Ioshikhes Ilya P, Albert Istvan, Zanton Sara J, Pugh B Franklin
Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.
Nat Genet. 2006 Oct;38(10):1210-5. doi: 10.1038/ng1878. Epub 2006 Sep 10.
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.
DNA序列长期以来一直被认为是核小体定位的重要因素，而核小体定位有可能调节基因的可及性。目前，人们正在研究启动子处的核小体结构在多大程度上由其潜在序列所界定。在此，我们利用比较基因组学报告了酿酒酵母所有基因附近的全基因组核小体定位序列（NPS）图谱。我们发现，潜在的DNA序列能很好地预测已通过实验定位到基因组一小部分的核小体位置。值得注意的是，不同类别的基因拥有NPS的特征性排列，这可能对其调控很重要。特别是，在启动子区域具有相对紧凑的NPS排列的基因，其TATA框往往埋藏在一个NPS中，并且往往受到染色质修饰和重塑因子的高度调控。
