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dc.contributor.authorYuan, Guo-Cheng
dc.contributor.authorLiu, Jun
dc.date.accessioned2010-09-30T17:19:38Z
dc.date.issued2008
dc.identifier.citationYuan, Guo-Cheng, and Jun S. Liu. 2008. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Computational Biology 4(1): e13.en_US
dc.identifier.issn1553-734Xen_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:4454676
dc.description.abstractThe regulation of DNA accessibility through nucleosome positioning is important for transcription control. Computational models have been developed to predict genome-wide nucleosome positions from DNA sequences, but these models consider only nucleosome sequences, which may have limited their power. We developed a statistical multi-resolution approach to identify a sequence signature, called the N-score, that distinguishes nucleosome binding DNA from non-nucleosome DNA. This new approach has significantly improved the prediction accuracy. The sequence information is highly predictive for local nucleosome enrichment or depletion, whereas predictions of the exact positions are only modestly more accurate than a null model, suggesting the importance of other regulatory factors in fine-tuning the nucleosome positions. The N-score in promoter regions is negatively correlated with gene expression levels. Regulatory elements are enriched in low N-score regions. While our model is derived from yeast data, the N-score pattern computed from this model agrees well with recent high-resolution protein-binding data in human.en_US
dc.description.sponsorshipStatisticsen_US
dc.language.isoen_USen_US
dc.publisherPublic Library of Scienceen_US
dc.relation.isversionofdoi:10.1371/journal.pcbi.0040013en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211532/pdf/en_US
dash.licenseLAA
dc.subjectcomputational biologyen_US
dc.subjectgenetics and genomicsen_US
dc.subjectmolecular biologyen_US
dc.subjectsaccharomycesen_US
dc.titleGenomic Sequence is Highly Predictive of Local Nucleosome Depletionen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalPLoS Computational Biologyen_US
dash.depositing.authorLiu, Jun
dc.date.available2010-09-30T17:19:38Z
dc.identifier.doi10.1371/journal.pcbi.0040013*
dash.contributor.affiliatedLiu, Jun


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