Abstract: The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

Abstract: The present invention concerns a genetic tool comprising at least two distinct nucleic acids optimized to facilitate the transformation and modification by homologous recombination of a bacterium of the genus Clostridium, typically a solventogenic bacterium.

Abstract: Provided are: a composition for DNA double-strand breaks (DSBs), comprising (1) a cytosine deaminase and an inactivated target-specific endonuclease, (2) a guide RNA, and (3) a uracil-specific excision reagent (USER); a method for producing DNA double-strand breaks by means of a cytosine deaminase using the composition; a method for analyzing a DNA nucleic acid sequence to which base editing has been introduced by means of a cytosine deaminase; and a method for identifying (or measuring or detecting) base editing, base editing efficiency at an on-target site, an off-target site, and/or target specificity by means of a cytosine deaminase.

Abstract: A proximity dependent split T7 RNAP (RNA polymerase) sensor using continuous molecular evolution is described. The versatility of the platform is described by creating robust light and small molecule-responsive genetic sensors. The activity-responsive RNAP platform dramatically simplifies and expands genetic circuit creation, and opens new opportunities in protein engineering, synthetic biology, and bioengineering.

Abstract: A guide RNA comprising: a gRNA spacer sequence at the 5? end of the guide RNA, wherein the spacer sequence is complementary to a target gene, a scaffold sequence that binds to Cas9, and an RNA capture and sequencing domain comprising: a barcode sequence, and a primer binding sequence; nucleic acids and vectors encoding the guide RNA; cells expressing the guide RNA; and a library comprising a plurality of guide RNAs. Also disclosed are methods of introducing a genetic perturbation into a cell, methods of assessing an effect of at least one genetic perturbation on RNA expression in a cell, methods of identifying nucleic acid sequences associated with a disease state and a method of identifying candidate therapeutic agents.

Abstract: Provided is a method of modifying a target site in the genome of a eukaryotic cell, the method comprising: (1) a step of introducing into the cell, introduction nucleic acids comprising (a) a template nucleic acid comprising a nucleic acid sequence encoding an RNA-guided nuclease, (b) a template nucleic acid comprising a nucleic acid sequence encoding a guide RNA, or a guide RNA, and (c) a template nucleic acid comprising a nucleic acid sequence encoding a selectable marker; and (2) a step of selecting a cell expressing the selectable marker, wherein the number of moles (C) of (c) the template nucleic acid comprising a nucleic acid sequence encoding a selectable marker, subjected to the step (1), is smaller than any of the number of moles (A) of (a) the template nucleic acid comprising a nucleic acid sequence encoding an RNA-guided nuclease and the number of moles (B) of (b) the template nucleic acid comprising a nucleic acid sequence encoding a guide RNA, or the guide RNA.

Abstract: The present disclosure provides compositions and methods for the treatment of PPARG activated cancer. For example, the present disclosure provides PPARG signaling modulators for the treatment of bladder cancer. In particular, therapeutic and/or prophylactic compositions and uses of PPARG inverse-agonists are described.

Abstract: A native Type I-B and heterologous Type II Clustered Regularly-Interspaced Short Palindromic Repeat/cas systems were developed and characterize to improve the ability to engineer C. thermocellum and other thermophilic microbes. The native Type I-B system was engineered for genome editing. For the Type I-B system, an engineered strain, termed LL1586, yielded 40% genome editing efficiency at the pyrF locus. When recombineering machinery was expressed the efficiency was increased to 71%. For the Type II GeoCas9 system, 12.5% genome editing efficiency was observed. When recombineering machinery was expressed, this increased to 94%. By combining the thermophilic CRISPR system (either Type I-B or Type II) with the recombinases, a new tool was developed that allows for efficient CRISPR editing. The tools provided herein enable CRISPR technologies to better engineer C. thermocellum, including engineering C. thermocellum for both increased lignocellulose degradation and biofuel production.

Abstract: Programmable guide RNAs (gRNAs) play a central role in the CRISPR revolution sweeping biology and medicine by directing the function of a Cas protein effector to a target gene of choice. To achieve programmable control over regulatory scope, the activity of a conditional guide RNA (cgRNA) depends on the presence or absence of an RNA trigger, allowing for cell-selective regulation of CRISPR/Cas function. Unlike a standard gRNA, a cgRNA is programmable at multiple levels, with the target-binding sequence controlling the target of Cas activity (edit, silence, induce, or bind a gene of choice) and the trigger binding sequence controlling the scope of Cas activity. cgRNA mechanisms that are allosteric allow for independent design of the target and trigger sequences, providing the flexibility to select the regulatory target and scope independently.

Abstract: Disclosed herein are genome editing systems and related methods which allow for the detection and quantitative measurement of all possible on-target gene editing outcomes, including targeted integration. The compositions and methods described herein rely on the use of donor templates comprising a 5? homology arm, a cargo, a one or more priming sites, a 3? homology arm, and optionally stuffer sequence.

Abstract: A method of selecting an agent for treating a disease of a subject is disclosed which includes identifying genes which bring about resistance to a cytotoxic agent in haploid human embryonic stem (ES) cells. Once the gene is identified, the method includes analyzing the sequence and/or expression of the gene in a cell sample of the subject, wherein an alteration in the sequence and/or level of expression of the gene as compared to the sequence and/or expression of the gene in a control sample is indicative that the agent should be ruled out as a monotherapy for treating the disease in the subject.

Abstract: The present disclosure generally relates to genome editing systems and methods and compounds and compositions for use in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) genome editing systems. Disclosed herein are modified nucleic acids that modulate the activity of genome editing.

Abstract: The present invention relates to a polypeptide comprising at least one at least one deletion selected from the group consisting of ?HNH (?775-909), ARuvCIII-b (?1002-1074), AREC1-a (?510-655), AREC1-b (?525-587), AREC1-c (?662-710), AREC2 (?180-308), AREC2-a (?212-244), AREC2-b (?244-276), AREC2-c (?276-308), AREC2-d (?199-283), AREC2-e (?198-257), AREC2-f (?235-286), AREC2-g (?217-266), AREC3 (?498-712) and combinations thereof, wherein the position numbering is in accordance with SEQ ID NO: 1 encoding for S. pyogenes Cas9, and wherein the polypeptide has CRISPR-Cas DNA-binding activity. The polypeptide may further comprises a missense mutations selected from G12R, T13K, T13R, N14K, N497K, T657K, T657R, N767K, T770K, T770R, Q920K, Q920R, S1109R, D1135K, D1135R, S1338R and combinations thereof. Also claimed are nucleic acid molecules encoding for said polypeptides, compositions and method of site-directed engineering of a target DNA thereof.

Abstract: Provided herein are gene-editing methods and compositions for improving the efficiency of deleting segments of DNA from cells, cells that are genetically modified using the disclosed methods and compositions, and methods of treatment using the genetically modified cells.

Abstract: The present invention refers to methods for selectively recognizing a base pair in a DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polypeptide and to uses of the polypeptide and DNA in specific DNA targeting as well as to methods of modulating expression of target genes in a cell.

Abstract: The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

Abstract: A CRISPR-Cas3 system was successfully established in a eukaryotic cell.

Abstract: The present invention relates to compositions and methods for increasing the rate of site specific insertion of a donor DNA sequence to the genome. More specifically, the method introduces a donor DNA template containing at least one transcription factor binding site to a cell in order to favor specific insertion of a donor template sequence at a target site by homology directed repair (HDR).

Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.

Abstract: The present invention provides inter alia methods for generating a library of cells producing polyketides and selecting for these strains based on binding to a protein target.