Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (ChIP-Seq). Mus musculus

The genome is organized via CTCF/cohesin binding sites, which partition chromosomes into 1-5Mb topologically associated domains (TADs), and further into smaller contact sub-domains within TADs (sub-TADs; 40-1000kb). Here we examined in vivo an ~80kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ~1Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF/cohesin sites which are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. Whereas the α-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 the adjacent upstream CTCF/cohesin binding site. The α-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 regulate both directionality and specificity of enhancer interactions with surrounding promoters. Overall design: ChIP-seq with indicated antibodies on chromatin isolated from primary erythroid ter119+ cells obtained from the spleens of acetylphenylhydrazine treated mice. Wild-type C57BL/6 mice were comparied with mice containing deletions for HS-29 (D29) or HS-38 and/or HS-39 (D38, D39,D3839) CTCF binding sites. Duplicate ChIP data is analysed for each antibody and genotype. (Third replicate of CTCF is provided, but was not used in the publication). Mutant data (Dxx) is compared to wild-type (C57) ChIP-seq.