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Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [Cut&Tag]

ABSTRACT: Here, we describe CRISPRpath, a CRISPR screening strategy for simultaneously characterizing CREs in multiple genomic loci by leveraging converging phenotypes resulted from transcriptional defects in genes linked to the same biological pathway.

ORGANISM(S): Homo sapiens

PROVIDER: GSE166836 | GEO | 2021/08/10

REPOSITORIES: GEO

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Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [ChIP-seq]

Project description:Here, we describe CRISPRpath, a CRISPR screening strategy for simultaneously characterizing CREs in multiple genomic loci by leveraging converging phenotypes resulted from transcriptional defects in genes linked to the same biological pathway.

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Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [ATAC-seq]

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Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath.

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Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [Cut&Tag]

Project description:Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [Cut&Tag]

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Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-08-10 | GSE166839 | GEO

Massively parallel cis-regulatory analysis in the mammalian central nervous system

Project description:Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of candidate CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery of candidate CREs to target organs in vivo. As a proof-of-concept, we introduce a capture library of ~46,000 constructs, corresponding to ~3,500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as non-human primates and human stem cell-derived organoids.

2015-10-15 | GSE68247 | GEO

H4K16ac activates retrotransposons and contributes to their cis regulatory function [CUT&TAG]

Project description:Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition, however, they have evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Here we show that the male-specific lethal (MSL) complex-mediated acetylation of histone H4 lysine 16 (H4K16ac) regulates the transcription of TEs. Furthermore, H4K16ac marked TEs function as a rich source of cis regulatory elements in the human genome, wherein H4K16ac acts by maintaining the permissive chromatin structure and promoting the transcription of these TEs.

2023-04-13 | GSE200768 | GEO

Multi-omic Analysis of Developing Human Retina and Organoids Reveals Cell-Specific Cis-Regulatory Elements and Mechanisms of Non-Coding Genetic Disease Risk.

Project description:Cis-regulatory elements (CREs) play a critical role in the development, maintenance, and disease-states of all human cell types. In the human retina, CREs have been implicated in a variety of inherited retinal disorders. To characterize cell-class-specific CREs in the human retina and elucidate their potential functions in development and disease, we performed single-nucleus (sn)ATAC-seq and snRNA-seq on the developing and adult human retina and on human retinal organoids. These analyses allowed us to identify cell-class-specific CREs, enriched transcription factor binding motifs, putative target genes, and to examine how these features change over development. By comparing DNA accessibility between the human retina and retinal organoids we found that CREs in organoids are highly correlated at the single-cell level, validating the use of organoids as a model for studying disease-associated CREs. As a proof of concept, we studied the function of a disease-associated CRE at 5q14.3 in organoids, identifying its principal target gene as the miR-9-2 primary transcript and demonstrating a dual role for this CRE in regulating neurogenesis and gene regulatory programs in mature glia. This study provides a rich resource for characterizing cell-class-specific CREs in the human retina and showcases retinal organoids as a model in which to study the function of retinal CREs that influence retinal development and disease.

2021-11-16 | GSE183684 | GEO

CRISPRi screen of prostate cancer associated risk cis-regulatory elements [CRISPRi]

Project description:Prostate cancer (PCa) associated risk SNPs are enriched in cis-regulatory elements (CREs). In this study, we screened 260 CREs that contain at least one PCa risk SNP for essentiality in V16A, 22Rv1 and A549 cells. We tiled the CREs and 14 control regions using 5,873 sgRNAs.

2020-12-16 | GSE142808 | GEO

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