Fig. 3

Common consequences of Kat5 and Ep400 inactivation on gene expression in O9-1 cells. a RRHO analysis for comparison of DEGs in Kat5 and Ep400 ko clones ranked by their degree of differential expression. The heatmap shows a strong and statistically significant overlap in the downregulated genes. b RRHO analysis of terms obtained by GSEA of preranked genes from Kat5 and Ep400 ko clones ranked by p value reveals a strong overlap in terms with low P value. c KEGG pathway analysis for the identification of the main cellular processes (gray dots, red terms) and the key components (blue dots, black terms) affected by both Kat5 and Ep400 inactivation. d Quantitative RT-PCR to validate expression changes of DEGs related to carbohydrate (left) and amino acid (middle) metabolism or protein biosynthesis (right) shared between Kat5 and Ep400 ko clones. Normalized transcript levels for each gene in wildtype O9-1 cells (WT) were set to 1, and levels in ko clones (n = 3) expressed relative to it. e, f Chromatin immunoprecipitation to determine the occupancy of H2A.Z (e) and acetylated H4 (H4ac, f) near the transcriptional start site of the Pck2, Aldh18a1, Asns, Aars and Eif4ebp1 genes in wildtype O9-1 cells, Kat5 ko clone Kat5/3 and Ep400 clone Ep400/2. Fasl and Gm5741 genes served as controls. Amounts in precipitates were normalized to input and are presented as enrichment with histone-specific antibodies over IgG controls. Statistical significance was determined by 2-way ANOVA and Dunett’s post test (e, f) (*P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001)