Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence.
Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence.
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DOI：
10.1186/1471-2164-10-15
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发表时间：
2009-01-10
期刊：
影响因子：
4.4
通讯作者：
He C
中科院分区：
文献类型：
--
作者：
Dai Z;Dai X;Xiang Q;Feng J;Wang J;Deng Y;He C
核小体是真核生物基因组的基本单位。它的定位在依赖于获得基因组DNA的各种细胞过程中发挥着核心作用。实验证据表明，基因组DNA序列是核小体定位的重要决定因素之一。然而，在不同启动子中，潜在DNA序列在核小体定位中的作用是否有所不同，目前还不太清楚。核小体定位的不同决定因素是否对核小体调控有独特的影响还有待阐明。我们在酵母中确定了两个典型的启动子类别，分别与核小体定位对潜在DNA序列的高或低依赖性相关。重要的是，这两类人分别对核小体具有较低或较高的本征序列偏好。这两类基因还具有多种启动子特征，包括核小体占有率、核小体模糊性、H_2A.Z占有率、转录扰动前后核小体位置的变化以及基因活性。这两类蛋白都有很高的组蛋白H3的周转率，但使用了不同的核小体调节模式：第一类是以高乙酰化为特征，而第二类是高度受依赖于ATP的染色质重塑调节。我们的结果，结合已知的核小体调制特征，表明不同基因选择性使用的两种不同的核小体调制模式与核小体的固有序列偏好有关。核小体调控方式的不同可以解释DNA序列对核小体定位的贡献在两类启动子之间的差异。
The nucleosome is the fundamental unit of eukaryotic genomes. Its positioning plays a central role in diverse cellular processes that rely on access to genomic DNA. Experimental evidence suggests that the genomic DNA sequence is one important determinant of nucleosome positioning. Yet it is less clear whether the role of the underlying DNA sequence in nucleosome positioning varies across different promoters. Whether different determinants of nucleosome positioning have characteristic influences on nucleosome modulation also remains to be elucidated. We identified two typical promoter classes in yeast associated with high or low dependence of nucleosome positioning on the underlying DNA sequence, respectively. Importantly, the two classes have low or high intrinsic sequence preferences for nucleosomes, respectively. The two classes are further distinguished by multiple promoter features, including nucleosome occupancy, nucleosome fuzziness, H2A.Z occupancy, changes in nucleosome positions before and after transcriptional perturbation, and gene activity. Both classes have significantly high turnover rates of histone H3, but employ distinct modes of nucleosome modulation: The first class is characterized by hyperacetylation, whereas the second class is highly regulated by ATP-dependent chromatin remodelling. Our results, coupled with the known features of nucleosome modulation, suggest that the two distinct modes of nucleosome modulation selectively employed by different genes are linked with the intrinsic sequence preferences for nucleosomes. The difference in modes of nucleosome modulation can account for the difference in the contribution of DNA sequence to nucleosome positioning between both promoter classes.
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