Supplementary Figure 3: Chromatin accessibility and histone modifications are both morphogen and p63 dependent.

a, Overlap in p63 binding sites (ChIP-seq) between day 0 p63GOF, day 7 p63WT, and keratinocytes (kc), n = 2. b, Only H3K27me3 histone marks are dependent on p63 presence, as is illustrated by the percent of differential peaks between day 7 p63WT and day 7 p63KO. c, Histograms depicting enrichment of histone modifications in day 7 p63WT and day 7 p63KO, in a 10-kb window, n = 2. H3K4me1, H3K4me3, and H3K27ac are similar between p63WT and p63KO, while H3K27me3 is noticeably reduced in p63KO. d, Western blots showing that global levels of H3K27me3 protein decrease in day 7 p63KO, while levels of Ezh2 do not (n = 4). Levels of Ezh2 protein are quantified relative to day 7 and are indicated above the blot. e, GO biological processes associated with H3K27me3 regions that are morphogen dependent. f, ChromHMM analysis indicates that the majority of p63 binding sites and sites that increase in accessibility upon morphogen treatment are located in strong enhancer regions. Conversely, the sites with differential H3K27me3 marks are not located in strong enhancer regions. g, By GREAT analysis, the majority of p63 binding sites at day 7 can be associated with differentially expressed genes. The reverse analysis interrogating how many differentially expressed genes are associated with a p63 binding site shows drastically different results. h, Genes that are associated with p63 binding sites and changing ATAC regions are more highly expressed in p63KO than p63WT, as analyzed by GREAT.