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Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [RNA-seq]

ABSTRACT: Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [RNA-seq]

PROVIDER: PRJNA862702 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20665024_1.fastq.gz	Fastqsanger.gz
	SRR20665024_2.fastq.gz	Fastqsanger.gz
	SRR20665025_1.fastq.gz	Fastqsanger.gz
	SRR20665025_2.fastq.gz	Fastqsanger.gz
	SRR20665026_1.fastq.gz	Fastqsanger.gz

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Regulation of cohesin-mediated chromosome structure by PDS5 in mammals

Project description:Regulation of cohesin-mediated chromosome structure by PDS5 in mammals

| PRJNA862699 | ENA

Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [RNA-seq]

Project description:Cohesin regulates sister chromatids cohesion but also contributes to chromosome folding by promoting the formation of chromatin loops, a process proposed to be mediated by loop extrusion. PDS5 plays a crucial role in regulating the cohesin dynamic on chromatin, mainly through WAPL-mediated release activity and the opponent ESCO1/2-sororin dependent pathway. However, the exact function of PDS5 on cohesin-mediated chromatin looping remains ambiguous. Two versions of PDS5 exist in vertebrates, PDS5A and PDS5B. Here, we construct cells for rapid PDS5A or PDS5B degradation in PLC/PRF/5 cell line with the FKBP12F36V-dTAG degron system to perform loss of function studies. Combining Hi-C, ChIP-seq for cohesin regulators, and RNA-seq data, we describe the redundant and discrete roles of PDS5A and PDS5B in three-dimensional genome organization and gene expression.

2022-10-08 | GSE209848 | GEO

Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [Hi-C]

2022-10-08 | GSE209846 | GEO

Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [ChIP-seq]

2022-10-08 | GSE209845 | GEO

Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [ChIP-seq]

Project description:Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [ChIP-seq]

| PRJNA862700 | ENA

Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [Hi-C]

Project description:Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [Hi-C]

| PRJNA862701 | ENA

Regulation of cohesin-mediated chromosome structure by PDS5 in mammals

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

2022-10-08 | GSE209849 | GEO

Regulation of cohesin-mediated chromosome folding by PDS5 in mammals

Project description:Cohesin regulates sister chromatid cohesion but also contributes to chromosome folding by promoting the formation of chromatin loops, a process mediated by loop extrusion. Although PDS5 regulates cohesin dynamics on chromatin, the exact function of PDS5 in cohesin-mediated chromatin looping remains unclear. Two paralogs of PDS5 exist in vertebrates, PDS5A and PDS5B. Here we show that PDS5A and PDS5B co-localize with RAD21 and CTCF at loop anchors. Rapid PDS5A or PDS5B degradation in liver cancer cells using an inducible degron system reduces chromatin loops and increases loop size. RAD21 enrichment at loop anchors is decreased upon depletion of PDS5A or PDS5B. PDS5B loss also reduces CTCF signals at loop anchors and has a stronger effect on loop enlargement compared with PDS5A. Co-depletion of PDS5A and PDS5B reduces RAD21 levels at loop anchors although the amount of cohesin on chromatin is increased. Our study provides insight into how PDS5 proteins regulate cohesin-mediated chromatin looping.

| S-SCDT-EMBOR-2022-54853V1 | biostudies-other

Structure of the Cohesin Loader Scc2-Scc4 and its Binding to a Folded Cohesin

Project description:The functions of cohesin are central to genome integrity, chromosome organization, and transcription regulation through its prevention of premature sister-chromatid separation and the formation of DNA loops. The loading of cohesin onto chromatin depends on the Scc2-Scc4 complex, however, little is known about how it stimulates the cohesin loading activity. Here we determine the large “hook” structure of Scc2 responsible for catalyzing cohesin loading. We identify key Scc2 surfaces that are crucial for DNA binding and for cohesin loading in vivo. Using previously determined structures and modeling, we derive a pseudo-atomic structure of the full-length Scc2-Scc4 complex. Finally, our crosslinking and electron microscopy analyses reveal that Scc2-Scc4 utilizes its modular structure to make multiple contacts with a folded cohesin at an interface created by the cohesin head-hinge interaction.

2017-01-11 | PXD004692 | Pride

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

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