Evolution of nucleosomes position in yeasts: conservation of global pattern and divergence of gene-specific patterns

This master project describes computational analysis of nucleosomes positioning in four yeast species: S. cerevisiae, S. kudriavzevii, S. bayanus (three relatively close species, ~75% of sequence similarity) and C. glabrata (more distant, ~57% of sequence similarity). We found that the global organization of nucleosomes previously described in S. cerevisiae (Nucleosome Depleted Region followed by an array of nucleosomes) was largely conserved among the different species also with the conservation of occupied/depleted promoters' classification from previous works redefined here in a more specific way. However, this conservation of general pattern does not reflect the evolution of gene specific pattern. Indeed, we show that nucleosome pattern diverged rapidly leaving practically no similarities between S. cerevisiae and C. glabrata orthologs. This was confirmed by different analysis and additional data from other species. In contrast, the pattern of gene expression and the response to stress were largely conserved among this species. Together, these results suggest that the general properties of nucleosome patterns and some specific features are conserved even if the gene specific patterns diverge much faster than the DNA sequence and the expression patterns. This argues strongly in favor of a model where different configurations of nucleosomes positions can encode the same expression output and where nucleosomes features evolve mainly by neutral drift