5formylcytosine

5-formylcytosine (5fC) is an oxidized derivative of the DNA base cytosine. It is produced by the oxidation of 5-methylcytosine (5mC) through the action of TET family dioxygenases, and it functions as part of the active DNA demethylation pathway in mammals and other organisms that possess TET enzymes.

In the common demethylation sequence, 5mC is first converted to 5-hydroxymethylcytosine (5hmC), then to 5fC, and further to 5-carboxylcytosine (5caC). 5fC is found at low abundance in genomic DNA and has been detected in various cell types and developmental stages, including embryonic stem cells. A major route for removing 5fC is thymine DNA glycosylase (TDG), which initiates base excision repair and ultimately restores unmodified cytosine, linking 5fC to dynamic regulation of DNA methylation and gene expression.

Beyond its role as an intermediate, 5fC may also participate in regulatory processes independent of demethylation, though its biological significance is still being investigated. Its distribution is nonuniform and can be enriched at certain regulatory regions in some cell types, but overall levels are low relative to 5hmC.

Analytical detection of 5fC relies on methods such as liquid chromatography–mass spectrometry (LC-MS/MS) for quantification and specialized sequencing approaches that map 5fC sites at high resolution. Studying 5fC contributes to understanding the turnover of DNA methylation and the broader landscape of epigenetic regulation.