Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE178982 | GEO | 2021/07/15
REPOSITORIES: GEO
Similar Datasets
Project description:Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1
| PRJNA741789 | ENA
Project description:We analysed the effect on the genomic localisation of cohesin (Stag1 and Scc1) and CTCF in CTCF, Smc3 and Wapl single depleted as well as CTCF Wapl double depleted mouse embryonic fibroblasts. Furthermore, we addressed the effect of CTCF and Smc3 depletion on gene expression as measured by RNA-Seq and the transcriptional activity in CTCF and Wapl double depleted cells by GRO-Seq.
2017-04-11 | GSE76303 | 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 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: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
Project description:Mammalian genomes contain several billion base pairs of DNA which are packaged in chromatin fibers. At selected gene loci, cohesin complexes have been proposed to arrange chromatin fibers into higher-order structures, but it is poorly understood how cohesin performs this task, how important this function is for determining the structure of chromosomes, and how this process is regulated to allow changes in gene expression. Here we show that the cohesin release factor Wapl controls chromatin structure and gene regulation at numerous loci throughout the mouse genome. Conditional deletion of the Wapl gene leads to stable accumulation of cohesin on chromatin, chromatin compaction, altered gene expression, cell cycle delay, chromosome segregation defects and embryonic lethality. In Wapl deficient chromosomes, cohesin accumulates in an axial domain, similar to how condensins form a M-bM-^@M-^\scaffoldM-bM-^@M-^] in mitotic chromosomes. We propose that Wapl controls chromatin structure and gene regulation by determining the residence time with which cohesin binds to DNA. 4 biological replicates for each genotype (Wapl +/F; Wapl -/F) treated with/without 4-OHT =16 samples
2013-08-09 | E-GEOD-41460 | biostudies-arrayexpress
Project description:Mammalian genomes contain several billion base pairs of DNA which are packaged in chromatin fibers. At selected gene loci, cohesin complexes have been proposed to arrange chromatin fibers into higher-order structures, but it is poorly understood how cohesin performs this task, how important this function is for determining the structure of chromosomes, and how this process is regulated to allow changes in gene expression. Here we show that the cohesin release factor Wapl controls chromatin structure and gene regulation at numerous loci throughout the mouse genome. Conditional deletion of the Wapl gene leads to stable accumulation of cohesin on chromatin, chromatin compaction, altered gene expression, cell cycle delay, chromosome segregation defects and embryonic lethality. In Wapl deficient chromosomes, cohesin accumulates in an axial domain, similar to how condensins form a “scaffold” in mitotic chromosomes. We propose that Wapl controls chromatin structure and gene regulation by determining the residence time with which cohesin binds to DNA. ChIP-Seq using two different antibodies (CTCF, Smc3); one (CTCF) and two (Smc3) replicates; two different genotypes (Wapl +/delta, Wapl -/delta). The control sample is a single-replicate INPUT for each genotype.
2013-08-09 | E-GEOD-41602 | biostudies-arrayexpress
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
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