Fig. 2

Changes in H3K27ac correlate with changes in genome organization and transcription within compartment switching regions. a Volcano plot showing differential analysis of all H3K27ac peaks in (i) WT and β-actin KO cells (ii) β-actin knockout and KO-actin cells iii) MEFs and ESCs. p-values based on two-tailed Wald test corrected for multiple testing using Benjamini–Hochberg procedure. Peaks showing log2FC >  = 2 and log2FC <  =  − 2 with padj <  = 0.05 were defined as upregulated and downregulated peaks respectively. b Barplots showing annotation of upregulated and downregulated H3K27ac peaks. c Boxplots showing average change in RNA-Seq expression for differentially expressed genes (FDR <  = 0.05) overlapping downregulated H3K27ac peaks, unchanging H3K27ac peaks, both upregulated and downregulated H3K27ac peaks and upregulated H3K27ac peaks: (i) average log2FC in KOvsWT expression for genes overlapping WT /KO H3K27ac peaks, (ii) average log2FC in KO-actin vs KO expression for genes overlapping WT/KO H3K27ac peaks, (iii) average log2FC in ESCvsMEF expression for genes overlapping ESC/MEF H3K27ac peaks. Number of genes in each category shown at the bottom. p-values based on two-tailed, two-sample Wilcoxon-rank sum test