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ChIP-seq data in mESCs show ZFP661 suppresses cohesin binding at CTCF barriers

ABSTRACT: ChIP-seq data in mESCs show ZFP661 suppresses cohesin binding at CTCF barriers

PROVIDER: PRJNA968171 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24461809_1.fastq.gz	Fastqsanger.gz
	SRR24461809_2.fastq.gz	Fastqsanger.gz
	SRR24461810_1.fastq.gz	Fastqsanger.gz
	SRR24461810_2.fastq.gz	Fastqsanger.gz
	SRR24461811_1.fastq.gz	Fastqsanger.gz

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ChIP-seq data in mESCs show ZFP661 suppresses cohesin binding at CTCF barriers

Project description:In this assay, we aimed to investigate the occupancy of ZFP661 in the mouse genome and its possible role in regulating the occupancies of CTCF and cohesin, which are two key factors in establishing 3D chromatin structures. To achieve this, we performed ChIP-seq in ZFP661-3HA endogenously tagged mESCs (for ZFP661), Zfp661 knockout (KO) mESCs (for CTCF and RAD21), and ZFP661-3HA overexpressing (OE) mESCs (for ZFP661, CTCF, RAD21, KAP1, and H3K9me3). Our results reveal that 1) ZFP661 binding peaks were co-occupied with those of CTCF; 2) ZFP661 binds exclusively inside the CTCF loop anchors; and 3) ZFP661 can suppress cohesin binding at CTCF barriers without altering CTCF binding.

2023-05-09 | GSE231866 | GEO

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Project description:In this assay, we aimed to investigate the impacts of ZFP661 on the permeability of CTCF barriers to chromatin interactions. To achieve this, we generated high-resolution Hi-C maps using empty vector (EV) control and ZFP661-3HA overexpressing (OE) mESCs. Our findings demonstrate that ZFP661 suppresses the trapping of cohesin at the CTCF barriers and modulates their permeability.

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Project description:In this assay, we aimed to investigate the impacts of ZFP661 on the permeability of CTCF barriers to chromatin interactions. To achieve this, we generated high-resolution Hi-C maps using WT and Zfp661 knockout (KO) mESCs. Our findings demonstrate that ZFP661 suppresses the trapping of cohesin at the CTCF barriers and modulates their permeability.

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Project description:This assay aimed to investigate the regulatory role of ZFP661 in modulating the permeability of CTCF barriers. To achieve this, we generated Capture Hi-C maps on several regions bound by ZFP661 using E16.5 forebrains from wild-type (WT) and Zfp661 knockout (KO) mice, as well as empty vector (EV) control and ZFP661-3HA overexpressing (OE) mESCs. Our findings reveal that ZFP661 modulates the permeability of CTCF barriers, thereby balancing between the interactions that are trapped at the barriers and those passing over them.

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ChIP-reChIP-seq data in mESCs show ZFP661 co-binds target regions with CTCF

Project description:In this assay, we aimed to investigate whether ZFP661 co-binds target regions with CTCF. To achieve this, we performed ChIP-reChIP-seq in ZFP661-3HA overexpressing (OE) mESCs, where the 1st ChIP utilized anti-HA antibody, and the 2nd ChIP involved the use of anti-IgG and anti-CTCF antibodies, respectively. Our results demonstrate that ZFP661 co-binds target regions with CTCF.

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Project description:ChIP-reChIP-seq data in mESCs show ZFP661 co-binds target regions with CTCF

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Project description:Eukaryotic genomes are compacted into loops and topologically associating domains (TADs), which contribute to transcription, recombination and genomic stability. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C of mouse zygotes revealed that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, suggesting loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, where MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned, partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Remarkably, chimaeric yeast MCMs harbouring a cohesin-interaction motif from human MCM3 induce cohesin pausing, suggesting that MCMs are “active” barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. Based on in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the 3D genome.

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