Independently of motif movements, nucleosome occupancy is correlated to expression divergence. A. Schematic of the alignment of the upstream regions to identify orthologous motifs between S. cerevisiae and S. bayanus. For the MBP1 binding site consensus [AGT][AT]CGCG[AT], a motif is considered to be conserved if the whole motif region is aligned and either the original motif is completely conserved, or it has changed into another form of the consensus. A motif is considered unconserved if the motif is not aligned or, despite complete alignment, the corresponding position does not constitute an MBP1 motif. B. All S. cerevisiae genes periodically expressed during the cell cycle and with an upstream MBP1 were first identified. Their orthologous motifs and genes in S. bayanus were then identified and only those genes with conserved motifs at aligned positions were considered. These S. bayanus orthologs were categorized into genes that show cyclic expression and those that do not. Nucleosome occupancy centered at these motifs of the two groups was plotted. C. We examined the conservation of expression patterns of S. cerevisiae from S. bayanus (a complementary comparison to B). The differential nucleosome occupancy levels of the two groups (conserved cyclic expression vs. non-cyclic expression) were depicted.