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Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo.


ABSTRACT: The genome is organized via CTCF-cohesin-binding sites, which partition chromosomes into 1-5?megabase (Mb) topologically associated domains (TADs), and further into smaller sub-domains (sub-TADs). Here we examined in vivo an ?80?kb sub-TAD, containing the mouse ?-globin gene cluster, lying within a ?1?Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF-cohesin sites that are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. Whereas the ?-globin regulatory elements normally act solely on promoters downstream of the enhancers, removal of a conserved upstream CTCF-cohesin boundary extends the sub-TAD to adjacent upstream CTCF-cohesin-binding sites. The ?-globin enhancers now interact with the flanking chromatin, upregulating expression of genes within this extended sub-TAD. Rather than acting solely as a barrier to chromatin modification, CTCF-cohesin boundaries in this sub-TAD delimit the region of chromatin to which enhancers have access and within which they interact with receptive promoters.

PROVIDER: S-EPMC5540176 | BioStudies |

REPOSITORIES: biostudies

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