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CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [ChIP-Seq, RNA-seq, Med-Seq]

ABSTRACT: CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [ChIP-Seq, RNA-seq, Med-Seq]

PROVIDER: PRJNA644803 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12172614.fastq.gz	Fastqsanger.gz
	SRR12172615.fastq.gz	Fastqsanger.gz
	SRR12172616.fastq.gz	Fastqsanger.gz
	SRR12172617.fastq.gz	Fastqsanger.gz
	SRR12172618.fastq.gz	Fastqsanger.gz

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CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [ChIP-Seq, RNA-seq, Med-Seq]

Project description:The eleven zinc finger (ZF) protein CTCF regulates topologically associating domain (TAD) formation and transcription through selective binding to thousands of genomic sites. We replaced endogenous CTCF in mouse embryonic stem (ES) cells with GFP-tagged wildtype or mutant proteins lacking individual ZFs. We examined the various ES cell lines using next generation sequencing methods (ChIP-Seq, RNA-Seq, MedSeq, HiC) in order to identify additional determinants of CTCF positioning and function.

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CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [Hi-C]

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Cell type specificity of chromatin organization mediated by CTCF and cohesin

Project description:CTCF sites are abundant in the genomes of diverse species but their function is enigmatic. We used chromosome conformation capture to determine long-range interactions among CTCF/cohesin sites over 2 Mb on human chromosome 11 encompassing the β-globin locus and flanking olfactory receptor genes. Although CTCF occupies these sites in both erythroid K562 cells and fibroblast 293T cells, the long-range interaction frequencies among the sites are highly cell type specific, revealing a more densely clustered organization in the absence of globin gene activity. Both CTCF and cohesins are required for the cell-type-specific chromatin conformation. Furthermore, loss of the organizational loops in K562 cells through reduction of CTCF with shRNA results in acquisition of repressive histone marks in the globin locus and reduces globin gene expression, whereas silent flanking olfactory receptor genes are unaffected. These results support a genome-wide role for CTCF/cohesin sites through loop formation that both influences transcription and contributes to cell-type-specific chromatin organization and function. Comparison of CTCF binding in K562 and 293T cells using ChIP-chip. 3 replicates each cell type, ChIP and input DNA for each replicate.

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