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このアイテムの引用には次の識別子を使用してください:
http://hdl.handle.net/10119/9210
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| タイトル: | Characterizing nucleosome dynamics from genomic and epigenetic information using rule induction learning |
| 著者: | Le, Ngoc Tu
Ho, Tu Bao
Tran, Dang Hung |
| 発行日: | 2009-12-03 |
| 出版者: | BioMed Central Ltd. |
| 誌名: | BMC Genomics |
| 巻: | 10 |
| 号: | Suppl 3 |
| 開始ページ: | article no.S27 |
| DOI: | 10.1186/1471-2164-10-S3-S27 |
| 抄録: | Background: Eukaryotic genomes are packaged into chromatin, a compact structure containing fundamental repeating units, the nucleosomes. The mobility of nucleosomes plays important roles in many DNA-related processes by regulating the accessibility of regulatory elements to biological machineries. Although it has been known that various factors, such as DNA sequences, histone modifications, and chromatin remodelling complexes, could affect nucleosome stability, the mechanisms of how they regulate this stability are still unclear. Results: In this paper, we propose a novel computational method based on rule induction learning to characterize nucleosome dynamics using both genomic and histone modification information. When applied on S. cerevisiae data, our method produced totally 98 rules characterizing nucleosome dynamics on chromosome III and promoter regions. Analyzing these rules we discovered that, some DNA motifs and post-translational modifications of histone proteins play significant roles in regulating nucleosome stability. Notably, these DNA motifs are strong determinants for nucleosome forming and inhibiting potential; and these histone modifications have strong relation with transcriptional activities, i.e. activation and repression. We also found some new patterns which may reflect the cooperation between these two factors in regulating the stability of nucleosomes. Conclusion: DNA motifs and histone modifications can individually and, in some cases, cooperatively regulate nucleosome stability. This suggests additional insights into mechanisms by which cells control important biological processes, such as transcription, replication, and DNA repair. |
| Rights: | BMC Genomics 2009, 10(Suppl 3):S27 doi: 10.1186/1471-2164-10-S3-S27 This article is available from: http://www.biomedcentral.com/1471-2164/10/S3/S27 © 2009 Le et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| URI: | http://hdl.handle.net/10119/9210 |
| 資料タイプ: | publisher |
| 出現コレクション: | a10-1. 雑誌掲載論文 (Journal Articles)
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このアイテムのファイル:
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記述 |
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| 14179.pdf | | 347Kb | Adobe PDF | 見る/開く |
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