Vertebrate CpG islands (CGIs) are short unevenly distributed DNA sequences that deviate significantly from the bulk DNA. The CpG islands are usually GC-rich, CpG-rich, and predominantly nonmethylated.

Image: By Helixitta - Own work, CC BY-SA 4.0,

The CpG sites or CG sites are regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide in the linear sequence of bases along its 5' → 3' direction. CpG is shorthand for 5'—C—phosphate—G—3', that is, cytosine and guanine are separated by only one phosphate group; phosphate links any two nucleosides together in DNA.

Most of these CGIs are transcription initiation sites because the CpG islands are core promoter elements in mammals. The shared DNA sequences in the region adapt CGIs as promoters by destabilizing the nucleosomes and attracting proteins that allow the transcriptionally permissive chromatin state.

The silencing of CGI promoters is usually by the methylation of CpG using their distinctive DNA sequence composition. Methylation followed by histone modifications results in imprinting.

This silencing alters the chromatin structure and therefore regulates the gene activity.

This dinucleotide pair is also the center for point mutation. CpG dinucleotides are usually methylated on cytosine. When Methyl-Cytosine undergoes spontaneous deamination, uracil is formed, which is then repaired by cellular mechanisms and altered to thymidine. The net result is a C to T mutation.

Image: By CFCF - Own work, CC BY-SA 3.0,

The vertebrate genomes being mostly methylated at the dinucleotide CpG, are mostly mutated and consequently are CpG deficient. However, the CGIs are about 1000 base pairs (bp) with higher G+C base composition and low CpG depletion, and the absence of DNA methylation allows them to be isolated as a homogeneous fraction of the genome. These are the most common promoter annotation sites in the vertebrate genome, which includes almost all housekeeping genes.


Kaushansky, Kenneth. "Glossary of Molecular Biology Terminology." ASH Education Program Book 2000.1 (2000): 438-456.

Deaton, Aimée M., and Adrian Bird. "CpG islands and the regulation of transcription." Genes & development 25.10 (2011): 1010-1022.