Role of Epigenetics in Cancer Genomics

Role of Epigenetics in Cancer Genomics

Amit Nagal (GVK Biosciences Private Limited, India)
Copyright: © 2016 |Pages: 13
DOI: 10.4018/978-1-4666-8726-4.ch011
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Epigenetics is the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself. ChIP-seq, is a method used to analyze protein interactions with DNA. It is a type of epigenetic analysis technique. Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is gaining popularity day by day because of its clinical significance. It is a very effective tool in diagnosis of disease such as cancer. ChIP-seq is found to be very effective tool in understanding basic regulatory mechanism, cell differentiation study and studying disease processes with the decreasing cost of sequencing, ChIP-seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms. The Present review explores epigenetic methods, pipeline and its role in cancer.
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In chromatin immunoprecipitation, cells are lysed and protein-DNA interactions are crosslinked to form covalent bonds by formaldehyde or other chemical reagents which explained by Solomon and Varshavsky (1998). Then the crosslinked DNA is sheared by sonication or DNA-cutting enzymes (e.g., micrococcal nuclease, often called MNase) into 150–500 bp-long fragments. Those DNA fragments crosslinked with the DNA-binding factor of interest are immunoprecipitated using an antibody specific to the factor. ChIP can be applied to a wide range of DNA binding factors, including TFs, transcription co-activators, co-repressors, chromatin regulators, and modified histones. After reverse cross-linking the protein-DNA complexes, the pulled-down DNA fragments are PCR amplified and then subjected to massively parallel sequencing it has been practiced that (Metzker, 2010, pp. 31-46) .Finally, when the resulting ChIP-seq reads are mapped back to the genome, the locations of the factor-DNA interactions can be identified.

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