ABSTRACT
Abstract One of the most fascinating aspects of biology is that the same genome can give rise to a diversity of cell types and cellular functions in a multicellular organism. This suggests that in addition to the DNA sequence there must be additional “epigenetic” features that are associated with cell type or condition specific gene regulation. In eukaryotic organisms, two important mechanisms for epigenetic regulation of gene expression are the dynamic regulation of chromatin organization and DNA methylation. A large number of sequencing-based assays, such as ChIP-seq, DNase-seq, Hi-C, whole genome bisulfite sequencing and Reduced Representation Bisulfite Sequencing (RRBS), have been developed to survey the epigenomes in a genome-wide fashion. In this chapter, we survey the state-of-the-art bioinformatics methodologies and tools for performing these epigenomic analyses. We also review the application of these epigenomic analyses, especially in terms of identifying the location and possible function of non-coding regulatory regions in a genome-wide fashion.
