5-carboxylcytosine (5caC) is the final oxidized derivative of 5-methylcytosine (5mC). 5mC is oxidized to 5-hydroxymethylcytosine (5hmC) which is then oxidized to 5-formylcytosine (5fC) then 5caC (Ito et al., 2011). Each of these oxidation steps are catalyzed by the Ten-Eleven Translocation (TET) family 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) or Thymine DNA glycosylase (TDG) by base excision repair (Zhang et al., 2012).
The active demethylation of DNA is particularly important in two places: embryonic development and the brain (Pastor et al., 2011; Song et al., 2011; Xu et al., 2011). 5caC is found in these contexts and may serve as in indicator of nearly complete 5mC demethylation. It does appear that 5caC also has its own functional significance. It has recently been shown that the 5caC and 5fC marks themselves cause increased pausing, backtracking, and reduced fidelity of RNAPII (Kellinger et al., 2012).
Future work needs to examine whether 5caC can act as its own epigenetic mark by binding its own reader proteins. There are already some indications that this may occur. The TDG enzyme is known to interact with transcription factors including the RNAPII-associated acetyltransferases CBP/P300 and damage response factors like GADD45a (Cortellino et al., 2011; Tini et al., 2002). TDG also interacts with de novo DNA methyltransferases and the deaminase AID (Cortellino et al., 2011; Li et al., 2007). It may be that TDG bound 5fC/5caC has some functional role in guiding these proteins to fulfill specific functions, such as further mediating pausing of RNAPII. Given the diverse roles of these proteins, much more work is needed to understand exactly what all these interactions mean.
5caC Additional Reading
This review focuses on how TET and TDG proteins in the context of DNA demethylation. It gives excellent details on the dynamics of each enzymatic process as wells as active DNA demethylation during development. The authors also briefly address the role of these processes in cancer, and touch on some remaining open questions.
Hashimoto, H., Hong, S., Bhagwat, A.S., Zhang, X., and Cheng, X. (2012). Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation. Nucleic Acids Res. 40, 10203-10214.
This paper examines the detailed mechanistic basis for the removal of 5caC by TdT. It’s a great read for those looking for an in depth look at the enzymatic functions of TdT.
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