5methylcytosine

5-methylcytosine (5mC) is a methylated form of the DNA base cytosine in which a methyl group is added to the 5-position of the ring. It is a primary epigenetic modification in many organisms and is involved in regulating gene expression and maintaining genome stability.

In animals, 5mC is most abundant in CpG dinucleotides, and clusters of CpG sites near gene promoters, called CpG islands, are often protected and remain unmethylated. Non-CpG methylation (in the CHG and CHH contexts) is also observed, especially in plants and some mammalian cells such as certain developmental stages and neurons.

DNA methyltransferases establish and maintain 5mC. DNMT3A and DNMT3B perform de novo methylation, while DNMT1 copies methylation patterns to the daughter strand during DNA replication. DNMT3L acts as a regulatory cofactor but lacks catalytic activity. In plants, additional enzymes mediate methylation across different sequence contexts (e.g., DRM2, MET1, CMT3).

5mC is associated with gene silencing, imprinting, X-chromosome inactivation, and suppression of transposable elements. The distribution and level of 5mC change during development and in response to environmental cues, contributing to cell-type–specific gene expression programs.

Active demethylation occurs through oxidation of 5mC by TET enzymes to 5-hydroxymethylcytosine and further through additional oxidation and base-excision repair. Spontaneous deamination of 5mC to thymine can create C>T mutations, making methylated cytosines mutation hotspots.

Abnormal DNA methylation patterns are linked to diseases such as cancer and neurological disorders. Detection methods include bisulfite sequencing, methylation-specific PCR, and array- or sequencing-based approaches; global and locus-specific methylation profiles serve as biomarkers and research tools.