CpG site

CpG sites are regions of the DNA where a cytosine nucleotide is situated next to a guanine nucleotide. "CpG" stands for cytosine and guanine separated by a phosphate which links the two nucleotides together in DNA.

Despite the high probability of a cytosine and guanine lying next to each other on DNA, there are actually very few CpG sites in the eukaryotic genomes. This is due to the action of DNA methyltransferase[?], which recognizes these CpG sites and methylates the cytosine, turning it into 5-methylcytosine. Following spontaenous deamination, the 5-methylcytosine converts into thymine. If this mutation has no effect (as in most cases), the error is not recognized by the repair machinery, thus resulting in the loss of the CpG site.

However, there are regions of the DNA which have a high concentration of CpG sites. These regions are known as CpG islands, and found at the promoters of eukaryotic genes. Surprisingly, these CpG sites are unmethylated, and therefore any spontaneous deaminations of cytosine to uracil are recognized by the repair machinery and the CpG site is restored.

Note: the mechanisms of methylation and de-methylatoin are largely unknown, as are the various enzymes and modes of regulation.