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CTCF binding polarity determines chromatin looping

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE72720 | GEO | 2015/10/29

SECONDARY ACCESSION(S): PRJNA294741

REPOSITORIES: GEO

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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

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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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