Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3′-end formation
Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3′-end formation
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DOI：
10.1073/pnas.1012674107
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发表时间：
2010-10-19
影响因子：
11.1
通讯作者：
Struhl, Kevin
中科院分区：
文献类型：
--
作者：
Fan, Xiaochun;Moqtaderi, Zarmik;Struhl, Kevin
微球菌核酸酶（MNase）产生的核小体的全基因组作图表明，酵母启动子和终止子区域是非常耗尽的核小体，主要是因为它们的DNA序列本质上不利于核小体的形成。然而，MNase具有很强的DNA序列特异性，有利于在启动子和终止子处切割，并解释了体内和体外组装的核小体占据模式之间的一些相关性。使用一种改进的方法来测量核小体占用在体内，不涉及MNase，我们证实，启动子区域强烈耗尽核小体，但发现终止子区域是比预期少得多耗尽。与启动子区域不同，终止子的核小体占有率与相邻基因的方向和距离密切相关。此外，核小体占用终止子的生长条件的强烈影响，这表明它不是主要由内在的组蛋白-DNA相互作用。RNA聚合酶II（pol II）的快速去除导致终止子处的核小体占据率增加，强烈表明核小体消耗的基于转录的机制。然而，终止子区域及其相应编码区域的不同行为表明，终止子处的核小体消耗不仅仅与pol II的通过相关，而是涉及与3 '端形成相关的不同机制。
Genome-wide mapping of nucleosomes generated by micrococcal nuclease (MNase) suggests that yeast promoter and terminator regions are very depleted of nucleosomes, predominantly because their DNA sequences intrinsically disfavor nucleosome formation. However, MNase has strong DNA sequence specificity that favors cleavage at promoters and terminators and accounts for some of the correlation between occupancy patterns of nucleosomes assembled in vivo and in vitro. Using an improved method for measuring nucleosome occupancy in vivo that does not involve MNase, we confirm that promoter regions are strongly depleted of nucleosomes, but find that terminator regions are much less depleted than expected. Unlike at promoter regions, nucleosome occupancy at terminators is strongly correlated with the orientation of and distance to adjacent genes. In addition, nucleosome occupancy at terminators is strongly affected by growth conditions, indicating that it is not primarily determined by intrinsic histone-DNA interactions. Rapid removal of RNA polymerase II (pol II) causes increased nucleosome occupancy at terminators, strongly suggesting a transcription-based mechanism of nucleosome depletion. However, the distinct behavior of terminator regions and their corresponding coding regions suggests that nucleosome depletion at terminators is not simply associated with passage of pol II, but rather involves a distinct mechanism linked to 3'-end formation.