Nucleosome positioning for 4 yeast species

We describe the genome-wide nucleosome profiles of four related yeast species. All species display the same global organization features first described in S. cerevisiae: a stereotypical nucleosome organization along genes, and the classification of promoters into these which contain or lack a pronounced Nucleosome Depleted region (NDR), with the latter displaying a more dynamic pattern of gene expression. This global similarity, however, does not reflect a static evolutionary pattern, as nucleosome positioning at specific genes diverged rapidly leaving practically no similarity between S. cerevisiae and C. glabrata orthologs (~50 Myr). We show that this rapid divergence in nucleosome positioning contrasts a conserved pattern of gene expression, consistent with the idea that divergence of nucleosome patterns has a limited effect on gene expression as many different configurations can support the same regulatory outcome. Overall design: Nucleosomes from 4 different yeast species were isolated and sequenced using the Illumina GAII platform. Replicates were performed for 3 of the species