Fig. 4

Epigenetic features of H2A.Zac re-distribution at genomic regulatory regions. LHS, Venn diagrams overlapping the H2A.Zac gained or lost peaks from each different regulatory region (from Fig. 3a) with the corresponding “unique” active enhancers a, poised enhancers b, active promoters c and bivalent promoters d. The terminology “unique” was used to call enhancers or promoters that were only present in LNCaP but not in PrEC, for the gained peaks; and the enhancers and promoters that were only present in PrEC but not in LNCaP for the lost peaks. Box plots were generated to address the correlation of gain and loss of H2A.Zac peaks at the unique enhancers (active, a and poised, b or promoters (active, c or bivalent d) with gene transcriptional regulation. The logarithmic fold change expression (logFC) of LNCaP minus PrEC was compared between all genes and the overlapping regions from the corresponding Venn diagrams. To associate gene expression with enhancers, all the genes upstream or downstream of a particular enhancer within a 25 kb window were assigned as an enhancer-gene association a and b RHS, two types of NOMe plots were generated to evaluate differential chromatin accessibility, (represented as 1 minus GpC methylation ratio) and differential DNA methylation 0–1 ratio) between LNCaP (red) and PrEC (green). The regions analyzed corresponded to the overlapping areas from the corresponding Venn diagrams for active enhancers a, poised enhancers b, active promoters c and bivalent promoters d. * t-test p-value < 0.05 ** t-test p-value < 0.001