Supplementary Figure 4: Positional conservation of enhancers and promoters in the brain across primate evolution.
From: Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
(a) Upper panels show the fraction of enhancers and promoters in cerebellum (CB) and prefrontal cortex (PFC) that is enriched, as defined by peak calling, in both human and rhesus macaque (blue box) or one species only (red box). Species-specific CREs are further subdivided using DESeq2 into significantly differentially enriched (DE higher in human, purple; DE lower in human, light brown) and not DE (grey). Lower panels show normalized RNA read counts, indicated for human and rhesus macaque by silhouettes, for genes close to DE and not DE enhancers. Dissimilarity between distributions was calculated using a Wilcoxon rank-sum test; *** P < 0.0005, ** P < 0.005, * P < 0.05, # P > 0.05. (b) Fraction of enhancers (left) and promoters (right) for each brain region that is positionally conserved between human and rhesus macaque (blue and grey). (c) Average PhastCons scores for all nucleotides within the indicated elements. (d) Fraction of reads within CREs that was mappable onto the other genome for (not) positionally conserved CREs. (e) Upper panels show the fraction of enhancers and promoters in CB and PFC that is enriched, as defined by peak calling, in both human and rhesus macaque (blue box) or one species only (red box). Shared CREs (blue) were further subdivided into DE, higher in human (purple), DE, lower in human (light brown) and not DE (grey) using DESeq2. Lower panels show normalized RNA read counts, indicated for human and rhesus macaque by the silhouettes, for genes close to (not) differentially enriched enhancers. Dissimilarity between distributions was calculated using a Wilcoxon rank-sum test; *** P < 0.0005, * P < 0.05, # P > 0.05.
