Epigenetic and transcriptional regulation of Rho GTPase pathway genes in Y. enterocolitica infected macrophages.
A, Bar plot showing fraction and number (in bars) of indicated Rho GTPase pathway genes with changes in expression only (RNA only), histone modification only (ChIP only), overlaps between RNA-seq and ChIP-seq (RNA & ChIP) and no overlap with neither ChIP-seq nor RNA-seq (no overlap). B, Bar plot showing number of Rho GTPase pathway genes with dynamic histone modifications at promoters, enhancers or both (overlap). C, Table showing number of Rho GTPase pathway genes with histone modification changes at enhancers and number of associated enhancers. “% total enhancer associated genes” indicates what fraction of all Rho GTPase pathway genes with changes at enhancers show a certain number of changed enhancers. D, E, Heatmaps of DEGs with associated histone modification changes at promoters or enhancers encoding Rho GTPase effectors (D) and GEFs (E). Associated classes are color coded on the left. The specificity of GEFs for Rho GTPases is color coded on the right (E). Gene rlog counts were row-scaled (row Z-score). F, Table showing specificity of Rho GTPase effectors associated with RNA-seq and ChIP-seq overlaps in (A) and Fig 4C.