An organism's DNA contains numerous regulatory sequences that are used to modulate gene expression; yet DNA sequence alone does not explain why some regulatory sequences are functional while others are not. Because most genomic DNA (80% on average) is tightly packaged into nucleosomes [1
], alternating nucleosome occupancy has been proposed as an important strategy to regulate gene expression since its initial discovery [2
]. Indeed, higher expression levels are commonly associated with nucleosome depletion at promoters and other genomic locations, e.g. rDNA [1
]. It has also been demonstrated that nucleosome occupancy affects the accessibility of DNA sequence motifs to transcriptional regulators; as a consequence different DNA sequences can display different nucleosome occupancy levels [1
]. Further, motifs recognized and bound by active transcription factors are more likely to be nucleosome-depleted than those recognized by inactive ones [1
]. Differential occupancy on many motifs has been observed in certain environmental conditions [14
] and following environmental stresses [16
]. However, it remains controversial whether changes of nucleosome occupancy [16
] or their initial positioning [14
] determines levels of gene expression.
Most previous studies have focused on measurements of average transcription levels and average nucleosome occupancy over regulatory regions. The one-to-one connection between the occupancy of individual motifs and the resulting effect on gene expression has been tested only for a small number of genes. A recent study demonstrated that nucleosome depletion at two cell cycle-regulated promoters, CLN2pr
, ensures periodic expression pattern of genes involved in cell-cycle progression [17
]. These experiments clearly linked a specific expression pattern (cell-cycle periodicity) to nucleosome occupancy. The generality of this phenomenon for genes containing cell cycle regulating motifs remains to be tested through genome-wide experiments.
An average correlation between expression level and nucleosome occupancy at promoters across species has been reported [18
], but it is not, however, clear how motif-specific nucleosome occupancy patterns affect the expression of individual genes across different species. To address this question, we sought an analysis approach that transcends the average expression level and targets the response at a specific class of motifs under specific conditions. Although predictions of nucleosome occupancy often assume that nucleosome positions are identical on conserved DNA sequences [19
], experimental data is needed to test this assumption to better understand how nucleosome occupancy on motifs relates to phenotypic evolution. Such comparison across species can provide insight that augments ongoing efforts to define the relative contributions of cis
acting factors in phenotype divergence.
In this study, we determined the genome-wide nucleosome positions in the yeast S. bayanus
, and compared these findings to patterns of gene expression during the cell cycle of S. cerevisiae
and S. bayanus
, two closely related sensu stricto
yeast species. We show that changes in nucleosome occupancy on motifs are correlated with phenotypic divergence between species. In particular, our results show that nucleosomes provide a conspicuous genome-wide signature of MBP1 cell-cycle motif recognition in these two yeasts and this signature distinguishes which motifs result in periodic, cyclic expression patterns of the downstream genes. Although averaged expression level has previously been negatively linked to nucleosome occupancy at promoters [1
], our data provide a high-resolution, genome-wide demonstration of how the interplay between nucleosome occupancy and motif content is related to a specific expression pattern (i.e
. in the cell cycle) of individual genes. Conserved transcription factor binding sites are more likely to be nucleosome-depleted, suggesting that patterns of nucleosome occupancy may reflect conservation of regulatory circuits across species. Finally, our cross-species comparison of transcription factor binding sites and nucleosome occupancy patterns reveals that changes in nucleosome-motif interactions are correlated to expression divergence, i.e. despite their conserved presence, motifs that become nucleosome-occupied during evolution no longer regulate downstream gene expression.