Supplementary Figure 5: Differential H3K27ac enrichment corresponds to changes in gene expression.
From: Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
(a) Heatmaps and boxplots for the eight brain regions illustrate (the ratio of) average read counts (normalized for number of reads in peaks) of replicates in human and rhesus macaque. Upper panels in purple depict DE enhancers, higher in human. Middle panels in light brown are DE enhancers, lower in human. Lower panels in grey represent enhancers that are not DE. (b) Percentage of human promoters per brain region that is (not) DE between human and rhesus macaque as defined by DESeq2 (≥ twofold change, FDR < 0.01). The number of analyzed promoters per subdivision is indicated in the color bar below the graph. (c) Boxplot showing the comparison of normalized RNA read counts from human and rhesus macaque brain samples as indicated by the silhouettes. Displayed are the closest genes to a (not) DE enhancer in the prefrontal cortex (PFC). Dissimilarity between distributions was calculated using a Wilcoxon rank-sum test; # P > 0.05. (d) Comparison of normalized RNA read counts for genes with (no) differential H3K27ac enrichment at their promoters (shown for CB and PFC). Dissimilarity between distributions was calculated using a Wilcoxon rank-sum test; *** P < 0.0005, ** P < 0.005, * P < 0.05, # P > 0.05. (e) Ratio of enhancer length between rhesus macaque and human for (not) DE enhancers. (f) Left panels show a RPM normalized ChIP-seq read distribution (axis limit 5 RPM) for H3K27ac at a genomic region spanning 115kb containing the DFNB31 gene. Eight tracks represent the different anatomical brain regions that were analyzed in both human (HS1) and rhesus macaque (RM1) as indicated by the silhouettes. Blue shade highlights the repurposed enhancer and promoter. The right panel displays RPKM normalized RNA sequencing reads for DFNB31 relative to the human cortex.
