Supplementary Figure 7: TSSs associated with p63-dependent H3K27me3 regions are not differentially regulated.

a, Changes in high-confidence cohesin connectivity strength between various cell types of the following contacts: p63–TSS, p63–p63-dependent (p63-dep) H3K27me3, and p63–p63-dep H3K27me3 where both elements are connected to the TSS. P values were calculated using a two-sample Anderson-Darling test. n is the number of contacts. b, ecdfs of the change in expression level (day 7 p63WT versus day 7 p63KO) of genes connected to a p63-dependent H3K27me3 region (left panel, red), both p63 and a p63-dependent H3K27me3 region (left panel, purple), or a morphogen-dependent (morph-dep) ATAC site (right panel, green) compared to all protein-coding genes (left and right panels, black). Genes connected to a p63-dependent H3K27me3 region or both p63 and a p63-dependent H3K27me3 region are not significantly differentially regulated relative to all genes. Genes connected to a morph-dependent ATAC region are significantly more likely to be negatively regulated by p63 compared to all genes. n is the number of genes, two-sided test. c, FDR of the change in strength of connectivity in high-confidence cohesin contacts between various cell types. d, Scatterplots of changes in connectivity strength of high-confidence cohesin contacts between various cell types; red depicts >2-fold change with P < 0.05, while blue depicts <–2-fold change with P < 0.05, in wild-type cells. CPM, counts per million. glmQLFit was performed, which builds a generalized linear model and then estimates the quasi-likelihood dispersion from the deviance.