Engineered pioneer factor proteins for improved multi-species induced pluripotent stem cell derivation

Abstract

Provided are designed proteins, derived from OCT4 and SOX2, which have enhanced stability and binding affinity for one another compared to the wild-type equivalents. These designed proteins are species-agnostic. Specifically provided are isolated SOX2 proteins having an artificial SOX2 DNA binding domain and isolated OCT4 proteins having an artificial OCT4 DNA binding domain. Also provided are uses of these proteins to generate induced pluripotent stem cells, vectors, and host cells containing these proteins.

Description

Attorney Docket No.: 069296.11211 / 34WO01ENGINEERED PIONEER FACTOR PROTEINS FOR IMPROVED MULTISPECIES INDUCED PLURIPOTENT STEM CELL DERIVATION CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Application No. 63 / 746,196, filed January 16, 2025, the disclosure of which is herein incorporated by reference in its entirety.FIELD OF THE INVENTION

[0002] This disclosure relates to SOX2 proteins having an artificial SOX2 domain and OCT4 proteins having an artificial OCT4 domain, and their uses in generating induced pluripotent stem cells.REFERENCE TO SEQUENCE LISTING

[0003] This application contains a sequence listing, which is submitted electronically. The contents of the electronic sequence listing (069296.34WO01 Sequence Lisitng.xml; size: 215,199 bytes; and creation date of December 30, 2025) is herein incorporated by reference in its entirety.BACKGROUND OF THE INVENTION

[0004] SOX2 (SRY (sex determining region Y)-box 2) is a transcription factor essential for maintaining self-renewal or pluripotency of undifferentiated embryonic stem cells. OCT4 (octamer-binding transcription factor 4, also known as POU5F1 (POU domain, class 5, transcription factor 1)) is a homeodomain transcription factor of the POU family, which is involved in the self-renewal of undifferentiated embryonic stem cells. SOX2 forms a trimeric complex with OCT4 on DNA and is known to control expression of various genes involved in embryonic development such as YES1, FGF4, UTF1, and ZFP206.

[0005] Experiments have shown that OCT4, along with SOX2 and KLF4 (SK), can induce pluripotency, but structurally similar factors like OCT6 cannot. See Malik et al., Nature Communication, 10: 3477 (2019). However, despite their ability to induce pluripotency, OCT4 and SOX2 are believed to be species specific, limiting their use as a tool for generating pluripotency in a variety7of species.

[0006] What is needed are OCT4 and SOX2 variants that can be used in a variety of different species to induce pluripotency.4918-0896-8837 1 1Attorney Docket No.: 069296.11211 / 34WO01SUMMARY OF THE INVENTION

[0007] Accordingly, this disclosure provides artificially designed OCT4 and SOX2 proteins with enhanced stability and binding affinity for one another compared to the wildtype equivalent. These enhancements were designed for stronger and more persistent binding to their DNA targets in cellulo. This leads to more potent induction of gene transcription towards pluripotency, and in turn faster and more efficient reprogramming to induced pluripotent stem cells (iPSCs). These proteins share as little as 70% sequence identity to the wild-ty pe proteins within the DNA-binding domains (DBD). They were designed to be species-agnostic.

[0008] Accordingly, one aspect of the disclosure is related to artificially designed SOX2 proteins, nucleic acids encoding such proteins, and vectors encoding such proteins. One embodiment is an isolated SOX2 protein having an artificial SOX2 DNA binding domain, wherein the artificial SOX2 DNA binding domain has an ammo acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 1-21. In certain embodiments, the artificial SOX2 DNA binding domain has the amino acid sequence of any one of SEQ ID NOs: 1-21.

[0009] In other embodiments, the SOX2 protein has an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs:43-62. Alternatively, the SOX2 protein has the amino acid sequence of any one of SEQ ID NOs:43-62. In certain embodiments, the isolated SOX2 protein is humanized.

[0010] Another embodiment of the disclosure is directed to nucleic acids encoding the isolated SOX2 protein. Yet another embodiment is a vector containing the nucleic acids encoding the isolated SOX2 protein. A further embodiment is a host cell containing the isolated nucleic acid.

[0011] Another aspect of the disclosure is related to artificially designed OCT4 proteins, nucleic acids encoding such proteins, and vectors encoding such proteins. One embodiment is an isolated OCT4 protein having an artificial OCT4 DNA binding domain, wherein the artificial OCT4 DNA binding domain has an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 83-103. In another embodiment, the artificial OCT4 DNA binding domain comprises the amino acid sequence of any one of SEQ ID NOs: 83-103.4918-0896-88371 2Attorney Docket No.: 069296.11211 / 34WO01

[0012] In yet another embodiment, the OCT4 protein has an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 125- 144. In further embodiments, the OCT4 protein has the amino acid sequence of any one of SEQ ID NOs: 125-144.

[0013] In certain embodiments, the isolated OCT4 protein is humanized.

[0014] Yet another embodiment of the disclosure is directed to an isolated nucleic acid encoding the isolated OCT4 protein. A further embodiment is a vector containing the nucleic acid encoding the isolated SOX2 protein. An additional embodiment is a host cell containing the isolated nucleic acid.

[0015] In certain embodiments, the disclosure is related to a vector containing one or more of the artificially designed OCT4 proteins of the disclosure and one or more of the artificially designed SOX2 proteins of the disclosure. The disclosure also includes host cells containing one or more of the artificially designed OCT4 proteins of the disclosure and one or more of the artificially designed SOX2 proteins of the disclosure. The disclosure further includes host cells containing the vectors.

[0016] Yet another aspect of the disclosure is directed to methods of generating induced pluripotent stem cells using the OCT4 and SOX2 proteins of the disclosure.

[0017] One embodiment is a method of generating induced pluripotent stem cells including:(a) transfecting a somatic cell with a polynucleotide encoding a SOX2 protein having an artificial SOX2 DNA binding domain and a polynucleotide encoding an OCT4 protein having an artificial OCT4 DNA binding domain;(b) culturing the cells in a culture medium to generate induced pluripotent stem cells;and optionally(c) selecting for the induced pluripotent stem cells,wherein the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 22-42; and wherein the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 104-124.

[0018] In certain embodiments, the polynucleotide encoding the SOX2 protein and the polynucleotide encoding the OCT4 protein are humanized.4918-0896-88371 3Attorney Docket No.: 069296.11211 / 34WO01

[0019] In other embodiments, the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes (i) a nucleic acid sequence at least 85%. at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 63-82 or (ii) a nucleic acid sequence encoding a protein having an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 43-62.

[0020] In further embodiments, the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes (iii) a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 145-164 or (iv) a nucleic acid sequence encoding a protein having an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 125-144.

[0021] In further embodiments of the methods:• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 1 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 83;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 2 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 84;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 3 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 85;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 4 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 86;4918-0896-88371 4Attorney Docket No.: 069296.11211 / 34WO01• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 5 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 87;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 6 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 88;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 7 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 89;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 8 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 90;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 9 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 91;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 10 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 92;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 11 and the polynucleotide encoding the OCT4 protein4918-0896-88371 5Attorney Docket No.: 069296.11211 / 34WO01containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 93;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 12 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 94;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 13 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 95;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 14 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 96;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 1 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 97;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 16 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 98;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 17 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 99;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA4918-0896-88371 6Attorney Docket No.: 069296.11211 / 34WO01binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 18 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 100;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 19 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 101;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 20 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 102; or• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 21 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 103.

[0022] In additional embodiments of the methods:• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 43 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 125;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 44 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 126;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 45 and the polynucleotide encoding the OCT4 protein4918-0896-88371 7Attorney Docket No.: 069296.11211 / 34WO01containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 127;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 46 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 128;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 47 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 129;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 48 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 130;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 49 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 131;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 50 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 132;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 51 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 133;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA4918-0896-88371 8Attorney Docket No.: 069296.11211 / 34WO01binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 52 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 134;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 53 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 135;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 54 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 136;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 55 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 137;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 56 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 138;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 57 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 139;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 58 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence4918-0896-88371 9Attorney Docket No.: 069296.11211 / 34WO01encoding a protein having the amino acid sequence of SEQ ID NO: 140;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 59 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 141;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 60 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 142;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 61 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 143; or• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 62 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 144.

[0023] In additional embodiments of the methods:• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 22 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 104;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 23 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 105;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 24 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding4918-0896-88371 10Attorney Docket No.: 069296.11211 / 34WO01domain includes the nucleic acid sequence of SEQ ID NO: 106;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 25 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 107;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 26 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 108;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 27 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 109;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 28 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 110;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 29 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 111;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 30 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 112;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 31 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 113;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 32 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 114;4918-0896-88371 11Attorney Docket No.: 069296.11211 / 34WO01• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 33 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 115;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 34 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 116;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 35 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 117;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 36 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 118;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 37 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 119;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 38 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 120;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 39 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 121;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 40 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 122;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA4918-0896-88371 12Attorney Docket No.: 069296.11211 / 34WO01binding domain includes the nucleic acid sequence of SEQ ID NO: 41 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 123; or• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 42 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 124.

[0024] In further embodiments of the methods:• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 63 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 145;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 64 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 146;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 65 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 147;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 66 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 148;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 67 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 149;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 68 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 150;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA4918-0896-88371 13Attorney Docket No.: 069296.11211 / 34WO01binding domain includes the nucleic acid sequence of SEQ ID NO: 69 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 151;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 70 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 152;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 71 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 153;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 72 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 154;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 73 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 155;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 74 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 156;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 75 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 157;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 76 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 158;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 77 and the4918-0896-88371 14Attorney Docket No.: 069296.11211 / 34WO01polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 159;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 78 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 160;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 79 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 161;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 80 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 162;• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 81 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 163; or• the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 82 and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain includes the nucleic acid sequence of SEQ ID NO: 164.

[0025] In additional embodiments, the method includes transfecting the somatic cells with a nucleic acid encoding one or more of KLF4, MYC, LIN28, and NANOG, such as e.g., a nucleic acid encoding KLF4 and MYC or a nucleic acid encoding KLF4, MYC, LIN28, and NANOG. For example, in certain embodiments, the method includes transfecting the cells with: (i) a nucleic acid encoding the SOX2 protein having the artificial SOX2 DNA binding domain, (ii) a nucleic acid encoding the OCT4 protein having an artificial OCT4 DNA binding domain; and (iii) either a polynucleotide encoding KLF4 an MYC or a polynucleotide encoding KLF4, MYC, LIN28, and NANOG.

[0026] In further embodiments, the method includes transfecting the somatic cells with a vector containing the polynucleotide encoding the SOX2 protein having an artificial SOX24918-0896-88371 15Attorney Docket No.: 069296.11211 / 34WO01DNA binding domain and a polynucleotide encoding the OCT4 protein containing an artificial OCT4 DNA binding domain.

[0027] In additional embodiments, the method further includes chemically reprogramming the cells prior to transfecting the cells. For example, in certain embodiments, the method further includes chemically reprogramming the cells by culturing the cells in a culture medium supplemented with an HD AC inhibitor, a GSK-3 inhibitor, a TGF-[3 inhibitor, a monoamine oxidase inhibitor, an activator of eukaryotic adenylyl cyclase, a retinoid, and a DOT1L inhibitor. In other embodiments, the method further includes chemically reprogramming the cells by culturing the cells in a culture medium supplemented with one or more of an HD AC inhibitor, a GSK-3 inhibitor, a TGF-[3 inhibitor, a monoamine oxidase inhibitor, an activator of eukaryotic adenylyl cyclase, a retinoid, and a DOT1L inhibitor.

[0028] A variety of cells can be used in the methods or with the SOX2 and / or OCT4 proteins of the disclosure. In one embodiment, the somatic cells are endothelial cells. In another embodiment, the somatic cell or cell is a mammalian cell. In some embodiments, the mammal is a mouse, a rat, a marsupial, a cow, an ovine, a caprine, a pig, an elephant, an equid, a cat, a dog, a wolf, a deer, or an antelope. In other embodiments, the mammal is mammal is Felis catus, Cants lupus familiaris, Cams lupus, Bison bison, Dama dama, Hippolragus equinus, Hippotragus niger, an Asian elephant (Elephas maximus), an African elephant (Loxodonta africana). an African forest elephant (Loxodonta cyclotis), or a Bornean elephant (Elephas maximus borneensis). In some embodiments, the mammal is an Asian elephant Elephas maximus), an African elephant (Loxodonta africana), an African forest elephant (Loxodonta cyclotis), or a Bornean elephant (Elephas maximus borneensis).

[0029] The disclosure also includes pluripotent stem cells produced by the methods of the disclosure.

[0030] Other features and advantages of the invention will be apparent from the detailed description and examples that follow.BRIEF DESCRIPTION OF THE DRAWINGS

[0031] The foregoing summary, as well as the following detailed description of the invention, will be better understood when read in conjunction with the appended figures. For the purpose of illustrating the invention, the figures demonstrate embodiments of the present invention. It should be understood, however, that the invention is not limited to the precise arrangements, examples, and instrumentalities shown.4918-0896-88371 16Attorney Docket No.: 069296.11211 / 34WO01

[0032] FIG. 1 shows a schematic diagram of the computational pipeline used to develop the redesigned Oct / Sox pairs of the disclosure.

[0033] FIG. 2 shows colony forming units after 7 days for certain OXT4 / SOX2 construct pairs of the disclosure.

[0034] FIG. 3 shows an MA plot for NANOG, KLF4, LIN28A, SOX2, and POUT5F1 for elephant primary cells transfected with one of the top performing engineered OCT4 / SOX2 pairs (em_int48 as above) after 28 days culture post-transfection.

[0035] FIG. 4 shows an MA plot for key pluripotency cells transfected with one of the top performing engineered OCT4 / SOX2 pairs (em_int48 as above) after 28 days culture posttransfection.

[0036] FIG. 5 shows the results of a metagenomic analysis of gene clusters upregulated in cells treated with engineered OCT4 / SOX2 pairs.DETAILED DESCRIPTION

[0037] This disclosure is directed to designed proteins, derived from OCT4 and SOX2. which have enhanced stability and binding affinity for one another compared to the wildtype equivalent. These enhancements enable stronger and more persistent binding to their DNA targets in cellulo, leading to more potent induction of gene transcription towards pluripotency, and in turn faster and more efficient reprogramming to induced pluripotent stem cells (iPSCs). These proteins, while derived from the structures of the DNA-binding domains (DBD) of mouse (crystal structure) and Asian elephant (modeled using ESMFold) OCT4 and SOX2, were redesigned using ProteinMPNN, and share as little as 70% sequence identity to the wild-type proteins within the DBD. They were designed to be speciesagnostic, and to that end they have been tested thus far in mouse and elephant cell lines, and several pairs work extremely well in both, establishing efficacy in highly divergent mammalian species.

[0038] The OCT4 and SOX2 derivatives provide faster and more efficient induction of iPSCs. Without being bound by theory, this allows both researchers and clinicians to spend less time and effort in generating stem cells for research or clinical purposes and potentially enables iPSC induction in previously recalcitrant species and cell lines, like elephants.

[0039] The general description and the following detailed description are exemplary and explanatory only and are not restrictive of the invention, as defined in the appended claims. Other aspects of the present invention will be apparent to those skilled in the art in view of the detailed description of the invention as provided herein.4918-0896-88371 17Attorney Docket No.: 069296.11211 / 34WO01

[0040] For clarity of disclosure, and not by way of limitation, the detailed description of the invention is divided into subsections that describe or illustrate certain features, embodiments, or applications of the present invention.Definitions

[0041] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, representative illustrative methods, and materials are now described.

[0042] All publications and patents cited in this specification are herein incorporated by reference as if each individual publication or patent were specifically and individually indicated to be incorporated by reference and are incorporated herein by reference to disclose and describe the methods and / or materials in connection with which the publications are cited. The citation of any publication is for its disclosure prior to the filing date and should not be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates, which may need to be independently confirmed.

[0043] It is noted that, as used herein and in the appended claims, the singular forms “a,” ■‘an,” and “the” include plural referents unless the context clearly dictates otherwise. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely.” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.

[0044] Each of the individual embodiments described and illustrated herein has discrete components and features which may be readily separated from or combined with the features of any of the other several embodiments without departing from the scope or spirit of the present invention. Any recited method can be carried out in the order of events recited or in any other order which is logically possible.

[0045] As used herein, the term “about” when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ± 20% or ± 10%, more preferably ± 5%, even more preferably ± 1%, and still more preferably ± 0.1%4918-0896-88371 18Attorney Docket No.: 069296.11211 / 34WO01from the specified value, as such variations are appropriate to perform the disclosed methods.

[0046] As used herein, the terms “comprising,’’ “including,” “containing” and “characterized by” are exchangeable, inclusive, open-ended and do not exclude additional, unrecited elements or method steps. Any recitation herein of the term “comprising,” particularly in a description of components of a composition or in a description of elements of a device, is understood to encompass those compositions and methods consisting essentially of and consisting of the recited components or elements.

[0047] Throughout this specification, unless the context requires otherwise, the word “comprise” or variations such as “comprises” or “comprising,” will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers.

[0048] As used herein, the term “consisting of’ excludes any element, step, or ingredient not specified in the claim element.

[0049] Before certain embodiments are described in greater detail, it is to be understood that this invention is not limited to certain embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing certain embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.

[0050] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

[0051] Ranges: throughout this disclosure, various aspects of the invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 14918-0896-88371 19Attorney Docket No.: 069296.11211 / 34WO01to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example. 1, 2, 2.7, 3, 4, 5, 5.3. and 6. This applies regardless of the breadth of the range.

[0052] Unless otherwise indicated, the term “at least” preceding a series of elements is to be understood to refer to every element in the series. Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the invention.

[0053] As used herein, the terms “comprises,” “comprising,” “includes,” “including,” “has,” “having,” “contains” or “containing,” or any other variation thereof, will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers and are intended to be non-exclusive or open-ended. For example, a composition, a mixture, a process, a method, an article, or an apparatus that comprises a list of elements is not necessarily limited to only those elements but can include other elements not expressly listed or inherent to such composition, mixture, process, method, article, or apparatus. Further, unless expressly stated to the contrary, “or” refers to an inclusive or and not to an exclusive or. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).

[0054] As used herein, the conjunctive term “and / or” between multiple recited elements is understood as encompassing both individual and combined options. For instance, where two elements are conjoined by “and / or,” a first option refers to the applicability of the first element without the second. A second option refers to the applicability of the second element without the first. A third option refers to the applicability of the first and second elements together. Any one of these options is understood to fall within the meaning, and therefore satisfy the requirement of the term “and / or” as used herein. Concurrent applicability of more than one of the options is also understood to fall within the meaning, and therefore satisfy the requirement of the term “and / or.”

[0055] As used herein, the term “consists of,” or variations such as “consist of’ or “consisting of,” as used throughout the specification and claims, indicate the inclusion of any recited integer or group of integers, but that no additional integer or group of integers can be added to the specified method, structure, or composition.

[0056] As used herein, the term “consists essentially of.” or variations such as “consist essentially of’ or “consisting essentially of,” as used throughout the specification and4918-0896-88371 20Attorney Docket No.: 069296.11211 / 34WO01claims, indicate the inclusion of any recited integer or group of integers, and the optional inclusion of any recited integer or group of integers that do not materially change the basic or novel properties of the specified method, structure or composition. See M.P.E.P. § 2111.03.

[0057] The words “right,” “left,” “lower,” and “upper” designate directions in the drawings to which reference is made.

[0058] It should also be understood that the terms “about,” “approximately.” “generally,” “substantially” and like terms, used herein when referring to a dimension or characteristic of a component of the preferred invention, indicate that the described dimension / characteristic is not a strict boundary or parameter and does not exclude minor variations therefrom that are functionally the same or similar, as would be understood by one having ordinary skill in the art. At a minimum, such references that include a numerical parameter would include variations that, using mathematical and industrial principles accepted in the art (e.g, rounding, measurement or other systematic errors, manufacturing tolerances, etc.), would not van’ the least significant digit.

[0059] The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection.

[0060] For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

[0061] Optimal alignment of sequences for comparison can be conducted, e.g, by the local homology’ algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology’ alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat 'I. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by visual inspection (see generally. Current Protocols in Molecular Biology, F.M. Ausubel et al., eds.. Current Protocols, a joint venture between4918-0896-88371 21Attorney Docket No.: 069296.11211 / 34WO01Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1995 Supplement) (Ausubel)).

[0062] Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1990) J. Mol. Biol. 215: 403-410 and Altschul et al. (1997) Nucleic Acids Res. 25: 3389-3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query' sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul etal., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased.

[0063] Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always > 0) and N (penalty score for mismatching residues; always < 0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity' and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=-4. and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).

[0064] In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat’l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to4918-0896-88371 22Attorney Docket No.: 069296.11211 / 34WO01the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.

[0065] A further indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the polypeptide encoded by the second nucleic acid, as described below. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules hybridize to each other under stringent conditions.

[0066] As used herein, the term ‘‘polynucleotide,’' synonymously referred to as “nucleic acid molecule,” “nucleotides” or “nucleic acids,” refers to any polyribonucleotide or poly deoxyribonucleotide, which can be unmodified RNA or DNA or modified RNA or DNA. “Polynucleotides” include, without limitation single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA. and RNA that is mixture of single- and double-stranded regions, hybrid molecules compnsing DNA and RNA that can be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. In addition, “polynucleotide” refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The term polynucleotide also includes DNAs or RNAs containing one or more modified bases and DNAs or RNAs with backbones modified for stability or for other reasons. “Modified” bases include, for example, tritylated bases and unusual bases such as inosine. A variety of modifications can be made to DNA and RNA; thus, “polynucleotide” embraces chemically, enzymatically, or metabolically modified forms of polynucleotides as typically found in nature, as well as the chemical forms of DNA and RNA characteristic of viruses and cells. “Polynucleotide” also embraces relatively short nucleic acid chains, often referred to as oligonucleotides.

[0067] As used herein, the term “vector” is a replicon in which another nucleic acid segment can be operably inserted so as to bring about the replication or expression of the segment.

[0068] As used herein, the term “host cell” refers to a cell comprising a nucleic acid molecule of the present disclosure, such as, for example an isolated vector comprising an isolated nucleic acid of the invention. The “host cell” can be any type of cell, e.g., a primary cell, a cell in culture, or a cell from a cell line. In one embodiment, a “host cell” is a cell transfected with a nucleic acid molecule of the invention. In another embodiment, a “host4918-0896-88371 23Attorney Docket No.: 069296.11211 / 34WO01cell” is a progeny or potential progeny of such a transfected cell. A progeny of a cell may or may not be identical to the parent cell, e.g, due to mutations or environmental influences that can occur in succeeding generations or integration of the nucleic acid molecule into the host cell genome. A host cell can be, for example, any type of prokaryotic, eukaryotic, or archaeal cell. In some instances, the host cell is a bacterial cell. In some instances, the host cell is a mammalian cell.

[0069] The term ‘"expression” as used herein, refers to the biosynthesis of a gene product. The term encompasses the transcription of a gene into RNA. The term also encompasses translation of RNA into one or more polypeptides, and further encompasses all naturally occurring post-transcriptional and post-translational modifications.

[0070] As used herein, the terms “peptide.” “polypeptide,” or “protein” can refer to a molecule comprised of amino acids and can be recognized as a protein by those of skill in the art. The conventional one-letter or three-letter code for amino acid residues is used herein. The terms “peptide,” “poly peptide,” and “protein” can be used interchangeably herein to refer to polymers of amino acids of any length. The polymer can be linear or branched, it can comprise modified amino acids, and it can be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component. Also included within the definition are. for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids, etc.), as well as other modifications known in the art.

[0071] The peptide sequences described herein are written according to the usual convention whereby the N-terminal region of the peptide is on the left and the C-terminal region is on the right. Although isomeric forms of the amino acids are known, it is the L-form of the amino acid that is represented unless otherwise expressly indicated.

[0072] The term “heterologous nucleic acid” or “heterologous polypeptide” refers to a nucleic acid or a polypeptide whose sequence is not identical to that of another nucleic acid or polypeptide naturally found in the same host cell or the same host. As used herein, the “heterologous nucleic acid” or “heterologous polypeptide” can be heterologous to the bacterial cell and / or the mammalian host.

[0073] As used herein, the term “transform” or “transformation” refers to the transfer of a nucleic acid fragment into a host cell, such as a host bacterial cell, resulting in genetically -4918-0896-88371 24Attorney Docket No.: 069296.11211 / 34WO01stable inheritance. Host cells comprising the transformed nucleic acid fragment are referred to as "‘recombinant’' or “transgenic” or “transformed” organisms.

[0074] As used herein, the term “isolated” means a biological component (such as a nucleic acid, peptide or protein) has been substantially separated, produced apart from, or purified away from other biological components of the organism in which the component naturally occurs, i.e., other chromosomal and extrachromosomal DNA and RNA. and proteins.Nucleic acids, peptides and proteins that have been “isolated” thus include nucleic acids and proteins purified by standard purification methods. “Isolated” nucleic acids, peptides and proteins can be part of a composition and still be isolated if the composition is not part of the native environment of the nucleic acid, peptide, or protein. The term also embraces nucleic acids, peptides and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.

[0075] As used herein, “gene” refers to a nucleic acid comprising an open reading frame encoding a polypeptide, including both exon and (optionally) intron sequences.

[0076] As used herein, a “promoter” is an example of a transcriptional regulatory sequence and is specifically a nucleic acid sequence generally described as the proximal region of a gene located 5' to the start codon. The transcription of an adjacent nucleic acid segment is initiated at the promoter region. A repressible promoter’s rate of transcription decreases in response to a repressing agent. An inducible promoter’s rate of transcription increases in response to an inducing agent. A constitutive promoter’s rate of transcription is not specifically regulated, though it can vary under the influence of general metabolic conditions.

[0077] The term “gene product,” as used herein, refers to any product encoded by a nucleic acid sequence. Accordingly, a gene product may, for example, be a primary transcript, a mature transcript, a processed transcript, or a protein or peptide encoded by a transcript. Examples for gene products, accordingly, include mRNAs, rRNAs, hairpin RNAs (e.g., microRNAs, shRNAs, siRNAs, tRNAs), and peptides and proteins, for example, reporter proteins or therapeutic proteins.

[0078] “Operably linked” as used herein means that expression of a gene is under the control of a promoter with which it is spatially connected. A promoter can be positioned 5' (upstream) or 3' (dow nstream) of a gene under its control. The distance between the promoter and a gene can be approximately the same as the distance between that promoter and the gene it controls in the gene from which the promoter is derived. As is known in the art, variation in this distance can be accommodated without loss of promoter function.4918-0896-88371 25Attorney Docket No.: 069296.11211 / 34WO01

[0079] As used herein, the term “stem cell” refers to a cell that can self-renew and differentiate to at least one more-differentiated or less developmentally-capable phenotype. The term “stem cell” encompasses stem cell lines, induced stem cells, non-human embryonic stem cells, pluripotent stem cells, multipotent stem cells, amniotic stem cells, placental stem cells, or adult stem cells. An “induced stem cell” is one derived from a non-pluripotent cell induced to a less-differentiated or more developmentally-capable phenotype by introduction of one or more reprogramming factors or genes. As the term is used herein, an induced stem cell need not be pluripotent, but has the capacity to differentiate, under appropriate conditions, to more than one more-highly-differentiated phenotype. It should be understood that the capacity' was not present prior to the introduction of reprogramming factors. An induced stem cell will express at least one stem cell marker not expressed by the parent cell prior to introduction of reprogramming factors. In this context, a stem cell marker is exclusive of a factor introduced by reprogramming. An induced pluripotent stem cell, or iPS cell, has the induced capacity to differentiate, under appropriate conditions, to a cell phenotype derived from each of the endoderm, mesoderm, and ectoderm germ layers.

[0080] The term “marker” as used herein is used to describe a characteristic and / or phenotype of a cell. Markers can be used for selection of cells comprising characteristics of interest and can vary with specific cells. Markers are characteristics, whether morphological, structural, functional, or biochemical (enzymatic) characteristics of the cell of a particular cell type, or molecules expressed by the cell type. In one aspect, such markers are proteins. Such proteins can possess an epitope for antibodies or other binding molecules available in the art. However, a marker can consist of any molecule found in or on a cell, including, but not limited to, proteins (peptides and polypeptides), lipids, polysaccharides, nucleic acids, and steroids. Examples of morphological characteristics or traits include, but are not limited to, shape, size, and nuclear to cytoplasmic ratio. Examples of functional characteristics or traits include, but are not limited to, the ability' to adhere to particular substrates, ability to incorporate or exclude particular dyes, ability' to migrate under particular conditions, and the ability to differentiate along particular lineages.Markers can be detected by any method available to one of skill in the art. Markers can also be the absence of a morphological characteristic or absence of proteins, lipids etc. Markers can be a combination of a panel of unique characteristics of the presence and / or absence of polypeptides and other morphological or structural characteristics. In one embodiment, the marker is a cell surface marker.4918-0896-88371 26Attorney Docket No.: 069296.11211 / 34WO01

[0081] The term ‘‘exogenous” refers to a substance present in a cell that was introduced by the hand of man. The term “exogenous” when used herein can refer to a nucleic acid (e.g., a nucleic acid encoding a polypeptide) or a polypeptide that has been introduced by a process involving the hand of man into a biological system such as a cell or organism in which it is not normally found. Alternatively, “exogenous” can refer to a nucleic acid or a polypeptide that has been introduced by a process involving the hand of man into a biological system such as a cell or organism in which it is found in relatively lower amounts and in which one wishes to increase the amount of the nucleic acid or polypeptide in the cell or organism, e.g., to create ectopic expression or levels.

[0082] As used herein, the term “reprogramming genes” or “reprogramming factors” refers to agents or nucleic acid molecules that can induce the reprogramming process in a somatic cell to re-express a less-differentiated, more stem-cell like phenotype. The reprogramming factor can be a nucleic acid, a polypeptide, or a small molecule that promotes a reprogrammed phenotype when introduced to a cell. Non-limiting examples of reprogramming factors include: OCT4 (Octamer binding transcription factor-4), SOX2 (Sex determining region Y)-box 2, KLF4 (Kruppel Like Factor-4), and c-MYC. These are the so-called “classical” or “standard” set of reprogramming factors used to derive, for example, induced pluripotent stem cells. Additional factors that can be considered reprogramming factors when introduced in the process of reprogramming cells to a less differentiated or stem cell phenotype include LIN28 + NANOG, Esrrb. Pax5 shRNA, C / EBPa, p53 siRNA, UTF1, DNMT shRNA, Wnt3a, SV40 LT(T), hTERT, small molecule chemical agents including, but not limited to BIX-01294, BayK8644, RG108, AZA, dexamethasone, VP A, TSA, SAHA, PD0325901 + CHIR99021(2i) and A-83-01. In some embodiments, the reprogramming genes or factors are OCT4, KLF4. SOX2, and c-MYC.

[0083] As used herein, the terms “dedifferentiation” or “retrodifferentiation” or “reprogramming” refer to a process that generates a cell that re-expresses a less differentiated phenoty pe than the cell from which it is derived and / or expresses at least one stem cell marker not expressed prior to that process. For example, a terminally-differentiated cell can be dedifferentiated to a multipotent cell. That is, dedifferentiation shifts a cell backward along the differentiation spectrum of totipotent cells to fully differentiated cells. Typically, reversal of the differentiation phenotype of a cell requires artificial manipulation of the cell, for example, by introducing or expressing exogenous polypeptide factors. Reprogramming is not typically observed under native conditions in vivo or in vitro.4918-0896-88371 27Attorney Docket No.: 069296.11211 / 34WO01

[0084] As used herein, a “reprogrammed cell’" is a cell that has been contacted with one or more reprogramming factors and expresses a less differentiated phenoty pe than the cell from which it was derived. The reprogrammed cell can also have the capacity to self-renew and will express at least one stem cell marker that was not delivered to the cell as a reprogramming factor. Furthermore, the reprogrammed cell will have the capacity to differentiate into a more-differentiated somatic cell type following differentiation protocols provided herein or described in the art.

[0085] As used herein, the term “somatic cell’’ refers to any cell other than a germ cell, a cell present in or obtained from a pre-implantation embryo, or a cell resulting from proliferation of such a cell in vitro. Stated another way, a somatic cell refers to any cells forming the body of an organism, excluding germ cells. Every cell type in the mammalian body-apart from the sperm and ova and the cells from which they are made (gametocytes)-is a somatic cell: internal organs, skin, bones, blood, and connective tissue are all substantially made up of somatic cells. In some embodiments the somatic cell is a “non-embryonic somatic cell,” by which is meant a somatic cell that is not present in or obtained from an embryo and does not result from proliferation of such a cell in vitro. In some embodiments the somatic cell is an “adult somatic cell,” by which is meant a cell that is present in or obtained from an organism other than an embryo or a fetus or results from proliferation of such a cell in vitro.

[0086] As used herein a “vector” is a nucleic acid construct designed for delivery to a host cell or for transfer of genetic material between different host cells. As used herein, a vector can be viral or non-viral. The term “vector” encompasses any genetic element that is capable of replication when associated with the proper control elements and that can transfer genetic material to cells. A vector can include, but is not limited to, a cloning vector, an expression vector, a plasmid, phage, transposon, cosmid, artificial chromosome, virus, virion, etc. In some embodiments of any of the aspects, the vector is selected from the group consisting of a plasmid, a cosmid, and a viral vector.

[0087] An expression vector is a vector that directs expression of an RNA or polypeptide (e.g, isolated SOX2 protein containing an artificial SOX2 DNA binding domain or an isolated OCT4 protein contain an artificial OCT4 DNA binding domain) from nucleic acid sequences contained therein linked to transcriptional regulatory sequences on the vector. The sequences expressed will often, but not necessarily, be heterologous to the cell; an artificial SOX2 protein and / or artificial OCT4 protein introduced to a viable cell is heterologous to the cell. An expression vector may comprise additional elements, for4918-0896-88371 28Attorney Docket No.: 069296.11211 / 34WO01example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms, for example in animal cells for expression and in a prokaryotic host for cloning and amplification. “Expression” refers to the cellular processes involved in producing RNA and proteins and as appropriate, secreting proteins, including where applicable, but not limited to, for example, transcription, transcript processing, translation and protein folding, modification and processing. “Expression products” include RNA transcribed from a gene, and polypeptides obtained by translation of mRNA transcribed from a gene.

[0088] In some embodiments, a vector is capable of driving expression of one or more sequences in a mammalian cell; i.e., the vector is a mammalian expression vector.Examples of mammalian expression vectors include pCDM8 (Seed. 1987. Nature 329: 840) and pMT2PC (Kaufman, et al., 1987. EMBO J. 6: 187-195). When used in mammalian cells, the expression vector’s control functions are typically provided by one or more regulatory elements. For example, commonly used promoters are derived from polyoma, adenovirus 2, cytomegalovirus, simian virus 40, and others disclosed herein and known in the art. For other suitable expression systems for both prokaryotic and eukaryotic cells see, e.g.. Chapters 16 and 17 of Sambrook, et al., MOLECULAR CLONING: A LABORATORY MANUAL. 2nd ed., Cold Spring Harbor Laboratory , Cold Spring Harbor Laboratory Press. Cold Spring Harbor, N.Y., 1989.SOX2 Proteins and Polynucleotides with Artificial SOX2 DNA Binding Domains

[0089] One aspect of the disclosure is directed to designed SOX2 proteins, which have enhanced stability and binding affinity. This aspect of the disclosure also includes nucleotides encoding these SOX2 proteins as well as vectors and cells containing these nucleotides. The proteins contain an artificial SOX2 DNA binding domain and are designed to be species-agnostic.

[0090] In certain embodiments, the disclosure is directed to isolated SOX2 protein having an artificial SOX2 DNA binding domain. The binding domain has an amino acid sequence that is 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%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 1-21. In certain embodiments, the binding domain has the amino acid sequence of any one of SEQ ID NOs: 1-21.4918-0896-88371 29Attorney Docket No.: 069296.11211 / 34WO01

[0091] In one certain embodiments of the isolated proteins, the artificial SOX2 DNA binding domain has an amino acid sequence that is 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%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 1-21 and is flanked by tail regions on either side of the SOX2 DNA binding domain. In other embodiments, the SOX2 DNA binding domain has the amino acid sequence of any one of SEQ ID NOs: 1-21 and is flanked by tail regions on either side of the SOX2 DNA binding domain. In one embodiment, the tail region is derived from a mouse, such as e.g, mouse SOX2. In another embodiment, the tail region is derived from an elephant, such as e.g., elephant SOX2.

[0092] In some embodiments, the disclosure is directed to isolated SOX2 proteins having an artificial SOX2 DNA binding domain. These proteins have an amino acid sequence 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%, or at least 99% identical to any one of SEQ ID NOs:43-62. In certain embodiments, the proteins have the amino acid sequence of any one of SEQ ID NOs:43-62.

[0093] Another embodiment of the disclosure is directed to nucleic acids encoding the SOX2 protein having an artificial SOX2 DNA binding domain of the disclosure. The nucleic acids encoding the SOX2 protein can be operably linked to a promoter and / or an enhancer.

[0094] Certain embodiments are directed to nucleic acids encoding a SOX2 protein having an artificial SOX2 domain 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%, or at least 99% identical to the amino acid sequence to any one of SEQ ID NOs: 1-21. Other embodiments are directed nucleic acid encoding a SOX2 protein having an artificial SOX2 domain that encodes the amino acid sequence of any one of SEQ ID NOs: 1-21.

[0095] In one embodiment, the nucleic acids (polynucleotides) encode an artificial SOX2 protein having the artificial SOX2 DNA binding domain that has a nucleic acid sequence 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%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 22-42.4918-0896-88371 30Attorney Docket No.: 069296.11211 / 34WO01

[0096] In another embodiment, the nucleic acids (polynucleotides) encode a SOX2 protein having the artificial SOX2 DNA binding domain and the nucleic acids (polynucleotides) have a nucleic acid sequence 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%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 63-82

[0097] In certain embodiments, the nucleic acid is DNA. In other embodiments, the nucleic acid is RNA. The disclosure also includes nucleic acids complementary to the nucleic acid sequence of any one of SEQ ID NOs: 22-42 or 63-82. In further embodiments, the disclosure includes nucleic acids 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%, or at least 99% complementary to the nucleic acid sequence of any one of SEQ ID NOs: 22-42 or 63-82.

[0098] The disclosure also provides for vectors containing the SOX2 protein having an artificial SOX2 DNA binding domain of the disclosure. The vector can have a nucleic acid sequence containing an origin of replication. The vector can be either a self-replicating extrachromosomal vector or a vector which integrates into a host genome.

[0099] The one or more vectors can be an expression construct, which is generally a plasmid that is used to introduce a specific gene into a target cell. Once the expression vector is inside the cell, the protein that is encoded by the gene is produced by the cellular-transcription and translation machinery ribosomal complexes. The plasmid is frequently engineered to contain regulatory sequences that act as enhancer and promoter regions and lead to efficient transcription of the gene carried on the expression vector. The vectors of the present invention express large amounts of stable messenger RNA, and therefore proteins. The vectors may have expression signals such as a strong promoter, a strong termination codon, adjustment of the distance between the promoter and the cloned gene, and the insertion of a transcription termination sequence and a PTIS (portable translation initiation sequence).

[0100] The disclosure also includes host cells containing the vector encoding the artificial SOX2 proteins and / or nucleic acids encoding the artificial SOX2 proteins. In certain embodiments, the host cell is a mammalian cell. In some embodiments, the mammal is a mouse, a rat, a marsupial, a cow, an ovine, a caprine, a pig, an elephant, an equid, a cat, a dog, a wolf, a deer, or an antelope. In some embodiments, the mammal is Felis catus, Cants4918-0896-88371 31Attorney Docket No.: 069296.11211 / 34WO01lupus familiaris, Canis lupus, Bison bison, Dama dama, Hippotragus equinus, Elephas maximus, or Hippotragus niger.OCT4 Proteins and Polynucleotides with Artificial OCT4 DNA Bindins Domains

[0101] One aspect of the disclosure is directed to designed OCT 4 proteins, which have enhanced stability' and binding affinity. This aspect of the disclosure also includes nucleotides encoding these OCT4 proteins as well as vectors and cells containing these nucleotides. The proteins contain an artificial OCT4 DNA binding domain and are designed to be species-agnostic.

[0102] In certain embodiments, the disclosure is directed to isolated OCT4 proteins having an artificial OCT4 DNA binding domain. The binding domain has an amino acid sequence that is 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%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 83-103. In certain embodiments, the binding domain has the amino acid sequence of any one of SEQ ID NOs: 83-103.

[0103] In one certain embodiments of the isolated proteins, the artificial OCT4 DNA binding domain has an amino acid sequence that is 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%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 83-103 and is flanked by tail regions on either side of the OCT4 DNA binding domain. In other embodiments, artificial OCT4 DNA binding domain has an amino acid sequence and is flanked by tail regions on either side of the OCT4 DNA binding domain. In one embodiment, the tail region is derived from a mouse, such as e.g., mouse OCT4. In another embodiment, the tail region is derived from an elephant, such as e.g., elephant OCT4.

[0104] In other embodiments, the disclosure is directed to isolated OCT4 proteins having an artificial OCT4 DNA binding domain. In certain embodiments, the isolated OCT4 proteins have an ammo acid sequence that is 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%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 125-144. In other embodiments, the isolated OCT4 proteins have an amino acid sequence of any one of SEQ ID NOs: 125-144. In certain embodiments, the OCT4 protein is humanized.4918-0896-88371 32Attorney Docket No.: 069296.11211 / 34WO01

[0105] In certain embodiments, the nucleic acid is DNA. In other embodiments, the nucleic acid is RNA. The disclosure also includes nucleic acids complementary to the nucleic acid sequence of any one of SEQ ID NOs: 83-103 orl45-164. In further embodiments, the disclosure includes nucleic acids 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%, or at least 99% complementary to the nucleic acid sequence of any one of SEQ ID NOs: 83-103 or 145-164.

[0106] Another embodiment of the disclosure is directed to nucleic acids encoding the OCT4 protein having an artificial OCT4 DNA binding domain of the disclosure. Certain embodiments are directed to nucleic acids encoding an OCT4 protein having an artificial OCT4 domain 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%, or at least 99% identical to the amino acid sequence to any one of SEQ ID NOs: 83-103. Other embodiments are directed to nucleic acids encoding an OCT4 protein having an artificial OCT4 domain that encodes the amino acid sequence of any one of SEQ ID NOs: 83-103.

[0107] In one embodiment, the nucleic acids (polynucleotides) encode an artificial OCT4 protein having the artificial OCT4 DNA binding domain that has a nucleic acid sequence 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%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 145-164. In further embodiments, the nucleic acids (polynucleotides) encode an artificial OCT4 protein having the artificial OCT4 DNA binding domain that has a nucleic acid sequence of any one of SEQ ID NOs: 145-164.

[0108] The disclosure also provides for vectors containing the OCT4 protein having an artificial OCT4 DNA binding domain of the disclosure. In certain embodiments, the vectors contain both a SOX2 protein encoding an artificial SOX2 DNA binding domain and an OCT4 protein having an artificial OCT4 DNA binding domain of the disclosure. The vector can have a nucleic acid sequence containing an origin of replication. The vector can be either a self-replicating extrachromosomal vector or a vector which integrates into a host genome.

[0109] The one or more vectors can be an expression construct, which is generally a plasmid that is used to introduce a specific gene into a target cell. Once the expression vector is inside the cell, the protein that is encoded by the gene is produced by the cellular4918-0896-88371 33Attorney Docket No.: 069296.11211 / 34WO01transcription and translation machinery ribosomal complexes. The plasmid is frequently engineered to contain regulatory sequences that act as enhancer and promoter regions and lead to efficient transcription of the gene carried on the expression vector. The vectors of the present invention express large amounts of stable messenger RNA, and therefore proteins. The vectors may have expression signals such as a strong promoter, a strong termination codon, adjustment of the distance between the promoter and the cloned gene, and the insertion of a transcription termination sequence and a PTIS (portable translation initiation sequence).

[0110] The disclosure also includes host cells containing the vector encoding the artificial OCT4 proteins and / or nucleic acids encoding the artificial OCT4 proteins. In certain embodiments, the host cell is a mammalian cell. In some embodiments, the mammal is a mouse, a rat, a marsupial, a cow, an ovine, a caprine, a pig, an elephant, an equid, a cat, a dog, a wolf, a deer, or an antelope. In some embodiments, the mammal is Felis catus, Canis lupus familiaris, Canis lupus, Bison bison, Dama dama, Hippotragus equinus, Hippotragus niger. an Asian elephant (Elephas maximus), an African elephant (Loxodonta africana), an African forest elephant (Loxodonta cyclotis), or a Bornean elephant (Elephas maximus borneensis).Recombinant host cells containing the artificial isolated SOX2 proteins and / or the artificial isolated OCT4 proteins[OHl] The artificial isolated SOX2 proteins and the artificial isolated OCT4 proteins described herein can be expressed by any viable cell that can accept exogenous genetic material. The cell can be. for example, a prokaryotic cell or a eukaryotic cell. In some embodiments, the cell is a eukaryotic cell. The cell can be a reprogrammed cell, a nonhuman oocyte, a cell of a non-human embryo or a cell of a non-human blastula. In some embodiments of any of the aspects, the cell is a fibroblast cell. In some embodiments, the cell is selected from the group consisting of a nerve cell, a cartilage cell, a bone cell, a muscle cell, a bone cell, a fat cell, an endothelial cell, and an epidermal cell. In other embodiments, the cell was previously differentiated into a cell selected from the group consisting of a nerve cell, cartilage cell, bone cell, muscle cell, bone cell, fat cell, an endothelial cell, and an epidermal cell.

[0112] The scientific literature provides guidance for one of ordinary skill in the art to isolate and prepare cells as necessary for use with the isolated nucleic acids and vectors described herein.4918-0896-88371 34Attorney Docket No.: 069296.11211 / 34WO01

[0113] The cells described herein can be from any viable non-human source or organism. Usually, the organism is an animal or vertebrate such as a wild animal, zoo animal, endangered animal, rodent, domestic animal, or bird. Animals can include, as non-limiting examples, an antelope, hippopotamus, hyrax, manatee, bear, panda, feline species (such as e.g, tiger, lion, cheetah, and bobcat), canine species (such as e.g, fox and wolf), avian species (such as e.g., ostrich, emu, penguin, and pigeon), and fish (such as e.g., trout, catfish, and salmon). In some embodiments, the cell described herein is from a mammal.

[0114] The cells described herein can be from any tissue isolated from an organism by methods known in the art. For example, placental tissue can be isolated from a given organism (e.g., an antelope), after full term delivery of young, and subsequently processed for cellular isolation and / or culture by methods known in the art. Additional exemplary cell types that can be used for the compositions and methods described herein include but are not limited to fibroblasts, skin cells, blood cells (e.g., leukocytes, monocytes, dendritic cells), stem cells, hematopoietic cells, liver cells, vascular cells, muscle cells, pancreatic cells, neural cells, ocular or retinal cells, epithelial or endothelial cells, lung cells, cardiac cells, intestinal cells, diaphragmatic cells, renal (i.e., kidney) cells, bone marrow cells, or any one or more selected tissues or cells of an organism for which genetic modification or gene is contemplated.

[0115] In certain embodiments, the isolated nucleic acids and vectors described herein are used in recombinant host cells. In other embodiments, the recombinant host cell is a fibroblast cell or a mesenchymal cell. In alternate embodiments, the recombinant host cell is selected from the group consisting of a nerve cell, a cartilage cell, a bone cell, a muscle cell, a bone cell, a fat cell, an endothelial cell, and an epidermal cell.Methods of Generating Induced Pluripotent Stem Cells

[0116] Yet another aspect of the disclosure is directed to using a SOX2 protein encoding an artificial SOX2 DNA binding domain and an OCT4 protein having an artificial OCT4 DNA binding domain of the disclosure in methods of generating induced pluripotent stem cells. The methods are species-agnostic.

[0117] In certain embodiments, the methods of inducing pluripotency generally involve transfecting a somatic cell with a nucleic acid encoding a SOX2 protein encoding an artificial SOX2 DNA binding domain and / or a nucleic acid encoding an OCT4 protein having an artificial OCT4 DNA binding domain.4918-0896-88371 35Attorney Docket No.: 069296.11211 / 34WO01

[0118] In other embodiments, the methods of inducing pluripotency involve transfecting a cell with a vector containing a nucleic acid encoding a SOX2 protein encoding an artificial SOX2 DNA binding domain and / or a vector containing a nucleic acid encoding an OCT4 protein having an artificial OCT4 DNA binding domain. In certain embodiments, the methods involve a vector containing a nucleic acid encoding a SOX2 protein encoding an artificial SOX2 DNA binding domain and a nucleic acid encoding an OCT4 protein having an artificial OCT4 DNA binding domain.

[0119] One embodiment of the disclosure is directed to methods of generating induced pluripotent stem cells including: transfecting a somatic cell with a polynucleotide encoding a SOX2 protein containing at least an artificial SOX2 DNA binding domain of the disclosure and a polynucleotide encoding an OCT4 protein containing an artificial OCT4 DNA binding domain of the disclosure; culturing the cells in a culture medium to generate induced pluripotent stem cells; and optionally selecting for the induced pluripotent stem cells. In certain embodiments, the methods include: transfecting a somatic cell with a polynucleotide encoding a SOX2 protein containing an artificial SOX2 DNA binding domain of the disclosure and a polynucleotide encoding an OCT4 protein containing an artificial OCT4 DNA binding domain of the disclosure; and culturing the cells in a culture medium to generate induced pluripotent stem cells.

[0120] The methods can also include isolating the induced pluripotent stem cells.Common techniques known in the art can be used to isolate the induced pluripotent stem cells. Examples of such techniques include, but are not limited to, fluorescence activated cell sorting (FACS), magnetic cell separation (MACs), or differential adherent culture.

[0121] Any of the polynucleotides (nucleic acids) described above can be used in the methods. In certain embodiments, the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain has a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 22-42; and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain has a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 104-124.

[0122] The nucleic acids encoding the SOX2 protein and the polynucleotide encoding the OCT4 protein can be further modified. In certain embodiments, the polynucleotide encoding the SOX2 protein and the polynucleotide encoding the OCT4 protein are humanized.4918-0896-88371 36Attorney Docket No.: 069296.11211 / 34WO01

[0123] In some embodiments, the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain has (i) a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 63-82 or (ii) a nucleic acid sequence encoding a protein having an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 43-62.

[0124] In other embodiments, the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain has (iii) a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 145-164 or (iv) a nucleic acid sequence encoding a protein having an amino acid sequence at least 85%, at least 90%. at least 95%. or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 125-144.

[0125] In some embodiments, the methods include transfecting the somatic cells with a vector containing the polynucleotide encoding the SOX2 protein having an artificial SOX2 DNA binding domain and a polynucleotide encoding the OCT4 protein having an artificial OCT4 DNA binding domain.

[0126] In certain embodiments, the methods of the disclosure use uniquely designed pairs of a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain. These specific pairs are shown in Table A below.

[0127] Each of these pairs are designed to be used together. For example, in embodiment A, a nucleic acid encoding a SOX2 protein containing the artificial SOX2 DNA binding with a domain sequence of SEQ ID NO: 22 is used with a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain of SEQ NO: 104. etc.4918-0896-88371 37Attorney Docket No.: 069296.11211 / 34WO01

[0128] In certain embodiments, amino acids 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%, or at least 99% identical to the SOX2 or OCT4 amino acid sequences identified in Table A, nucleic acids 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%, or at least 99% identical to the SOX2 or OCT4 nucleic acid sequences identified in Table A, or nucleic acids encoding amino acids at least 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%, or at least 99% identical to the SOX2 or OCT4 amino acid sequences identified in Table A can be used.

[0129] In further embodiments, the methods include transfecting the somatic cells with:• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding4918-0896-8837 1 38Attorney Docket No.: 069296.11211 / 34WO01a protein having the amino acid sequence of SEQ ID NO: 1 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 83;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 2 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 84;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 3 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 85;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 4 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 86;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 5 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 87;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 6 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having4918-0896-88371 39Attorney Docket No.: 069296.11211 / 34WO01the amino acid sequence of SEQ ID NO: 88;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 7 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 89;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 8 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 90;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 9 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the ammo acid sequence of SEQ ID NO: 91;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 10 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 92;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 11 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 93;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding4918-0896-88371 40Attorney Docket No.: 069296.11211 / 34WO01a protein having the amino acid sequence of SEQ ID NO: 12 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 94;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 13 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 95;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 14 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 96;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 15 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 97;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 16 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 98;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 17 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having4918-0896-88371 41Attorney Docket No.: 069296.11211 / 34WO01the amino acid sequence of SEQ ID NO: 99;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 18 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 100;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 19 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 101;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 20 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the ammo acid sequence of SEQ ID NO: 102; or• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 21 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 103.

[0130] In further embodiments, the methods include transfecting the somatic cells with:• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 43 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 125;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA4918-0896-88371 42Attorney Docket No.: 069296.11211 / 34WO01binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 44 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 126;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 45 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 127;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 46 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 128;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 47 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 129;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 48 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 130;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 49 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain,4918-0896-88371 43Attorney Docket No.: 069296.11211 / 34WO01wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 131;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 50 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 132;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 51 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 133;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 52 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 134;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 53 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 135;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 54 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 136;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA4918-0896-88371 44Attorney Docket No.: 069296.11211 / 34WO01binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 55 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 137;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 56 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 138;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 57 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 139;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 58 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 140;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 59 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 141;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 60 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain,4918-0896-88371 45Attorney Docket No.: 069296.11211 / 34WO01wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 142;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 61 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 143; or• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 62 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 144.

[0131] In additional embodiments, the methods include transfecting the somatic cells with:• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 22 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 104;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 23 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 105;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 24 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 106;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ4918-0896-88371 46Attorney Docket No.: 069296.11211 / 34WO01ID NO: 25 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 107;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 26 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 108;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 27 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 109;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 28 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 110;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 29 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 111;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 30 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 112;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 31 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 113;4918-0896-88371 47Attorney Docket No.: 069296.11211 / 34WO01• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 32 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 114;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 33 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 115;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 34 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 116;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 35 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 117;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 36 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 118;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 37 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 119;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 38 and a polynucleotide encoding the OCT4 protein containing the artificial4918-0896-88371 48Attorney Docket No.: 069296.11211 / 34WO010CT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 120;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 39 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 121;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 40 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 122;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 41 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 123; or• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 42 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 124.

[0132] In further embodiments, the methods include transfecting the somatic cells with:• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 63 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 145;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 64 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 146;4918-0896-88371 49Attorney Docket No.: 069296.11211 / 34WO01• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 65 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 147;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 66 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 148;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 67 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 149;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 68 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 150;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 69 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 151;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 70 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 152;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 71 and a polynucleotide encoding the OCT4 protein containing the artificial4918-0896-88371 50Attorney Docket No.: 069296.11211 / 34WO010CT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 153;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 72 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 154;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 73 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 155;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 74 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 156;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 75 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 157;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 76 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 158;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 77 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 159;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA4918-0896-88371 51Attorney Docket No.: 069296.11211 / 34WO01binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 78 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 160;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 79 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 161;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 80 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 162;• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 81 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 163; or• a polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 82 and a polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain, wherein the polynucleotide includes the nucleic acid sequence of SEQ ID NO: 164.

[0133] The polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain can be on the same vector. Accordingly, in certain embodiments, the methods include transfecting somatic cells with a vector having both the polynucleotide encoding the SOX2 protein containing the artificial SOX2 DNA binding domain and the polynucleotide encoding the OCT4 protein containing the artificial OCT4 DNA binding domain.

[0134] In certain embodiments, the methods also include transfecting the somatic cells with one or more nucleic acids encoding a pluripotency-inducing factor. In one4918-0896-88371 52Attorney Docket No.: 069296.11211 / 34WO01embodiment, the method includes transfecting the somatic cells with a nucleic acid encoding one or more of KLF4, MYC, LIN28, and NANOG, such as e.g., a nucleic acid encoding KLF4 and MYC. In other embodiments, the method includes transfecting the somatic cells with a nucleic acid encoding each of KLF4, MYC, LIN28, and NANOG. The nucleic acids can be contained on a vector or a plurality of vectors.

[0135] In certain embodiments, the methods include transfecting the cells with a nucleic acid encoding the SOX2 protein having the artificial SOX2 DNA binding domain, a nucleic acid encoding the OCT4 protein having an artificial OCT4 DNA binding domain, and either a polynucleotide encoding KLF4 and MYC or a polynucleotide encoding KLF4, MYC, LIN28, and NANOG.

[0136] The methods can also include chemically reprogramming the somatic cells prior to transfecting the cells. For example, in certain embodiments, the methods include chemically reprogramming the cells by culturing the cells in a culture medium supplemented with one or more or each of an HD AC inhibitor, a GSK-3 inhibitor, a TGF-inhibitor, a monoamine oxidase inhibitor, an activator of eukaryotic adenylyl cyclase, a retinoid, and a DOT1L inhibitor.

[0137] A variety of HD AC inhibitors may be used. In one embodiment, the HD AC inhibitor is valproic acid (2-propylpentanoic acid). Other suitable HD AC inhibitors include, but are not limited to, suberanilohydroxamic acid, trichostatin (A), cyclic tetrapeptides, benzamides, electrophilic ketones, sodium butyrate, and phenylbutyrate. In certain embodiments, the media contains from about 0.1 to about 1 mM of the HDAC inhibitor.

[0138] In one embodiment, the GSK-3 inhibitor is CHIR-99021 (6-((2-((4-(2,4-Dichlorophenyl)-5-(4-methyl-lH-imidazol-2-yl)pyrimidin-2-yl)amino)ethyl)amino)nicotinonitrile). A variety of other GSK-3 inhibitors may be used in place of CHIR-99021. In certain embodiments, the media contain from about 10 to about 25 pM of the GSK-3 inhibitor.

[0139] A variety of monoamine oxidase inhibitor inhibitors may be used in the media. In one embodiment, monoamine oxidase inhibitor is tranylcypromine (2-PCPA) HC1 (also known as tranylcypromine). In other embodiments, the monoamine oxidase inhibitor is selegiline. In yet another embodiment, the monoamine oxidase inhibitor is phenelzine. In certain embodiments, the cell culture media are supplemented with from about 5 to about 25 pM of the monoamine oxidase inhibitor.

[0140] Similarly, a variety of activators of eukaryotic adenylyl cyclase may be used in the media. Suitable examples include, but are not limited to, forskolin4918-0896-88371 53Attorney Docket No.: 069296.11211 / 34WO01([(3R,4aR,5S,6S,6aS, 1 OS, lOaR, 10bS)-3-ethenyl-6, 10, 1 Ob-trihy droxy-3,4a,7,7, 1 Oa-pentamethyl-I-oxo-5,6,6a,8,9,10-hexahydro-2H-benzo[f]chromen-5-yl] acetate) and 3-isobutyl-1 -methylxanthine. In one embodiment, the activator of eukaryotic adenylyl cyclase (cAMP agonist) in the culture media is forskolin. The culture media may be supplemented with from about 10 to about 30 pM of the activator of eukaryotic adenylyl cyclase.

[0141] The culture media are also supplemented with a retinoid. In one embodiment, the retinoid is Ch 55 (4-[(lE)-3-[3,5-bis(l,l-Dimethylethyl)phenyl]-3-oxo-l-propenyl]benzoic acid). In other embodiments, the retinoid is all-trans-retinoic acid. Other examples of suitable retinoids include, but are not limited, to Re 80 (4-[l-hydroxy-3-oxo-3-(5,6.7,8-tetrahydro-3-hydroxy-5,5,8,8-tetramethyl- 2- naphthalenyl)- 1 -propenyl] benzoic acid), Am 580 (4-[(5,6,7,8-tetrahydro- 5,5,8,8-tetramethyl-2-naphthalenyl)carboxamido]benzoic acid) and Am 80 (4-[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)carbamoyl] benzoic acid. In certain embodiments, the culture media may be supplemented with from about 0.5 to about 3 pM of a retinoid.

[0142] In one embodiment, the DOT1L inhibitor is EPZ004777 (l-[3-[[(2R,3S,4R,5R)-5-(4-aminopyrrolo[2,3-d]pyrimidin-7-yl)-3,4-dihydroxyoxolan-2-yl]methyl-propan-2-ylamino]propyl]-3-(4-tert-butylphenyl)urea). Other suitable DOT1L inhibitors include SGC0946 (l-(3-((((2R,3S,4R,5R)-5-(4-Amino-5-bromo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-3.4-dihydroxytetrahydrofuran-2-yl)methyl)(isopropyl)amino)propyl)-3-(4-(tert-butyl)phenyl)urea). The culture media may be supplemented with from about 2 to about 10 pM of the DOT IL inhibitor.

[0143] One embodiment of a suitable TGF-(3 inhibitor for use in the media is RepSox (2-(3-(6-Methylpyridin-2-yl)-IH-pyrazol-4-yl)-1.5-naphthyridine). Other exemplary TGF-(3 inhibitors include, but are not limited to, SB431542 (4-(4-(benzo[d][l,3]dioxol-5-yl)-5-(8yridine-2-yl)-lH-imidazol-2-yl)benzamide), LY2157299 (4-[2-(6-methylpyridin-2-yl)-5,6-dihydro-4H-pyrrolo[l,2-b]pyrazol-3-yl]quinoline-6-carboxamide), A83-01 3-(6-methylpyridin-2-yl)-N-phenyl-4-(quinoline-4-yl)-IH-pyrazole-l -carbothioamide), and tranilast. In some embodiments, the cell culture media is supplemented with from about 0.5 to about 4 pM of the TGF-0 inhibitor.

[0144] In certain embodiments, the somatic cells are endothelial cells. In other embodiments, the somatic cells are mammalian cells. In certain embodiments, the mammal is a mouse, a rat, a marsupial, a cow. an ovine, a caprine, a pig, an elephant, an equid, a cat, a dog, a wolf, a deer, or an antelope. In some embodiments, the mammal is Felis cams.4918-0896-88371 54Attorney Docket No.: 069296.11211 / 34WO01Cctnis lupus familiaris, Canis lupus, Bison bison, Dama dama, Hippotragus equinus, Hippotragus niger, an Asian elephant (Elephas maximus). an African elephant (Loxodonta africana), an African forest elephant (Loxodonta cyclotis , or a Bornean elephant (Elephas maximus borneensis).

[0145] The mammalian cells can be elephant cells or rodent cells. For example, the elephant cells are selected from Asian elephant (Elephas maximus) cells, African elephant (Loxodonta africana) cells, African forest elephant (Loxodonta cyclotis) cells, and Bornean elephant (Elephas maximus borneensis) cells.

[0146] In certain embodiments, the methods are used to generate induced pluripotent stem cells from somatic elephant cells. In these embodiments, the methods include transfecting the somatic cells with (i) elephant HRAS, (ii) at least one of C4 or C6, and (iii) SV40LT and / or an agent targeting TP53 and / or TP53 retrogenes. In one embodiment, C4 is a nucleotide encoding Elephas maximus OCT4ISOX2IKLF4IMYC and C6 is a nucleotide encoding Elephas maximus OCT4ISOX2IKLF4IMYCILIN28AINANOG. In other embodiments, the OCT4 and / or SOX2 can be replaced with an artificial OCT4 of the disclosure and an artificial SOX2 of the disclosure. In certain embodiments, the methods use an artificial OCT4 of the disclosure and an artificial SOX2 of the disclosure as well as C4 or C6.

[0147] The disclosure also includes induced pluripotent stem cells produced by the methods of the disclosure.

[0148] In certain aspects of the disclosure, the methods also include differentiating the induced pluripotent stem cells. In certain embodiments, the iPSCs can be differentiated into each germ layer (endoderm, mesoderm, and ectoderm). In other embodiments, embry oid bodies are formed from the cells. In further embodiments, the iPSCs are used to generate embryos. The cells may also be further edited using multiplex editing. In further embodiments, the elephant iPSCs can be used to generate chimeras, embryos, germ cell progenitors, and gametes.

[0149] In certain embodiments, the iPSCs are differentiated into neurons, neuronal precursors, and / or cardiomyocyte precursors.

[0150] Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative examples, make and utilize the present invention and practice the claimed methods. The following working examples, therefore, specifically’ point out the preferred embodiments of the present invention, and are not to be construed as limiting in any way the remainder of the disclosure.4918-0896-88371 55Attorney Docket No.: 069296.11211 / 34WO01ExamplesExample 1: Generation of SOX2 and OCT4 constructs of the disclosure

[0151] The SOX2 and OCT4 constructs of the disclosure were generated using the process shown in FIG. 1.

[0152] Models of Oct4 (Pou5fl) in complex with Sox2 in the transcription-competent state bound to their DNA target were either retrieved from the protein data base (PDB) for the mouse complex (code 6ht5) or generated using RosettaFold2NA (RF2NA) in the case of the elephant complex. Amino acids in the DNA binding domains of the Oct / Sox proteins were classified: in the dimeric protein interface, in the protein-DNA interface, both, or neither, on the basis of distance (8 A) from the dimeric partner or DNA. respectively. For each of the mouse (mm) and elephant (em) Oct / Sox dimers, two different redesign strategies were pursued- redesign of only the protein-protein interface residues while avoiding any protein-DNA interface residues (int), or redesign of any residues outside of the protein-DNA interface (full). Redesign was performed using ProteinMPNN on identified residues, yielding 400 designs based on the elephant scaffolds and 800 based on the mouse scaffolds. RF2NA was used to produce folding simulations of the designed TF pairs along with their target DNA sequence, and the resulting predicted structures w ere aligned against the input structures using USalign. For each of the four sets, the highest-scoring five designs were calculated as those with the maximum geometnc mean value of the RF2NA fold simulation’s pLDDT (confidence) value and the USalign TMscore of the fold simulation’s alignment against the input structure, for a total of 20 designs selected for synthesis and testing.

[0153] These proteins share as little as 70% sequence identity to the wild-lvpe proteins within the DBD. They w ere designed to be species-agnostic, and to that end they have been tested thus far in mouse and elephant cell lines, and several pairs work extremely well in both, establishing efficacy in highly divergent mammalian species.Example 2 - Testing of SOX2 and OCT4 Constructs

[0154] As noted in Example 1 above, tw enty of the SOX2 and OCT4 constructs were tested.

[0155] First, engineered OCT4 / SOX2 pairs were cloned into a doxycycline inducible PiggyBac integration vector and then integrated into the genome of a Mus musculus cell line that has a GFP expression cassette downstream of the endogenous OCT4 locus. Once4918-0896-88371 56Attorney Docket No.: 069296.11211 / 34WO01these cells are reprogrammed, the resulting iPSC colonies fluoresce green. Cell lines containing the engineered OCT4 / SOX2 constructs were generated, and the expression of the engineered factors was induced for 7 days. At this time, resulting number of colonies visible in each 6-well plate well was counted. The results of this testing are shown in FIG. 1.

[0156] The following OCT4 / SOX2 pairs w ere cloned:

[0157] After this testing, one of the top performing Engineered OCT4 / SOX2 pairs (em_int48 as above), was delivered to elephant induced pluripotent stem cells in a transient, doxycycline-inducible, non-genome integrating vector. After 28 days, sub-populations of these cells with improved stem cell morphology were isolated and expanded.

[0158] These cells underwent bulk RNA sequencing, and the resulting transcriptome w as analyzed. The MA plots in FIG. 3 and FIG.4 show gene expression of all coding genes compared to primary elephant endothelial cells. Key pluripotency genes are called out. The4918-0896-8837 1 57Attorney Docket No.: 069296.11211 / 34WO01expression of each of these genes was a marked improvement over the transcriptome of the starting elephant induced pluripotent stem cells.

[0159] Furthermore, a metagenomic analysis of gene clusters upregulated in cells treated with an engineered OCT4 / SOX2 pairs was carried out. The results of this analysis are shown in FIG. 5. Compared to starting primary cells, cells treated with the engineered OCT4 / SOX2 pairs (labelled as boost) uniquely upregulated gene networks associated with telomere maintenance and germ cell proliferation, reinforcing the hypothesis that these protein pairs can improve pluripotent stem cells.

[0160] While the invention has been described and illustrated herein by references to various specific materials, procedures and examples, it is understood that the invention is not restricted to the particular combinations of material and procedures selected for that purpose. Numerous variations of such details can be implied as will be appreciated by those skilled in the art. It is intended that the specification and examples be considered as exemplar^', only, with the true scope and spirit of the invention being indicated by the following claims. All references, patents, and patent applications referred to in this application are herein incorporated by reference in their entirety.EMBODIMENTS

[0161] The invention provides also the following non-limiting embodiments.

[0162] Embodiment 1 is an isolated SOX2 protein comprising an artificial SOX2 DNA binding domain, wherein the artificial SOX2 DNA binding domain comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 1-21.

[0163] Embodiment 2 is the isolated SOX2 protein of embodiment 1. wherein the artificial SOX2 DNA binding domain comprises the amino acid sequence of any one of SEQ ID NOs: 1-21.

[0164] Embodiment 3 is the isolated SOX2 protein of embodiment 1 or 2, wherein the SOX2 protein comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs:43-62.

[0165] Embodiment 4 is the isolated SOX2 protein of embodiment 3, wherein the SOX2 protein comprises the amino acid sequence of any one of SEQ ID NOs:43-62.

[0166] Embodiment 5 is the isolated SOX2 protein of any one of embodiments 1-4, wherein the protein is humanized.4918-0896-88371 58Attorney Docket No.: 069296.11211 / 34WO01

[0167] Embodiment 6 is an isolated nucleic acid encoding the isolated SOX2 protein of any one of embodiments 1-5.

[0168] Embodiment 7 is a vector comprising the isolated nucleic acid of embodiment 6.

[0169] Embodiment 8 is a host cell comprising the isolated nucleic acid of embodiment 6 or the vector of embodiment 7.

[0170] Embodiment 9 is an isolated OCT4 protein comprising an artificial OCT4 DNA binding domain, wherein the artificial OCT4 DNA binding domain comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 83-103.

[0171] Embodiment 10 is the isolated OCT4 protein of embodiment 9, wherein the artificial OCT4 DNA binding domain comprises the amino acid sequence of any one of SEQ ID NOs: 83-103.

[0172] Embodiment 11 is the isolated OCT4 protein of embodiment 9 or 10, wherein the OCT4 protein comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 125-144.

[0173] Embodiment 12 is the isolated OCT4 protein of embodiment 11, wherein the OCT4 protein comprises the amino acid sequence of any one of SEQ ID NOs: 125-144.

[0174] Embodiment 13 is the isolated OCT4 protein of any one of embodiments 9-12, wherein the protein is humanized.

[0175] Embodiment 14 is an isolated nucleic acid encoding the isolated OCT4 protein of any one of embodiments 9-13.

[0176] Embodiment 15 is a vector comprising the isolated nucleic acid of embodiment 14.

[0177] Embodiment 16 is a host cell comprising the isolated nucleic acid of embodiment 14 or the vector of embodiment 15.

[0178] Embodiment 17 is a method of inducing pluripotency in a cell comprising transfecting the cell with the isolated nucleic acid of embodiment 6 and / or 14 or a vector of embodiment 7 and 15.

[0179] Embodiment 18 is the method of embodiment 17, wherein the cell is a mammalian cell.

[0180] Embodiment 19 is a method of generating induced pluripotent stem cells comprising: (a) transfecting a somatic cell with a polynucleotide encoding a SOX2 protein comprising an artificial SOX2 DNA binding domain and a polynucleotide encoding an OCT4 protein comprising an artificial OCT4 DNA binding domain; (b) culturing the cells in a culture medium to generate induced pluripotent stem cells; and optionally (c) selecting for4918-0896-88371 59Attorney Docket No.: 069296.11211 / 34WO01the induced pluripotent stem cells, wherein the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 22-42; and wherein the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 104-124.

[0181] Embodiment 20 is the method of embodiment 19, wherein the polynucleotide encoding the SOX2 protein and the polynucleotide encoding the OCT4 protein are humanized.

[0182] Embodiment 21 is the method of embodiments 19 or 20. wherein the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises (i) a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 63-82 or (ii) a nucleic acid sequence encoding a protein having an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 43-62.

[0183] Embodiment 22 is the method of any one of embodiments 19 to 21, wherein the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises (hi) a nucleic acid sequence at least 85%, at least 90%. at least 95%. or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 145-164 or (iv) a nucleic acid sequence encoding a protein having an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 125-144.

[0184] Embodiment 23 is the method of embodiments 19 or 20, wherein:• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 1 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 83;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 2 and the polynucleotide encoding the OCT4 protein4918-0896-88371 60Attorney Docket No.: 069296.11211 / 34WO01comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 84;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 3 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 85;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 4 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 86;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 5 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 87;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 6 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 88;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 7 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 89;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 8 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 90;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA4918-0896-88371 61Attorney Docket No.: 069296.11211 / 34WO01binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 9 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 91;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 10 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 92;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 11 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 93;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 12 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 94;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 13 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 95;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 14 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 96;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 15 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence4918-0896-88371 62Attorney Docket No.: 069296.11211 / 34WO01encoding a protein having the amino acid sequence of SEQ ID NO: 97;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 16 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 98;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 17 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 99;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 18 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 100;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 19 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 101;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 20 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 102; or• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 21 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 103.

[0185] Embodiment 24 is the method of embodiments 19 or 20, wherein:4918-0896-88371 63Attorney Docket No.: 069296.11211 / 34WO01• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 43 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 125;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 44 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 126;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 45 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 127;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 46 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 128;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 47 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 129;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 48 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 130;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 49 and the poly nucleotide encoding the OCT4 protein4918-0896-88371 64Attorney Docket No.: 069296.11211 / 34WO01comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 131;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 50 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 132;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 51 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 133;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 52 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 134;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 53 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 135;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 54 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 136;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 55 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 137;4918-0896-88371 65Attorney Docket No.: 069296.11211 / 34WO01• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 56 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 138;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 57 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 139;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 58 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 140;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 59 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 141;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 60 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 142;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 61 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 143; or• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 62 and the polynucleotide encoding the OCT4 protein4918-0896-88371 66Attorney Docket No.: 069296.11211 / 34WO01comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 144.

[0186] Embodiment 25 is the method of embodiments 19 or 20, wherein:• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 22 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 104;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 23 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 105;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 24 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 106;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 25 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 107;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 26 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 108;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 27 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 109;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 28 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 110;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 29 and the4918-0896-88371 67Attorney Docket No.: 069296.11211 / 34WO01polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 111;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 30 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 112;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 31 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 113;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 32 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 114;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 33 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 115;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 34 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 116;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 35 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 117;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 36 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 118;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 37 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding4918-0896-88371 68Attorney Docket No.: 069296.11211 / 34WO01domain comprises the nucleic acid sequence of SEQ ID NO: 119;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 38 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 120;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 39 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 121;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 40 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 122;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 41 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 123; or• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 42 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 124.

[0187] Embodiment 26 is the method of embodiments 19 or 20. wherein:• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 63 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 145;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 64 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 146;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 65 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding4918-0896-88371 69Attorney Docket No.: 069296.11211 / 34WO01domain comprises the nucleic acid sequence of SEQ ID NO: 147;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 66 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 148;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 67 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 149;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 68 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 150;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 69 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 151;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 70 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 152;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 71 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 153;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 72 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 154;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 73 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 155;4918-0896-88371 70Attorney Docket No.: 069296.11211 / 34WO01• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 74 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 156;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 75 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 157;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 76 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 158;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 77 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 159;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 78 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 160;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 79 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 161;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 80 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 162;• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 81 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 163; or• the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA4918-0896-88371 71Attorney Docket No.: 069296.11211 / 34WO01binding domain comprises the nucleic acid sequence of SEQ ID NO: 82 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 164.

[0188] Embodiment 27 is the method of any one of embodiments 19-26, further comprising transfecting the somatic cells with a nucleic acid encoding one or more of KI.1 '4. MYC, LIN28, and NANOG.

[0189] Embodiment 28 is the method of any one of embodiments 19-27, wherein the method comprises transfecting the cells with: a nucleic acid encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain; a nucleic acid encoding the OCT4 protein comprising an artificial OCT4 DNA binding domain; and a polynucleotide encoding KLF4 and MYC or a polynucleotide encoding KI.F4MYC. LIN28. and NANOG.

[0190] Embodiment 29 is the method of any one of embodiments 19-27, wherein the method comprises transfecting the somatic cells with a vector comprising the polynucleotide encoding the SOX2 protein comprising an artificial SOX2 DNA binding domain and the polynucleotide encoding the OCT4 protein comprising an artificial OCT4 DNA binding domain.

[0191] Embodiment 30 is the method of any one of embodiments 19-27, wherein the method further comprises chemically reprogramming the cells prior to transfecting the cells.

[0192] Embodiment 31 is the method of embodiment 30, wherein the method further comprises chemically reprogramming the cells by culturing the cells in a culture medium supplemented with an HD AC inhibitor, a GSK-3 inhibitor, a TGF- inhibitor, a monoamine oxidase inhibitor, an activator of eukaryotic adenylyl cyclase, a retinoid, and a DOT1L inhibitor.

[0193] Embodiment 32 is the method of any one of embodiments 19-31, wherein the somatic cells are endothelial cells.

[0194] Embodiment 33 is the method of embodiment 32, wherein the somatic cell is a mammalian cell.

[0195] Embodiment 34 is the method of embodiment 33, wherein the mammal is a mouse, a rat, a marsupial, a cow, an ovine, a caprine, a pig, an elephant, an equid, a cat, a dog, a wolf, a deer, or an antelope.

[0196] Embodiment 35 is the method of embodiment 34, wherein the mammal is Felis catus, Cants lupus familiaris, Cants lupus, Bison bison, Dama dama, Hippotragus equinus, Hippotragus niger. an Asian elephant Elephas maximus), an African elephant Loxodonta4918-0896-88371 72Attorney Docket No.: 069296.11211 / 34WO01africana), an African forest elephant (Loxodonta cyclotis), or a Bornean elephant (Elephas maximus borneensis).

[0197] Embodiment 36 is the method of embodiment 34, wherein the mammal is an Asian elephant (Elephas maximus), an African elephant (Loxodonta africana), an African forest elephant (Loxodonta cyclotis), or a Bornean elephant (Elephas maximus borneensis).

[0198] Embodiment 37 is an induced pluripotent stem cell produced by the method of any one of embodiments 19-36.4918-0896-8837 1 73

Claims

1. Attorney Docket No.: 069296.11211 / 34WO01CLAIMSWhat is claimed is:

1. An isolated SOX2 protein comprising an artificial SOX2 DNA binding domain, wherein the artificial SOX2 DNA binding domain comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs : 1 -21.

2. The isolated SOX2 protein of claim 1, wherein the artificial SOX2 DNA binding domain comprises the amino acid sequence of any one of SEQ ID NOs: 1-21.

3. The isolated SOX2 protein of claim 1, wherein the SOX2 protein comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs:43-62.

4. The isolated SOX2 protein of claim 3, wherein the SOX2 protein comprises the amino acid sequence of any one of SEQ ID NOs:43-62.

5. The isolated SOX2 protein of any one of claims 1-4, wherein the protein is humanized.

6. An isolated nucleic acid encoding the isolated SOX2 protein of any one of claims 1-4.

7. A vector comprising the isolated nucleic acid of claim 6.

8. A host cell comprising: (a) the isolated nucleic acid of claim 6; or (b) a vector comprising the isolated nucleic acid of claim 6.

9. An isolated OCT4 protein comprising an artificial OCT4 DNA binding domain, wherein the artificial OCT4 DNA binding domain comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 83-103.

10. The isolated OCT4 protein of claim 9, wherein the artificial OCT4 DNA binding domain comprises the amino acid sequence of any one of SEQ ID NOs: 83-103.4918-0896-88371 74Attorney Docket No.: 069296.11211 / 34WO0111. The isolated OCT4 protein of claim 9, wherein the OCT4 protein comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 125-144.

12. The isolated OCT4 protein of claim 11, wherein the OCT4 protein comprises the amino acid sequence of any one of SEQ ID NOs: 125-144.

13. The isolated OCT4 protein of any one of claims 9-11, wherein the protein is humanized.

14. An isolated nucleic acid encoding the isolated OCT4 protein of any one of claims 9-11.

15. A vector comprising the isolated nucleic acid of claim 14.

16. A host cell comprising: (a) the isolated nucleic acid of claim 14; or (b) a vector comprising the isolated nucleic acid of claim 14.

17. A method of inducing pluripotency in a cell comprising transfecting the cell with an isolated nucleic acid of encoding a SOX2 protein comprising an artificial SOX2 DNA binding domain and / or an isolated nucleic acid encoding an OCT4 protein comprising an artificial OCT4 DNA binding domain or a vector comprising the isolated nucleic acid of encoding a SOX2 protein and / or the isolated nucleic acid encoding an OCT4 protein comprising, wherein:the artificial SOX2 DNA binding domain comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 1-21;the SOX2 protein comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs:43-62;the artificial OCT4 DNA binding domain comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 83-103; and / or4918-0896-88371 75Attorney Docket No.: 069296.11211 / 34WO01the OCT4 protein comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 125-144.

18. The method of claim 17, wherein the cell is a mammalian cell.

19. A method of generating induced pluripotent stem cells comprising:(a) transfecting a somatic cell with a polynucleotide encoding a SOX2 protein comprising an artificial SOX2 DNA binding domain and a polynucleotide encoding an OCT4 protein comprising an artificial OCT4 DNA binding domain;(b) culturing the cells in a culture medium to generate induced pluripotent stem cells;and optionally(c) selecting for the induced pluripotent stem cells,wherein the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 22-42; andwherein the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 104-124.

20. The method of claim 19, wherein the polynucleotide encoding the SOX2 protein and the polynucleotide encoding the OCT4 protein are humanized.

21. The method of claim 19, wherein the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises: (i) a nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 63-82; or (ii) a nucleic acid sequence encoding a protein having an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 43-62.

22. The method of any one of claims 19 to 21, wherein the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises: (iii) a4918-0896-88371 76Attorney Docket No.: 069296.11211 / 34WO01nucleic acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the nucleic acid sequence of any one of SEQ ID NOs: 145-164; or (iv) a nucleic acid sequence encoding a protein having an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 125-144.

23. The method of claims 19 or 20, wherein:the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 1 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 83;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 2 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 84;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 3 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 85;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 4 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 86;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 5 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 87;4918-0896-88371 77Attorney Docket No.: 069296.11211 / 34WO01the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 6 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 88;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 7 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 89;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 8 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 90;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 9 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 91;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 10 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 92;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 11 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 93;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino4918-0896-88371 78Attorney Docket No.: 069296.11211 / 34WO01acid sequence of SEQ ID NO: 12 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 94;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 13 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 95;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 14 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 96;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 15 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 97;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 16 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 98;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 17 and the poly nucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 99;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 18 and the polynucleotide encoding the OCT4 protein4918-0896-88371 79Attorney Docket No.: 069296.11211 / 34WO01comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 100;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 19 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 101;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 20 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 102; orthe polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 21 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 103.

24. The method of claims 19 or 20. wherein:the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 43 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 125;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 44 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 126;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 45 and the poly nucleotide encoding the OCT4 protein4918-0896-88371 80Attorney Docket No.: 069296.11211 / 34WO01comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 127;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 46 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 128;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 47 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 129;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 48 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 130;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 49 and the poly nucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 131;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 50 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 132;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 51 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 133;4918-0896-88371 81Attorney Docket No.: 069296.11211 / 34WO01the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 52 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 134;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 53 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 135;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 54 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 136;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 55 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 137;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 56 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 138;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 57 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 139;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino4918-0896-88371 82Attorney Docket No.: 069296.11211 / 34WO01acid sequence of SEQ ID NO: 58 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 140;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 59 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 141;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 60 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 142;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 61 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 143; orthe polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 62 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises a nucleic acid sequence encoding a protein having the amino acid sequence of SEQ ID NO: 144.

25. The method of claims 19 or 20. wherein:the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 22 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 104;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 23 and the4918-0896-88371 83Attorney Docket No.: 069296.11211 / 34WO01polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 105;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 24 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 106;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 25 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 107;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 26 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 108;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 27 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 109;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 28 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 110;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 29 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 111;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 30 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 112;4918-0896-88371 84Attorney Docket No.: 069296.11211 / 34WO01the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 31 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 113;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 32 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 114;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 33 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 115;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 34 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 116;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 35 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 117;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 36 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 118;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 37 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 119;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 38 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 120;4918-0896-88371 85Attorney Docket No.: 069296.11211 / 34WO01the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 39 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 121;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 40 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 122;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 41 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 123; orthe polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 42 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 124.

26. The method of claims 19 or 20, wherein:the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 63 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 145;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 64 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 146;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 65 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 147;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 66 and the4918-0896-88371 86Attorney Docket No.: 069296.11211 / 34WO01polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 148;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 67 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 149;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 68 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 150;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 69 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 151;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 70 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 152;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 71 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 153;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 72 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 154;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 73 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 155;4918-0896-88371 87Attorney Docket No.: 069296.11211 / 34WO01the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 74 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 156;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 75 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 157;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 76 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 158;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 77 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 159;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 78 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 160;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 79 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 161;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 80 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 162;the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 81 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 163; or4918-0896-88371 88Attorney Docket No.: 069296.11211 / 34WO01the polynucleotide encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 82 and the polynucleotide encoding the OCT4 protein comprising the artificial OCT4 DNA binding domain comprises the nucleic acid sequence of SEQ ID NO: 164.

27. The method of any one of claims 19-21 , further comprising transfecting the somatic cells with a nucleic acid encoding one or more of KLF4,MYC, LIN28, and NANOG.

28. The method of any one of claims 19-21, wherein the method comprises transfecting the cells with:a nucleic acid encoding the SOX2 protein comprising the artificial SOX2 DNA binding domain;a nucleic acid encoding the OCT4 protein comprising an artificial OCT4 DNA binding domain; anda polynucleotide encoding KLF4 and MYC or a polynucleotide encoding KI. 4N1YC. LIN28, and NANOG.

29. The method of any one of claims 19-21, wherein the method comprises transfecting the somatic cells with a vector comprising the polynucleotide encoding the SOX2 protein comprising an artificial SOX2 DNA binding domain and the polynucleotide encoding the OCT4 protein comprising an artificial OCT4 DNA binding domain.

30. The method of any one of claims 19-21 , wherein the method further comprises chemically reprogramming the cells prior to transfecting the cells.

31. The method of claim 30, wherein the method further comprises chemically reprogramming the cells by culturing the cells in a culture medium supplemented with an HD AC inhibitor, a GSK-3 inhibitor, a TGF-0 inhibitor, a monoamine oxidase inhibitor, an activator of eukaryotic adenylyl cyclase, a retinoid, and a DOT1L inhibitor.

32. The method of any one of claims 19-21, wherein the somatic cells are endothelial cells.

33. The method of claim 32, wherein the somatic cell is a mammalian cell.4918-0896-88371 89Attorney Docket No.: 069296.11211 / 34WO0134. The method of claim 33, wherein the mammal is a mouse, a rat, a marsupial, a cow, an ovine, a caprine, a pig, an elephant, an equid, a cat. a dog, a wolf, a deer, or an antelope.

35. The method of claim 34, wherein the mammal is Felis catus, Canis lupus familiaris. Cants lupus, Bison bison, Dama dama, Hippotragus equinus, Hippotragus niger, an Asian elephant (Elephas rn.axim.us). an African elephant (Loxodonta africana). an African forest elephant (Loxodonta cyclotis), or a Bornean elephant (Elephas maximus borneensis).

36. The method of claim 34, wherein the mammal is an Asian elephant (Elephas maximus), an African elephant (Loxodonta africana), an African forest elephant (Loxodonta cyclotis), or a Bornean elephant (Elephas maximus borneensis).

37. An induced pluripotent stem cell produced by the method of any one of claims 19- 21.4918-0896-88371 90

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