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A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [Hi-C]

ABSTRACT: Purpose: Chromatin architecture is an important regulator of gene expression, but details of how DNA loops form and function remain unclear. The purpose of this study is to assess the role of Widely Interspaced Zinc-fingers protein (WIZ) in gene regulation and DNA looping. Method: Genome wide chromatin looping patterns in the presence or absence of WIZ were assessed via Hi-C in both wildtype and CRISPR-Cas9 genome edited WIZ deletion mouse embryonic stem cells (mESCs).

ORGANISM(S): Mus musculus

PROVIDER: GSE137274 | GEO | 2020/04/14

REPOSITORIES: GEO

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A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [RNA-Seq]

Project description:Purpose: Chromatin architecture is an important regulator of gene expression, but details of how DNA loops form and function remain unclear. The purpose of this study is to assess the role of Widely Interspaced Zinc-fingers protein (WIZ) in gene regulation and DNA looping. Method: The role of WIZ in gene regulation was assessed by performing RNA-seq in both wildtype and CRISPR-Cas9 genome edited WIZ deletion mouse embryonic stem cells (mESCs).

2020-04-14 | GSE137271 | GEO

A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [ChIP-Seq]

Project description:Purpose: Chromatin architecture is an important regulator of gene expression, but details of how DNA loops form and function remain unclear. The purpose of this study is to assess the role of Widely Interspaced Zinc-fingers protein (WIZ) in gene regulation and DNA looping. Method: Genome wide binding patterns of known architectural proteins in the presence or absence of WIZ were assessed via chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) in both wildtype and CRISPR-Cas9 genome edited WIZ deletion mouse embryonic stem cells (mESCs).

2020-04-14 | GSE137272 | GEO

A WIZ/Cohesin/CTCF Complex Anchors DNA Loops to Define Gene Expression and Cell Identity.

Project description:Chromosome structure is a key regulator of gene expression. CTCF and cohesin play critical roles in structuring chromosomes by mediating physical interactions between distant genomic sites. The resulting DNA loops often contain genes and their cis-regulatory elements. Despite the importance of DNA loops in maintaining proper transcriptional regulation and cell identity, there is limited understanding of the molecular mechanisms that regulate their dynamics and function. We report a previously unrecognized role for WIZ (widely interspaced zinc finger-containing protein) in DNA loop architecture and regulation of gene expression. WIZ forms a complex with cohesin and CTCF that occupies enhancers, promoters, insulators, and anchors of DNA loops. Aberrant WIZ function alters cohesin occupancy and increases the number of DNA loop structures in the genome. WIZ is required for proper gene expression and transcriptional insulation. Our results uncover an unexpected role for WIZ in DNA loop architecture, transcriptional control, and maintenance of cell identity.

| S-EPMC7212317 | biostudies-literature

A role for Widely Interspaced Zinc finger (WIZ) in retention of the G9a methyltransferase on chromatin

Project description:G9a and GLP lysine methyltransferases form a heterodimeric complex that is responsible for the bulk of cellular mono- and di-methylation on histone H3 lysine 9 (H3K9me1/me2). Widely Interspaced Zinc finger (WIZ) associates with the G9a/GLP protein complex, but its role in lysine methylation is poorly defined. Here, we show that WIZ regulates global H3K9me2 levels through a mechanism that involves retention of G9a on chromatin. We also show that WIZ-mediated chromatin loss of G9a/GLP results in altered gene expression and protein-protein interactions that are distinguishable from that of using a molecule-induced enzymatic inhibitor towards G9a/GLP – thus providing evidence that the G9a/GLP/WIZ complex has unique functions when bound to chromatin that are independent of the H3K9me2 mark DMSO, UNC0638, NS, and siWIZ treatments to HEK293T cells, assessing G9a and H3K9me2 localization, each performed in duplicate, plus one input control for each cell condition. 30 samples total.

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A role for Widely Interspaced Zinc finger (WIZ) in retention of the G9a methyltransferase on chromatin

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A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity

Project description:A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity

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A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity

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

2020-04-14 | GSE137285 | GEO

Widely Interspaced Zinc Finger Motifs, Wiz, binds active promoters and CTCF-binding sites and is required for normal neural function in the mouse

Project description:Mice heterozygous for a null mutation in Widely-interspaced zinc finger, Wiz, were produced in a screen for modifiers of epigenetic reprogramming; expression of the GFP reporter transgene decreased in mutants, suggesting a role in transcriptional activation (Daxinger et al., 2013). These mice are viable and fertile, with no overt abnormalities and homozygosity for the mutation is embryonic lethal (Daxinger et al, 2013). Wiz is expressed at high levels in the brain, both in the embryo and in the adult, but there have been no reports of its role in neural tissue. To address this, ChIP-seq, using an anti-Wiz antibody, was carried out in adult cerebellum. Wiz peaks were found at tens of thousands of sites across the genome, many of which are gene promoters that show enrichment for the pioneer transcription factor CTCF. RNA-seq, using WizMommeD30/+ and Wiz+/+ mice, revealed that some genes were affected by haploinsufficiency of Wiz; ~30 in the brains of mid-gestation embryos and ~80 in adult cerebellum. Most genes that were deregulated in embryonic brain of heterozygous mutants decreased in expression and include a group of clustered protocadherin genes that were also down-regulated in adult cerebellum. The enhancer of this gene cluster has a strong Wiz peak in the ChIP-seq data and has been reported, by others, to be activated by CTCF in neurons.

2016-07-14 | GSE76909 | GEO

A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [RNA-Seq]

Project description:A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [RNA-Seq]

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A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [ChIP-Seq]

Project description:A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [ChIP-Seq]

| PRJNA565019 | ENA