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

ABSTRACT: The structural basis for cohesin/CTCF anchored loops [ChIP-seq]

PROVIDER: PRJNA522780 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10043141.fastq.gz	Fastqsanger.gz
	SRR10043142.fastq.gz	Fastqsanger.gz
	SRR10043143.fastq.gz	Fastqsanger.gz
	SRR10043144.fastq.gz	Fastqsanger.gz
	SRR10043145.fastq.gz	Fastqsanger.gz

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The structural basis for cohesin/CTCF anchored loops [ChIP-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 | GSE126634 | GEO

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

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The structural basis for cohesin/CTCF anchored loops

Project description:The structural basis for cohesin/CTCF anchored loops

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The structural basis for cohesin/CTCF anchored loops [Hi-C]

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

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The structural basis for cohesin-CTCF-anchored loops.

Project description:Cohesin catalyses the folding of the genome into loops that are anchored by CTCF1. 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 human cohesin. We report a crystal structure of SA2-SCC1 in complex with CTCF at a resolution of 2.7 Å, which 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 newly identified cohesin ligands, including the cohesin release factor WAPL2,3. Our data suggest that CTCF enables the formation of chromatin loops by protecting cohesin against loop release. These results provide fundamental insights into the molecular mechanism that enables the dynamic regulation of chromatin folding by cohesin and CTCF.

| S-EPMC7035113 | biostudies-literature

The structural basis for cohesin/CTCF anchored loops

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

2020-01-06 | GSE126637 | GEO

Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL and PDS5 proteins

Project description:Mammalian genomes are organized into compartments, topologically-associating domains (TADs) and loops to facilitate gene regulation and other chromosomal functions. Compartments are formed by nucleosomal interactions, but how TADs and loops are generated is unknown. It has been proposed that cohesin forms these structures by extruding loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here we show that cohesin suppresses compartments but is essential for TADs and loops, that CTCF defines their boundaries, and that WAPL and its PDS5 binding partners control the length of chromatin loops. In the absence of WAPL and PDS5 proteins, cohesin passes CTCF sites with increased frequency, forms extended chromatin loops, accumulates in axial chromosomal positions (vermicelli) and condenses chromosomes to an extent normally only seen in mitosis. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.

2017-12-07 | GSE102884 | GEO

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin-STAG1 from WAPL

Project description:The human genome folds to create thousands of loops connecting sites that are bound by the insulator protein CTCF and the ring-shaped cohesin complex. It is thought that most of these loops emerge through a process whereby cohesin extrudes chromatin, forming an initially small loop that grows larger and larger until the loop’s expansion is arrested by CTCF. Cohesin rings comprise four proteins: SMC1, SMC3, SCC1, and, in higher eukaryotes, either STAG1 or STAG2. We explore differential roles of especially STAG1, STAG2 and ESCO1 proteins in chromatin organization.

2020-02-27 | GSE138405 | GEO

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