5hmC

5-hydroxymethylcytosine (5hmC) is a modified DNA base produced by the oxidation of 5-methylcytosine (5mC). It is generated primarily by the TET family of dioxygenases (TET1, TET2, TET3) and requires Fe2+ and alpha-ketoglutarate as cofactors. 5hmC can be further oxidized to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), and these products can be removed by base excision repair to restore unmodified cytosine. In many contexts, 5hmC also acts as a stable epigenetic mark, not merely an intermediate in demethylation.

Distribution and function: 5hmC is enriched in embryonic stem cells and is particularly abundant in the mammalian brain, with tissue- and cell-type–specific patterns. It is found within gene bodies and at regulatory elements such as enhancers and promoters. In some contexts, 5hmC correlates with active transcription and plays a role in development, neural function, and plasticity. Alterations in 5hmC patterns have been associated with developmental disorders and cancer, indicating a role in gene regulation and genome stability.

Detection and significance: Genome-wide maps of 5hmC can be generated with methods such as TAB-seq and oxidative bisulfite sequencing, which distinguish 5hmC from 5mC. 5hmC levels reflect TET activity and cellular metabolism and can change with development, aging, and disease. Ongoing research investigates its potential as a biomarker and its precise contributions to epigenetic regulation.