Nucleosome positions predicted through comparative genomics
Nucleosome positions predicted through comparative genomics
复制标题
DOI：
10.1038/ng1878
复制
发表时间：
2006-10-01
期刊：
影响因子：
30.8
通讯作者：
Pugh, B. Franklin
中科院分区：
文献类型：
--
作者：
Ioshikhes, Ilya P.;Albert, Istvan;Pugh, B. Franklin
长期以来，DNA序列一直被认为是核小体定位的重要因素，核小体定位具有调节基因获取的潜力。启动子的核小体结构在多大程度上被潜在的序列描绘出来，现在正在研究中。在这里，我们使用比较基因组学来报告位于所有酿酒酵母基因附近的核小体定位序列(NPSS)的全基因组图谱。我们发现，潜在的DNA序列提供了一个非常好的预测核小体位置的方法，这些位置已经被实验地映射到基因组的一小部分。值得注意的是，不同类别的基因具有NPSS的特征排列，这可能对它们的调控很重要。特别是，在启动子区域具有相对紧凑的NPS排列的基因往往有一个埋在NPS中的TATA盒，并且往往受到染色质修饰和重塑因子的高度调控。
DNA sequence has long been recognized as an important contributor to nucleosome positioning, which has the potential to regulate access to genes. The extent to which the nucleosomal architecture at promoters is delineated by the underlying sequence is now being worked out. Here we use comparative genomics to report a genome-wide map of nucleosome positioning sequences (NPSs) located in the vicinity of all Saccharomyces cerevisiae genes. We find that the underlying DNA sequence provides a very good predictor of nucleosome locations that have been experimentally mapped to a small fraction of the genome. Notably, distinct classes of genes possess characteristic arrangements of NPSs that may be important for their regulation. In particular, genes that have a relatively compact NPS arrangement over the promoter region tend to have a TATA box buried in an NPS and tend to be highly regulated by chromatin modifying and remodeling factors.