Epigenetics and DNA Methylation

Epigenetics is a wide term representing molecular processes leading to modification of gene expression without bringing any DNA base sequence alterations. Major epigenetic mechanisms involved in gene expression modifications are DNA methylation, histone modification, gene imprinting, epigenetic writers, and transcription regulators. In this chapter, protocols for detection of all the epigenetic mechanisms have been discussed. The principle involved in DNA methylation includes conversion of methylated cytosine into thymine by sodium bisulfite treatment; each CpG site is targeted by two different probes. A histone modification is the process of a covalent post-translational modification (PTM) to histone protein including methylation, phosphorylation, acetylation, ubiquitylation, and sumoylation, which is the cause of alteration chromatin structure or recruiting histone modifiers. Genomic imprinting is an epigenetic phenomenon that leads to genes to be expressed in a parent-of-origin-specific manner. Both genomic region compaction and gene expression are regulated by epigenetic modifications, deposited by specific enzymes (known as “writers”) and subsequently recognized by effector proteins (“readers”) and removal of these marks by erasers, which all together regulate gene transcription, and defects may cause cancer initiation and progression. Epigenetic regulation through various nutritive substance leads to the development of a separate study referred to as nutrigenomics, which are discussed in Chapter 12.