Epigenetic approach for reconfiguring gene regulatory network

Abstract

Gene expression is a coordinated work of whole processes of gene regulation. To conquer gene expression completely, there are many ways to describe and understand this phenomena. Inferring gene regulatory network is most well known and powerful approach to configurate the process of gene regulation. However, the increasing study about epigenetics shows that not only the genetic mechanism but also epigenetic mechanism, such as DNA methylation, histone modification, chromatin remodeling, etc are significantly influencing the gene regulation. Such foundation leads us to deeper understanding of gene regulation in the view point of epigenetics. In this study, we attempt to find the relation between the gene regulatory network and epigenetic states analyzing histone modification data. We used well known network model, ARACNE, which is based on information theoretic approach to obtain direct interaction between genes. To analyze the epigenetic states of each nodes in the regulatory network, we use the histone modification data from the Yeast chromatin database, Chrom DB.