Fig. 5: MyoD mediates primed architectural chromatin loops in proliferating muscle cells.

a Aggregated Hi-C maps generated around chromatin loops with enhanced, reduced, or static internal interactions (measure by domain score) between WT and MKO myoblasts (MKO-GM vs. WT-GM). b Percentage of chromatin loops with differential internal interactions (MKO-GM vs. WT-GM) that are occupied by MyoD at anchors. MyoD bound at both anchors (Both, red), one of the two anchors (Xor, blue), or neither of the two anchors (Neither, green). Pseudo-peaks of MyoD binding identified from combined ChIP-seq data obtained from public datasets and our study were used for this analysis (see Methods). c Boxplot showing the corresponding expression changes of genes within chromatin loops having enhanced, reduced, or static internal interactions (domain score) identified in b (MKO-GM vs. WT-GM). Considering that a single loop may contain several genes and the domain scores of nested loops are associated with one another, we assigned each gene to its most dynamic nested loop. The loop domain-containing gene 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. d Scatter plot showing the domain score fold changes and gene expression fold changes of MyoD-bound chromatin loops between WT-GM and MKO-GM cells. Internal interaction-reduced MyoD-bound chromatin loops whose associated genes did not show significantly differential expression in MKO-GM cells compared with WT-GM cells are shown as blue dots. In contrast, internal interaction-reduced MyoD-bound chromatin loops whose associated genes showed significant down-regulation in MKO-GM cells compared with WT-GM cells are shown as red dots. e The Rbm24 locus as a representative internal interaction-reduced MyoD-bound chromatin loop associated with genes that were significantly downregulated in MKO-GM cells compared with WT-GM cells. f Heatmap showing expression (FPKM) Z-scores among the four indicated sample types for genes within internal interaction-reduced MyoD-bound chromatin loops whose associated genes did not show differential expression in MKO-GM cells compared with WT-GM cells. g The Lmrt1 locus as a representative internal interaction-reduced MyoD-bound chromatin loop that is primed in proliferating muscle cells, comparing MKO-GM cells with WT-GM cells.