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This article is part of the supplement: Eighth International Conference on Bioinformatics (InCoB2009): Computational Biology

Open Access Proceedings

Characterizing nucleosome dynamics from genomic and epigenetic information using rule induction learning

Ngoc Tu Le12*, Tu Bao Ho13 and Dang Hung Tran12

Author Affiliations

1 School of Knowledge Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan

2 Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam

3 Vietnamese Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam

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BMC Genomics 2009, 10(Suppl 3):S27  doi:10.1186/1471-2164-10-S3-S27

Published: 3 December 2009

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.