Abstract: The present disclosure, at least in part, relates to compositions (e.g., engineered nucleic acids and engineered proteins) and methods for increasing gene expression. The engineered proteins include RNA-binding proteins (e.g., RNA-binding proteins that comprise a Interleukin Enhancer Binding Factor 3 (ILF3) sequence, a Cas sequence, or a combination thereof). In some aspects, the disclosure provides methods of identifying engineered nucleic acids that are shorter in length than a gene of interest to induce expression of the gene of interest and also provides RNA-binding proteins for inducing gene expression.

Abstract: The disclosure provides, in various embodiments, fusion proteins comprising a DNA-binding domain, a DNMT3A-binding domain, and a H3K4me0; and polynucleotides and vectors encoding one or more of the fusion proteins. The disclosure also provides, in various embodiments, gene-delivery systems, cells, compositions (e.g., pharmaceutical compositions) and kits comprising one or more of the fusion proteins polynucleotides, or vectors; methods of epigenetically modifying a genomic locus in a cell; and methods of treating a subject (e.g., a human) in need thereof.

Abstract: The disclosure provides, in various embodiments, fusion proteins comprising a DNA-binding domain, a DNMT3A-binding domain, and a H3K4me0; and polynucleotides and vectors encoding one or more of the fusion proteins. The disclosure also provides, in various embodiments, gene-delivery systems, cells, compositions (e.g., pharmaceutical compositions) and kits comprising one or more of the fusion proteins polynucleotides, or vectors; methods of epigenetically modifying a genomic locus in a cell; and methods of treating a subject (e.g., a human) in need thereof.

Abstract: The disclosure provides, in various embodiments, fusion proteins comprising a DNA-binding domain, a DNMT3A-binding domain, and a H3K4me0; and polynucleotides and vectors encoding one or more of the fusion proteins. The disclosure also provides, in various embodiments, gene-delivery systems, cells, compositions (e.g., pharmaceutical compositions) and kits comprising one or more of the fusion proteins polynucleotides, or vectors; methods of epigenetically modifying a genomic locus in a cell; and methods of treating a subject (e.g., a human) in need thereof.

Abstract: The disclosure provides, in various embodiments, fusion proteins comprising a DNA-binding domain, a DNMT3A-binding domain, and a H3K4me0; and polynucleotides and vectors encoding one or more of the fusion proteins. The disclosure also provides, in various embodiments, gene-delivery systems, cells, compositions (e.g., pharmaceutical compositions) and kits comprising one or more of the fusion proteins polynucleotides, or vectors; methods of epigenetically modifying a genomic locus in a cell; and methods of treating a subject (e.g., a human) in need thereof.

Abstract: Provided herein are, inter alia, fusion proteins, compositions and methods for manipulation of genomes of living organisms.

Abstract: The disclosure provides, in various embodiments, fusion proteins comprising a DNA-binding domain, a DNMT3A-binding domain, and a H3K4me0; and polynucleotides and vectors encoding one or more of the fusion proteins. The disclosure also provides, in various embodiments, gene-delivery systems, cells, compositions (e.g., pharmaceutical compositions) and kits comprising one or more of the fusion proteins polynucleotides, or vectors; methods of epigenetically modifying a genomic locus in a cell; and methods of treating a subject (e.g., a human) in need thereof.

Abstract: Provided herein are, inter alia, compositions and methods for modulating gene expression.

Abstract: Provided herein are, inter alia, compositions and methods for manipulation of genomes of living organisms.

Abstract: Provided herein are, inter alia, compositions and methods for manipulation of genomes of living organisms.

Abstract: Provided herein are, inter alia, compositions and methods for manipulation of genomes of living organisms.

Abstract: The present disclosure provides methods and compositions for precisely controlling the expression levels of mammalian genes using CRISPRi or CRISPRa and one or more modified sgRNAs. The methods and compositions are useful for, inter alia, titrating the expression of a gene of interest, identifying drug targets and mechanisms of drug resistance, and enabling the analysis of and control over metabolic and signaling pathway fluxes.

Abstract: The present invention provides tools and methods for the systematic analysis of genetic interactions, including higher order interactions. The present invention provides tools and methods for combinatorial probing of cellular circuits, for dissecting cellular circuitry, for delineating molecular pathways, and/or for identifying relevant targets for therapeutics development.

Abstract: Provided herein are, inter alia, compositions and methods for manipulation of genomes of living organisms.

Abstract: Provided herein are methods directed to multiplexed detection of the modulation of transcriptional activity using perturbation elements.

Abstract: Provided herein are compositions and methods for CRISPR-based screening.

Abstract: The present invention provides tools and methods for the systematic analysis of genetic interactions, including higher order interactions. The present invention provides tools and methods for combinatorial probing of cellular circuits, for dissecting cellular circuitry, for delineating molecular pathways, and/or for identifying relevant targets for therapeutics development.

Abstract: The present invention provides methods for conducting screens using nucleic acid elements (e.g., interfering RNAs) to confidently identify hit genetic elements. The present invention further comprises constructing vectors that contain two or more nucleic acid elements to knock down all pairwise combinations of the hit genetic elements identified from the screen. Following quantitation of the single and double-knockdown phenotypes, genetic interactions between all gene pairs can be calculated. Genes can then be clustered according to the similarity of the pattern of their interactions with all of the other genes to obtain a genetic interaction map, which can advantageously be used to predict functional associations between genes and identify drug targets for therapy such as combination cancer therapy.

Abstract: Methods are provided for, inter alia, detecting nucleic acid molecules resistant to degradation, such as a plurality of RNA molecules bound to a ribosome, using various technologies including deep sequencing.

Abstract: Provided herein are methods directed to multiplexed detection of the modulation of transcriptional activity using perturbation elements.