Extended Data Fig. 3: Comparative chromatin accessibility.

a. A workflow schematic for classifying level 0 (sequence conserved), level 1 (tissue conserved), and level 2 (cell type conserved), epigenome elements across both mammals and primates. b. A workflow schematic for classifying level 3 (matched patterns across all cell types) conserved elements in both mammals and primates. c. A schematic illustrating the workflow for identifying human-biased cCREs. d. Stacked bar plots representing the breakdown of human cCREs from ATAC-seq peaks for each indicated group for Level 0 and Level 1 conservation. e. Level 2 conservation of human cCREs from ATAC-seq peaks showing the overlap between each species for the same cell type (outer circle stacked bars). Inner circles show the breakdown for mammal and primate comparisons for all human ATAC-seq cCREs f. Scatter plots highlighting the pairwise divergence vs. conservation index of human ATAC-seq peaks for each species pair. g. Scatter plots comparing the conservation index and divergence index of all mammal level 0 peaks highlighting human biased (top left), level 1 (top right), level 2 (bottom left) or level 3 (bottom right). h. Scatter plot displaying the relationship between the conservation index (mean GLS T-statistic across comparisons) and divergence index (maximum absolute fold change across cell types) for primate level 0 cCREs. i. A scatter plot showing the relationship between conservation of epigenome signals (open chromatin conservation index), and conservation of motif sequence (PhastCons) averaged over all motifs of each transcription factor found in peaks. j. A scatterplot showing the relationship between sequence conservation (PhastCons) and ATAC conservation index among mammal level 0 CCREs. Density plots highlight the difference in ATAC conservation index (top) and PhastCons (right) between promoters and distal elements. Species silhouettes in a, b, c, e and f created in BioRender.