Combinatorial Roles of DNA Methylation and Histone Modifications on Gene Expression
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Gene regulation, despite being investigated in a large number of works, is still yet to be well understood. The mechanisms that control gene expression is one of the open problems. Epigenetic factors, among others, are assumed to have a role to play. In this work, we focus on DNA methylation and post-translational histone modifications (PTMs). These individually have been shown to contribute to controlling of gene expression. However, neither can totally account for the expression levels, i.e. low or high. Therefore, the hypothesis of their combinatorial role, as two of the most influencing factors, has been established and discussed in literature. Taking a computational approach based on rule induction, we derived \(83\) rules and identified some key PTMs that have considerable effects such as H2BK5ac, H3K79me123, H4K91ac, and H3K4me3. Also, some interesting patterns of DNA methylation and PTMs that can explain the low expression of genes in CD4\(+\) T cell. The results include previously reported patterns as well as some new valid ones which could give some new insights to the process in question.
KeywordsDNA methylation Histone modification Gene regulation Gene expression
We would like to gratefully thank Prof. Nada Lavrac and Dr. Branko Kavsek for sharing CN2-SD software. The first author has received funding from Institute of Information and Technology and support from Centre for Informatics and Computing, Vietnam Academy of Science and Technology to conduct this research.
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