Computational Epigenomics and Its Application in Regulatory Genomics
Over the years, with increasing knowledge of molecular mechanisms underlying the regulation of gene expression, the epigenetic landscape has undergone an evolution. In contrast to the early epigenetics that was originated exclusively in embryology and development, the modern epigenetics emphasizes on defining mechanisms of transmission of information that are not encoded in DNA. Epigenetic mechanisms such as DNA methylation and histone modifications introduce heritable changes in gene expression by regulating the wrapping of DNA inside the nucleus. The epigenetic machinery may result in either activation or repression, by acting upon euchromatin and dense heterochromatin part of chromatin, respectively. Epigenetics has provided novel understandings into the key mechanisms of development, cellular differentiation, and cell fate decisions. Moreover, recent studies have suggested their significant contribution in causing diseases such as cancer and neurodegenerative and autoimmune diseases. Recent overwhelming experimental and computational technological advancements have enabled us to resolve epigenome maps with increasing accuracy, comprehensiveness, and throughput manner across multiple cell types and tissues. This chapter provides a brief overview of the current technological advancements and resources available to perform epigenetic research with particular application in regulatory genomics.
KeywordsEnhancer Regulatory elements Epigenetics DNA methylation ChIP-seq ATAC-seq Chromatin conformation
I thank Ajinkya Deogade and Sachin Pundhir for their useful comments while writing this book chapter. I appreciate La Caixa international Ph.D. scholarship program at the Centre for Genomic Regulation (CRG), Barcelona, Spain, for providing financial support.
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