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

Abstract

The genome is organised via CTCF/Cohesin binding sites, which partition chromosomes into 1-5Mb topologically associated domains (TADs), and further into smaller sub-domains (sub-TADs). 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 adjacent upstream CTCF/cohesin binding sites. 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 delimit the region of chromatin to which enhancers have access and within which they interact with receptive promoters.

The Role of Bromodomain and Extraterminal Motif (BET) Proteins in Chromatin Structure

“…Single-molecule mRNA FISH confirmed these findings by demonstrating that, at the single-cell level, the expression of these two genes becomes increasingly correlated with either deletion of the intervening CTCF/BRD2 cooccupied site or with BRD2 depletion. Conceptually analogous findings were recently reported at another erythroid gene locus, in which mutation of CTCF sites at the α-globin gene cluster in mice resulted in the formation of new contacts between the α-globin enhancer and the promoters of adjacent genes normally protected from its influence (Hanssen et al 2017).…”

Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene

“…Interestingly, AMIGO2 and its SEs are located within the same putative topologically associating domain (TAD) (Dekker and Heard, 2015) and lamina-associated domain (Fu et al, 2015), as suggested by flanking H3K27me3, macroH2A1, and macroH2A2 repressive domains, respectively, as well as CTCF occupancy (Hanssen et al, 2017) (Figure 6A). This region also contains PCED1B , which is not expressed (Table S1) and therefore unlikely to be regulated by these SEs.…”

Dynamics of the 4D genome during lineage specification, differentiation and maturation in vivo

“…We focused our analysis on a ~3.3 Mb region containing the well-characterized a-globin genes and their associated regulatory elements. The a-globin genes are regulated by five erythroidspecific enhancer elements (R1-R4 and Rm), which classify as a super-enhancer 20 , and interact with the gene promoters within a TAD flanked by multiple CTCF-binding elements [21][22][23][24] (Supplementary Figure 2). We generated a single-cell RNA-seq dataset 25 , which is the first scRNA-seq dataset to include the full course of in vivo erythroid differentiation through to terminal differentiation in the mouse (Supplementary Figure 5).…”