Nature Genetics
- 38, 1210 - 1215 (2006)
Published online: 10 September 2006; | doi:10.1038/ng1878
Nucleosome positions predicted through comparative genomicsIlya P Ioshikhes1, Istvan Albert2, Sara J Zanton3 & B Franklin Pugh31
Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA. 2
Bioinformatics Consulting Center, Huck Institutes for Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. 3
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Correspondence should be addressed to B Franklin Pugh bfp2@psu.edu 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.
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