Extended Data Fig. 7: Enhancer and chromatin accessibility analysis in the absence of macroH2A in CAFs.
a) Metagene profile of H3K27ac levels in serum-stimulated cultured CAFs across genes binned into quartiles according to their expression levels. Genes not detected are either not expressed or not mappable. n = 3000 randomly selected genes within each group. b) Changes in H3K27ac signal at all detected enhancers in cultured CAFs depicted by MA plot. TEs and SEs are separated by a vertical dashed line. Enhancers with a log2 fold change > 0.75 are shown in color for the respective genotype. c) Heatmap of H3K27ac ChIP signal in serum-stimulated cultured CAFs centered around ATAC peaks located in enhancers that gain, lose or maintain static H3K27ac levels in dKO vs. WT, ndKO up = 6659, ndKO down = 5211, nStatic = 18961. Number of TEs and SEs noted for each cluster. d) ATAC-seq signals at peaks in (c). e) Hockey plot highlighting TEs and SEs gaining H3K27ac in dKO within 50 kb of upregulated inflammatory genes (red) among all TEs and SEs ranked by H3K27ac signal in cultured CAFs. f) Average profile of ATAC-seq signal at differentially accessible regions in dKO vs. WT sorted CAFs, ndKO up = 667, ndKO down = 668, nStatic = 3000 randomly selected non-changing peaks. g) Top 3 hits of HOMER TF motif analysis of regions of increased accessibility in dKO vs. WT sorted CAFs. Fisher Exact test P-values shown. h) H3K27ac ChIP signal in serum-stimulated cultured CAFs at ATAC-seq regions defined in (j). The same scale was used as in (g) for comparison.
