The cohesin release factor WAPL restricts chromatin loop extension.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA375736 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5266530.fastq.gz | Fastqsanger.gz | |||
| SRR5266570.fastq.gz | Fastqsanger.gz | |||
| SRR5266580.fastq.gz | Fastqsanger.gz | |||
| SRR5266590_1.fastq.gz | Fastqsanger.gz | |||
| SRR5266590_2.fastq.gz | Fastqsanger.gz |
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Project description:The spatial organization of chromosomes influences many nuclear processes including gene expression. The ring-shaped cohesin complex shapes the 3D genome by looping together convergent CTCF sites along chromosomes. We show here with high-resolution Hi-C analysis that chromatin loop size can be increased, and that cohesin’s DNA release factor WAPL restricts the degree of this extension. WAPL alsoincreased, and that cohesin’s DNA release factor WAPL restricts the degree of this extension. WAPL also prevents looping between incorrectly oriented CTCF sites. Through haploid genetics we find that WAPL deficiency bypasses the need for cohesin’s DNA loader SCC4 and we reveal that SCC4 promotes the extension of chromatin loops. We provide functional evidence in support of the model that chromatin loops are processively enlarged by the extrusion of DNA from cohesin rings. We conclude that the balanced activity of SCC4 and WAPL enables cohesin to correctly structure chromosomes to ensure proper transcriptional control.
2017-05-03 | GSE95521 | GEO
Project description:The spatial organization of chromosomes influences many nuclear processes including gene expression. The ring-shaped cohesin complex shapes the 3D genome by looping together convergent CTCF sites along chromosomes. We show here with high-resolution Hi-C analysis that chromatin loop size can be increased, and that cohesin’s DNA release factor WAPL restricts the degree of this extension. WAPL alsoincreased, and that cohesin’s DNA release factor WAPL restricts the degree of this extension. WAPL also prevents looping between incorrectly oriented CTCF sites. Through haploid genetics we find that WAPL deficiency bypasses the need for cohesin’s DNA loader SCC4 and we reveal that SCC4 promotes the extension of chromatin loops. We provide functional evidence in support of the model that chromatin loops are processively enlarged by the extrusion of DNA from cohesin rings. We conclude that the balanced activity of SCC4 and WAPL enables cohesin to correctly structure chromosomes to ensure proper transcriptional control.
2017-05-03 | GSE95520 | GEO
Project description:The spatial organization of chromosomes influences many nuclear processes including gene expression. The ring-shaped cohesin complex shapes the 3D genome by looping together convergent CTCF sites along chromosomes. We show here with high-resolution Hi-C analysis that chromatin loop size can be increased, and that cohesin’s DNA release factor WAPL restricts the degree of this extension. WAPL alsoincreased, and that cohesin’s DNA release factor WAPL restricts the degree of this extension. WAPL also prevents looping between incorrectly oriented CTCF sites. Through haploid genetics we find that WAPL deficiency bypasses the need for cohesin’s DNA loader SCC4 and we reveal that SCC4 promotes the extension of chromatin loops. We provide functional evidence in support of the model that chromatin loops are processively enlarged by the extrusion of DNA from cohesin rings. We conclude that the balanced activity of SCC4 and WAPL enables cohesin to correctly structure chromosomes to ensure proper transcriptional control.
2017-05-03 | GSE95518 | GEO
Project description:The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show here that chromatin loop size can be increased, and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin’s DNA release factor WAPL restricts the degree of this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.
2017-05-03 | GSE95014 | GEO
Project description:The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show here that chromatin loop size can be increased, and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin’s DNA release factor WAPL restricts the degree of this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.
2017-05-03 | GSE94993 | GEO
Project description:The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show here that chromatin loop size can be increased, and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin’s DNA release factor WAPL restricts the degree of this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.
2017-05-03 | GSE94992 | GEO
Project description:The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show here that chromatin loop size can be increased and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin's DNA release factor WAPL restricts this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.
| S-EPMC5422210 | biostudies-literature
Project description:Cohesin structures the genome through the formation of chromatin loops and by holding together the sister chromatids. The acetylation of cohesin’s SMC3 subunit is a dynamic process that involves the acetyltransferase ESCO1 and deacetylase HDAC8. Here we show that this cohesin acetylation cycle controls the 3D genome. ESCO1 restricts the length of chromatin loops and architectural stripes, while HDAC8 promotes the extension of such loops and stripes. This role in controlling loop length turns out to be distinct from the canonical role of cohesin acetylation that protects against WAPL-mediated DNA release. We reveal that acetylation rather controls cohesin’s interaction with PDS5A to restrict chromatin loop length. Our data supports a model in which this PDS5A-bound state acts as a brake that enables the pausing and restart of loop enlargement. The cohesin acetylation cycle hereby provides punctuation in the process of genome folding.
2022-03-14 | PXD032185 | Pride
Project description:Cohesin’s association with chromosomes is determined by loading dependent on the Scc2/4 complex and release due to Wapl. We show here that Scc2 also actively maintains cohesin on chromosomes during G1. It does so by blocking a Wapl-independent release reaction that requires opening the cohesin ring at its Smc3/Scc1 interface as well as the D loop of Smc1’s ATPase. The Wapl-independent release mechanism is switched off as cells activate Cdk1 and enter G2/M and cannot be turned back on without cohesin’s dissociation from chromosomes. The latter phenomenon enabled us to show that in the absence of release mechanisms, cohesin rings that have already captured DNA in a Scc2-dependent manner before replication no longer require Scc2 to capture sister DNAs during S phase.
2019-06-06 | GSE132221 | GEO
Project description:Cohesin is essential for genome folding and chromosome inheritance through cell divisions. In somatic cells, both of these functions are mediated by Scc1-cohesin, which in mitosis is released from chromosomes by Wapl and separase. In mammalian oocytes, cohesion is mediated by Rec8-cohesin. Scc1 is also expressed but neither required nor sufficient for cohesion, and its function in oocytes is unknown. Likewise, it is unknown whether Wapl regulates one or both cohesin complexes and chromosome segregation in mature oocytes. Using conditional mouse mutagenesis, we show that in meiosis I Wapl is required for proper chromosome segregation, predominantly releases Scc1-cohesin from chromosomes and promotes production of euploid eggs. Using single-nucleus Hi-C, we found that Scc1 is essential for chromatin loops and topologically associating domains (TADs) in oocytes. Increasing Scc1 residence time on chromosomes by Wapl depletion leads to vermicelli formation and intra-loop structures but, unlike in mitotic cells, does not increase loop size. This implies that loop size has reached a maximum in oocytes, possibly because it is limited by barriers such as cohesive cohesin. We conclude that distinct cohesin complexes generate loops and cohesion in mammalian oocytes and propose that the same principle applies to all cell types and species.
2020-03-04 | GSE132264 | GEO