleotides of claim 73, wherein said RNA polynucleotide is a circRNA.

76. One or more vectors comprising the one or more polynucleotides of any one of claims 1-72.

77. The one or more vectors of claim 76, wherein said one or more vectors further comprise at least one nucleotide sequence encoding a polymerase editing guide RNA (PEgRNA), wherein said PEgRNA comprises an extension arm, wherein said extension arm comprises a primer binding site and a DNA synthesis template sequence, and wherein said PEgRNA is capable of binding to said RGN of said PE.

78. The one or more vectors of claim 77, wherein said extension arm is at the 3’ end of said PEgRNA.

79. The one or more vectors of claim 77 or 78, wherein said DNA synthesis template sequence is 19, 22, 23, 24, 25, 26, 29, 30, 32, 34, 37, 38, 39, 40, 42, or 46 nucleotides in length.

80. The one or more vectors of any one of claims 77-79, wherein said DNA synthesis template sequence comprises an RT template (RTT) sequence.

81. The one or more vectors of any one of claims 77-80, wherein said primer binding site is 9, 11, 12, 13, or 15 nucleotides in length.

82. The one or more vectors of any one of claims 77-81, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising a nucleotide sequence of any one of SEQ ID NOs: 3, 470, and 471, or that differs from any one of SEQ ID NOs: 3, 470, and 471 by 1 to 5 nucleotides, wherein said RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 7, 579, 583, 584, or 591.

83. The one or more vectors of any one of claims 77-82, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of any one of SEQ ID NOs: 3, 470, and 471, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO: 1, 7, 579, 583, 584, or 591.

84. The one or more vectors of claims 82 or 83, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to any one of SEQ ID NOs: 4, 472, 473, and 474.

85. The one or more vectors of any one of claims 82-84, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to any one of SEQ ID NOs: 4, 472, 473, and 474. 1026 Atty Dkt No: L1034381390WO (0330.1)86. The one or more vectors of any one of claims 82-85, wherein the PEgRNA comprises a tracrRNA comprising the nucleotide sequence of any one of SEQ ID NOs: 4, 472, 473, and 474.

87. The one or more vectors of any one of claims 77-81, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising a nucleotide sequence of any one of SEQ ID NOs: 5, 475, and 476 or that differs from any one of SEQ ID NOs: 5, 475, and 476 by 1 to 5 nucleotides, wherein said RGN polypeptide comprises the amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO:

2.

88. The one or more vectors of any one of claims 77-81 and 87, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of any one of SEQ ID NOs: 5, 475, and 476, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO:

2.

89. The one or more vectors of claim 87 or 88, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to any one of SEQ ID NOs: 6, 477, 478, 479, and 480.

90. The one or more vectors of claim 87 or 88, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to any one of SEQ ID NOs: 6, 477, 478, 479, and 480.

91. The one or more vectors of any one of claims 87-90, wherein the PEgRNA comprises a tracrRNA comprising the nucleotide sequence of any one of SEQ ID NOs: 6, 477, 478, 479, and 480.

92. The one or more vectors of any one of claims 77-81, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising a nucleotide sequence of SEQ ID NO: 571, or that differs from SEQ ID NO: 571 by 1 to 5 nucleotides, wherein said RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO:

565.

93. The one or more vectors of any one of claims 77-81 and 92, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of SEQ ID NO: 571, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO:

565.

94. The one or more vectors of claims 92 or 93, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO:

572.

95. The one or more vectors of any one of claims 92-94, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO:

572.

96. The one or more vectors of any one of claims 92-95, wherein the PEgRNA comprises a tracrRNA comprising the nucleotide sequence of SEQ ID NO:

572. 1027 Atty Dkt No: L1034381390WO (0330.1)97. The one or more vectors of any one of claims 77-81, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising a nucleotide sequence of SEQ ID NO: 573 or 1180, or that differs from SEQ ID NO: 573 or 1180 by 1 to 5 nucleotides, wherein said RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO:

566.

98. The one or more vectors of any one of claims 77-81 and 97, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of SEQ ID NO: 573 or 1180, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO:

566.

99. The one or more vectors of claims 97 or 98, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 574 or 1181.

100. The one or more vectors of any one of claims 97-99, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 574 or 1181.

101. The one or more vectors of any one of claims 97-100, wherein the PEgRNA comprises a tracrRNA comprising the nucleotide sequence of SEQ ID NO: 574 or 1181.

102. The one or more vectors of any one of claims 76-101, wherein said one or more vectors further comprise a nucleotide sequence encoding a nicking guide RNA.

103. The one or more vectors of any one of claims 76-102, wherein said one or more vectors further comprise a nucleotide sequence encoding a dominant negative MLH1.

104. The one or more vectors of any one of claims 76-103, wherein the one or more vectors are adeno-associated viral (AAV) vectors.

105. A cell comprising the one or more polynucleotides of any one of claims 1-75 or the one or more vectors of any one of claims 76-104.

106. The cell of claim 105, wherein the cell is a prokaryotic cell.

107. The cell of claim 105, wherein the cell is a eukaryotic cell.

108. The cell of claim 107, wherein the eukaryotic cell is a mammalian cell.

109. The cell of claim 108, wherein the mammalian cell is a human cell.

110. The cell of claim 108, wherein the human cell is an immune cell.

111. The cell of claim 108, wherein the human cell is a stem cell.

112. The cell of claim 111, wherein the stem cell is an induced pluripotent stem cell.

113. The cell of claim 107, wherein the eukaryotic cell is an insect or avian cell.

114. The cell of claim 107, wherein the eukaryotic cell is a fungal cell.

115. The cell of claim 107, wherein the eukaryotic cell is a plant cell.

116. A plant or plant part comprising the plant cell of claim 115. 1028 Atty Dkt No: L1034381390WO (0330.1)117. A method for making a PE comprising culturing the cell of claim 105 under conditions in which the PE is expressed.

118. The method of claim 117, further comprising purifying said PE.

119. The method of claim 117, wherein said cell further expresses one or more guide RNAs capable of binding to said RGN polypeptide of said PE to form a ribonucleoprotein complex.

120. The method of claim 119, further comprising purifying said ribonucleoprotein complex.

121. A polymerase editor (PE) comprising a DNA polymerase and an RNA-guided nuclease (RGN) polypeptide, wherein said RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179.

122. The PE of claim 121, wherein said RGN polypeptide comprises an amino acid sequence having: a) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1 and comprises: i) a S at a position corresponding to amino acid position 1020 in SEQ ID NO: 1; ii) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1; iii) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1; iv) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1; and v) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1; b) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 579, wherein said RGN polypeptide comprises a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 579; c) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 584, wherein said RGN polypeptide comprises a T at a position corresponding to amino acid position 1021 in SEQ ID NO: 584 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 584; d) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 583, wherein said RGN polypeptide comprises an N at a position corresponding to amino acid position 1021 in SEQ ID NO: 583 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 583; or 1029 Atty Dkt No: L1034381390WO (0330.1)e) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 591, wherein said RGN polypeptide comprises: i) a Q at a position corresponding to amino acid position 975 in SEQ ID NO: 591; ii) an A at a position corresponding to amino acid position 1020 in SEQ ID NO: 591; iii) a G at a position corresponding to amino acid position 1022 in SEQ ID NO: 591; and iv) a Q at a position corresponding to amino acid position 1023 in SEQ ID NO:

591.

123. The PE of claim 121, wherein said RGN polypeptide comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179.

124. The PE of claim 121 or 123, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO: 1, 2, 7, 565, 566, 579, 583, 584, 591, or 1165-1179.

125. The PE of any one of claims 121-124, wherein said DNA polymerase and said RGN polypeptide are two separate polypeptides.

126. The PE of claim 125, wherein said DNA polymerase, said RGN polypeptide, or both said DNA polymerase and said RGN polypeptide are operably fused to one or more nuclear localization signals (NLSs).

127. The PE of claim 126, wherein said one or more NLSs is selected from the group consisting of SEQ ID NOs: 107-109, 2086-2101, 2118, and 2119.

128. The PE of claim 126 or 127, wherein said DNA polymerase, said RGN polypeptide, or both said DNA polymerase and said RGN polypeptide are operably fused to said NLS at its N- terminus, C-terminus, or both its N-terminus and C-terminus.

129. The PE of any one of claims 126-128, wherein said DNA polymerase, said RGN polypeptide, or both said DNA polymerase and said RGN polypeptide are further operably linked to one or more linker sequences between said NLS and said DNA polymerase, said RGN polypeptide, or both said DNA polymerase and said RGN polypeptide.

130. The PE of any one of claims 121-124, wherein said DNA polymerase is operably fused to said RGN polypeptide.

131. The PE of claim 130, wherein said PE comprises said DNA polymerase fused at the amino terminus of said RGN polypeptide.

132. The PE of claim 130, wherein said PE comprises said DNA polymerase fused at the carboxy terminus of said RGN polypeptide.

133. The PE of any one of claims 130-132, wherein said PE is operably fused to one or more NLSs. 1030 Atty Dkt No: L1034381390WO (0330.1)134. The PE of claim 133, wherein said NLS is selected from the group consisting of SEQ ID NOs: 107-109, 2086-2101, 2118, and 2119.

135. The PE of claim 133 or 134, wherein said PE is operably fused to said NLS at its N- terminus, C-terminus, within said PE, or a combination thereof.

136. The PE of any one of claims 131-135, wherein said PE is further operably fused to one or more linker sequences.

137. The PE of claim 136, wherein at least one or said one or more linker sequences is between said DNA polymerase and said RGN polypeptide.

138. The PE of claim 137, wherein said one or more linker sequences has a formula of - (SGGS)x-NLSm-(SGGS)y-NLSn-(SGGS)z-, wherein each of x, y, or z is 0, 1, 2, 3, or 4; and wherein each of m or n is 0 or 1.

139. The PE of claim 137, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide comprises one or more copies of amino acid sequence SGGS.

140. The PE of any one of claims 137-139, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide has a length of 42 amino acids.

141. The PE of any one of claims 137-140, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide comprises at least one NLS.

142. The PE of claim 141, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide comprises two NLSs.

143. The PE of any one of claims 137-142, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide comprises the sequence set forth as SEQ ID NO: 110, 366, 603, 605, 2120, or 2126.

144. The PE of claim 130, wherein said PE comprises said DNA polymerase inserted within said RGN polypeptide.

145. The PE of claim 144, wherein said DNA polymerase is inserted within a linker domain 2, a wedge domain, a RuvC domain, an HNH domain, a Rec-2 domain, or a PAM-interacting domain of said RGN polypeptide or wherein said DNA polymerase is inserted between a linker domain 2, a wedge domain, a RuvC domain, an HNH domain, a Rec-2 domain, or a PAM-interacting domain of said RGN polypeptide and another domain 5' or 3' to said linker domain 2, wedge domain, RuvC domain, HNH domain, Rec-2 domain, or PAM-interacting domain.

146. The PE of claim 145, wherein said RuvC domain is a RuvCIII domain.

147. The PE of claim 145, wherein said DNA polymerase is inserted within a linker domain 2, a wedge domain, or a RuvCIII domain of said RGN polypeptide.

148. The PE of claim 144, wherein said DNA polymerase is inserted within said RGN polypeptide immediately after an amino acid at a position selected from the group consisting of: a) an amino acid position corresponding to position 678 of SEQ ID NO: 2; b) an amino acid position corresponding to position 736 of SEQ ID NO: 2; 1031 Atty Dkt No: L1034381390WO (0330.1)c) an amino acid position corresponding to position 922 of SEQ ID NO: 2; d) an amino acid position corresponding to position 642 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; e) an amino acid position corresponding to position 772 of SEQ ID NO: 1, 7, 579, 583, 584, or 591; f) an amino acid position corresponding to position 739 of SEQ ID NO: 565; g) an amino acid position corresponding to position 744 of SEQ ID NO: 565; h) an amino acid position corresponding to position 680 of SEQ ID NO: 566; i) an amino acid position corresponding to position 785 of SEQ ID NO: 566; and j) an amino acid position corresponding to position 910 of SEQ ID NO:

566.

149. The PE of any one of claims 144-148, wherein said PE is operably fused to one or more NLSs.

150. The PE of claim 149, wherein said NLS is selected from the group consisting of SEQ ID NOs: 107-109, 2086-2101, 2118, and 2119.

151. The PE of claim 149 or 150, wherein said PE is operably fused to said NLS at its N- terminus, C-terminus, within said PE, or a combination thereof.

152. The PE of any one of claims 149-151, wherein said PE is further operably linked to one or more linker sequences.

153. The PE of claim 152, wherein at least one of said one or more linker sequences is between said DNA polymerase and a fragment of said RGN polypeptide.

154. The PE of claim 153, wherein said one or more linker sequences between said DNA polymerase and said RGN polypeptide comprises one or more copies of amino acid sequence SGGS.

155. The PE of any one of claims 121-154, wherein said RGN polypeptide is capable of binding a target sequence in a target polynucleotide in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA), wherein said target sequence comprises a target strand and a non-target strand, and wherein said gRNA is capable of hybridizing to the target strand of the target sequence.

156. The PE of claim 155, wherein said RGN polypeptide recognizes a protospacer adjacent motif (PAM) that is 3′ of said target sequence.

157. The PE of claim 156, wherein: a) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 recognizes the PAM having a consensus nucleotide sequence set forth as NNNNCY; b) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 7 recognizes the PAM having a consensus nucleotide sequence set forth as NNNNCC; 1032 Atty Dkt No: L1034381390WO (0330.1)c) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 2 recognizes the PAM having a consensus nucleotide sequence set forth as NNRYA; d) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 565 recognizes the PAM having a consensus nucleotide sequence set forth as NNGRR; or e) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 566 recognizes the PAM having a consensus nucleotide sequence set forth as NNGG; f) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 579 or 583 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNC; g) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 584 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCM; or h) the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 591 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCT.

158. The PE of any one of claims 155-157, wherein said RGN polypeptide is capable of cleaving said target polynucleotide upon binding.

159. The PE of claim 158, wherein said RGN polypeptide is capable of generating a double-stranded break.

160. The PE of claim 158, wherein said RGN polypeptide is capable of generating a single-stranded break.

161. The PE of claim 160, wherein said RGN polypeptide comprises an RGN nickase comprising an HNH domain with at least one mutation that reduces or eliminates nuclease activity.

162. The PE of claim 160, wherein said RGN polypeptide does not comprise an HNH domain.

163. The PE of claim 162, wherein said HNH domain of an RGN polypeptide has been replaced with said DNA polymerase.

164. The PE of claim 163, wherein said DNA polymerase is operably fused to one or more linker sequences.

165. The PE of claim 164, wherein at least one of said one or more linker sequences is between said DNA polymerase and said RGN polypeptide.

166. The PE of claim 161, wherein said RGN nickase comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 8, 106, 365, 567, or 568. 1033 Atty Dkt No: L1034381390WO (0330.1)167. The PE of claim 161 or 166, wherein said RGN nickase comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 8, 106, 365, 567, or 568.

168. The PE of any one of claims 161, 166, and 167, wherein said RGN nickase comprises the amino acid sequence set forth as SEQ ID NO: 8, 106, 365, 567, or 568.

169. The PE of claim 161, wherein said HNH domain comprises at least two mutations that reduce nuclease activity.

170. The PE of claim 169, wherein said RGN nickase comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 367, 368, 369, 569, or 570.

171. The PE of claim 169 or 170, wherein said RGN nickase comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 367, 368, 369, 569, or 570.

172. The PE of any one of claims 169-171, wherein said RGN nickase comprises the amino acid sequence set forth as SEQ ID NO: 367, 368, 369, 569, or 570.

173. The PE of any one of claims 155-157, wherein said RGN polypeptide is nuclease inactive.

174. The PE of any one of claims 121-173, wherein said DNA polymerase is a reverse transcriptase (RT).

175. The PE of claim 174, wherein said RT is a Moloney murine leukemia virus RT (MMLV RT).

176. The PE of claim 174, wherein said RT has an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 174, and 2127-2131.

177. The PE of claim 174 or 176, wherein said RT has an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 174, and 2127-2131.

178. The PE of any one of claims 174, 176, and 177, wherein said RT has the amino acid sequence set forth as any one of SEQ ID NOs: 174, and 2127-2131.

179. The PE of claim 174, wherein said RT lacks an RNase H domain.

180. The PE of claim 179, wherein said RT is truncated after an amino acid at a position corresponding to D497 in SEQ ID NO:

174.

181. The PE of claim 179 or 180, wherein said RT has an amino acid sequence having at least 90% sequence identity to SEQ ID NO:

175.

182. The PE of any one of claims 179-181, wherein said RT has an amino acid sequence having at least 95% sequence identity to SEQ ID NO:

175.

183. The PE of any one of claims 179-182, wherein said RT has the amino acid sequence set forth as SEQ ID NO:

175.

184. The PE of any one of claims 121-183, wherein said PE has an amino acid sequence having at least 90% sequence identity or at least 95% sequence identity to any one of SEQ ID NOs: 9- 11, 111-130, 137-173, 364, 774-787, 790-814, 817-901, 926, 1143-1155, 1164, 1182-1185, 1189- 2085, and 2121-2125. 1034 Atty Dkt No: L1034381390WO (0330.1)185. The PE of any one of claims 121-184, wherein said PE has an amino acid sequence having at least 90% sequence identity or at least 95% sequence identity to any one of SEQ ID NOs: 364, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 1432, 1443, 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718.

186. The PE of any one of claims 121-185, wherein said PE has the amino acid sequence set forth as any one of SEQ ID NOs: 9-11, 111-130, 137-173, 364, 774-787, 790-814, 817-901, 926, 1143-1155, 1164, 1182-1185, 1189-2085, 2121-2125, 1208, 1209, 1210, 1221, 1224, 1225, 1226, 1337, 1361, 1371, 1425, 1432, 1443, 1444, 1445, 1447, 1448, 1516, 1577, 1592, 1622, 1640, 1658, 1666, 1682, 1683, 1692, 1694, 1696, and 1718.

187. A ribonucleoprotein (RNP) complex comprising the PE of any one of claims 121-186 and a PEgRNA bound to the RGN polypeptide, wherein said PEgRNA comprises a primer binding site (PBS) and a DNA synthesis template.

188. The RNP complex of claim 187, wherein the PEgRNA comprises a spacer that hybridizes to a eukaryotic target sequence.

189. The RNP complex of claim 188, wherein the eukaryotic target sequence comprises a mammalian target sequence.

190. A PE system for modifying one or more target sequences in a target polynucleotide, said system comprising: a) one or more PEgRNAs, or one or more polynucleotides comprising one or more nucleotide sequences encoding the one or more PEgRNAs, wherein the one or more PEgRNAs comprise an extension arm, wherein the extension arm comprises a primer binding site (PBS) and a DNA synthesis template sequence; and b) a PE of any one of claims 121-186; wherein said one or more PEgRNAs are capable of binding to said RGN polypeptide of said PE.

191. The PE system of claim 190, wherein each of the one or more PEgRNAs is capable of hybridizing to the target strand of said target sequence and forming a complex with the RGN polypeptide to direct said RGN polypeptide to bind to said target sequence.

192. The PE system of claim 190 or 191, wherein the spacer hybridizes to a eukaryotic target sequence.

193. The PE system of claim 192, wherein the eukaryotic target sequence comprises a mammalian target sequence.

194. The PE system of any one of claims 190-193, wherein said extension arm is at the 3' end of said PEgRNA.

195. The PE system of any one of claims 190-194, wherein said DNA synthesis template sequence is 19, 22, 23, 24, 25, 26, 29, 30, 32, 34, 37, 38, 39, 40, 42, or 46 nucleotides in length. 1035 Atty Dkt No: L1034381390WO (0330.1)196. The PE system of any one of claims 190-195, wherein said DNA synthesis template sequence comprises an RT template sequence (RTT).

197. The PE system of any one of claims 190-196, wherein said primer binding site is 9, 11, 12, 13, or 15 nucleotides in length.

198. The PE system of any one of claims 190-197, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of any one of SEQ ID NOs: 3, 470, and 471, or that differs from any one of SEQ ID NOs: 3, 470, and 471 by 1 to 5 nucleotides, wherein said RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 7, 579, 583, 584, or 591.

199. The PE system of any one of claims 190-198, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of any one of SEQ ID NOs: 3, 470 and 471, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO: 1, 7, 579, 583, 584, or 591.

200. The PE system of claim 198 or 199, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to any one of SEQ ID NOs: 4, 472, 473, and 474.

201. The PE system of any one of claims 198-200, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to any one of SEQ ID NOs: 4, 472, 473, and 474.

202. The PE system of any one of claims 198-201, wherein the PEgRNA comprises a tracrRNA comprising the nucleotide sequence of any one of SEQ ID NOs: 4, 472, 473, and 474.

203. The PE system of any one of claims 190-197, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of any one of SEQ ID NOs: 5, 475, and 476 or that differs from any one of SEQ ID NOs: 5, 475, and 476 by 1 to 5 nucleotides, wherein said RGN polypeptide comprises the amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO:

2.

204. The PE system of any one of claims 190-197 and 203, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of any one of SEQ ID NOs: 5, 475, and 476, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO:

2.

205. The PE system of claim 203 or 204, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to any one of SEQ ID NOs: 6, 477, 478, 479, and 480.

206. The PE system of any one of claims 203-205, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to any one of SEQ ID NOs: 6, 477, 478, 479, and 480. 1036 Atty Dkt No: L1034381390WO (0330.1)207. The PE system of any one of claims 203-206, wherein the PEgRNA comprises a tracrRNA comprising the nucleotide sequence of any one of SEQ ID NOs: 6, 477, 478, 479, and 480.

208. The PE system of any one of claims 190-197, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of SEQ ID NO: 571 or that differs from SEQ ID NO: 571 by 1 to 5 nucleotides, wherein said RGN polypeptide comprises the amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO:

565.

209. The PE system of any one of claims 190-197 and 208, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of SEQ ID NO: 571, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO:

565.

210. The PE system of claim 208 or 209, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO:

572.

211. The PE system of any one of claims 208-210, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO:

572.

212. The PE system of any one of claims 208-211, wherein the PEgRNA comprises a tracrRNA comprising the nucleotide sequence of SEQ ID NO:

572.

213. The PE system of any one of claims 190-197, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of SEQ ID NO: 573 or 1180 or that differs from SEQ ID NO: 573 or 1180 by 1 to 5 nucleotides, wherein said RGN polypeptide comprises the amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO:

566.

214. The PE system of any one of claims 190-197 and 213, wherein the PEgRNA comprises a CRISPR RNA comprising a CRISPR RNA (crRNA) repeat comprising the nucleotide sequence of SEQ ID NO: 573 or 1180, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO:

566.

215. The PE system of claim 213 or 214, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 574 or 1181.

216. The PE system of any one of claims 213-215, wherein the PEgRNA comprises a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 574 or 1181.

217. The PE system of any one of claims 213-216, wherein the PEgRNA comprises a tracrRNA comprising the nucleotide sequence of SEQ ID NO: 574 or 1181.

218. The PE system of any one of claims 190-217, wherein said polynucleotide encoding said one or more PEgRNAs and said polynucleotide encoding said PE are on a single vector. 1037 Atty Dkt No: L1034381390WO (0330.1)219. The PE system of any one of claims 190-217, wherein said polynucleotide encoding said one or more PEgRNAs and said polynucleotide encoding said PE are on separate vectors.

220. The PE system of any one of claims 190-217, wherein said polynucleotide encoding said DNA polymerase and said polynucleotide encoding said RGN polypeptide are on separate vectors.

221. The PE system of any one of claims 190-217, wherein said polynucleotide encoding said one or more PEgRNAs, said polynucleotide encoding said DNA polymerase, and said polynucleotide encoding said RGN polypeptide are all on separate vectors.

222. The PE system of any one of claims 190-217, wherein said polynucleotide encoding said PE is an RNA polynucleotide.

223. The PE system of claim 222, wherein said RNA polynucleotide is an mRNA.

224. The PE system of claim 222, wherein said RNA polynucleotide is a circRNA.

225. The PE system of any one of claims 190-224, wherein said PE system further comprises a nicking guide RNA or a polynucleotide comprising a nucleotide sequence encoding a nicking guide RNA.

226. The PE system of any one of claims 190-225, wherein said PE system further comprises a dominant negative MLH1 or a polynucleotide comprising a nucleotide sequence encoding a dominant negative MLH1.

227. A cell comprising the PE of any one of claims 121-186, the RNP complex of any one of claims 187-189, or the PE system of any one of claims 190-226.

228. The cell of claim 227, wherein the cell is a prokaryotic cell.

229. The cell of claim 227, wherein the cell is a eukaryotic cell.

230. The cell of claim 229, wherein the eukaryotic cell is a mammalian cell.

231. The cell of claim 230, wherein the mammalian cell is a human cell.

232. The cell of claim 231, wherein the human cell is an immune cell.

233. The cell of claim 231, wherein the human cell is a stem cell.

234. The cell of claim 233, wherein the stem cell is an induced pluripotent stem cell.

235. The cell of claim 229, wherein the eukaryotic cell is an insect or avian cell.

236. The cell of claim 229, wherein the eukaryotic cell is a fungal cell.

237. The cell of claim 229, wherein the eukaryotic cell is a plant cell.

238. A plant or plant part comprising the plant cell of claim 237.

239. A pharmaceutical composition comprising the one or more polynucleotides of any one of claims 1-75, the one or more vectors of any one of claims 76-104, the PE of any one of claims 121-186, the RNP complex of any one of claims 187-189, the cell of any one of claims 107-112 and 229-234, or the PE system of any one of claims 190-226, and a pharmaceutically acceptable carrier.

240. A method for modifying a target polynucleotide comprising a target sequence, said method comprising delivering a PE system according to any one of claims 190-226 to said target 1038 Atty Dkt No: L1034381390WO (0330.1)sequence or a cell comprising the target sequence, wherein said method generates a modified target polynucleotide, and wherein components of said PE system are delivered simultaneously or sequentially to said target sequence or said cell.

241. The method of claim 240, wherein said modified target polynucleotide comprises insertion of heterologous DNA into the target polynucleotide.

242. The method of claim 240, wherein said modified target polynucleotide comprises deletion of at least one nucleotide from the target polynucleotide.

243. The method of claim 240, wherein said modified target polynucleotide comprises mutation of at least one nucleotide in the target polynucleotide.

244. A method for modifying one or more target sequences in a target polynucleotide , said method comprising: a) assembling a ribonucleoprotein (RNP) complex by combining: i) a PEgRNA comprising an extension arm, wherein said extension arm comprises a primer binding site (PBS) and a DNA synthesis template; and ii) a PE of any one of claims 121-186; under conditions suitable for formation of the RNP complex; and b) contacting said target polynucleotide or a cell comprising said target polynucleotide with the assembled RNP complex; thereby modifying said one or more target sequence with said PE.

245. The method of any one of claims 240-244, wherein said method is performed in vitro, in vivo, or ex vivo.

246. The method of any one of claims 240-244, wherein said target polynucleotide is within a cell.

247. The method of claim 246, wherein the cell is a eukaryotic cell.

248. The method of claim 247, wherein the eukaryotic cell is a mammalian cell.

249. A cell produced according to the method of claim 246, wherein said target polynucleotide has been modified at said target sequence.

250. The cell of claim 249, wherein the cell is a prokaryotic cell.

251. The cell of claim 249, wherein the cell is a eukaryotic cell.

252. The cell of claim 251, wherein the eukaryotic cell is a mammalian cell.

253. The cell of claim 252, wherein the mammalian cell is a human cell.

254. The cell of claim 253, wherein the human cell is an immune cell.

255. The cell of claim 253, wherein the human cell is a stem cell.

256. The cell of claim 255, wherein the stem cell is an induced pluripotent stem cell.

257. The cell of claim 249, wherein the eukaryotic cell is an insect or avian cell.

258. The cell of claim 249, wherein the eukaryotic cell is a fungal cell.

259. The cell of claim 249, wherein the eukaryotic cell is a plant cell. 1039 Atty Dkt No: L1034381390WO (0330.1)260. A plant or plant part comprising the plant cell of claim 259.

261. A pharmaceutical composition comprising the cell of any one of claims 251-256 and a pharmaceutically acceptable carrier.

262. A method for treating a subject having or at risk of developing a disease, disorder, or condition, the method comprising: administering to the subject the one or more polynucleotides of any one of claims 1-75, the one or more vectors of any one of claims 76-104, the PE of any one of claims 121-186, the RNP complex of any one of claims 187-189, the PE system of any one of claims 190-226, the cell of any one of claims 107-112, 229-234, and 251-256, or the pharmaceutical composition of claim 239 or 261.

263. The method of claim 262, wherein said disease, disorder, or condition is associated with a mutation and said treating comprises correcting said mutation.

264. Use of the one or more polynucleotides of any one of claims 1-75, the one or more vectors of any one of claims 76-104, the PE of any one of claims 121-186, the RNP complex of any one of claims 187-189, the PE system of any one of claims 190-226, the cell of any one of claims 107-112, 229-234, and 251-256, or the pharmaceutical composition of claim 239 or 261 for the treatment of a disease, disorder, or condition in a subject having or at risk of developing said disease, disorder, or condition.

265. The use of claim 264, wherein said disease, disorder, or condition is associated with a mutation and said treating comprises correcting said mutation.

266. Use of the one or more polynucleotides of any one of claims 1-75, the one or more vectors of any one of claims 76-104, the PE of any one of claims 121-186, the RNP complex of any one of claims 187-189, the PE system of any one of claims 190-226, or the cell of any one of claims 107-112, 229-234, and 251-256, or the pharmaceutical composition of claim 239 or 261 for the manufacture of a medicament useful for treating a disease, disorder, or condition.

267. The use of claim 266, wherein said disease, disorder, or condition is associated with a mutation and an effective amount of said medicament corrects said mutation.

268. A polynucleotide comprising a nucleotide sequence encoding an RNA-guided nuclease (RGN) polypeptide comprising an amino acid sequence having: a) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, wherein said RGN polypeptide comprises: i) a S at a position corresponding to amino acid position 1020 in SEQ ID NO: 1; ii) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1; iii) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1; iv) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1; and v) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1; 1040 Atty Dkt No: L1034381390WO (0330.1)b) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 579, wherein said RGN polypeptide comprises a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 579; c) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 584, wherein said RGN polypeptide comprises a T at a position corresponding to amino acid position 1021 in SEQ ID NO: 584 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 584; d) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 583, wherein said RGN polypeptide comprises an N at a position corresponding to amino acid position 1021 in SEQ ID NO: 583 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 583; or e) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 591, wherein said RGN polypeptide comprises: i) a Q at a position corresponding to amino acid position 975 in SEQ ID NO: 591; ii) an A at a position corresponding to amino acid position 1020 in SEQ ID NO: 591; iii) a G at a position corresponding to amino acid position 1022 in SEQ ID NO: 591; and iv) a Q at a position corresponding to amino acid position 1023 in SEQ ID NO:

591.

269. The polynucleotide of claim 268, wherein said RGN polypeptide comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 579, 583, 584, or 591.

270. The polynucleotide of claim 268 or 269, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO: 1, 579, 583, 584, or 591.

271. The polynucleotide of any one of claims 268-270, wherein said polynucleotide encoding an RGN polypeptide comprises an mRNA further comprising a heterologous 5’ untranslated region (UTR) and / or a heterologous 3’ UTR.

272. The polynucleotide of any one of claims 268-271, wherein said polynucleotide encoding an RGN polypeptide is operably linked to a promoter heterologous to said polynucleotide.

273. The polynucleotide of any one of claims 268-272, wherein said RGN polypeptide is capable of binding a target sequence in a target polynucleotide in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA), wherein said target sequence comprises a target strand and a non-target strand, and wherein said gRNA is capable of hybridizing to the target strand of the target sequence. 1041 Atty Dkt No: L1034381390WO (0330.1)274. The polynucleotide of claim 273, wherein said RGN polypeptide recognizes a protospacer adjacent motif (PAM) that is 3′ of said target sequence.

275. The polynucleotide of claim 274, wherein the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCY.

276. The polynucleotide of claim 274, wherein the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 579 or 583 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNC.

277. The polynucleotide of claim 274, wherein the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 584 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCM.

278. The polynucleotide of claim 274, wherein the RGN polypeptide comprising an amino acid sequence having at least 90% sequence idenetity to SEQ ID NO: 591 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCT.

279. The polynucleotide of any one of claims 273-278, wherein said RGN polypeptide is capable of cleaving said target polynucleotide upon binding.

280. The polynucleotide of claim 279, wherein said RGN polypeptide is capable of generating a double-stranded break.

281. The polynucleotide of claim 279, wherein said RGN polypeptide is capable of generating a single-stranded break.

282. The polynucleotide of any one of claims 273-278, wherein said RGN polypeptide is nuclease inactive.

283. The polynucleotide of any one of claims 268-282, wherein said RGN polypeptide is operably fused to a heterologous polypeptide.

284. The polynucleotide of claim 283, wherein said heterologous polypeptide is a deaminase.

285. The polynucleotide of claim 284, wherein said deaminase is a cytosine deaminase or an adenine deaminase.

286. The polynucleotide of claim 283, wherein said heterologous polypeptide is a detectable label.

287. The polynucleotide of claim 283, wherein said heterologous polypeptide is an expression modulator.

288. The polynucleotide of any one of claims 268-287, wherein the RGN polypeptide is operably fused to one or more nuclear localization signals.

289. The polynucleotide of any one of claims 268-288, wherein the nucleotide sequence encoding the RGN polypeptide is codon optimized for expression in a eukaryotic cell.

290. The polynucleotide of claim 289, wherein the eukaryotic cell is a mammalian cell. 1042 Atty Dkt No: L1034381390WO (0330.1)291. The polynucleotide of any one of claims 268-290, wherein the polynucleotide is an isolated polynucleotide.

292. A vector comprising the polynucleotide of any one of claims 268-291.

293. The vector of claim 292, wherein the vector further comprises at least one nucleotide sequence encoding a guide RNA (gRNA).

294. The vector of claim 293, wherein the gRNA comprises a CRISPR RNA (crRNA) comprising a crRNA repeat comprising a nucleotide sequence set forth as any one of SEQ ID NOs: 3, 470, and 471, or that differs from any one of SEQ ID NOs: 3, 470, and 471 by 1 to 5 nucleotides.

295. The vector of claim 294, wherein the gRNA comprises a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to any one of SEQ ID NOs: 4, 472, 473, and 474.

296. The vector of any one of claims 292-295, wherein the vector is an adeno-associated viral (AAV) vector.

297. A cell comprising the polynucleotide of any one of claims 268-291 or the vector of any one of claims 292-296.

298. The cell of claim 297, wherein the cell is a prokaryotic cell.

299. The cell of claim 297, wherein the cell is a eukaryotic cell.

300. The cell of claim 299, wherein the eukaryotic cell is a mammalian cell.

301. The cell of claim 300, wherein the mammalian cell is a human cell.

302. The cell of claim 301, wherein the human cell is an immune cell.

303. The cell of claim 301, wherein the human cell is a stem cell.

304. The cell of claim 303, wherein the stem cell is an induced pluripotent stem cell.

305. The cell of claim 299, wherein the eukaryotic cell is an insect or avian cell.

306. The cell of claim 299, wherein the eukaryotic cell is a fungal cell.

307. The cell of claim 299, wherein the eukaryotic cell is a plant cell.

308. A plant or plant part comprising the plant cell of claim 307.

309. A method for making an RGN polypeptide comprising culturing the cell of claim 297 under conditions in which the RGN polypeptide is expressed.

310. A method for making an RGN polypeptide comprising introducing into a cell a heterologous polynucleotide comprising a nucleotide sequence encoding an RNA-guided nuclease (RGN) polypeptide comprising an amino acid sequence having: a) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, wherein said RGN polypeptide comprises: i) a S at a position corresponding to amino acid position 1020 in SEQ ID NO: 1; ii) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1; iii) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1; iv) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1; and 1043 Atty Dkt No: L1034381390WO (0330.1)v) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1; b) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 579, wherein said RGN polypeptide comprises a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 579; c) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 584, wherein said RGN polypeptide comprises a T at a position corresponding to amino acid position 1021 in SEQ ID NO: 584 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 584; d) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 583, wherein said RGN polypeptide comprises an N at a position corresponding to amino acid position 1021 in SEQ ID NO: 583 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 583; or e) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 591, wherein said RGN polypeptide comprises: i) a Q at a position corresponding to amino acid position 975 in SEQ ID NO: 591; ii) an A at a position corresponding to amino acid position 1020 in SEQ ID NO: 591; iii) a G at a position corresponding to amino acid position 1022 in SEQ ID NO: 591; and iv) a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 591; and culturing said cell under conditions in which the RGN polypeptide is expressed.

311. The method of claim 310, wherein said heterologous polynucleotide comprising a nucleotide sequence encoding an RNA-guided nuclease (RGN) polypeptide comprises an mRNA, further comprising a heterologous 5’ untranslated region (UTR) and / or a heterologous 3’ UTR.

312. The method of claim 310 or 311, wherein said RGN polypeptide is capable of binding a target sequence in a target polynucleotide in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA), wherein said target sequence comprises a target strand and a non-target strand, and wherein said gRNA is capable of hybridizing to the target strand of the target sequence.

313. The method of any one of claims 310-312, further comprising purifying said RGN polypeptide.

314. The method of any one of claims 310-312, wherein said cell further expresses one or more guide RNAs capable of binding to said RGN polypeptide to form an RGN ribonucleoprotein complex.

315. The method of claim 314, further comprising purifying said RGN ribonucleoprotein complex. 1044 Atty Dkt No: L1034381390WO (0330.1)316. An RNA-guided nuclease (RGN) polypeptide, wherein said RGN polypeptide comprises an amino acid sequence having: a) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, wherein said RGN polypeptide comprises: i) a S at a position corresponding to amino acid position 1020 in SEQ ID NO: 1; ii) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1; iii) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1; iv) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1; and v) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1; b) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 579, wherein said RGN polypeptide comprises a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 579; c) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 584, wherein said RGN polypeptide comprises a T at a position corresponding to amino acid position 1021 in SEQ ID NO: 584 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 584; d) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 583, wherein said RGN polypeptide comprises an N at a position corresponding to amino acid position 1021 in SEQ ID NO: 583 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 583; or e) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 591, wherein said RGN polypeptide comprises: i) a Q at a position corresponding to amino acid position 975 in SEQ ID NO: 591; ii) an A at a position corresponding to amino acid position 1020 in SEQ ID NO: 591; iii) a G at a position corresponding to amino acid position 1022 in SEQ ID NO: 591; and iv) a Q at a position corresponding to amino acid position 1023 in SEQ ID NO:

591.

317. The RGN polypeptide of claim 316, wherein said RGN polypeptide comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, 579, 583, 584, or 591.

318. The RGN polypeptide of claim 316 or 317, wherein said RGN polypeptide comprises the amino acid sequence set forth as SEQ ID NO: 1, 579, 583, 584, or 591.

319. The RGN polypeptide of any one of claims 316-318, wherein said RGN polypeptide is operably fused to a heterologous polypeptide. 1045 Atty Dkt No: L1034381390WO (0330.1)320. The RGN polypeptide of any one of claims 316-319, wherein said RGN polypeptide is capable of binding a target sequence in a target polynucleotide in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA), wherein said target sequence comprises a target strand and a non-target strand, and wherein said gRNA is capable of hybridizing to the target strand of the target sequence.

321. The RGN polypeptide of claim 320, wherein said RGN polypeptide recognizes a protospacer adjacent motif (PAM) that is 3′ of said target sequence.

322. The RGN polypeptide of claim 321, wherein the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCY.

323. The RGN polypeptide of claim 321, wherein the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 579 or 583 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNC.

324. The RGN polypeptide of claim 321, wherein the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 584 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCM.

325. The RGN polypeptide of claim 321, wherein the RGN polypeptide comprising an amino acid sequence having at least 90% sequence idenetity to SEQ ID NO: 591 recognizes a PAM having a consensus nucleotide sequence set forth as NNNNCT.

326. An RNA-guided nuclease (RGN) polypeptide comprising a protospacer adjacent motif (PAM) interacting domain that recognizes a PAM site comprising the nucleotide sequence set forth as NNNNCY, wherein said RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO:

1.

327. An RNA-guided nuclease (RGN) polypeptide comprising a protospacer adjacent motif (PAM) interacting domain that recognizes a PAM site comprising the nucleotide sequence set forth as NNNNC, wherein said RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 479 or 583.

328. An RNA-guided nuclease (RGN) polypeptide comprising a protospacer adjacent motif (PAM) interacting domain that recognizes a PAM site comprising the nucleotide sequence set forth as NNNNCM, wherein said RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO:

584.

329. An RNA-guided nuclease (RGN) polypeptide comprising a protospacer adjacent motif (PAM) interacting domain that recognizes a PAM site comprising the nucleotide sequence set forth as NNNNCT, wherein said RGN polypeptide comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO:

591.

330. The RGN polypeptide of any one of claims 316-329, wherein said RGN polypeptide is capable of cleaving said target polynucleotide upon binding. 1046 Atty Dkt No: L1034381390WO (0330.1)331. The RGN polypeptide of claim 330, wherein cleavage by said RGN polypeptide generates a double-stranded break.

332. The RGN polypeptide of claim 330, wherein cleavage by said RGN polypeptide generates a single-stranded break.

333. The RGN polypeptide of any one of claims 316-329, wherein said RGN polypeptide is nuclease inactive.

334. The RGN polypeptide of any one of claims 316-333, wherein said RGN polypeptide is operably fused to a heterologous polypeptide.

335. The RGN polypeptide of claim 334, wherein said heterologous polypeptide is a deaminase.

336. The RGN polypeptide of claim 335, wherein said deaminase is a cytosine deaminase or an adenine deaminase.

337. The RGN polypeptide of claim 334, wherein said heterologous polypeptide is a detectable label.

338. The RGN polypeptide of claim 334, wherein said heterologous polypeptide is an expression modulator.

339. The RGN polypeptide of any one of claims 316-338, wherein the RGN polypeptide is operably fused to one or more nuclear localization signals.

340. The RGN polypeptide of any one of claims 316-339, wherein the RGN polypeptide is an isolated RGN polypeptide.

341. A ribonucleoprotein (RNP) complex comprising the RGN polypeptide of any one of claims 316-340 and a guide RNA bound to the RGN polypeptide.

342. The RNP complex of claim 341, wherein the guide RNA and the RGN polypeptide are not found complexed to one another in nature.

343. The RNP complex of claim 341 or 342, wherein the guide RNA comprises a spacer that hybridizes to a eukaryotic target sequence.

344. The RNP complex of claim 343, wherein the eukaryotic target sequence comprises a mammalian target sequence.

345. An RNA-guided nuclease (RGN) system for binding one or more target sequences, said system comprising: a) one or more guide RNA (gRNA)s, or one or more polynucleotides comprising one or more nucleotide sequences encoding the one or more gRNAs, wherein each of the one or more gRNAs comprises a CRISPR RNA (crRNA) comprising a crRNA repeat and a spacer; and b) an RGN polypeptide comprising an amino acid sequence having: i) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1, or a polynucleotide comprising a nucleotide sequence encoding the RGN polypeptide, wherein said RGN polypeptide comprises: 1047 Atty Dkt No: L1034381390WO (0330.1)A) a S at a position corresponding to amino acid position 1020 in SEQ ID NO: 1; B) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1; C) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1; D) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1; and E) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1; ii) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 579, wherein said RGN polypeptide comprises a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 579; iii) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 584, wherein said RGN polypeptide comprises a T at a position corresponding to amino acid position 1021 in SEQ ID NO: 584 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 584; iv) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 583, wherein said RGN polypeptide comprises an N at a position corresponding to amino acid position 1021 in SEQ ID NO: 583 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 583; or v) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 591, wherein said RGN polypeptide comprises: A) a Q at a position corresponding to amino acid position 975 in SEQ ID NO: 591; B) an A at a position corresponding to amino acid position 1020 in SEQ ID NO: 591; C) a G at a position corresponding to amino acid position 1022 in SEQ ID NO: 591; and D) a Q at a position corresponding to amino acid position 1023 in SEQ ID NO:

591.

346. The RGN system of claim 345, wherein each of the one or more gRNAs is capable of hybridizing to the target strand of said target sequence and forming a complex with the RGN polypeptide to direct said RGN polypeptide to bind to said target sequence.

347. The RGN system of claim 345 or 346, wherein the spacer hybridizes to a eukaryotic target sequence. 1048 Atty Dkt No: L1034381390WO (0330.1)348. The RGN system of claim 347, wherein the eukaryotic target sequence comprises a mammalian target sequence.

349. The RGN system of any one of claims 345-348, wherein at least one of said one or more nucleotide sequences encoding the one or more gRNAs and said nucleotide sequence encoding the RGN polypeptide is operably linked to a promoter heterologous to said nucleotide sequence.

350. The RGN system of any one of claims 345-349, wherein said polynucleotide comprising a nucleotide sequence encoding the RGN polypeptide comprises an mRNA further comprising a heterologous 5’ untranslated region (UTR) and / or a heterologous 3’ UTR.

351. The RGN system of any one of claims 345-350, wherein said one or more gRNA comprises a crRNA repeat comprising a nucleotide sequence of any one of SEQ ID NOs: 3, 470, and 471, or that differs from any one of SEQ ID NOs: 3, 470 and 471 by 1 to 5 nucleotides.

352. The RGN system of claim 351, wherein said gRNA comprises a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to any one of SEQ ID NOs: 4, 472, 473, and 474.

353. The RGN system of any one of claims 345-352, wherein said RGN polypeptide and said one or more gRNAs are not found complexed to one another in nature.

354. The RGN system of any one of claims 345-353, wherein said target sequence is a eukaryotic target sequence.

355. The RGN system of any one of claims 345-354, wherein said RGN polypeptide recognizes a protospacer adjacent motif (PAM) that is 3′ of said target sequence.

356. The RGN system of claim 355, wherein the RGN polypeptide comprising an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 recognizes the PAM having a consensus nucleotide sequence set forth as NNNNCY.

357. The RGN system of any one of claims 345-356, wherein the system directs cleavage of the target polynucleotide.

358. The RGN system of claim 357, wherein the cleavage generates a double-stranded break.

359. The RGN system of claim 357, wherein the cleavage generates a single-stranded break.

360. The RGN system of any one of claims 345-356, wherein said RGN polypeptide is nuclease inactive.

361. The RGN system of any one of claims 345-360, wherein said RGN polypeptide is operably fused to a heterologous polypeptide.

362. The RGN system of claim 361, wherein said heterologous polypeptide is a deaminase.

363. The RGN system of claim 362, wherein said deaminase is a cytosine deaminase or an adenine deaminase. 1049 Atty Dkt No: L1034381390WO (0330.1)364. The RGN system of claim 361, wherein said heterologous polypeptide is a detectable label.

365. The polynucleotide of claim 361, wherein said heterologous polypeptide is an expression modulator.

366. The RGN system of any one of claims 345-365, wherein the RGN polypeptide is operably fused to one or more nuclear localization signals.

367. The RGN system of any one of claims 345-366, wherein the polynucleotide comprising the nucleotide sequence encoding the RGN polypeptide is codon optimized for expression in a eukaryotic cell.

368. The RGN system of any one of claims 345-367, wherein said system further comprises one or more donor polynucleotides.

369. A cell comprising the RGN polypeptide of any one of claims 316-340, the RNP complex of any one of claims 341-344, or the RGN system of any one of claims 345-368.

370. The cell of claim 369, wherein the cell is a prokaryotic cell.

371. The cell of claim 369, wherein the cell is a eukaryotic cell.

372. The cell of claim 371, wherein the eukaryotic cell is a mammalian cell.

373. The cell of claim 372, wherein the mammalian cell is a human cell.

374. The cell of claim 373, wherein the human cell is an immune cell.

375. The cell of claim 373, wherein the human cell is a stem cell.

376. The cell of claim 375, wherein the stem cell is an induced pluripotent stem cell.

377. The cell of claim 371, wherein the eukaryotic cell is an insect or avian cell.

378. The cell of claim 371, wherein the eukaryotic cell is a fungal cell.

379. The cell of claim 371, wherein the eukaryotic cell is a plant cell.

380. A plant or plant part comprising the plant cell of claim 379.

381. A pharmaceutical composition comprising the polynucleotide of any one of claims 268-291, the vector of any one of claims 292-296, the RGN polypeptide of any one of claims 316- 340, the RNP complex of any one of claims 341-344, the cell of any one of claims 299-304 and 371- 376, or the RGN system of any one of claims 345-368, and a pharmaceutically acceptable carrier.

382. A method for binding a target sequence in a target polynucleotide comprising delivering an RGN system according to any one of claims 345-368, to said target sequence or a cell comprising the target sequence.

383. The method of claim 382, wherein said RGN polypeptide or said one or more gRNAs further comprise a detectable label, thereby allowing for detection of said target sequence.

384. The method of claim 382, wherein said RGN polypeptide or said one or more gRNAs further comprise an expression modulator, thereby modulating expression of a target gene comprising said target sequence. 1050 Atty Dkt No: L1034381390WO (0330.1)385. A method for cleaving and / or modifying a target polynucleotide comprising a target sequence, said method comprising delivering a RGN system according to any one of claims 345-368 to said target sequence or a cell comprising the target sequence.

386. The method of claim 385, wherein said modified target polynucleotide comprises insertion of heterologous DNA into the target polynucleotide.

387. The method of claim 385, wherein said modified target polynucleotide comprises deletion of at least one nucleotide from the target polynucleotide.

388. The method of claim 385, wherein said modified target polynucleotide comprises mutation of at least one nucleotide in the target polynucleotide.

389. A method for binding one or more target sequence in a target polynucleotide with an RNA-guided nuclease (RGN) polypeptide, said method comprising: a) assembling a ribonucleoprotein (RNP) complex by combining: i) a guide RNA (gRNA); and ii) an RGN polypeptide comprising an amino acid sequence having: A) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 1 wherein said RGN polypeptide comprises: I) a S at a position corresponding to amino acid position 1020 in SEQ ID NO: 1; II) a G at a position corresponding to amino acid position 1021 in SEQ ID NO: 1; III) a N at a position corresponding to amino acid position 1022 in SEQ ID NO: 1; IV) a K at a position corresponding to amino acid position 1023 in SEQ ID NO: 1; and V) a E at a position corresponding to amino acid position 1025 in SEQ ID NO: 1; B) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 579, wherein said RGN polypeptide comprises a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 579; C) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 584, wherein said RGN polypeptide comprises a T at a position corresponding to amino acid position 1021 in SEQ ID NO: 584 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 584; D) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 583, wherein said RGN polypeptide comprises an N at a position corresponding to amino acid position 1021 in SEQ ID NO: 583 and an N at a position corresponding to amino acid position 1023 in SEQ ID NO: 583; or 1051 Atty Dkt No: L1034381390WO (0330.1)E) at least 90% sequence identity to the amino acid sequence set forth as SEQ ID NO: 591, wherein said RGN polypeptide comprises: I) a Q at a position corresponding to amino acid position 975 in SEQ ID NO: 591; II) an A at a position corresponding to amino acid position 1020 in SEQ ID NO: 591; III) a G at a position corresponding to amino acid position 1022 in SEQ ID NO: 591; and IV) a Q at a position corresponding to amino acid position 1023 in SEQ ID NO: 591; under conditions suitable for formation of the RNP complex; and b) contacting said target polynucleotide or a cell comprising said target polynucleotide with the assembled RNP complex; thereby binding said one or more target sequence with said RGN polypeptide.

390. The method of any one of claims 382-389, wherein said method is performed in vitro, in vivo, or ex vivo.

391. The method of any one of claims 382-389, wherein said target polynucleotide is within a cell.

392. The method of claim 391, wherein the cell is a eukaryotic cell.

393. The method of claim 392, wherein the eukaryotic cell is a mammalian cell.

394. A cell produced according to the method of any one of claims 391-393, wherein said target polynucleotide has been cleaved and / or modified at said target sequence.

395. The cell of claim 394, wherein the cell is a prokaryotic cell.

396. The cell of claim 394, wherein the cell is a eukaryotic cell.

397. The cell of claim 396, wherein the eukaryotic cell is a mammalian cell.

398. The cell of claim 397, wherein the mammalian cell is a human cell.

399. The cell of claim 398, wherein the human cell is an immune cell.

400. The cell of claim 398, wherein the human cell is a stem cell.

401. The cell of claim 400, wherein the stem cell is an induced pluripotent stem cell.

402. The cell of claim 396, wherein said eukaryotic cell is an insect or avian cell.

403. The cell of claim 396, wherein the eukaryotic cell is a fungal cell.

404. The cell of claim 396, wherein the eukaryotic cell is a plant cell.

405. A plant or plant part comprising the plant cell of claim 404.

406. A pharmaceutical composition comprising the cell of any one of claims 396-401 and a pharmaceutically acceptable carrier.

407. A method for treating a subject having or at risk of developing a disease, disorder, or condition, the method comprising: 1052 Atty Dkt No: L1034381390WO (0330.1)administering to the subject the polynucleotide of any one of claims 268-291, the vector of any one of claims 292-296, the RGN polypeptide of any one of claims 316-340, the RNP complex of any one of claims 341-344, the RGN system of any one of claims 345-368, the cell of any one of claims 299-304, 371-376, and 396-401, or the pharmaceutical composition of claim 381 or 406.

408. The method of claim 407, wherein said disease, disorder, or condition is associated with a mutation and said treating comprises correcting said mutation.

409. Use of the polynucleotide of any one of claims 268-291, the vector of any one of claims 292-296, the RGN polypeptide of any one of claims 316-340, the RNP complex of any one of claims 341-344, the RGN system of any one of claims 345-368, the cell of any one of claims 299-304, 371-376, and 396-401, or the pharmaceutical composition of claim 381 or 406 for the treatment of a disease, disorder, or condition in a subject having or at risk of developing said disease, disorder, or condition.

410. The use of claim 409, wherein said disease, disorder, or condition is associated with a mutation and said treating comprises correcting said mutation.

411. Use of the polynucleotide of any one of claims 268-291, the vector of any one of claims 292-296, the RGN polypeptide of any one of claims 316-340, the RNP complex of any one of claims 341-344, the RGN system of any one of claims 345-368, the cell of any one of claims 299-304, 371-376, and 396-401, or the pharmaceutical composition of claim 381 or 406 for the manufacture of a medicament useful for treating a disease, disorder, or condition.

412. The use of claim 411, wherein said disease, disorder, or condition is associated with a mutation and an effective amount of said medicament corrects said mutation.

413. A dual polymerase editing (DPE) system comprising: a) a first polymerase editing (PE) system comprising a first PE, or a polynucleotide encoding the same, and a first PEgRNA comprising a first DNA synthesis template, or a polynucleotide encoding the same; and b) a second PE system comprising a second PE, or a polynucleotide encoding the same, and a second PEgRNA comprising a second DNA synthesis template, or a polynucleotide encoding the same; wherein said first and said second PEgRNAs bind to opposite strands of a target DNA and wherein said first DNA synthesis template encodes a first single-stranded DNA sequence and said second DNA synthesis template encodes a second single-stranded DNA sequence, wherein the first and second single-stranded DNA sequences are at least partially complementary to each other and form a replacement sequence; wherein said first PE, said second PE, or both said first and said second PE are a PE of any one of claims 121-186.

414. The DPE system of claim 413, wherein said first PE and said second PE are the same. 1053 Atty Dkt No: L1034381390WO (0330.1)415. The DPE system of claim 413, wherein said first PE and said second PE are different from each other.

416. A dual polymerase editing (DPE) system comprising a PE, or a polynucleotide encoding the same, and a first PEgRNA comprising a first DNA synthesis template, or a polynucleotide encoding the same; and a second PEgRNA comprising a second DNA synthesis template, or a polynucleotide encoding the same; wherein said first and said second PEgRNAs bind to opposite strands of a target DNA and wherein said first DNA synthesis template encodes a first single-stranded DNA sequence and said second DNA synthesis template encodes a second single-stranded DNA sequence, wherein the first and second single-stranded DNA sequences are at least partially complementary to each other and form a replacement sequence; wherein said PE is a PE of any one of claims 121-186.

417. The DPE system of any one of claims 413-416, wherein said replacement sequence comprises a first recombinase site.

418. The DPE system of claim 417, wherein said DPE system further comprises a donor DNA, wherein said donor DNA comprises a second recombinase site.

419. The DPE system of claim 418, wherein said DPE system further comprises a recombinase that recognizes said first and said second recombinase sites.

420. A cell comprising the DPE system of any one of claims 413-419.

421. The cell of claim 420, wherein the cell is a prokaryotic cell.

422. The cell of claim 420, wherein the cell is a eukaryotic cell.

423. The cell of claim 422, wherein the eukaryotic cell is a mammalian cell.

424. The cell of claim 423, wherein the mammalian cell is a human cell.

425. The cell of claim 424, wherein the human cell is an immune cell.

426. The cell of claim 424, wherein the human cell is a stem cell.

427. The cell of claim 426, wherein the stem cell is an induced pluripotent stem cell.

428. The cell of claim 422, wherein the eukaryotic cell is an insect or avian cell.

429. The cell of claim 422, wherein the eukaryotic cell is a fungal cell.

430. The cell of claim 422, wherein the eukaryotic cell is a plant cell.

431. A plant or plant part comprising the plant cell of claim 430.

432. A pharmaceutical composition comprising the DPE system of any one of claims 413- 419 or the cell of any one of claims 423-427, and a pharmaceutically acceptable carrier.

433. A method for modifying a target polynucleotide comprising a target sequence, comprising delivering a DPE system according to any one of claims 413-419 to said target sequence or a cell comprising the target sequence, wherein said method generates a modified target polynucleotide, and wherein components of said DPE system are delivered simultaneously or sequentially to said target sequence or said cell. 1054 Atty Dkt No: L1034381390WO (0330.1)434. The method of claim 433, wherein said method is performed in vitro, in vivo, or ex vivo.

435. The method of claim 433 or 434, wherein said target polynucleotide is within a cell.

436. The method of claim 435, wherein the cell is a eukaryotic cell.

437. The method of claim 436, wherein the eukaryotic cell is a mammalian cell.

438. A cell produced according to the method of claim 435, wherein said target polynucleotide has been modified at said target sequence.

439. The cell of claim 438, wherein the cell is a prokaryotic cell.

440. The cell of claim 438, wherein the cell is a eukaryotic cell.

441. The cell of claim 440, wherein the eukaryotic cell is a mammalian cell.

442. The cell of claim 441, wherein the mammalian cell is a human cell.

443. The cell of claim 442, wherein the human cell is an immune cell.

444. The cell of claim 442, wherein the human cell is a stem cell.

445. The cell of claim 444, wherein the stem cell is an induced pluripotent stem cell.

446. The cell of claim 440, wherein the eukaryotic cell is an insect or avian cell.

447. The cell of claim 440, wherein the eukaryotic cell is a fungal cell.

448. The cell of claim 440, wherein the eukaryotic cell is a plant cell.

449. A plant or plant part comprising the plant cell of claim 448.

450. A pharmaceutical composition comprising the cell of any one of claims 440-445 and a pharmaceutically acceptable carrier.

451. A method for treating a subject having or at risk of developing a disease, disorder, or condition, the method comprising: administering to the subject the DPE system of any one of claims 413-419, the cell of any one of claims 423-427 and 440-445, or the pharmaceutical composition of claim 432 or 450.

452. The method of claim 451, wherein said disease, disorder, or condition is associated with a mutation and said treating comprises correcting said mutation.

453. Use of the DPE system of any one of claims 413-419, the cell of any one of claims 423-427 and 440-445, or the pharmaceutical composition of claim 432 or 450 for the treatment of a disease, disorder, or condition in a subject having or at risk of developing said disease, disorder, or condition.

454. The use of claim 453, wherein said disease, disorder, or condition is associated with a mutation and said treating comprises correcting said mutation.

455. Use of the DPE system of any one of claims 413-419, the cell of any one of claims 423-427 and 440-445, or the pharmaceutical composition of claim 432 or 450 for the manufacture of a medicament useful for treating a disease, disorder, or condition.

456. The use of claim 455, wherein said disease, disorder, or condition is associated with a mutation and an effective amount of said medicament corrects said mutation. 1055 Atty Dkt No: L1034381390WO (0330.1)