Co-variation of chromatin marks. a Correlation of epigenomic profiles in each strain. Colors represent Spearman coefficients of pairs of histone marks, computed on the genome-wide vectors of nucleosome-level ChIP/MNase signal. Low or negative correlations correspond to marks located on different nucleosomes. b Correlation between inter-strain difference in one histone mark and inter-strain difference in another mark. In each strain–strain comparison, the divergence of one mark was quantified on every nucleosome, while accounting for differential nucleosomal abundance (Fig. 6). Color Spearman correlation coefficient between such estimates of two histone marks, across all nucleosomes. c Fraction of SNEPs co-varying with another mark. For each strain pair, the set of nucleosomes harboring an SNEP of mark (1) was analyzed by counting how many showed significant divergence in mark (2) (at p value <0.01) in the same direction [higher level of mark (2) in the strain with higher level of mark (1)]. The p value corresponded to the nominal test used to detect SNEPs of mark (2). d Co-variation of specific H3K14ac SNEPs with other active marks. All ‘labile’ and ‘persistent’ SNEPs described in  were matched to nucleosomes of the current study and retained if matching was unambiguous and if H3K14ac SNEP significance in the current study verified p value <0.001. They were then analyzed by counting how many of them co-varied consistently with H3K9ac, H4K12ac, or H3K4me3 in the BY–RM comparison. e Co-variation with H3K4me3 is more frequent among persistent H3K14ac SNEPs than among labile H3K14ac SNEPs even when accounting for genetic control. The 327 persistent SNEPs (d) were split according to whether they were under the control of an aceQTL or not . Stars indicate the significance of a Chi square test of independence at p = 0.012 (*) and p < 10−13 (**).