Divergence in nucleosome positioning. Our nucleosome mapping method defined two types of nucleosomal regions: well-positioned nucleosomes and UNRs, which correspond to conserved and variable positioning across biological replicates, respectively. a Shift in dyad position between strains for matched well-positioned nucleosomes. Lines show the distribution of the shifts between two strains. This panel considers the well-positioned nucleosomes of both strains that could be reliably matched. b Positioning divergence of nucleosomes that are well positioned in BY, but did not match a well-positioned nucleosome of RM. For all such BY nucleosomes (gray ellipse), two measures were retrieved that reflect distance to the nearest UNR (red rectangle) and nearest well-positioned nucleosome (red ellipse) in RM. Cases of full overlap (>99%) with a UNR from RM are not displayed because they correspond to conserved occupancy between the two strains. The blue line distinguishes a subpopulation of BY nucleosomes (pink dots) whose positions differ in RM [poorly matching a well-positioned nucleosome of RM (high x-axis value) or incomplete overlap with a nucleosomal region of RM (low y-axis value)]. c Average genic location of nucleosomes with differential positioning. The distributions show the location of well-positioned BY nucleosomes along an average gene. Gray all. Pink subset of nucleosomes whose positions differ in RM (pink flagged nucleosomes in a, combined with pink flagged nucleosomes in b). The fraction of nucleosomes that are not shifted (orange smoothed line) reflects conservation. d Transcriptional divergence between BY and RM. X-axis: log2 ratio of mRNA levels (data from ). Y-axis: density of genes. Black all genes. Pink 411 genes containing at least one nucleosome with differential positioning (from c). Shoulders in the pink distribution indicate matches between differential positioning and differential expression. The mode at zero shows that, for most of these genes, differential positioning is not accompanied by differential expression.