PT  - JOURNAL ARTICLE
AU  - Fabio Spada
AU  - Sarah Schiffers
AU  - Angie Kirchner
AU  - Yingqian Zhang
AU  - Olesea Kosmatchev
AU  - Eva Korytiakova
AU  - René Rahimoff
AU  - Charlotte Ebert
AU  - Thomas Carell
TI  - Oxidative and non-oxidative active turnover of genomic methylcytosine in distinct pluripotent states
AID  - 10.1101/846584
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 846584
4099  - http://biorxiv.org/content/early/2019/11/18/846584.short
4100  - http://biorxiv.org/content/early/2019/11/18/846584.full
AB  - Epigenetic plasticity underpins cell potency, but the extent to which active turnover of DNA methylation contributes to such plasticity is not known and the underlying pathways are poorly understood. Here we use mass spectrometry in combination with isoptope tracing to quantitatively address the global turnover of genomic methylcytidine (mdC), hydroxymethylcytidine (hmdC) and formylcytidine (fdC) across mouse pluripotent cell states. High rates of mdC/hmdC oxidation and fdC turnover characterize a formative-like pluripotent state. In primed pluripotent cells the global mdC turnover rate is about 3-6% faster than can be explained by passive dilution through DNA synthesis. While this active component is largely dependent on Tet-mediated mdC oxidation, we also unveiled an additional mdC oxidation-independent turnover process based on DNA repair. This process accelerates upon acquisition of primed pluripotency and returns to low levels in lineage committed cells. Thus, in pluripotent cells active mdC turnover involves both mdC oxidation-dependent and -independent processes.