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Modulation of CTCF barrier permeability by ZFP661 enhances protocadherin diversity for proper cortical dendritic projection in mammals

ABSTRACT: Modulation of CTCF barrier permeability by ZFP661 enhances protocadherin diversity for proper cortical dendritic projection in mammals

PROVIDER: PRJNA968170 | 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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High-resolution Hi-C maps in EV and ZFP661-3HA OE mESCs

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.

2023-05-09 | GSE231867 | GEO

Modulation of CTCF barrier permeability by ZFP661 enhances protocadherin diversity for proper cortical dendritic projection in mammals

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

2023-05-09 | GSE231869 | GEO

Hi-C and Capture Hi-C maps in WT and Zfp661 knockout mESCs

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.

2024-02-24 | GSE256450 | GEO

Capture Hi-C in (EV and ZFP661-3HA OE) mESCs and E16.5 mouse forebrains

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.

2023-05-09 | GSE231864 | GEO

Single-cell 5’ RNA-seq profiles of E16.5 forebrains in WT and Zfp661 knockout mice

Project description:In this assay, we aimed to investigate the impact of ZFP661 on the expression diversity of clustered protocadherin genes (Pcdhs). To accomplish this, we conducted single-cell 5’ RNA-seq analysis on developing mouse forebrains at embryonic day 16.5 (E16.5). Our findings reveal that ZFP661 enhances the expression diversity of Pcdhs by balancing the usage of Pcdh isoforms.

2023-05-09 | GSE231868 | GEO

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

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.

2023-05-09 | GSE231865 | GEO

CTCF barrier breaking by ZFP661 promotes protocadherin diversity in mammalian brains.

Project description:Mammalian brains are larger and more densely packed with neurons than reptiles, but the genetic mechanisms underlying the increased connection complexity amongst neurons are unclear. The expression diversity of clustered protocadherins (Pcdhs), which is controlled by CTCF and cohesin, is crucial for proper dendritic arborization and cortical connectivity in vertebrates. Here, we identify a highly-conserved and mammalian-restricted protein, ZFP661, that binds antagonistically at CTCF barriers at the Pcdh locus, preventing CTCF from trapping cohesin. ZFP661 balances the usage of Pcdh isoforms and increases Pcdh expression diversity. Loss of Zfp661 causes cortical dendritic arborization defects and autism-like social deficits in mice. Our study reveals both a novel mechanism that regulates the trapping of cohesin by CTCF and a mammalian adaptation that promoted Pcdh expression diversity to accompany the expanded mammalian brain.

| S-EPMC11343191 | biostudies-literature

ChIP-seq data in WT and Zfp661 knockout E16.5 mouse forebrains

Project description:In this assay, we aimed to investigate the occupancy of ZFP661 and CTCF at the clustered Pcdh locus during mouse brain development.

2024-02-24 | GSE256449 | GEO

Elucidation of molecular functions of the protocadherin CDHR5 in intestinal epithelial cells

Project description:Intestinal epithelial cells are covered by the brush border, which consists of densely packed microvilli. The Intermicrovillar Adhesion Complex (IMAC) connects the microvilli and is required for proper organization of the brush border. The protocadherin CDHR5 is an important member of the IMAC, but it is unclear whether CDHR5 has mainly structural functions or is also involved in cellular signaling. This issue was resolved with a CDHR5 knockout mouse model. Intestinal epithelial cells were isolated from the small intestine of four wild-type and four CDHR5 knockout mice. Bulk RNA sequencing was performed to provide insight into the functions of CDHR5 in cellular signaling and gene regulation.

2023-04-13 | E-MTAB-12525 | biostudies-arrayexpress

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