title: Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns.
abstract: To examine the role of nucleosome occupancy in the evolution of gene expression, we measured the genome-wide nucleosome profiles of four yeast species, three belonging to the Saccharomyces sensu stricto lineage and the more distantly related Candida glabrata. Nucleosomes and associated promoter elements at C. glabrata genes are typically shifted upstream by ∼20 bp, compared to their orthologs from sensu stricto species. Nonetheless, all species display the same global organization features first described for Saccharomyces cerevisiae: a stereotypical nucleosome organization along genes and a division of promoters into those that contain or lack a pronounced nucleosome-depleted region (NDR), with the latter displaying a more dynamic pattern of gene expression. Despite this global similarity, however, nucleosome occupancy at specific genes diverged extensively between sensu stricto and C. glabrata orthologs (∼50 million years). Orthologs with dynamic expression patterns tend to maintain their lack of NDR, but apart from that, sensu stricto and C. glabrata orthologs are nearly as similar in nucleosome occupancy patterns as nonorthologous genes. This extensive divergence in nucleosome occupancy contrasts with a conserved pattern of gene expression. Thus, while some evolutionary changes in nucleosome occupancy contribute to gene expression divergence, nucleosome occupancy often diverges extensively with apparently little impact on gene expression.
authors: Donnelly Centre for Cellular & Biomolecular Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
authors: Kyle
authors: K
authors: Tsui
authors: Sébastien
authors: S
authors: Dubuis
authors: Marinella
authors: M
authors: Gebbia
authors: Randall H
authors: RH
authors: Morse
authors: Naama
authors: N
authors: Barkai
authors: Itay
authors: I
authors: Tirosh
authors: Corey
authors: C
authors: Nislow
mesh_terms: D041221:Candida glabrata / Q000145:classification / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics; D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D040961:Genetic Drift; D016681:Genome, Fungal; D055106:Genome-Wide Association Study; D009707:Nucleosomes / Q000235:genetics*; D012440:Saccharomyces / Q000145:classification / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes