5mC

5-methylcytosine (5mC) is a chemically modified form of the DNA base cytosine in which a methyl group is added to the 5-position of the pyrimidine ring. In mammals, 5mC is predominantly found at CpG dinucleotides, although non-CpG methylation occurs in certain cell types such as embryonic stem cells and neurons.

DNA methylation is established and maintained by DNA methyltransferases (DNMTs). De novo methyltransferases DNMT3A and DNMT3B establish methylation patterns, while DNMT1 maintains them during DNA replication. 5mC plays a central role in epigenetic regulation, influencing gene expression, imprinting, X-chromosome inactivation, and suppression of transposable elements. Typically, promoter-associated CpG methylation correlates with transcriptional repression, whereas methylation in gene bodies can have more complex effects.

5mC can be oxidized by TET family enzymes (TET1-3) to 5-hydroxymethylcytosine (5hmC) and further to 5-formylcytosine and 5-carboxylcytosine, steps that are part of active DNA demethylation pathways. These oxidized forms can be processed by base excision repair to restore unmodified cytosine, enabling dynamic regulation of methylation.

Spontaneous deamination of 5mC yields thymine, creating C>T transitions and contributing to mutation patterns, particularly at CpG sites. This mutational tendency has implications for aging and cancer.

Detection methods include bisulfite sequencing, which differentiates methylated from unmethylated cytosine; whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) are widely used. 5mC is a foundational epigenetic mark studied in development, imprinting, cancer, and aging.