Abstract: Recombinant adeno-associated viral (AAV) capsid proteins are provided. Methods for generating the recombinant adeno-associated viral capsid proteins and a library from which the capsids are selected are also provided.

Abstract: The present invention relates to variant AAV capsid polypeptides, wherein the variant AAV capsid polypeptides exhibit increased transduction and/or tropism in human pancreatic tissue or human islets as compared non-variant parent capsid polypeptides.

Abstract: Provided are methods and compositions for reducing proliferation of a target cell (e.g., target cancer cell), e.g., for treating an individual who has cancer. The subjects include the use of an agent that increases activity of long non-coding RNA 122 (lnc122) in the targeted cell(s). As such, a subject method can include a step of administering to the individual a subject composition, which includes an agent that increases activity of lnc122. In some cases, a subject agent is a genome targeting fusion protein (e.g., Zinc Finger, TALE, or CRISPR effector protein fused to a transcriptional activator) that causes increased transcription of lnc122 from its endogenous locus. In some cases, a subject agent is lnc122, or a functional equivalent thereof. In some cases, a subject agent is a nucleic acid that encodes lnc122 or a functional equivalent thereof.

Abstract: Recombinant adeno-associated viral (rAAV) vectors expressing recombinant capsid proteins, having enhanced transduction properties in humans and mice are provided. Methods for generating the rAAV capsid proteins and assays to assess transduction efficiency are also provided. Also described are methods for determining the therapeutic efficacy for a gene of interest in two species of mammals by delivering to them the rAAV carrying the gene of interest encapsidated in the recombinant capsid protein.

Abstract: Methods and compositions are provided for editing the genome of a cell without the use of an exogenously supplied nuclease. Aspects of the methods include contacting a cell with a targeting vector comprising nucleic acid sequence to be integrated into the target locus, where the cell is not also contacted with a nuclease. In addition, reagents, devices and kits thereof that find use in practicing the subject methods are provided.

Abstract: The present invention relates to variant AAV capsid polypeptides, wherein the variant AAV capsid polypeptides exhibit increased transduction and/or tropism in human pancreatic tissue or human islets as compared non-variant parent capsid polypeptides.

Abstract: The present invention relates to variant AAV capsid polypeptides, wherein the variant AAV capsid polypeptides exhibit increased transduction and/or tropism in human pancreatic tissue or human islets as compared non-variant parent capsid polypeptides.

Abstract: The present disclosure provides variant adeno-associated virus (AAV) capsid polypeptides that provide an AAV particle with the ability to traverse the human blood brain barrier (BBB) and transduce cells of the CNS. In some embodiment, a subject variant AAV capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 96% or more, 97% or more, 98% or more, 99% or more, 99.5% or more, or 100% sequence identity) with the amino acid sequence set forth in any one of SEQ ID NOs: 1-27. Also provided are nucleic acids, AAV vectors, viral particles, cells, kits, and methods.

Abstract: The present disclosure provides methods and compositions for facilitating efficient adeno-associated virus (AAV)-based homologous recombination (HR). Subject methods include a step of contacting a cell (e.g., a population of cells) with a ribonucleotide reductase inhibitor, which provides for increased HR efficiency compared to performing HR in the absence of the inhibitor. The cell is also contacted with a recombinant adeno-associated vims (rAAV) that includes a donor DNA having a sequence cassette (i.e., a nucleotide sequence of interest) flanked by homology arms that facilitate integration of the sequence cassette into a target genomic locus via HR.

Abstract: Compositions and methods are provided for integrating one or more genes of interest into cellular DNA without substantially disrupting the expression of the gene at the locus of integration, i.e., the target locus. These compositions and methods are useful in any in vitro or in vivo application in which it is desirable to express a gene of interest in the same spatially and temporally restricted pattern as that of a gene at a target locus while maintaining the expression of the gene at the target locus, for example, to treat disease, in the production of genetically modified organisms in agriculture, in the large scale production of proteins by cells for therapeutic, diagnostic, or research purposes, in the induction of iPS cells for therapeutic, diagnostic, or research purposes, in biological research, etc. Reagents, devices and kits thereof that find use in practicing the subject methods are also provided.

Abstract: Recombinant adeno-associated viral (AAV) capsid proteins are provided. Methods for generating the recombinant adeno-associated viral capsid proteins and a library from which the capsids are selected are also provided.

Abstract: Methods and compositions are provided for editing the genome of a cell without the use of an exogenously supplied nuclease. Aspects of the methods include contacting a cell with a targeting vector comprising nucleic acid sequence to be integrated into the target locus, where the cell is not also contacted with a nuclease. In addition, reagents, devices and kits thereof that find use in practicing the subject methods are provided.

Abstract: Provided are nucleic acids and expression vectors having a non-silencing selectable marker gene, and methods of using the same. A subject expression vector includes an expression cassette and a non-silencing selectable marker gene. In some cases, the non-silencing selectable marker gene provides for drug resistance for prokaryotic cells, and includes a nucleotide sequence that (i) encodes a drug selectable marker protein; (ii) is operably linked to a promoter functional in prokaryotic cells, and (iii) includes an increased A/T content relative to a corresponding wild type nucleotide sequence. In some cases, the non-silencing selectable marker gene provides for drug resistance for prokaryotic cells, and includes a nucleotide sequence that (i) encodes a drug selectable marker protein; (ii) is operably linked to a promoter functional in prokaryotic cells, and (iii) has an A/T content in a range of from 52% to 70%.

Abstract: AAV vectors that encode a modified Factor IX (FIX) polypeptide for gene therapy for treatment of hemophilia B are provided. The modified FIX polypeptide has increased potency compared to the wild-type FIX polypeptide. The nucleic acid encoding the modified FIX polypeptide includes a portion of an intron. The AAV vectors were generated and selected to infect islet cells, but were found to effectively transduce hepatocytes upon systemic administration, and to express high levels of FIX polypeptide. Relatively low doses of the AAV vectors can be administered to achieve a therapeutic effect. The gene therapy treatment can result in normal or near normal coagulation pharmacokinetics and normal levels of FIX, or mild hemophilia B. Combining an AAV vector with improved properties for transducing hepatocytes, and modified FIX polypeptides with enhanced potency, improves transgene expression and effectively lowers the viral dose needed to achieve therapeutically relevant FIX activity levels.

Abstract: Compositions and methods are provided for integrating one or more genes of interest into cellular DNA without substantially disrupting the expression of the gene at the locus of integration, i.e., the target locus. These compositions and methods are useful in any in vitro or in vivo application in which it is desirable to express a gene of interest in the same spatially and temporally restricted pattern as that of a gene at a target locus while maintaining the expression of the gene at the target locus, for example, to treat disease, in the production of genetically modified organisms in agriculture, in the large scale production of proteins by cells for therapeutic, diagnostic, or research purposes, in the induction of PS cells for therapeutic, diagnostic, or research purposes, in biological research, etc. Reagents, devices and kits thereof that find use in practicing the subject methods are also provided.

Abstract: Recombinant adeno-associated viral (AAV) capsid proteins are provided. Methods for generating the recombinant adeno-associated viral capsid proteins and a library from which the capsids are selected are also provided.

Abstract: The present invention features compositions and methods relating to tRNA-derived small RNAs (tsRNAs). Provided herein are oligonucleotide compositions that are complementary to tsRNAs, in particular leuCAGtsRNA, and methods of using the oligonucleotides for the regulation of respective tsRNA. Further provided are methods of inducing apoptosis through the inhibition of leuCAGtsRNA.

Abstract: Methods and compositions are provided for editing the genome of a cell without the use of an exogenously supplied nuclease. Aspects of the methods include contacting a cell with a targeting vector comprising nucleic acid sequence to be integrated into the target locus, where the cell is not also contacted with a nuclease. In addition, reagents, devices and kits thereof that find use in practicing the subject methods are provided.

Abstract: Methods and compositions are provided for modulating, e.g., reducing, coding sequence expression in mammals. In the subject methods, an effective amount of an RNAi agent, e.g., an interfering ribonucleic acid (such as an siRNA or shRNA) or a transcription template thereof, e.g., a DNA encoding an shRNA, is administered to a non-embryonic mammal, e.g., via a hydrodynamic administration protocol. Also provided are RNAi agent pharmaceutical preparations for use in the subject methods. The subject methods and compositions find use in a variety of different applications, including academic and therapeutic applications.

Abstract: Methods and compositions are provided for modulating, e.g., reducing, coding sequence expression in mammals. In the subject methods, an effective amount of an RNAi agent, e.g., an interfering ribonucleic acid (such as an siRNA or shRNA) or a transcription template thereof, e.g., a DNA encoding an shRNA, is administered to a non-embryonic mammal, e.g., via a hydrodynamic administration protocol. Also provided are RNAi agent pharmaceutical preparations for use in the subject methods. The subject methods and compositions find use in a variety of different applications, including academic and therapeutic applications.