Cytosine Modifications in Development and Stem Cells
Methylation of cytosine to form 5-methylcytosine (5mC) on genomic DNA plays important roles in regulating gene expression. Although DNA methylation has been well studied, the reverse process has only recently been revealed in mammalian cells. A group of iron (II)/αKG-dependent dioxygenases, the TET proteins, oxidize 5mC to 5-hydroxymethylcytosine (5hmC), and then to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). The resulting 5fC and 5caC can be recognized by mammalian DNA glycosylase, thymine DNA glycosylase (TDG), in a base excision repair process to convert back to cytosine, providing an active demethylation pathway.
In collaboration with Dr. Chuan He at U. Chicago, we developed a suite of new technologies to map the genome-wide distribution of these modified cytosines and study the active demethylation process. These methods provide the community the tools to investigate 5mC oxidation and active DNA demethylation.