5-Formylcytosine

5-Formylcytosine (5fC) is a pyrimidine nitrogen base derived from cytosine. In the context of nucleic acid chemistry and biology, it is regarded as an epigenetic marker. Discovered in 2011 in mammalian embryonic stem cells by Thomas Carell's research group the modified nucleoside was more recently confirmed to be relevant both as an intermediate in the active demethylation pathway and as a standalone epigenetic marker. In mammals, 5fC is formed by oxidation of 5-Hydroxymethylcytosine (5hmC) a reaction mediated by TET enzymes. Its molecular formula is C5H5N3O2.

Localization
Similarly to the related cytosine modifications 5-Methylcytosine (5mC) and 5hmC, 5fC is broadly distributed across the mammalian genome, although it is much more rarely occurring. The specific concentration values vary significantly depending on the cell type. 5fC can be aberrantly expressed in distinct sets of tissue that can indicate different tumor onsets and canceration.

Functions
The exact functions of 5fC have not been yet precisely defined, although it is likely to play key roles in at least two distinct frameworks. Firstly, 5fC serves as an intermediate of the active demethylation pathway, a process that contributes to the DNA maintenance and integrity by replacing 5mC with canonical cytosine. A central dilemma regarding 5fC (and epigenetics in general) is how reader proteins recognise their substrates with such high specificity over the overwhelming background. Thymine-DNA glycosylase (TDG), a protein which is involved in the removal of 5fC from DNA in mammals, is especially interesting in this context. Secondly, 5fC can exist as an independent, stable modification, but its role in this context is still blurry.

5fC impact on DNA structure and flexibility
The understanding of the impact of 5fC on DNA physical properties is to date limited. Recent studies have reported contradictory findings regarding the structural impact of 5fC on DNA. On the other hand, several researchers working independently have identified 5fC to distinctly increase DNA flexibility. 5fC also curtails DNA double helix stability and increases base pair opening.