Nucleosome-coupled expression differences in closely-related species

Abstract

Background: Genome-wide nucleosome occupancy is negatively related to the average level of transcription factor motif binding based on studies in yeast and several other model organisms. The degree to which nucleosome-motif interactions relate to phenotypic changes across species is, however, unknown.

Results: We address this challenge by generating nucleosome positioning and cell cycle expression data for Saccharomyces bayanus and show that differences in nucleosome occupancy reflect cell cycle expression divergence between two yeast species, S. bayanus and S. cerevisiae. Specifically, genes with nucleosome-depleted MBP1 motifs upstream of their coding sequence show periodic expression during the cell cycle, whereas genes with nucleosome-shielded motifs do not. In addition, conserved cell cycle regulatory motifs across these two species are more nucleosome-depleted compared to those that are not conserved, suggesting that the degree of conservation of regulatory sites varies, and is reflected by nucleosome occupancy patterns. Finally, many changes in cell cycle gene expression patterns across species can be correlated to changes in nucleosome occupancy on motifs (rather than to the presence or absence of motifs).

Conclusions: Our observations suggest that alteration of nucleosome occupancy is a previously uncharacterized feature related to the divergence of cell cycle expression between species.

Figure 1

Absence of cyclic expression pattern correlates with nucleosome occupancy in A. S. bayanus and B. S. cerevisiae. Genes with MBP1/SWI4 consensus sites within the upstream region of the coding sequence start site were ranked from top to bottom by accordance to their cell cycle periodicity. Nucleosome level from -300 to 300 bp of the motif positions (arrow) for those genes (left) were laid in parallel to their expression level (right).

Figure 2

Correspondence between MBP1 motif binding, nucleosome depletion and expression pattern. A. Comparison of nucleosome occupancy between MBP1 bound motifs (blue line) [29] and unbound (black line) consensus sites CGCGT[CT] over the S. cerevisiae intergenic region. Comparison of nucleosome signals from -300 to 300 reveals that overall the bound (B) motifs (arrow) are more nucleosome-depleted than unbound (C) motifs although exceptions occur. D. Comparison of expression patterns during the cell cycle for genes with at least one bound MBP1 motif (blue line, as assessed by chromatin immuno-precipitation) in the region upstream of the start site, and genes (black line) that have an MBP1 consensus-match in the upstream intergenic region but that are not bound by the MBF protein complex. The cyclic expression patterns of genes with bound Mbp1p (E) are more apparent than the genes with an MBP1 motif present but without evidence of binding (F).

Figure 3

Non-conserved cell cycle motifs are more nucleosome-occupied. A. Genes containing the SWI4 DNA sequence binding consensus [AGT]ACGCG[AT][ACG]A in the upstream region in S. bayanus were divided into two categories, depending on motif occurrence in the orthologous upstream region in S. cerevisiae. The genes without the SWI4 consensus motif in S. cerevisiae (black line, C, arrow points to motif positions) tend to be more nucleosome-occupied on the motif position than the genes with conserved SWI4 motifs (blue line, B). D. The MBP1 DNA sequence consensus [AGT][AT]CGCGT[CT][AGT] observed in S. bayanus (similar to the MBP1 motif identified in S. cerevisiae) was divided into two categories: conserved (E) versus not present in S. bayanus (F). The genes with an MBP1 motif present in only S. cerevisiae (black line) are consistently more nucleosome occupied compared to the genes for which MBP1 binding sites are conserved in both species (blue line).

Figure 4

Difference of cell cycle expression pattern across species achieved by either differences in motif content or occupancy by nucleosomes. A. We identified MBP1 sites absent in S. bayanus but present in S. cerevisiae. The nucleosome signal around these sites (left) is compared against the expression profiles (right). B. The S. bayanus orthologous sequences of the functional motif sites from S. cerevisiae were ranked according to whether the downstream genes show a periodic expression pattern during the cell cycle. The nucleosome signal centered at the MBP1 motif (left) and the expression pattern of the downstream genes (right) was plotted.

Figure 5

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.