JAIST Repository >
School of Knowledge Science >
Articles >
Journal Articles >

Please use this identifier to cite or link to this item: http://hdl.handle.net/10119/9210

Title: Characterizing nucleosome dynamics from genomic and epigenetic information using rule induction learning
Authors: Le, Ngoc Tu
Ho, Tu Bao
Tran, Dang Hung
Issue Date: 2009-12-03
Publisher: BioMed Central Ltd.
Magazine name: BMC Genomics
Volume: 10
Number: Suppl 3
Start page: article no.S27
DOI: 10.1186/1471-2164-10-S3-S27
Abstract: 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
Material Type: publisher
Appears in Collections:a10-1. 雑誌掲載論文 (Journal Articles)

Files in This Item:

File Description SizeFormat
14179.pdf347KbAdobe PDFView/Open

All items in DSpace are protected by copyright, with all rights reserved.


Contact : Library Information Section, Japan Advanced Institute of Science and Technology