Inter-strain distances according to five epigenomic marks. a Hierarchical clustering of strains. For each histone modification, the distance between two samples was determined as 1 − ρ, where ρ is the Spearman rank-based correlation coefficient between the profiles of the two samples. Profiles comprised ChIP counts computed at every nucleosome by NucleoMiner2.0  (see “Methods”). b–f ChIP coverage profiles of the indicated marks along an average gene (in per-million reads, normalized and averaged across replicates). Colors correspond to strains as in a. g Same representation but for MNase average profile. h H3K14 acetylation differences between the BY and RM strains, before and after the transient reprogramming described in . The distribution of log2(RM/BY) of ChIP-CHIP intensities is shown for all nucleosomes (gray) and for the subset of nucleosomes (magenta) located in the second half of the body of 529 genes responsible for the specific pattern of RM. Magenta and gray distributions significantly differ (Kolmogorov–Smirnov p value <10−15) both before and after reprogramming. i Genomic QTL scan for regulators of the RM-specific K14ac profile in f. Red line significance threshold determined by permutations. Linkage score: −log10(P), where P is the nominal QTL p value.