Gene clustering according to BY–RM epigenomic divergence. For each gene, the ChIP/MNase log ratio in each strain was computed on genomic bins covering the gene body (from TSS to TES, orange box, divided in percentiles) together with 500 bp of their upstream and downstream regions. The difference in signal between the two strains was computed (black to red color scale). Genes were clustered by their similarity in this differential signal across the five chromatin marks. a Average pattern of the 23 clusters described in Table 1. b Details of three clusters with previously measured differential mRNA expression . Cyan missing mRNA data. c Correlation between gene expression (y-axis) and histone modification (x-axis) variation. For each modification, inter-strain difference was computed as the mean of (log2(ChIP/Mnase) of strain 1 − log2(ChIP/Mnase) strain 2) from the TSS to the TES. Each plot corresponds to one histone modification compared between two strains, with dots representing genes. Only genes for which the mean log ratio was above zero in at least one strain were considered. Upper panels BY versus RM. Lower panels BY versus YJM. ρ Pearson correlation coefficient. Lines linear fits. d Same analysis as in c but for the expression of non-coding transcripts in BY and YJM .