Abstract: Provided herein are compositions and methods for regulating protein translation. The compositions include a cap-conjugated oligonucleotide comprising an m7G cap or a variant or analog thereof conjugated to an oligonucleotide, wherein the oligonucleotide is capable of specifically hybridizing with a target sequence in an RNA molecule. The disclosure further provides methods of regulating translation of an mRNA in a cell, the method comprising contacting the cell with a cap-conjugated oligonucleotide comprising an m7G cap or a variant or analog thereof conjugated to an oligonucleotide, wherein the oligonucleotide comprises a sequence capable of specifically hybridizing with a target sequence in an RNA molecule.

Abstract: 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.

Abstract: Provided are RNA recognition complexes that include an RNA-targeting agent; and a coronavirus-derived protein. In some embodiments, the RNA recognition complex further includes a linker. In some embodiments, the RNA-targeting agent includes CRISPR/Cas9 components (e.g., a Cas9 protein, a Cas 13b protein, or a Cas 13d protein). Also provided herein are methods of upregulating gene expression of a target RNA that include delivering a RNA recognition complex into a cell, wherein the RNA recognition complex comprises a RNA-targeting agent, and a coronavirus-derived protein, and wherein the RNA recognition complex binds to the target RNA and upregulates gene expression of the target RNA in the cell.

Abstract: Provided herein is a molecule for use in directing splicing event. More specifically, provided herein is a molecule for use in targeted exon inclusion during mRNA splicing, along with compositions and methods of using the same.

Abstract: Provided are compositions and methods of treating Coronavirus disease 2019 (COVID-19) in a subject, the method including administering to the subject a therapeutically effective amount of a composition comprising an exogenous nucleic acid and delivering the exogenous nucleic acid into a cell, wherein the exogenous nucleic acid comprises an antisense oligonucleotide, a small interfering RNA (siRNA), or locked nucleic acid, and wherein the exogenous nucleic acid binds to a target RNA and modulates gene expression of the target RNA, thereby treating Coronavirus disease 2019 (COVID-19) in the subject.

Abstract: Provided herein are methods of regulating alternative polyadenylation (APA) of a target RNA in a cell, increasing stability of a target RNA in a cell, preventing degradation of a target RNA in a cell, preventing degradation of a target RNA in a cell, modifying localization of a target RNA in a cell, or increasing synthesis of a protein encoded by a target RNA in a cell, by administering to the cell an RNA regulation unit, wherein the RNA regulation unit comprises an RNA binding protein (RBP) and a gene-targeting agent, wherein the RNA binding protein binds proximal to a poly(A) signal and/or site.

Abstract: Provided herein are zinc finger peptides comprising the amino acid sequence of SEQ ID NO: 1 (SDGDWICPDKKCGN-VNFARRTSCNRCGREKTT) and at least one substitution compared to SEQ ID NO: 1, wherein the zinc finger peptide is an engineered zinc finger peptide.

Abstract: Provided herein are methods of treating Huntington's disease in a subject, the method comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising: (a) a guide RNA (gRNA), wherein the guide RNA comprises a repeat sequence complementary to a target CAG-expansion RNA, and wherein the gRNA allele-selectively targets the target CAG-expansion RNA; and (b) a CRISPR-associated protein or a nucleic acid sequence encoding the CRISPR-associated protein, wherein the CRISPR-associated protein comprises a Cas13d polypeptide.

Abstract: Provided herein are nuclear expressed antisense RNAs for interfering with a target repetitive RNA, the nuclear expressed antisense RNA comprising: (a) an oligonucleotide encoding an RNA-targeting guide comprising a sequence complementary to the target repetitive RNA; and (b) an oligonucleotide encoding a RNA binding protein (RBP)/ribonucleoprotein (RNP)-recruiting motif.

Abstract: Provided are methods of modulating gene expression of a target RNA in a cell comprising (a) recruiting a modulation unit, wherein the modulation unit comprises an RNA binding protein (RBP), an exogenous RNA binding moiety, and a gene-editing agent; (b) delivering the modulation unit into the cell; and (c) detecting change in the target RNA translation, wherein the modulation unit modulates gene expression of the target RNA in the cell.

Abstract: Disclosed herein is a technology to perform programmable RNA editing at single-nucleotide resolution using RNA-targeting CRISPR/Cas9. This approach, which Applicants have termed “Cas9-directed RNA editing” or “CREDIT,” provides a means to reversibly alter genetic information in a temporal manner, unlike traditional CRISPR/Cas9 driven genomic engineering which relies on permanently altering DNA sequence.

Abstract: Provided are methods of modulating gene expression of a target RNA in a cell comprising (a) recruiting a modulation unit, wherein the modulation unit comprises an RNA binding protein (RBP), an exogenous RNA binding moiety, and a gene-editing agent; (b) delivering the modulation unit into the cell; and (c) detecting change in the target RNA translation, wherein the modulation unit modulates gene expression of the target RNA in the cell.

Abstract: Disclosed are compositions and methods for simultaneously providing a gene therapy and preventing an adaptive immune response to a cell modified by the gene therapy by the immune system of a subject. In some embodiments, compositions of the disclosure modify a level of expression of an RNA molecule associated with a disease or disorder as well as inhibit expression or activity of a component of an adaptive immune response to mask the modified cell from a subject's immune system.

Abstract: Provided are methods of inhibiting activity of a RNA binding protein in a cell that include (a) generating a RNA binding N protein (RBP) binding agent comprising an RNA molecule comprising a binding site for the RNA binding protein; and (b) delivering the RBP binding agent into the cell, wherein the RBP binding agent binds to the RNA binding protein, thereby inhibiting the activity of the RNA binding protein in the cell.

Abstract: Provided are methods for identifying an RNA nucleobase that interacts with an RNA binding protein (RBP) including (a) crosslinking the RNA binding protein to an RNA fragment in a biological sample; (b) detecting an RNA-RBP complex, wherein the RNA-RBP complex comprises the RNA fragment bound by the RNA binding protein; (c) isolating the RNA fragment of the RNA-RBP complex; and (d) profiling the isolated RNA fragment bound by the RNA binding protein, thereby identifying the RNA nucleobase of the RNA fragment that interacts with the RNA binding protein.

Abstract: Cas9 polypeptides which target RNA and methods of using them are provided.

Abstract: Described herein are efficient methods for preparing a library for use in comprising performing gene targeting or massively parallel reporter assays. The methods comprise performing hybrid capture of a library constant region.

Abstract: The present invention provides methods, antibodies and kits for detecting and/or quantifying expression of both non-nucleic acid molecules, such as proteins, and nucleic acid molecules in a single sample or single cell. The antibody is covalently conjugated to an oligonucleotide, such as a single-stranded DNA molecule, which comprises an identification tag and a blocking group, such as a ddNTP or an inverted dTTP, which prevents extension of the oligonucleotide by a polymerase. The method comprises the steps of reverse transcribing the conjugated oligonucleotide and the target nucleic acid simultaneously, amplifying both transcription production, and detecting the amplicons thereof. The method is also useful for detecting and/or quantifying the number of cells in a sample expressing a given non -nucleic acid molecule (e.g. protein).

Abstract: Cas9 polypeptides which target RNA and method of using them are provided.

Abstract: 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.