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A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [RNA-Seq]

ABSTRACT: A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [RNA-Seq]

PROVIDER: PRJNA565018 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10099877_1.fastq.gz	Fastqsanger.gz
	SRR10099877_2.fastq.gz	Fastqsanger.gz
	SRR10099878_1.fastq.gz	Fastqsanger.gz
	SRR10099878_2.fastq.gz	Fastqsanger.gz
	SRR10099879_1.fastq.gz	Fastqsanger.gz

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A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity

Project description:A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity

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A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [ChIP-Seq]

Project description:A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [ChIP-Seq]

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A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [Hi-C]

Project description:A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [Hi-C]

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A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [RNA-Seq]

Project description:Purpose: Chromatin architecture is an important regulator of gene expression, but details of how DNA loops form and function remain unclear. The purpose of this study is to assess the role of Widely Interspaced Zinc-fingers protein (WIZ) in gene regulation and DNA looping. Method: The role of WIZ in gene regulation was assessed by performing RNA-seq in both wildtype and CRISPR-Cas9 genome edited WIZ deletion mouse embryonic stem cells (mESCs).

2020-04-14 | GSE137271 | GEO

A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [Hi-C]

Project description:Purpose: Chromatin architecture is an important regulator of gene expression, but details of how DNA loops form and function remain unclear. The purpose of this study is to assess the role of Widely Interspaced Zinc-fingers protein (WIZ) in gene regulation and DNA looping. Method: Genome wide chromatin looping patterns in the presence or absence of WIZ were assessed via Hi-C in both wildtype and CRISPR-Cas9 genome edited WIZ deletion mouse embryonic stem cells (mESCs).

2020-04-14 | GSE137274 | GEO

A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [ChIP-Seq]

Project description:Purpose: Chromatin architecture is an important regulator of gene expression, but details of how DNA loops form and function remain unclear. The purpose of this study is to assess the role of Widely Interspaced Zinc-fingers protein (WIZ) in gene regulation and DNA looping. Method: Genome wide binding patterns of known architectural proteins in the presence or absence of WIZ were assessed via chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) in both wildtype and CRISPR-Cas9 genome edited WIZ deletion mouse embryonic stem cells (mESCs).

2020-04-14 | GSE137272 | GEO

Eco1-dependent cohesin acetylation anchors chromatin loops and cohesion to define functional meiotic chromosome domains

Project description:Eco1-dependent cohesin acetylation anchors chromatin loops and cohesion to define functional meiotic chromosome domains

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A WIZ/Cohesin/CTCF Complex Anchors DNA Loops to Define Gene Expression and Cell Identity.

Project description:Chromosome structure is a key regulator of gene expression. CTCF and cohesin play critical roles in structuring chromosomes by mediating physical interactions between distant genomic sites. The resulting DNA loops often contain genes and their cis-regulatory elements. Despite the importance of DNA loops in maintaining proper transcriptional regulation and cell identity, there is limited understanding of the molecular mechanisms that regulate their dynamics and function. We report a previously unrecognized role for WIZ (widely interspaced zinc finger-containing protein) in DNA loop architecture and regulation of gene expression. WIZ forms a complex with cohesin and CTCF that occupies enhancers, promoters, insulators, and anchors of DNA loops. Aberrant WIZ function alters cohesin occupancy and increases the number of DNA loop structures in the genome. WIZ is required for proper gene expression and transcriptional insulation. Our results uncover an unexpected role for WIZ in DNA loop architecture, transcriptional control, and maintenance of cell identity.

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Computational prediction of CTCF/cohesin-based intra-TAD (sbTAD) loops that insulate chromatin contacts and gene expression in mouse liver

Project description:This SuperSeries is composed of the SubSeries listed below, and presents the high throuput sequencing datasets that were generated as part of a larger study that investigates the role of CTCF and cohesin as key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. This study presents and validates a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues. The intra-TAD loops are proposed to be formed by the same loop extrusion mechanism as the larger TAD loops; their shorter length enables finer regulatory control in restricting enhancer-promoter interactions, which enables selective, high-level expression of gene targets of super-enhancers and genes located within repressive nuclear compartments. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization associated with widespread insulation of distal enhancer activity.

2018-05-11 | GSE102999 | GEO

The structural basis for cohesin/CTCF anchored loops [RNA-seq]

Project description:Cohesin catalyses the folding of the genome into loops that are anchored by CTCF. The molecular mechanism of how cohesin and CTCF structure the 3D genome has remained unclear. Here we show that a segment within the CTCF N terminus interacts with the SA2-SCC1 subunits of cohesin. A 2.6 Å crystal structure of SA2-SCC1 in complex with CTCF reveals the molecular basis of the interaction. We demonstrate that this interaction is specifically required for CTCF-anchored loops and contributes to the positioning of cohesin at CTCF-binding sites. A similar motif is present in a number of established and novel cohesin ligands, including the cohesin release factor WAPL. Our data suggest that CTCF enables chromatin loop formation by protecting cohesin against loop release. These results provide fundamental insights into the molecular mechanism that enables dynamic regulation of chromatin folding by cohesin and CTCF.

2020-01-07 | GSE126635 | GEO

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