Fig. 6: The regulatory loops specified by MyoD are functionally required for muscle cell differentiation.

a APA plots showing the aggregated Hi-C contacts around chromatin loops that are enhanced (n = 5754) and reduced (n = 488) in WT-DM cells compared with WT-GM cells. Differential loops were identified based on DESeq2 (see Methods). b Boxplot showing expression changes of genes associated with MyoD-induced chromatin loops in WT-DM cells compared with WT-GM cells (left) and in MKO-DM cells compared with WT-DM cells (right). The gene numbers related to the MyoD-induced loops 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. c MyoD and H3K27ac ChIP-seq signals at the anchors of MyoD-induced loops. Heatmaps showing signal enrichment centralized at the anchors within a ± 100 kb genomic region. d, e The Mef2c and Dyrk2 loci as representatives of MyoD-induced loops occurring during muscle cell differentiation. The MyoD-induced loops detected by our algorithm are presented in red in the loop track, while differentiation-induced loops are shown in orange. Other loops are presented in gray. f Mef2c and Dyrk2 gene expression among WT and MKO cells cultured in GM and DM. Data are presented as mean ± SD. n = 3 biologically independent samples.