Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion Export

@article{Yuan2008, abstract = {The 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.}, author = {Yuan, Guo-Cheng and Liu, Jun S.}, citeulike-article-id = {2297339}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.0040013}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18225943}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18225943}, day = {1}, doi = {10.1371/journal.pcbi.0040013}, journal = {PLoS Computational Biology}, keywords = {chip-seq, hmm, nucleosome, sequences}, month = {January}, number = {1}, pages = {e13+}, posted-at = {2009-04-23 10:31:05}, priority = {2}, title = {Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion}, url = {http://dx.doi.org/10.1371/journal.pcbi.0040013}, volume = {4}, year = {2008} }

TY - JOUR ID - Yuan2008 L3 - citeulike-article-id:2297339 N2 - The 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. IS - 1 JF - PLoS Computational Biology TI - Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion VL - 4 SP - e13 KW - chip-seq KW - hmm KW - nucleosome KW - sequences AU - Yuan, Guo-Cheng AU - Liu, Jun PY - 2008/01/01/ UR - http://dx.doi.org/10.1371/journal.pcbi.0040013 ER -