Qualitatively Predicting Acetylation and Methylation Areas in DNA Sequences

Tho Hoan Pham[1] (h-pham@jaist.ac.jp)
Dang Hung Tran[2] (tran@jaist.ac.jp)
Tu Bao Ho[2],[3] (bao@jaist.ac.jp)
Kenji Satou[2],[3] (ken@jaist.ac.jp)
Gabriel Valiente[4] (valiente@lsi.upc.edu)

[1]Faculty of Information Technology, Hanoi University of Pedagogy, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
[2]School of Knowledge Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
[3]Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Agency (JST), Japan
[4]Department of Software, Technical University of Catalonia, E-08034 Barcelona, Spain


Abstract

Eukaryotic genomes are packaged by the wrapping of DNA around histone octamers to form nucleosomes. Nucleosome occupancy, acetylation, and methylation, which have a major impact on all nuclear processes involving DNA, have been recently mapped across the yeast genome using chromatin immunoprecipitation and DNA microarrays. However, this experimental protocol is laborious and expensive. Moreover, experimental methods often produce noisy results. In this paper, we introduce a computational approach to the qualitative prediction of nucleosome occupancy, acetylation, and methylation areas in DNA sequences. Our method uses support vector machines to discriminate between DNA areas with high and low relative occupancy, acetylation, or methylation, and rank k-gram features based on their support for these DNA modifications. Experimental results on the yeast genome reveal genetic area preferences of nucleosome occupancy, acetylation, and methylation that are consistent with previous studies. Supplementary files are available from http://www.jaist.ac.jp/~tran/nucleosome/.

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Japanese Society for Bioinformatics