5-formylcytosine (5fC) is one the oxidized derivatives of 5-methylcytosine (5mC) demethylation. 5mC is oxidized to 5-hydroxymethylcytosine (5hmC) which is then oxidized to 5fC (Ito et al., 2011). Each of these oxidation steps are catalyzed by the Ten-eleven translocation (TET) trio of enzymes. 5fC can then be further oxidized to 5-carboxylcytosine (5caC) by TET. Both 5fC and 5caC can be converted to unmodified cytosine by Terminal deoxynucleotidyl transferase (TdT) by base excision repair.
TET enzymes facilitate active DNA demethylation. Passive DNA demethylation occurs by methyltransferases failing to maintain methylation on newly synthesized DNA. Active DNA methylation occurs by the removal of the methyl group from 5mC (Kohli and Zhang, 2013). The intermediate derivatives of this process have come under intense investigation since their discovery in mammalian cells. They may simply be intermediates in the DNA demethylation process, or could serve functional roles and each act as their own epigenetic mark.
Recently, technologies have been developed to examine each derivative on its own. One application of these technologies has been to map the progress of active DNA demethylation. Each derivate appears to have different distributions. 5fC in mouse embryonic stem cells is enriched at poised enhancers and other regulatory elements (Song et al., 2013). An increase in 5fC also co-occurs with p300-based activation of enhancer chromatin (Song et al., 2013). This may indicate that the committed demethylation that 5fC indicates is permissive to transcriptional activators acting at enhancers; however this work is still correlation-based and more research is needed to elucidate the mechanisms involved.
It may be that 5fC binds its own reader proteins. This would allow 5fC to act as its own de facto epigenetic modification. Research is currently underway to address these possibilities. Work has been done on the effect of the 5fC mark itself on transcription. It appears that 5fC and 5caC affect the rate and specificity of RNA polymerase II (RNAPII). Specifically, both 5fC and 5caC cause increased RNAPII backtracking, increased pausing, and reduced fidelity in nucleotide incorporation (Kellinger et al., 2012).
5fC Additional Reading
Raiber, E.A., Beraldi, D., Ficz, G., Burgess, H.E., Branco, M.R., Murat, P., Oxley, D., Booth, M.J., Reik, W., and Balasubramanian, S. (2012). Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase. Genome Biol. 13, R69.
This paper describes a purification and sequencing-based method to find regions associated with 5fC modification. The authors also examine the distribution of 5fC in embryonic stem cells in and find enrichment regions associated with epigenetic reprograming and transcriptional activation.
This review goes over some of the basics of the TET protein family and their oxidation of 5mC to each derivative. It also discusses each derivative in some detail including their genomic distribution and potential roles.
- Ito, S., Shen, L., Dai, Q., Wu, S.C., Collins, L.B., Swenberg, J.A., He, C., and Zhang, Y. (2011). Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300-1303.
- Kellinger, M.W., Song, C.X., Chong, J., Lu, X.Y., He, C., and Wang, D. (2012). 5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 19, 831-833.
- Kohli, R.M., and Zhang, Y. (2013). TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502, 472-479.
- Song, C.X., Szulwach, K.E., Dai, Q., Fu, Y., Mao, S.Q., Lin, L., Street, C., Li, Y., Poidevin, M., Wu, H., et al. (2013). Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell 153, 678-691.