Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (Capture-C". 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: NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments; in this case promoters, enhancers and CTCF binding sites in the alpha-globin subTAD were used as viewpoints. The method was applied to wild type mouse erythroid and mES cells and to in vivo models in which CTCF sites -HS38 and -HS39 were deleted in combination. ------------------------- A1_R1_ESvsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.) A4_HS38_ESvsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.) A5_CTCF48_ESvsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.) mpg_ESvsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.) rhbd_ESvsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.) A1_R1_DEL3839vsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.) A5_CTCF48_DEL3839vsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.) mpg_DEL3839vsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.) rhbd_DEL3839vsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)