ABSTRACT
Acquisition of cell identity is associated with a remodeling of the epigenome in part through active DNA demethylation. The T:G mismatch DNA glycosylase (TDG) participates to this process by removing 5-methylcytosines that have been oxidized by Ten-Eleven-Translocation (TET) enzymes. Despite this well-defined molecular function, a comprehensive view of the biological function of TDG is still lacking, especially during cell differentiation. Here, we combined transcriptomic and epigenomic approaches in a Tdg knock-out epiblast stem-like cell model to decipher TDG function in pluripotent cells and their retinoic acid-induced progeny. We determined that TDG occupies a majority of active promoters, a large fraction of which are also engaged by the transcription factor ATF4. Consistently, neural fate commitment upon retinoic acid treatment is associated with a TDG-dependent sustained expression of ATF4-dependent genes, in relation with a TDG-associated nucleosome positioning at promoters. We further evidenced that TDG maintains ATF4 pathway activity by positively regulating the mammalian target of rapamycin complex 1 (mTORC1), favoring neural cell fate commitment. These observations highlight the central role of TDG in cell differentiation and support a model linking metabolic reprogramming to cell fate acquisition.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
New experiments related to to Figure 1 (kinetic study of Nodal, Lefty 1 and Lefty 2 expression), Figure 2 (ferroptosis regulation), Figure 3 (epiblast and nascent mesoderm module analysis) Figure 4 (new heatmaps and average ChIP-seq profiles including CHD2 and CHD4 remodelers) and Figure 5 (new analysis of TDG expression correlation with gene effect and protein levels in human cancer cell lines) have been added. A supplementary Figure 5 has also been created.
