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CTCF binding polarity determines chromatin looping

ABSTRACT: CTCF binding polarity determines chromatin looping

PROVIDER: PRJNA294741 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2121304.fastq.gz	Fastqsanger.gz
	SRR2121305.fastq.gz	Fastqsanger.gz
	SRR2220270.fastq.gz	Fastqsanger.gz
	SRR2220280.fastq.gz	Fastqsanger.gz
	SRR2220290.fastq.gz	Fastqsanger.gz

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CTCF binding polarity determines chromatin looping [ChIP-seq]

Project description:CTCF binding polarity determines chromatin looping CTCF ChIPseq was performed in E14 embryonic stem cells and neural precursor cells

2015-10-29 | E-GEOD-71158 | biostudies-arrayexpress

CTCF binding polarity determines chromatin looping [ChIP-seq]

Project description:CTCF binding polarity determines chromatin looping

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CTCF binding polarity determines chromatin looping [4C]

Project description:CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentally stable and dynamic chromatin loops. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR-Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher order chromatin structure. 4C-seq was performed on a large number of viewpoints in E14 embryonic stem cells, neural precursor cells and primary fetal liver cells

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Molecular basis of CTCF binding polarity in genome folding

Project description:Current models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin. While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize loops, the molecular basis of this polarity remains mysterious. Here we report that CTCF positions cohesin but does not control its overall binding dynamics on chromatin by single molecule live imaging. Using an inducible complementation system, we found that CTCF mutants lacking the N-terminus cannot insulate TADs properly. Cohesin remained at CTCF sites in this mutant, albeit with reduced enrichment. Given that the orientation of the CTCF motif presents the CTCF N-terminus towards cohesin as it translocates from the interior of TADs, these observations explain how the orientation of CTCF binding sites determines the genomic distribution of chromatin loops.

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CTCF binding polarity determines chromatin looping

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-10-29 | E-GEOD-72720 | biostudies-arrayexpress

Mus musculus

Project description:CTCF binding polarity determines chromatin looping [4C]

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CTCF binding polarity determines chromatin looping

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

2015-10-29 | GSE72720 | GEO

Mus musculus

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An RNA binding region in CTCF regulates chromatin looping and CTCF nuclear organization

Project description:The study investigates CTCF/cohesin binding and chromatin looping by ChIP-seq and Micro-C. By ChIP-seq, we determined the genome-wide binding profiles of CTCF and Smc1a cohesin subunit in a knock-in mouse ES cell line (wt-CTCF; clone C59) with endogenously tagged wild type CTCF (FLAG-Halo-mCTCF) and Rad21 (mRad21-SNAPf-V5), and compared them to the same ES line expressing a mutant CTCF (ΔRBR-CTCF; clone C59D2), where we replaced a previously described RNA binding region with a short linker (GDGAGLINS) followed by a 3xHA tag (N576_D611del::3xHA). By Micro-C, we compared nucleosome-resolution chromosome folding maps of the same ES cell lines C59 and C59D2 described above, to determine the effect of deleting CTCF RNA binding region on chromatin looping.

2019-05-30 | GSE123636 | GEO

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