Fig. 5: Identification of super-silencers and characterization of super-silencer-associated chromatin contacts.
From: Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity
a Ranked H3K27me3 and H3K9me2 ChIP-Seq signals. Regions with exceptionally high densities of H3K27me3 and H3K9me2 ChIP-Seq signals are defined as SuReR and SuHeR, respectively. b Boxplots showing the sizes of SuReR (n = 1130), TyReR (n = 15,958), SuHeR (914) and TyHeR (n = 33,729). ***p < 0.001 from two-way ANOVA. c Metaplots of H3K27ac, H3K4me1, and ATAC enrichment signals at SuReR and SuHeR. d Venn diagram of SuReR-associated genes across myotube, IMR-90, and LSCs. e Pie charts showing the fractions of the indicated SuReR-anchored and SuHeR-anchored loops. f Boxplots showing the interaction densities of SuReR (n = 1130), SuHeR (914), TyReR (n = 15,958) and TyHeR (33,729). ***p < 0.001 from two-way ANOVA. g Fractions of the indicated loops with CTCF/SMC1, SMC1 only and CTCF only at the interaction anchors and without CTCF and SMC1 at the interaction anchors. h Boxplots showing the gene expression levels of the indicated groups. ***p < 0.001 from two-way ANOVA. All the boxplots indicate the 25th percentile (bottom of box), median (horizontal yellow line inside box), and 75th percentile (top of box). Whiskers indicate 1.5 times the interquartile range.
