The regulation of transcription and translation of a gene under a given
environment is dependent on several factors and epigenetics is one such factor,
responsible for the differential expression of several genes in health and in various
diseases. DNA methylation, an important epigenetics mechanism has been shown to
play a vital role in numerous cellular processes, and the abnormal patterns of
methylation have been linked to the number of human diseases. CpG islands, a short
stretch of DNA enriched with CpG sites in the 5’ end of a gene, although remains
unmethylated but tends to methylate aberrantly upon certain environmental exposures.
The methylation of the promoter region bearing transcriptional start sites of those genes
that encodes tumor suppressors such as tumor protein p53, retinoblastoma-associated
protein 1, tumor protein p16, breast cancer 1 and many more result in the reduced
expression of these genes and have been implicated in a large number of cancers like
retinoblastoma, colon, lung and ovarian. A growing number of human diseases have
been found to be associated with the aberrant DNA methylation. Hence, a deep insight
into the individual’s epigenetic profile is the need of the hour. Several approaches have
been developed to map DNA methylation patterns genome-wide. Some of these
approaches include enzymatic digestion with methylation-sensitive restriction
enzymes, the capture of 5-mC by methylated DNA-binding proteins followed by nextgeneration
sequencing and methyl-DNA immunoprecipitation followed by sequencing
of precipitated fragments. However, this chapter is going to describe the most
recommended method for studying DNA methylation pattern, the method based on
bisulfite sequencing. The bisulfite treatment of DNA converts unmethylated cytosine(s)
to uracil(s), which are subsequently amplified as Ts by PCR. Hence, the bisulfitetreated
DNA has mutations specifically at unmethylated Cs that can be mapped by
Next-Generation sequencing.
Keywords: Bisulfite conversion, CpG island, DNA methylation, Deep
sequencing, Epigenetics, Genomics, Immunoprecipitation, Next-Generation
Sequencing, PCR, Retinoblastoma, Restriction enzymes, Transcription,
Unmethylated.
