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CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [MicroC]

ABSTRACT: CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [MicroC]

PROVIDER: PRJNA1212539 | ENA |

REPOSITORIES: ENA

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			Action	DRS
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	SRR32044700_1.fastq.gz	Fastqsanger.gz
	SRR32044700_2.fastq.gz	Fastqsanger.gz
	SRR32044701_1.fastq.gz	Fastqsanger.gz
	SRR32044701_2.fastq.gz	Fastqsanger.gz

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Project description:CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [iCLIP2]

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Project description:CCCTC-binding factor (CTCF) is essential for chromatin organization, but its role in dynamically shaping chromatin loops during cellular differentiation is not fully understood. We previously demonstrated that CTCF interacts with endogenous RNAs, and deletion of its ZF1 RNA-binding region disrupts chromatin loops in mouse embryonic stem cells (ESCs). Using an ESC-to-neural progenitor cell (NPC) differentiation model, we show that the ZF1 RNA-binding region of CTCF is crucial for maintaining cell-type specific chromatin loops. Expression of CTCF-∆ZF1 leads to dysregulation of genes within these disrupted loops, particularly those involved in neuronal development and function. We identified NPC-specific, CTCF-interacting RNAs and chose Podxl and Grb10 for further study. We found that CRISPR-Cas9-mediated truncation of Podxl and Grb10 disrupts chromatin loops in cis, similar to the disruption seen in the NPC-∆ZF1 mutant. Our study underscores the importance of CTCF-ZF1 RNA interactions in preserving cell-specific genome structure and cellular identity.

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R-loop associated G-quadruplexes reinforce CTCF interactions

Project description:We report that three-stranded R-loop structures facilitate CTCF binding genome-wide through the formation of G-quadruplex (G4) structures. Genome-wide assays of CTCF and R-loop formation under various treatment conditions reveal that R-loop removal and G4 stabilization can both alter CTCF occupancy, and these changes are associated with alterations in gene expression and chromatin organization.

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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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