79 results about "Mitochondrial RNA editing" patented technology

The invention discloses a chloroplast RNA edited gene OsPPR7 for temperature-sensitive regulation and control of rice and application of the gene OsPPR7, and belongs to the technical field of gene engineering. The CDS sequence of the OsPPR7 gene is as shown in SEQ ID NO. 1. The OsPPR7 is an RNA (Ribonucleic Acid) editing factor which has a bidirectional regulation and control function and is sensitive to temperature. Editing of multiple sites on the rpoB gene is negatively regulated and controlled, and meanwhile RNA editing of multiple genes such as ndhB and ndhD which are crucial to the chloroplast function is positively regulated and controlled under high-temperature stress. Under the stress of high temperature of 35 DEG C, the loss of functions can lead to obvious reduction of RNA editing efficiency of a plurality of ndh genes, and serious yellowing of seedlings is caused. The key function of the rice OsPPR7 gene in regulation and control of rice growth and development and high-temperature response is clarified for the first time, the importance of the OsPPR7 gene in maintenance of chloroplast functions under high-temperature stress is clarified, and a new gene resource and a technical path are provided for cultivation of new varieties of high-temperature-resistant rice.

The present disclosure relates generally to (CRISPR) RNA (crRNA) for the precision silencing of transcripts. In some embodiments, the crRNA are enriched for guanosine (G) nucleotides at key spacer positions, which is useful in enhancing the silencing efficacy of otherwise inefficient crRNA, thereby expanding the targeting spectrum of Cas13 endonucleases, e.g., Cas13b and Cas13d. In other embodiments, the crRNA comprise a spacer sequence having at least one nucleotide mismatch relative to the target RNA sequence, wherein the target RNA sequence is a wild-type transcript and / or a variant transcript (e.g., a transcript comprising a single nucleotide variant (SNV)). The present disclosure also provides RNA editing systems comprising the crRNA described herein in complex a Cas13 effector protein and a target RNA sequence, methods for the selective targeting of transcripts encoding proteins that are difficult to target, or are not amenable to pharmacological targeting, e.g., oncogenic fusion transcripts or oncogenic transcripts comprising single nucleotide variant(s), and methods for the design and selection of potent crRNA.

The present invention relates to a method for the differential diagnosis of bipolar versus unipolar disorder in a human patient during a depressive phase from a biological sample of the patient, comprising determining the relative proportions of RNA editing variants of at least the A-to-I-edited RNA ZNF267 gene. The present invention also relates to a method for monitoring the treatment of a depressed patient exhibiting bipolar or unipolar disorder. Finally, the present invention provides a kit for the differential diagnosis of bipolar versus unipolar disorder in a patient during a depressive phase.

The application discloses a fusion protein, which comprises an antibody binding domain and an RNA editing domain, wherein the antibody binding domain is a pAG domain, which comprises the functional domains of Protein A and Protein G, and the RNA editing domain comprises a rat APOBEC1 enzyme deamination domain and / or a human ADAR2 enzyme deamination domain. The fusion protein can be used to simultaneously identify RBP targets and provide transcriptome information in the same sample, can characterize the RNA-protein interaction spectrum, has high reliability and sensitivity, is suitable for studying the RBP functions in tissue sections and single cells, and has wide application prospects in the functional mechanism research of RBP in the development and disease processes.

The present disclosure provides novel adenine base editors that retain ability to edit DNA efficiently but show greatly reduced off-target effects, such as reduced RNA editing activity, as well as lower off-target DNA editing activity and reduced indel by product formation. Also provided are base editing methods comprising contacting a nucleic acid molecule with an adenine base editor and a guide RNA that has complementarity to a target sequence. Further provided are complexes comprising a guide RNA bound to a base editor provided herein; and kits and pharmaceutical compositions for the administration of adenine base editor variants to a host cell.

A sequence for forming an editing substrate together with a target RNA editing site. The sequence and the upstream and downstream portions of the target RNA editing site form a specific double-chain secondary structure, so that efficient editing of the target RNA editing site is realized.

This disclosure provides methods for treating neurodegenerative diseases and restoring neuronal synaptic function by administering adenosine-to-inosine editing modifiers.

Disclosed herein are SnRNA systems containing RNA-binding sequences for RNA editing.

The invention discloses a corn ZmMORF3 gene, an excellent haplotype of the corn ZmMORF3 gene and application of the corn ZmMORF3 gene in grain development regulation and molecular breeding. A key gene ZmMORF3 which affects mitochondrial gene RNA editing is cloned by using a grain mutant m497 found in a corn field breeding line selection process, and the gene encodes MORF protein and regulates assembly and activity of a mitochondrial compound I, so that corn grain development is affected; the excellent allelic variation genotype of the ZmMORF3 gene in the aspect of the row grain number is further excavated, and the row grain number can be increased by utilizing the ZmMORF3 gene, so that the yield is increased. In addition, distribution and utilization potentials of different haplotypes in a selfing line are researched, and technical support and excellent germplasm resources are provided for utilization of the gene.

Provided is an RNA editing system activating a Wnt signaling pathway, relating to the field of gene editing. Provided is an RNA editing element, comprising an Axin1-targeting RNA fragment and an Axin2-targeting RNA fragment. A gRNA that targets both Axin1 and Axin2 is constructed, which, compared with gRNAs targeting Axin1 or Axin2 alone, can significantly up-regulate Wnt activity. An AAV6 vector is screened from three AAV vectors of different serotypes, and exhibits relatively high expression intensity and efficiency and high infection efficiency with respect to airway epithelial cells and alveolar epithelial cells while exhibiting very low infection efficiency with respect to immune cells and endothelial cells. The AAV vector is assembled with a Cre-LoxP recombinase system to together infect a host cell, thereby facilitating the measurement of Cas13d knockdown efficiency by means of fluorescent labeling.

The present invention relates to methods and compositions for disrupting interaction of an NRF2 protein and a KEAP1 protein. The methods include contacting at least one polynucleotide selected from the group consisting of a polynucleotide encoding the NRF2 protein and a polynucleotide encoding the KEAP1 protein with a guide oligonucleotide that effects one or more (e.g., at least two) adenosine deaminase acting on RNA (ADAR)-mediated adenosine to inosine alterations in said at least one polynucleotide, wherein the adenosine to inosine alterations generate a mutant amino acid, thereby disrupting interaction of the NRF2 protein and the KEAP1 protein. The invention also relates to methods of treating a KEAP1-NRF2 pathway related disease in a subject in need thereof, the method comprising contacting, within the subject, at least one polynucleotide selected from the group consisting of a polynucleotide encoding an NRF2 protein and a polynucleotide encoding a KEAP1 protein with a guide oligonucleotide that effects an adenosine deaminase acting on RNA (ADAR)-mediated adenosine to inosine alteration in said at least one polynucleotide, wherein the adenosine to inosine alteration generates a mutant amino acid, thereby disrupting interaction of the NRF2 protein and the KEAP1 protein and treating the disease in the subject; and compositions thereof.

The invention relates to chemically modified oligonucleotides for use in site-directed A-to-I editing of a target RNA inside a cell with endogenous adenosine deaminase acting on RNA (ADAR), the oligonucleotide comprising a sequence capable of binding to a target sequence in a target RNA and a central base triplet (CBT) of 3 nucleotides (N−1N0N+1), wherein N0 is the central nucleotide directly opposite to a target adenosine in the target RNA that is to be edited, wherein the oligonucleotide comprises at least one internucleoside linkage that is a methanesulfonyl (mesyl) linkage.

Provided herein are RNA editing oligonucleotides capable of effecting ADAR-mediated deamination of a target adenosine comprised in a target RNA, wherein the oligonucleotide comprises a sequence that is capable of hybridizing with a region in the target RNA comprising said target adenosine, and wherein the oligonucleotide comprises at least one conformationally restricted nucleotide (CRN) positioned at the 5' and / or at the 3' terminus of the oligonucleotide and / or internally. In particular, the target adenosine may be part of a therapeutic target codon in the MECP2 protein-coding RNA. Provided herein are RNA editing oligonucleotides capable of effecting ADAR-mediated deamination of a target adenosine in a target RNA molecule encoding a target protein, wherein the oligonucleotide comprises a sequence that is capable of hybridizing with a region in the target RNA molecule comprising said target adenosine, and wherein the target adenosine is part of a codon encoding a posttranslational modification site in the target protein. In particular, the target adenosine may be part of a ubiquitination site in the frataxin (FXN) protein. Provided herein are RNA editing oligonucleotides capable of effecting ADAR-mediated deamination of a target adenosine in a target RNA molecule encoding a target protein, wherein the oligonucleotide comprises a sequence that is capable of hybridizing with a region in the target RNA molecule comprising said target adenosine, and wherein the target adenosine is part of a start codon in the 5' untranslated region of the target RNA molecule. In particular, the target adenosine may be part of the start codon of an untranslated ORF (uORF) in the human Sodium-dependent phosphate transporter 2 protein (SLC20A2).

The invention discloses a modified linear arRNA (Ribonucleic Acid) or cyclized arRNA and an application of the modified linear arRNA or cyclized arRNA in RNA (Ribonucleic Acid) editing. The invention provides an RNA (referred to as a modified arRNA), comprising n copies of arRNA truncated bodies; and n is a natural number greater than 2. The modified arRNA can be a linear RNA (Ribonucleic Acid) or a circular RNA (Ribonucleic Acid). To minimize the effect of bystanders without reducing the editing efficiency. The RNA sequence structure is modified by minimizing the specific sequence, the recruitment structural domain is combined, and the cyclization mechanism is optimized. Compared with the existing ADAR technology, the method and the device have the advantage that the editing efficiency is remarkably improved.

The disclosure relates to the field of chronic pain and the treatment thereof. The disclosure involves antisense oligonucleotides and the use thereof in pre-mRNA and mRNA modulation, in one aspect related to RNA editing using endogenous ADAR enzymes, in targeting an adenosine in a (pre-) mRNA for human Nav1.7, preferably to change from a lysine residue to an arginine residue in the protein at position 1406 (K1406R), thereby impairing the ability of the Nav1.7 protein to act as a sodium ion channel. In another aspect the disclosure relates to exon skipping wherein antisense oligonucleotides are used to induce skipping of exon 23 in the generation of human SCN9A mRNA thereby generating a shortened Nav1.7 protein with an impaired ability to act as a sodium ion channel. The disclosure relates to methods and means to alter the Nav1.7 protein in cells of the peripheral nervous system, preferably large nociceptor cells (type Aα / Aβ), to provide a treatment of chronic pain.

Disclosed are methods and compositions for promoting trans-splicing. In some embodiments, the composition comprises an engineered small nuclear RNA that promotes trans-splicing of a target RNA molecule. The composition may further comprise an RNA donor molecule.

SnRNA systems comprising RNA binding sequences for RNA editing are disclosed herein.

The present invention relates to an RNA editing method and a reagent. The method uses a type III CRISPR complex and introduces a bulge loop structure of at least one base onto gRNA to edit a target RNA molecule. The method can bypass the characteristics of a 6-nucleotide-based cleavage rule, thereby enabling cleavage and ligation of RNA bases that are not multiples of 6 nucleotides.

Systems and methods for predicting deamination efficiency or specificity associated with a guide RNA (gRNA) are provided. A nucleic acid sequence for the gRNA is received. Responsive to inputting a data structure into a model, a metric for an efficiency or specificity of deamination by a first Adenosine Deaminase Acting on RNA (ADAR) protein of a target nucleotide position in mRNA transcribed from a target gene is obtained as output from the model. The data structure includes an encoding of the nucleic acid sequence for the gRNA.

The present invention relates to a method for differential diagnosis of bipolar and monophasic disorders in a human patient during a depressive period from a biological sample of said patient, the method comprising at least determining the relative proportion of RNA editing variants of the A to I editing RNA ZNF267 gene. The invention also relates to a method for monitoring the treatment of a depressive patient exhibiting a bipolar disorder or a monophasic disorder. Finally, the present invention provides a kit for differential diagnosis of bipolar disorder and monophasic disorder in a patient during the depressive phase.

The invention discloses an OsDYW2 gene for maintaining chloroplast RNA editing and splicing of rice at high temperature and application of the OsDYW2 gene, and belongs to the technical field of gene engineering. The CDS sequence of the OsDYW2 gene is as shown in SEQ ID NO. 1. The invention reveals that the OsDYW2 is used as a key regulation factor under high temperature stress and guarantees the double functions of chloroplast RNA editing and splicing for the first time, and provides a new gene resource with high application value for heat-resistant genetic improvement of crops. Based on the discovery of the invention, the molecular marker related to the function of the OsDYW2 gene can be developed and is used for rapidly screening the heat-resistant potential of a breeding material, and the breeding efficiency is greatly improved. Meanwhile, the function-deleted mutant also provides an ideal tool material for further researching related mechanisms.

Provided are methods for using chimeric proteins to produce RNA modifications that can be detected by sequencing methods, including methods detecting relative translation rates of various mRNAs. Also provided herein are compositions comprising chimeric proteins, wherein the chimeric proteins comprise a RNA editing protein and a ribosomal protein.

Disclosed herein is a readrRNA (RNA sensing by Endogenous ADAR) molecule comprising a modular RNA molecule that facilitates sensing and detection of a cell type or its status, including a cell of a mammalian nervous system, including neurons and / or neuronal cells of the area postrema of the mammalian brain, and / or facilitates delivery of an effector protein to the selected cell. A composition that includes such a modular RNA molecule and another nucleic acid (linked or unlinked to the modular RNA molecule) is a CellREADR (Cell access through RNA sensing by Endogenous ADAR). CellREADR senses the presence of a selected cell RNA in a cell of a mammalian nervous system via readrRNA and leverages RNA editing mediated by ADAR (adenosine deaminase acting on RNA) for coupling the detection of a cell-defining RNA with translation of one or more effector proteins in a cell of a mammalian nervous system.

The invention discloses a primer group with three blood RNA editing markers, a kit and application. The primer group and the kit are used for early lung cancer detection and pulmonary nodule progress risk assessment. Lung cancer early diagnosis and pulmonary nodule risk assessment are clinical problems, and RNA editing as a novel non-invasive marker and related functions of the RNA editing are still to be clarified. According to the research, three RNA editing sites of the application are identified through 15 pairs of blood RNA sequencing of early lung cancer and healthy control; and the diagnostic value is evaluated through 100 early-stage lung cancer review queues and 313 sub-centimeter-level pulmonary nodule look-ahead queues in combination with machine learning. In the review queue, the AUC of the early lung cancer detected by the RNA editing sites reaches 0.984; in the look-ahead queue, the AUC of the RNA editing sites for pulmonary nodule progress risk assessment is 0.778, and the AUC is improved to 0.891 after the RNA editing sites are combined with imaging features. Compared with a traditional marker, the RNA editing marker has the advantages of high specificity, interference resistance, low cost and the like, and a novel clinical solution is provided for lung cancer early diagnosis and pulmonary nodule risk stratification.

The invention discloses a CRISPR-Cas13d gRNA design method and system based on an intracellular dynamic environment and application, and relates to the technical field of RNA editing and deep learning. The method comprises the following steps: acquiring secondary structure information and RBP binding site distribution condition of target RNA in a cell line; constructing a gRNA design model based on a deep learning algorithm, and learning a gRNA recognition process, an RNA structure of a target site and a correlation among an RBP binding process by using the gRNA design model according to secondary structure information of the target RNA in the cell line and a distribution condition of the RBP binding site to obtain a gRNA efficiency prediction result; and introducing an efficiency difference threshold to evaluate a gRNA efficiency prediction result. According to the method, the gRNA efficiency can be efficiently predicted in different cell environments.

The present invention relates to a single-stranded antisense oligonucleotide (ASO) for targeted RNA editing, in which the ASO comprises a specific domain (SD) and a secondary binding domain (BHD), in which the SD is complementarily paired with a targeted RNA region, and the BHD is complementarily paired with a non-targeted RNA region, and in which the specific domain (SD) and the BHD are complementarily paired with the non-targeted RNA region, in which the specific domain (SD) and the BHD are in one-to-one correspondence with the specific domain (SD) and the BHD are in one-to-one correspondence with the specific domain (SD) and the BHD are in one-to-one correspondence with the specific domain (SD) and the BHD are in one-to-one correspondence. Methods of editing RNA, compositions, and uses thereof are also provided.

The application discloses a marker for the severity and complication of mycoplasma pneumoniae pneumonia infection and application thereof in the preparation of a mycoplasma pneumoniae infection diagnosis kit, and belongs to the field of epigenetics and microbiology. In the application, the editing levels of six RNA editing sites of five genes in the severe side and the control side of MPP patients, i.e. CCRL2:chr3:46408483, CCNI:chr4:77058527, CTSS:chr1:150732881 / 150732032, IRAK3:chr12:66194142 and LYN:chr8:56010885, are obviously different, the five different genes are related to the severity and complication of MPP, and the combination of RNA editing has a very high accuracy in diagnosing the severity and complication of MPP.

The present application provides methods, compositions, and systems for targeted pseudouridylation of RNA. In some aspects, the present application provides methods for editing a target RNA (e.g., mRNA) in a host cell, comprising introducing an engineered guide small nucleolar RNA (gsnoRNA) into the host cell, wherein the gsnoRNA recruits a DKC1 protein to modify a target uridine residue in the target RNA to a pseudouridine residue. In some embodiments, the DKC1 protein has cytoplasmic localization in the host cell.