Computational Methods for Epigenetic Studies
The epigenome has increasingly been the focus of research over the past decade. Epigenetic control occurs in two primary ways: DNA methylation and chemical modification of histones. The latter mechanism determines whether the chromatin is tightly packed, in which case gene expression is repressed, or relaxed, in which case gene expression is enhanced. DNA methylation is the addition of the methyl groups to cytocines. Methylation of DNA is involved in a variety of biological processes, including embryogenesis and development, silencing of transposable elements, and regulation of gene transcription. In our research, we developed a set of computational methods and software tools that enable genome-wide epigenetic studies. In particular, our computational methods and software tools allow for (1) the determination of dynamic nucleosome positioning and the analysis of the correlation between the nucleosome landscape and gene expression, (2) the identification of methylation patterns from raw data obtained from next-generation sequencing technologies such as the Illumina Genome Analyzer, and (3) the discovery of transcription factors binding sites from data on the dynamic chromatin structure remodeling. Our methods and tools were used to study nucleosome landscape, methylation and control of transcription in the human malaria parasite which is responsible to one million deaths world-wide every year.