Cell Cycle–Specified Fluctuation of Nucleosome Occupancy at Gene Promoters

The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence.

DNA包装为核小体（nucleosome）会影响其下游调控信息的可及性。目前对核小体占据率与定位的最佳研究来自出芽酵母——酿酒酵母（Saccharomyces cerevisiae），不过此类研究多基于异步细胞群体或针对单个启动子（如PHO5与GAL1–10）展开。本研究借助FAIRE（甲醛辅助调控元件分离术，formaldehyde-assisted isolation of regulatory elements）与全基因组微阵列技术，对同步化培养的酿酒酵母群体中，有丝分裂细胞周期全程的核小体占据率变化进行了检测。令人意外的是，不同细胞周期阶段的核小体占据率并未出现大范围的全局差异。不过，细胞周期调控基因的启动子区域的核小体占据率，会特异性降低至该基因达到表达峰值的细胞周期阶段，S期基因（S-phase genes）是显著例外。我们所提交的数据证实，FAIRE可作为一种高通量的核小体占据率检测方法。本研究首次在任意生物系统中实现了全细胞周期范围内的全基因组核小体占据率图谱绘制。多数细胞周期调控基因的启动子区域核小体占据率的波动，为这些基因的周期性表达主要受转录水平调控提供了独立证据。G2/M期基因（G2/M genes）的启动子与其他细胞周期启动子的区别在于，其在整个细胞周期中均呈现异常低的基础核小体占据率。这一观察结果，结合编码与非编码基因座之间固有的典型核小体占据率状态在细胞周期中得以维持的现象，表明核小体占据率变异的最大组成部分是“固有固定”的，其调控可能发生在DNA序列层面。