Methods in epigenetics-based systems biology and their applications

The large-scale advancement of high-throughput sequencing technologies has enabled the interrogation of different regulatory layers. Especially the development of computational models of Gene Regulatory Networks has enabled the disentangling of a complex interplay between these interconnected levels of regulation by interpreting large quantities of biomedical information in a systematic way. These approaches provide a systems-level view of the underlying regulatory mechanisms controlling the development and maintenance of complex biological processes. In particular, epigenetics-based computational approaches allowed to obtain an overview of the crosstalk among various epigenetics components contributing to the regulation of a particular gene expression program. This chapter will provide an overview of computational approaches that have been or can be used for interrogating the interplay of epigenetic and transcriptional regulation, and shows applications in which the exploitation of epigenetic information yielded considerable advancements in both basic and translational research.