Fig. 3: SEs and SE-associated loops in the human developing brain.

a Ten-kb resolution O/E interaction heatmaps around ZIC1/ZIC4 gene overlaid with brain H3K27ac ChIP-seq tracks, brain CTCF ChIP-seq and H1/IMR90 H3K27ac ChIP-seq tracks. Green arrows indicated dynamic loops mediated by H3K27ac-marked SEs in the CB region. b The ZIC1/ZIC4 gene expression barplot of PFC, V1 and CB samples from the GW11 to GW26 stage. c The violin plots for SE-linked genes and TE-linked genes in the developing human brain region. d H3K27ac signal enrichment heatmaps around the differential SEs between the developing PFC/V1 region and the CB region at the GW13 stage. e Barplots of GO biological process enrichment for region-specific SE-linked genes at the GW13 stage. The top panel is for GW13 PFC/V1-specific SE-linked genes, and the bottom panel is for GW13 CB-specific SE-linked genes. f The respective enrichment plot for interactions between identified SEs and interactions between TEs in the GW26 PFC, the GW26 V1, and the GW26 CB. g An example for TAD crossing interactions between SEs. h Boxplots of the interaction enrichment for cis SE − SE interactions and trans SE–SE interactions from the GW13 to the GW26 stage. One-sided Wilcox. test for calculating the statistical significance.