DNA methylation has been undergoing dramatic change lately. 6mA shook things up by showing Cytosine can’t claim all the glory and now a talented team from the UK have shown 5-formylcytosine (5fC) is starting to follow in 5hmC’s independent footsteps.
The team profiled 5hmC, 5fC, and 5caC using:
- in vivo isotope labeling of methionine to penetrate the one carbon pool and be deposited as radioactive methylation. Using these isotopes, they determined the turnover rate by examining the uptake of isotopes.
- nano high-performance liquid chromatography–tandem high-resolution mass spectrometry (nanoHPLC-MS/HRMS) to discriminate the rare bases at their low level.
All this fancy technology was used to analyze C57BL/6J mice at newborn, adolescent, and adult life stages. Interestingly, 5hmC levels depend on tissue proliferation rate and thus age. The team also analyzed different tissues like the brain, heart, liver, kidney, and colon.
Finally, they also examined embryos lacking thymine-DNA glycosylase (TDG), which is involved in removing 5fC and 5caC.
Here’s what the interdisciplinary set-up revealed:
- 5fC is present in all mouse tissues at all stages but is most abundant in the brain, just like 5hmC.
- In cultured embryonic cells 5fC differs from 5hmC and 5mC by taking longer to reduce its turnover rate.
- Interestingly, the turnover rate of 5fC is lower in the developing brain when compared to other developing tissues.
- 5fC also has a lower turnover rate in adult tissues, when compared to 5mC and 5hmC, which attests to its stability.
- 5fC appears to have no turnover in adult brains, unlike 5mC and 5hmC, and as assessed by 5mC RNA labeling control.
The findings leave the authors hypothesizing that 5fC is present in two distinct cell populations; one that is not dividing (the brain) and one (the other tissues) with lower levels that is actively dividing.
Since 5fC was stable, this experimentation suggests that it could be creating a unique epigenetic landscape. This leaves us wondering if 5fC is being repurposed in the brain and how long it will be before 5caC is caught in the act of being more stable.
Learn more about this stable modification in Nature Chemical Biology, June 2015