Supplementary Figure 6: Changes in active chromatin at predicted CREs occurred mainly before the human-chimpanzee separation.
From: Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
(a) t-Distributed Stochastic Neighbor Embedding (t-SNE) analysis for all human, chimpanzee and rhesus macaque brain samples using normalized H3K27ac enrichment at 60,702 predicted human and rhesus CREs with orthologues on all three genomes. (b) Upper panels show scaled H3K27ac enrichment of (not) DE enhancers as indicated between human and rhesus macaque in prefrontal cortex (PFC). In purple, DE enhancers, higher in human. In light brown, DE enhancers, lower in human. In grey, not DE enhancers. Lower panels display normalized RNA read counts from human, rhesus macaque and chimpanzee brain samples for genes close to (not) DE enhancers. Dissimilarity between distributions was calculated using a Wilcoxon rank-sum test; * P < 0.05, # P > 0.05. (c) Fraction of (not) DE enhancers in cortical and subcortical samples defined between human and rhesus macaque with a twofold difference in normalized read counts (mean of replicates) between human and the indicated species.
