Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. is performed by DNA-methyltransferases that catalyze transfer of a methyl group from S-adenosyl-l-methionine to cytosine bases in DNA.
Most of mammalian and plant DNA methylation is restricted to symmetrical CG sequences, but plants also have significant levels of cytosine methylation in the symmetric context CHG (where H is A, C or T) and even in asymmetric sequences.
Methylation in symmetrical sequences is preserved though cycles of DNA replication by maintenance DNA methyltransferases, which show a preference for hemimethylated substrates and methylate cytosines in the newly synthesized strand. Maintenance mechanisms for asymmetric methylation patterns are unknown, but they must include de novo methylation after each cell division.
recent study (October 25, 2013) results showed that CpG methylation is always symmetrically methylated, whereas non-CpG sites are strand-specifically methylated in introns, SINE elements and LINE elements. Even though hydroxymethylcytosine (hmC) could not be distinguished from methylcytosine by the current bisulfite conversion method showed that hmC is unlikely to occur in non-CpG sites; thus, we do not expect hmC to influence our main conclusions. We also showed that the skew of non-CpG methylation in intron is more pronounced at the boundaries and more significant for highly expressed genes.