CpG island

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CpG islands are regions of DNA in and near approximately 40% of promoters of mammalian genes (about 70% in human promoters). They are regions where there are a large number of cytosine and guanine adjacent to each other, linked by phosphodiester bonds, in the backbone of the DNA. The "p" in CpG notation refers to the phopshodiester bond between the cytosine and the guanine.

The length of a CpG island is typically 300-3000 base pairs. These regions are characterized by CpG dinucleotide content equal to or greater than what would be statistically expected (≈6%), whereas the rest of the genome has much lower CpG frequency (≈1%), a phenomenon called CG suppression. Unlike CpG sites in the coding region of a gene, in most instances, the CpG sites in the CpG islands of promoters are unmethylated if genes are expressed. This observation led to the speculation that methylation of CpG sites in the promoter of a gene may inhibit the expression of a gene.

The usual formal definition of a CpG island is a region with at least 200 bp and with a GC percentage that is greater than 50% and with an observed/expected CpG ratio that is greater than 0.6. The majority of these islands are associated with genes, and can be used as recognition sites for restriction enzymes.