Fig. 2: Chromatin multiscale organization of LSCs.
From: Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity
a Chromatin interaction heatmaps of chromosome 2 at 100-kb, 50-kb, and 10-kb resolution. b Chromatin compartments and Pearson correlation heatmap of cis-interactions on chromosome 19. Positive first principal component (PC1) values represent compartment A (blue), and negative PC1 values represent compartment B (red). c Violin and boxplots showing GC content (left) of A (n = 13,613) and B (n = 14,149) compartments and gene expression levels in A (n = 16,462) and B (n = 6,084) compartments. ***p < 0.001 from two-way analysis of variance (ANOVA). The boxplots indicate the 25th percentile (bottom of box), median (horizontal yellow line inside box), mean value (dark spot inside box), and 75th percentile (top of box). Whiskers indicate 1.5 times the interquartile range. TPM: transcripts per kilobase million. d Chromatin interaction heatmap, identified TADs, and chromatin compartments at the indicated gene loci. e, f Chromatin interaction heatmaps of the TADs at the indicated gene loci. The upregulated genes produced by RUNX1 or SMAD3 knockdown (e) and the genes activated in CECs (f) were marked in red. g Chromatin interaction heatmap, TADs, and DNA loops at the indicated genomic loci. h Percentages of inter-TAD and intra-TAD cis-interactions.
