Donnelly Centre for Cellular & Biomolecular Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
Mol Cell Biol. 2011 Nov;31(21):4348-55. doi: 10.1128/MCB.05276-11. Epub 2011 Sep 6.
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.
为了研究核小体占据在基因表达进化中的作用，我们测量了四个酵母物种的全基因组核小体图谱，其中三个属于酿酒酵母谱系，另一个是亲缘关系较远的光滑球拟酵母。与来自酿酒酵母谱系的同源基因相比，光滑球拟酵母基因的核小体和相关启动子元件通常向前移动约 20 个碱基对。然而，所有物种都表现出与最初在酿酒酵母中描述的相同的全局组织特征：基因上存在典型的核小体组织，以及将启动子分为包含或缺乏明显核小体缺失区域（NDR）的两种类型，后者显示出更动态的基因表达模式。然而，尽管存在这种全局相似性，但在酿酒酵母谱系和光滑球拟酵母的同源基因之间，特定基因的核小体占据情况存在广泛的差异（约 5000 万年）。具有动态表达模式的同源基因往往保持其缺乏 NDR，但除此之外，酿酒酵母谱系和光滑球拟酵母的同源基因在核小体占据模式上与非同源基因非常相似。这种核小体占据的广泛差异与保守的基因表达模式形成对比。因此，虽然核小体占据的一些进化变化有助于基因表达的分化，但核小体占据经常发生广泛的变化，而对基因表达的影响似乎很小。
