Fig. 2: Comparative analysis of chromatin accessibility across species.
From: Conserved and divergent gene regulatory programs of the mammalian neocortex
a, The levels of conservation for ATAC–seq peaks. b, Human cCREs from ATAC–seq peaks for each indicated group for human-specific, level 0 (sequence conserved), level 1 (tissue conserved), level 2 (cell type conserved) and level 3 (matched patterns across all the cell types) across mammals. c, The relationship between the average conservation index (x axis) and the average divergence index across species (y axis). The density of all mammal-conserved gene cCREs is highlighted. d, The relationship between the average conservation index across species (x axis) and the average divergence index across species (y axis) for each level 0 (sequence conserved) peak. Human-biased peaks are highlighted. e, Heat maps ordered by cell type with highest signal for mammal level 3 distal cCREs (top) and human-biased distal cCREs (bottom). For visualization of cell type patterns of accessibility, log2[counts per million (CPM) + 1] values are row scaled. Non-N, non-neuronal. f, The proportion of promoter-proximal (≤1 kb from a TSS) or promoter distal (>1 kb from a TSS) cCREs for the indicated group (left). The density plots show the cell specificity scores (Methods) for cCREs in each group. g, The percentage of human cCREs in TEs for different conservation groups. h, The average conservation and divergence index for all cCREs containing a given TF motif from JASPAR CORE. Motifs are coloured by TF class. i, The weighted cell type chromatin accessibility divergence across distal cCREs as a function of weighted cell type TF divergence for each cell type. Distal cCREs and TF genes were weighted by CPM. j, The weighted chromatin accessibility conservation in distal peaks as a function of weighted cell type PhastCons among distal peaks. For i and j, P values were calculated using two-sided Pearson correlation.
