Fan, S., Zhang, M. Q., Zhang, X. (2008) Histone methylation marks play important roles in predicting the methylation status of CpG islands. Biochemical and Biophysical Research Communications, 374 (3). pp. 559-564. ISSN 0006291X
Abstract
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. © 2008 Elsevier Inc. All rights reserved.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | CpG island DNA methylation Epigenetics Histone methylation |
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering organism description > animal > mammal > primates > hominids > human bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein methylation bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > zinc finger proteins |
| CSHL Authors: | |
| Communities: | CSHL labs > Zhang lab |
| Depositing User: | Tom Adams |
| Date: | 2008 |
| Date Deposited: | 26 Jul 2011 19:37 |
| Last Modified: | 13 Mar 2018 20:52 |
| PMCID: | PMC2974564 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/7729 |
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