Figure 7. Compaction domains correlate with PRC1 occupancy.

A, Primer interactions mapped at HoxA and Nkx2.4-Nkx2.2-Pax1 regions in WT ESC show that boundaries of interaction domains correlate well with PRC1 occupancy. ChIP-Seq enrichments for Ring1b, Cbx7, H3K27me3 and H2AK119Ub are shown. Grey lines – mapped primer interactions with Z-score above significance threshold. Light grey lines represent an interaction between the Nkx2.2 locus and a nearby CTCF binding site. This interaction is independent of PRC1 occupancy and also celltype invariant. Red bars – computationally identified interaction domains. Blue-red-green colored bar marks restriction fragments assigned to Forward, Reverse and Unused 5C primers respectively. B, Cumulative distribution function plots showing distance of ESC TAD boundaries (blue) compared with distance of PRC1 associated domain boundaries (red) from nearest CTCF (left) and Smc1a binding sites (right) in ESC. Indicated p-values (Wilcoxon Rank Sum test) show that the distributions are significantly different. Black line is the expected distribution of random genomic loci from the relevant protein. Source of publicly available data: ESC TAD – (Dixon et al., 2012); CTCF and Smc1a binding sites – (Kagey et al., 2010). Also see Figure S6. C, Distribution of PRC1 subunits Cbx7 and Ring1b and PcG associated histone modifications H3K27me3 and H2AK119Ub across PRC1 associated domains. Boundaries of all four marks correlate well with boundaries of PRC1 associated domains. D, Model to describe interpretation of presented data; see discussion for a description of the hypothesis presented. See also Figure S7 for our analysis of a high-resolution Hi-C dataset generated in GM12878 cells by (Rao et al., 2014), and discussion for a description.