Fig. 7: H3K27ac enhancement in MKO cells is not sufficient to drive the formation of MyoD-bound chromatin loops.

a Motif enrichment at loop-anchor H3K27ac peaks gained or lost in WT-DM cells compared with WT-GM cells. p-values of motif enrichment were determined using cumulative binomial distributions, as applied by Homer. b Heatmaps showing H3K27ac peaks found to be enhanced and reduced on ChIP-seq analysis of MKO-DM cells versus WT-DM cells. MyoD-binding peaks at those differential H3K27ac peaks are also shown. c Heatmaps showing H3K27ac peaks enhanced and reduced on ChIP-seq analysis of MKO cells treated with the selective class I HDAC inhibitor, Tacedinaline (Tac), in DM for 12 h. DMSO-treated MKO cells served as a control. d Loop-strength fold changes of the loops with gained, lost, static or no H3K27ac marks on their anchors between MKO cells treated with Tac or DMSO. Loop strength was defined as relative Hi-C contacts found at loop pixels compared with those at surrounding donut-shaped background pixels (see Methods). The loop numbers are marked in red. p-values were calculated by the one-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file. e APA plots showing aggregated Hi-C contacts around the four types of chromatin loops (classified in 2d) in MKO cells treated with Tac or DMSO (control). f Representative dCas9-mediated DNA images visualizing the chromatin loops linking MyoG (red) and Mybph (green) in WT and MKO cells transfected with dCas9-p300core and cultured in DM for 24 h. dCas9-EGFP served as a control. g The distance between the two anchors visualized in f. The scale bar represents 5 μm. Data are presented as mean ± SEM. p-values were determined by ANOVA followed by Tukey’s multiple comparison test, ***p < 0.001. Source data are provided as a Source Data file. h Relative expression of MyoG and Mybph in the cells described in f, as determined by qRT-PCR. Data are presented as mean ± SEM. p-values were determined by ANOVA followed by Tukey’s multiple comparison test. n = 3 biologically independent samples. Source data are provided as a Source Data file.