CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation

Abstract

Polycomb and trithorax group proteins encode the epigenetic memory of cellular positional identity by establishing inheritable domains of repressive and active chromatin within the Hox clusters. Here, we demonstrate that the CCCTC-binding factor (CTCF) functions to insulate these adjacent yet antagonistic chromatin domains during embryonic stem cell differentiation into cervical motor neurons. Deletion of CTCF binding sites within the Hox clusters results in the expansion of active chromatin into the repressive domain. CTCF functions as an insulator by organizing Hox clusters into spatially disjoint domains. Ablation of CTCF binding disrupts topological boundaries such that caudal Hox genes leave the repressed domain and become subject to transcriptional activation. Hence, CTCF is required to insulate facultative heterochromatin from impinging euchromatin to produce discrete positional identities.

Spatial Organization of Epigenomes

“…Furthermore, removal of TAD boundaries can lead to spreading of activating histone marks and transcription of genes in the neighbouring TAD [38]. Although these findings support the compartmentalization of genes and regulatory elements into TADs, they do not exclude the possibility of regulatory contacts across TADs.…”

CTCF-mediated topological boundaries during development foster appropriate gene regulation

“…1A). We did so in MNs derived from wild-type mouse ESCs, as we had already developed 4C (circularized chromatin conformation capture) maps of the local topology and chromatin structure of the Hox loci for these cells (Mazzoni et al 2013;Narendra et al 2015). TAD boundaries were determined by calculating an "insulation score" at each position along the 4-Mb scan, which reflects the aggregate of interactions (within an ∼160-kb window) occurring across each genomic position (Crane et al 2015).…”

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

“…3b) are particularly unable to explain the matrices of contacts detected experimentally across the gene-dense HoxB locus, although they may contribute to the overall folding as seen in the other Hox loci 16 , and may have deterministic roles in gene-poor areas, as those recently explored 15 . Our detailed analyses of physical distances across the HoxB locus suggest that homotypic (Active-Active and Poised-Poised) contacts are highly predominant within ES cell nuclei, and are not explained by independent contacts in separate cells or even separate alleles within the same cells.…”

“…Although the molecular mechanisms that underlie promoter co-associations and their functional purpose remain unclear, they suggest that gene activation states may help to establish cell-type specific chromatin folding configurations that partition active from Polycomb-repressed chromatin domains. CTCF binding has important roles in the formation of chromatin loops and enhancer-promoter interactions [9][10][11][12][13][14] , and has been proposed to organise chromatin domains through loop extrusion mechanisms in gene-poor areas 15 and to help insulate spreading of active marks into Polycomb repressed domains 16 . However, CTCF .…”