The control of gene expression in mammals relies in part on modifications to cytosine residues in DNA, which exist in at least five forms: cytosine (C), 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5- formylcytosine (5fC) and 5-carboxylcytosine (5caC). DNA methyltransferases methylate cytosine at the 5- position, generating 5mC in the genome. Ten-eleven translocation (Tet) dioxygenases convert 5mC to 5hmC, 5fC, and 5caC in three consecutive oxidation reactions. These modifications are dynamically regulated during development and cell differentiation. To understand the function of these modifications and the regulatory mechanisms that control the levels and genomic distribution of the five forms of the cytosine, we propose to study the enzymes/proteins that generate, read, and remove these DNA modifications as well as associated histone methylation.
During the development, mammalian cells undergo a series of cellular and molecular events that lead to the erasure and re-establishment of epigenetic programs. It is postulated that the active erasure and the re- establishment of DNA methylation marks during germ line differentiation, T-cell differentiation and brain development from fetus to young adult involve dynamic changes of methylated cytsoine into oxidative marks, and that these modified cytosine residues in DNA are recognized by specific transcription factors with distinct roles in the maintenance of epigenetic memory. A detailed biochemical and structural analyses of generation, recognition, alteration and erasure of these marks should shed light on this issue.