Extended Data Fig. 3: Related to Figure 3.
a. HiGlass visualization of H3K27ac HiChIP results around a TSC related hub (Cdx2) and a XEN-related hub (Gata6) in TSC, ESC, and XEN along with the corresponding H3K27ac HiChIP derived arcs and H3K27ac ChIP-seq signals. Interacting scores are presented in 5 kb resolution. b. Barplot showing the percentages of essential genes -as identified in two recent studies83,84- within the least (Q1) versus most (Q10) connected hubs. The preferential enrichment of essential genes in Q10 is significant (p-value < 0.001, two-sided Fisher’s exact test). c. Stacked barplots showing the proportions of different HiChIP loop subtypes in TSC, ESC and XEN cells. Loops were separated into 5 chromatin interaction categories based on the presence of regulatory elements, such as promoter/TSS (P) or putative enhancer (E, H3K27ac peak). X- anchors were defined as anchors that do not contain any TSS nor an H3K27ac peak. d. Boxplot showing the size distribution of X loops (X-E and X-P) compared to E-E, E-P and P-P loops in all cell lines. (n = 60,909 (TSC), 81,679 (ESC), 77,124 (TSC) loops across n = 2 independent HiChIP experiments). e. Boxplots showing expression changes between any two cell types around multiconnected genes (n > =5 in both cell types of interest), when at least one of their conserved anchors switches chromatin states: either from X-to-E (enhancer gain) or from E-to-X (enhancer loss) Asterisks indicate significance < 0.05 by two-sided Wilcoxon rank-sum test. (See also Supplementary Table 8). Note: all statistics are provided in Supplementary Table 8.
