Fig. 6

Hi-C data upon Beaf32 depletion confirms its role in specific long-range depending on presence of co-factors. a Aggregation of Hi-C data in control cells (right plot) and Beaf32-depleted cells (left plot) [20] highlighting genome-wide long-range interactions between all Beaf32 sites and GAF/dCTCF sites. The higher density of Hi-C reads in the middle region (red arrow) highlights specific looping (LRIs-3) between Beaf32 and GAF or dCTCF sites, which is reduced upon Beaf-KD (see panel b for a control). b Same as panel a except aggregation of Hi-C was performed between GAF and Pc/Polycomb (see “Methods”) [33]. Note that LRIs-3 were not significantly reduced in this instance. c Beaf32 depletion alters ΔLRIs between its binding sites and those of GAF or dCTCF, CP190, indirect peaks shown to predict loops (“P-loop”) with Beaf32 sites [50], dCTCF (lone) or cohesin, estimated as variations in LRIs-1 (compartments), LRIs-2 (TAD strength), or LRIs-3 (specific loops). LRIs-3 define the most significant parameter for detecting the impact of Beaf32 depletion (p values by the Wilcoxon pairwise test). d Genome-wide long-range interactions between distant Beaf32 sites and micro-domains as measured from Hi-C in control cells (upper panel) compared to Hi-C in Beaf32 depleted cells (Beaf-KD, lower APA panel). Note that LRIs were significantly reduced upon depletion (the *** indicates a significant p value <1e−4 as obtained by the Wilcoxon pairwise test)