Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

TLDR

5‑methylcytosine regulates gene expression, imprinting, and transposon silencing, and Tet proteins oxidize it to 5‑hydroxymethylcytosine. The study demonstrates that Tet enzymes can oxidize 5‑methylcytosine to 5‑formylcytosine and 5‑carboxylcytosine in an activity‑dependent manner. We detected 5‑formylcytosine and 5‑carboxylcytosine in mouse embryonic stem cells and tissues, showed that their levels are regulated by Tet expression, identified them as novel Tet products, and suggested a Tet‑mediated demethylation pathway.

Abstract

5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable elements. 5mC can be converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins. Here, we show that, in addition to 5hmC, the Tet proteins can generate 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic activity-dependent manner. Furthermore, we reveal the presence of 5fC and 5caC in genomic DNA of mouse embryonic stem cells and mouse organs. The genomic content of 5hmC, 5fC, and 5caC can be increased or reduced through overexpression or depletion of Tet proteins. Thus, we identify two previously unknown cytosine derivatives in genomic DNA as the products of Tet proteins. Our study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation.