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Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [Capture Hi-C]

ABSTRACT: Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [Capture Hi-C]

PROVIDER: PRJNA543246 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9070112_1.fastq.gz	Fastqsanger.gz
	SRR9070112_2.fastq.gz	Fastqsanger.gz
	SRR9070113_1.fastq.gz	Fastqsanger.gz
	SRR9070113_2.fastq.gz	Fastqsanger.gz
	SRR9070114_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development

Project description:Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development

| PRJNA542478 | ENA

Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [Capture Hi-C]

Project description:The ubiquitously expressed transcription factor CTCF maintains higher-order chromatin structure in multiple cell types and species through well-established common mechanisms. Here we define a new role for CTCF in tissue-specific gene regulation revealed by serial examinations of genome-wide CTCF occupancy during red blood cell (RBC) differentiation of human CD34+ hematopoietic stem/progenitor cells (HSPCs). We identified 1753 dynamic, erythroid developmental stage-specific CTCF chromatin occupancy sites that occur through both direct DNA binding and indirectly via interactions with lineage-specific transcription factors. These dynamic sites display features of transcriptional enhancers, function as hubs of cis-regulatory elements (CREs) interactome, and are enriched for single nucleotide polymorphisms (SNPs) associated with RBC traits. Precise deletion of CTCF binding motifs from those dynamically bound sites alternated local CRE-interactions and disrupted erythropoiesis. Our study highlights novel, lineage-specific functions for CTCF and provides new insights into how genetic variation regulates erythropoiesis

2021-01-18 | GSE131324 | GEO

Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [HiChIP]

Project description:Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [HiChIP]

| PRJNA542482 | ENA

Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [ChIP-seq]

Project description:Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [ChIP-seq]

| PRJNA542480 | ENA

Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [ATAC-seq]

Project description:Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [ATAC-seq]

| PRJNA542481 | ENA

Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [HiChIP]

2021-01-18 | GSE131054 | GEO

Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [ATAC-seq]

2021-01-18 | GSE131053 | GEO

Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [ChIP-seq]

2021-01-18 | GSE131052 | GEO

Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development

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

2021-01-18 | GSE131055 | GEO

Acute depletion of CTCF rewires genome-wide chromatin accessibility

Project description:Accumulated data suggest that transcription factor CTCF is indispensable to define topologically associated domain (TAD) boundaries and to maintain intra-TAD chromatin loop structures. However, upon genome-wide acute depletion of CTCF, the discrepancy between global reduction of chromatin interactions and minimal alteration of transcription has been evidently observed. To understand CTCF’s direct role in chromatin accessibility and global transcriptional regulation, we have systematically integrated data collected from ATAC-seq, RNA-seq, whole genome bisulfite-seq, Cut&Run and HiC in a previously established CTCF-miniAID knock-in cell lines. Acute degradation of CTCF markedly rewires genome-wide chromatin accessibility but not DNA methylation. Differentially altered ATAC-seq peaks are highly associated with adjacent CTCF binding sites, supporting the direct link between CTCF occupancy and its surrounding chromatin accessibility. Increased ATAC-seq peaks upon CTCF loss are notably associated with enhanced transcription at promoter regions and insulator sites, while decreased ATAC-seq peaks are significantly enriched at DNA loops. Furthermore, using CTCF associated multi-Omics data we have established a combinatorial data analysis pipeline to discover novel CTCF mediated insulators in the genome, by which we have successfully identified 67 novel insulators at non-coding regions distal to promoters. Functional CRISPR interference (CRISPRi) unconstrained the repressive transcriptional regulation of target genes. In sum, using CTCF acute depletion cell model and multi-Omics analysis, we concluded that CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role for transcriptional regulation.

2021-08-26 | GSE153237 | GEO

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