Nucleosome positions predicted through comparative genomics

Ilya P. Ioshikhes, Istvan Albert, Sara J. Zanton, B. Franklin Pugh

Research output: Contribution to journalArticle

252 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1210-1215
Number of pages6
JournalNature Genetics
Volume38
Issue number10
DOIs
StatePublished - Oct 1 2006

All Science Journal Classification (ASJC) codes

  • Genetics

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