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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]

ABSTRACT: The aim of the project was to investigate the effect of nuclear receptor activation, particularly of the vitamin D receptor, on CTCF-defined 3D chromatin structure, and associated functional changes in the transcriptional response of THP-1 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE188380 | GEO | 2022/04/27

REPOSITORIES: GEO

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [Hi-C]

Project description:The aim of the project was to investigate the effect of nuclear receptor activation, particularly of the vitamin D receptor, on chromatin structure, and associated functional changes in the transcriptional response of THP-1 cells.

2022-04-27 | GSE190463 | GEO

Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]

Project description:Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [Hi-C]

Project description:Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [Hi-C]

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure

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

2022-04-27 | GSE190464 | GEO

CTCF ChIP-seq in human monocytic THP-1 cells

Project description:ChIP-seq for the insulator protein CTCF in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) THP-1 cells were treated for 24 h with 100 nM 1,25(OH)2D3 before ChIP assay

2016-07-04 | E-GEOD-69962 | biostudies-arrayexpress

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [HiChIP]

Project description:The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF depletion, revealed that ZNF143 and CTCF collaborate to regulate higher-order genome organization. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate TAD formation and genome compartmentalization whereas directional recognition of DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.

2023-11-07 | GSE236635 | GEO

Acute depletion of CTCF rewires genome-wide chromatin accessibility

Project description:The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription. Here we systematically integrated multi-omics data including ATAC-seq, RNA-seq, WGBS, Hi-C, Cut&Run, CRISPR-Cas9 survival dropout screening, time-solved deep proteomic and phosphoproteomic analyses in cells carrying auxin-induced degron at endogenous CTCF locus. Acute CTCF protein degradation markedly rewired genome-wide chromatin accessibility. Increased accessible chromatin regions were largely located adjacent to CTCF-binding sites at promoter regions and insulator sites and were associated with enhanced transcription of nearby genes. In addition, we used CTCF-associated multi-omics data to establish a combinatorial data analysis pipeline to discover CTCF co-regulatory partners in regulating downstream gene expression. We successfully identified 40 candidates, including multiple established partners (i.e., MYC) supported by all layers of evidence. Interestingly, many CTCF co-regulators (e.g., YY1, ZBTB7A) that have evident alterations of respective downstream gene expression do not show changes at their expression levels across the multi-omics measurements upon acute CTCF loss, highlighting the strength of our system to discover hidden co-regulatory partners associated with CTCF-mediated transcription. This study highlights CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation

2021-07-04 | PXD026484 | Pride

CTCF ChIP-seq in human monocytic THP-1 cells with replicates (4)

Project description:ChIP-seq for the insulator protein CTCF in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)

2016-01-02 | GSE69962 | GEO

CUT&RUN and HiChIP of CTCF and histone modifications in Wnt ON and Wnt OFF in HEK293T cells

Project description:We aimed to compare CTCF binding patterns, chromatin states and 3D genome structure in the absence and after activation of Wnt signaling in HEK293T cells.

2024-02-16 | E-MTAB-13727 | biostudies-arrayexpress

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