CpG island

Across most of the genome, the DNA letter C followed by G is surprisingly rare. A CpG island is a short stretch where this CG pairing is unusually common, like an island of dense punctuation in an otherwise sparse text. These islands often sit right at the start of genes.

The name uses a small p to mark the phosphate linking the cytosine to the guanine along one strand, distinguishing a CpG site from a C paired with a G across the double helix. Islands are typically a few hundred to a couple of thousand bases long and are found near the promoters of a large share of human genes.

What makes CpG islands special is their methylation. In healthy cells, islands at active genes are usually kept unmethylated, leaving the gene available for transcription. When an island becomes methylated, the associated gene tends to be switched off, and this silencing can be inherited by daughter cells.

Abnormal methylation of CpG islands is a hallmark of many cancers, where islands at tumor-suppressor genes can be wrongly silenced. They are therefore closely watched both in basic research and in efforts to develop diagnostic markers.