Journal
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Volume 374, Issue 3, Pages 559-564Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.bbrc.2008.07.077
Keywords
DNA methylation; CpG island; histone methylation; epigenetics
Categories
Funding
- National Natural Science Foundation of China [60540420569, 30625012, 60721003]
- National Basic Research Program of China [2004CB518605]
- Hi-tech Research and Development Program of China [2006AA02Z325]
- National Institutes of Health [HG01696]
- Changjiang Scholar Award of China
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The methylation status of CpG islands is highly correlated with gene expression. Current methods for computational prediction of DNA methylation only utilize DNA sequence features. In this study, besides 35 DNA sequence features, we added four histone methylation marks to predict the methylation status of CpG islands, and improved the accuracy to 89.94%. Also we applied our model to predict the methylation pattern of all the CpG islands in the human genome, and the results are consistent with the previous reports. Our results imply the important roles of histone methylation marks in affecting the methylation status of CpG islands. H3K4me enriched in the methylation-resistant CpG islands could disrupt the contacts between nucleosomes, unravel chromatin and make DNA sequences accessible. And the established open environment may be a prerequisite for or a consequence of the function implementation of zinc finger proteins that could protect CpG islands from DNA methylation. (C) 2008 Elsevier Inc. All rights reserved.
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