Fig. 3

Switching compartments show significant gain or loss of enhancer-promoter contacts. a Venn diagrams comparing the number of unique enhancers annotated in WT versus β-actin KO MEFs and MEFs versus ESCs using the ABC model. b Bar plot showing the distribution of all enhancer-promoter contacts by distance. c Boxplots showing the change in the number of enhancers annotated per gene in different compartments for (i) β-actin KOvsWT, (ii) KO-actin vs β-actin KO, and (iii) ESCvsMEF. Boxes represent first and third quartiles with line in the box showing median and whiskers showing data within 1.5 × interquartile range. p-values based on two-tailed, two-sample Wilcoxon-rank sum test. DEG, differentially expressed genes (absolute log2FC > 2 and padj <  = 0.05), NDE, non-differentially expressed genes