Extended Data Fig. 5: Patterns of DNA methylation conservation.
From: Conserved and divergent gene regulatory programs of the mammalian neocortex
a. Proportions of level 0 (sequence conserved) and level 1 (tissue conserved) DMRs across mammals and primates. b. Level 2 conservation of human DMRs 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 DMRs. c. Distance from nearest TSS with conservation level for all mammal conserved (left) or primate conserved (right) DMRs. Upper and lower plots display different genomic scales on the X-axis. d. Proportion of TEs in different levels of primate conserved DMRs. e. Dot plots showing the percentage of all (left) or human-specific (right) DMRs overlapping different subclasses of TEs for each cell type. N = 519,456, 371,964, 343,711, 64,138 DMRs in each category. f. Heatmaps in each species highlighting distal mammal level three DMRs (above) and primate level three DMRs (below). Each DMR is ordered by the cell type with the lowest methylation level in the human data. g. Pie charts showing the proportion of promoter-proximal (≤ 1 kb from a TSS) and promoter distal (> 1 kb from a TSS) elements for each level of mammal conservation (above) and primate conservation (below). Density plots show distribution of cell specificity scores (methods) for DMRs in each conservation group. h. Box plots showing the fraction of methylated CGs at all DMRs that intersect indicated group of promoter distal chromatin accessible cCREs. Box plots encompass 25th to 75th percentiles; central lines represent medians; whiskers represent 1.5 times the interquartile interval. Species silhouettes in a, b and f created in BioRender.
