Extended Data Fig. 3: Human gained enhancers consist of traditional and super-enhancers during cardiomyocyte differentiation.
From: Human-gained heart enhancers are associated with species-specific cardiac attributes
a, HGEs are enriched in intergenic and intronic regions during cardiomyocyte differentiation. b, HGEs consist of both traditional (TE) and super-enhancers (SE). c, Violin plots reveal comparable activity of HGEs compared to all other mouse stages combined. Dashed line in violin plots indicates the mean and dotted lines indicate quartiles. d, Shannon entropy calculations show stage-specific expression of genes near gained or stable enhancers. Lower entropy indicates more stage-specific gene expression. Horizontal line in boxplots represents the median, the box indicates the interquartile range and the dots represent outliers. Data was compared using Wilcoxon rank sum test (****p value < 0.0001). PSC-Stable, n = 7339; PSC-Gained, n = 1240; Mes-Stable, n = 6436; Mes-Gained, n = 1924; CP-Stable, n = 7525; CP-Stable, n = 1531; CM-Gained, n = 7531; CM-Gained, n = 1653. e, Stable and gained super-enhancer domains are primarily associated with transcription factors based on GO-term analysis. f, Representative super-enhancer TADs with HGEs (blue boxes) are shown at various cardiomyocyte developmental stages. HGE, human-gained enhancer; PSC, pluripotent stem cells; Mes, mesoderm; CP, cardiac progenitor; CM, cardiomyocyte; UTR, untranslated region; pseudo, pseudogene; TTS, transcription termination site; enh., enhancers; TAD, topologically associated domain; hs, human; ms, mouse.
