**3. DNA methylation**

DNA methylation involves transfer of a methyl group from S-adenosylmethionine to the 5'position of cytosine residues in DNA. DNA methylation is one of the most prominent epigenetic events that take place within the cells and has been shown to play important roles in various cellular processes like genome integrity, genome imprinting, X chromosome inactivation and development [7–9].

DNA methylation at 5 methyl cytosine is catalyzed by two groups of methyltransferases.


Another member of the DNMT family of enzymes is DNMT 3 L. It was discovered in 2000. DNMT 3 L lacks an intrinsic methyltransferase activity but assists DNMNT3a and 3b in methylating retrotransposons [12].

In eukaryotes, DNA methylation occurs predominantly within repetitive sequences in order to maintain genomic integrity [13]. Methylation on cytosine residues usually takes place in the context of CG dinucleotides (Known as CpG) and around 75% of CpG dinucleotides in humans remain methylated. These CpG dinucleotides are unevenly distributed but are concentrated in stretches of high frequency known as CpG islands. These islands remain mostly unmethylated and can be found in the promoters of constitutively expressed genes like housekeeping genes [14]. In humans, almost half of the estimated 29,000 CpG islands remains unmethylated under normal conditions [15–17].

Methycytosine residues often co-operate with other effectors to bring about a silenced chromatin state. Methyl binding domain (MBD) proteins recognize and bind to methylated cytosines. These MBD proteins act as a signal/binding platform for histone modifying and chromatin remodeling enzymes to bring about further compaction of chromatin [18]. Apart from binding methylated DNA, MBD 2 (a member of MBD family of proteins) has also been shown to promote the DNA methyltransferase activity of NuRD (chromatin remodeling complex) by interacting with NuRD [19, 20]. This interaction brings NuRD complex in close proximity of cytosine residues which are later methylated by NuRD. Till date, six members of methyl binding domain proteins have been identified that include MBD1, MBD2, MBD3, MBD4, methylcytosine binding protein 2 (MECP2) and Kaiso [21]. All of these proteins are under intense investigation and efforts are being made to identify more members of the family.

Various genes contain regions of CpG dinucleotides in their promoters with variable degrees of methylation levels [14]. These levels are crucial for normal functioning of the cells and any mis-regulation in this level is associated with a number of physiological outcomes. Methylated DNA elements often co-operate with other epigenetic elements to ensure proper silencing of chromatin and any increase in levels of DNA methylation are often involved in silencing of cognate genes which can lead to carcinogenesis [15, 22]. For example, it has been observed that increase in the levels of promoter DNA methylation in tumor suppressor genes leads to a decrease in their expression and hence a steady decline in their cellular activity is observed [15, 23–25]. Hypermethylated promoters can also serve as targets for transition mutations due to spontaneous deamination of 5'methyl cytosine into thymine [7, 26]. This leads to transmission of DNA with errors during replication to new cells. These cells are genomically unstable and with time, accumulate more and more mutations which in the absence of proper surveillance, eventually lead to cancer initiation [7, 16, 27]. Decrease in the DNA methylation of tumor suppressor genes has been observed in a number of primary tissues from cancer patients at various geographical locations.

Global hypomethylation can also ensue which can lead to loss of repression from the repetitive DNA sequences (like transposons) and imprinted genomic sequences. This can be accompanied by loss of methylation from genomic regions involved in maintaining chromosome stability like peri centromere. This can cause gross genomic instability which is a characteristic of many forms of cancer. Though the relationship between global loss of DNA methylation and cancer has not been very well studied and needs more research (**Figure 3**) [16, 28, 29].

Alternatively, certain genes undergo hypomethylation and therefore experience increase in expression that has been associated with carcinogenesis. Genes predominantly affected by hypomethylation include developmentally critical genes, enzymes, growth regulatory genes and tissue-specific genes such as germ cell-specific tumour antigen genes [30]. Various other genes which have been shown to be involved in carcinogenesis as a result of aberrant DNA methylation are listed in **Table 1**.

### **Figure 3.**

*Schematic of two broad mechanisms involved in cancer progression through DNA methylation. Hypermethylation and silencing of tumor suppressor gene promoters to allow unchecked growth of damaged cells to accumulate more damage and generate cancer phenotype. Hypomethylation of proto-oncogenes to favor uncontrolled proliferation of cells to generate cancer mass.*


**Table 1.**

*Changes in DNA methylation of different genes in different forms of cancer.*
