Role of Epigenetics in Cancer Genomics

Background

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.