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Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation (RNA-seq)

ABSTRACT: Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation (RNA-seq)

PROVIDER: PRJNA1127578 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32269447_1.fastq.gz	Fastqsanger.gz
	SRR32269447_2.fastq.gz	Fastqsanger.gz
	SRR32269448_1.fastq.gz	Fastqsanger.gz
	SRR32269448_2.fastq.gz	Fastqsanger.gz
	SRR32269449_1.fastq.gz	Fastqsanger.gz

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Project description:Here we used a series of CTCF mutations to explore CTCF’s relationship with chromatin and its contribution to gene regulation. CTCF’s impact depends on the genomic context of bound sites and the unique binding properties of WT and mutant CTCF proteins. Specifically, CTCF’s signal strength is linked to changes in accessibility, and the ability to block cohesin is linked to its binding stability. Multivariate modelling reveals that both CTCF and accessibility contribute independently to cohesin binding and insulation, however CTCF signal strength has a stronger effect. CTCF and chromatin have a bidirectional relationship such that at CTCF sites, accessibility is reduced in a cohesin-dependent, mutant specific fashion. In addition, each mutant alters TF binding and accessibility in an indirect manner, changes which impart the most influence on rewiring transcriptional networks and the cell’s ability to differentiate. Collectively, the mutant perturbations provide a rich resource for determining CTCF’s site-specific effects.

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Project description:Although only a fraction of CTCF motifs are bound in any cell type, and approximately half of the occupied sites overlap cohesin, the mechanisms underlying cell-type specific attachment and ability to function as a chromatin organizer remain unknown. To investigate the relationship between CTCF and chromatin we applied a combination of imaging, structural and molecular approaches, using a series of brain and cancer associated CTCF mutations that act as CTCF perturbations. We demonstrate that binding and the functional impact of WT and mutant CTCF depend not only on the unique properties of each protein, but also on the genomic context of bound sites. Our studies also highlight the reciprocal relationship between CTCF and chromatin, demonstrating that the unique binding properties of WT and mutant proteins have a distinct impact on accessibility, TF binding, cohesin overlap, chromatin interactivity and gene expression programs, providing insight into their cancer and brain related effects.

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