Interspecies differences in H3K4me3, compared to H3K9ac, better predict expression divergence.

<p><b>(A)</b> Correlation between interspecies expression differences and either H3K9ac (<i>red</i>) or H3K4me3 (<i>blue</i>) changes, at different regions along a gene, as indicated. Correlations were calculated for significant changes in expression and modifications (absolute differences greater than 0.4 (log₂ scale)). <b>(B)</b> Scatter plot of interspecies differences in mRNA levels against changes in ‘peak’ H3K9ac. Genes showing consistent changes between <i>S. cerevisiae</i> and <i>S. paradoxus</i> (<i>dark red</i>), opposite changes (<i>pink</i>), no changes in either parameter (<i>light grey</i>), changes in only in H3K9ac (<i>light red</i>), and changes only in expression (<i>dark grey</i>) are marked. The numbers of genes showing consistent or opposite changes are noted, and the relative proportions of each group are indicated in the adjacent pie chart. <b>(C)</b> As in (B), but for H3K4me3 changes. Genes showing consistent changes (<i>dark blue</i>), opposite changes (<i>light blue</i>), no changes in either parameter (<i>light grey</i>), changes in only in H3K9ac (<i>blue</i>), and changes only in expression (<i>dark grey</i>) are marked. <b>(D)</b><i>Upper panel</i>, Interspecies correlation between expression differences and H3K9ac (<i>red</i>) or H3K4me3 (<i>blue</i>) differences at different regions along a gene, as indicated, calculated at increasing absolute thresholds (for both expression and modification changes). <i>Middle panel</i>, Graph depicting the proportion of genes for which interspecies changes in expression and modifications (at different regions) are consistent (in the same direction). Percentages were calculated for an increasing threshold of absolute modification differences, and considering significant expression differences (> 0.4). <i>Lower panel,</i> Genes with the largest and smallest differences in expression <i>S. cerevisiae</i> and <i>S. paradoxus</i> (‘<i>divergent</i>’ and ‘<i>non-divergent</i>’; 1000 genes each) were taken. Thereafter, for an increasing threshold of absolute differences in modifications at different regions, the fold enrichment of divergent over non-divergent genes was calculated at each threshold. <b>(E)</b> Enrichment (<i>upper panels</i>) or depletion (<i>lower panels</i>) of sets of genes defined according to patterns of H3K9ac/mRNA changes (<i>left</i>) or H3K4me3/mRNA changes (<i>right</i>) amongst the indicated architectural or phenomenological gene classes; <i>p</i> values were calculated using a hypergeometric test. <b>(F)</b> Genes were classified based on interspecies variation in all three parameters (H3K9ac, H3K4me3, expression): those showing no change in either (<i>light grey</i>), consistent changes amongst all three (<i>purple</i>), consistent changes between H3K9ac and H3K4me3 but not expression (<i>dark grey</i>), consistent changes between H3K9ac and expression but not H3K4me3 (<i>light red</i>), and those showing consistent changes between H3K4me3 and expression but not H3K9ac (<i>blue</i>). Gene sets were subsequently analyzed as in (E).