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 in the context of CpG dinucleotides, 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 embryonic development and enriched in brain. 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 modifications. Specifically, the three aims of this proposal are to determine central aspects, enzymatically and structurally, of (1) 5mC oxidation by Tet proteins, (2) modification-specific recognition by C2H2 zinc-finger and SRA-domain proteins, and (3) 5mC and 5hmC base excision by DNA glycosylases.
During the development, mammalian germ line cells and brains undergo a series of cellular and molecular events that lead to the erasure and re-establishment of epigenetic programs and the mechanism by which erasure of 5-methylcytosine (5mC) marks takes place is not well understood. It is possible that the active erasure and the re-establishment of 5mC marks during germ line differentiation and brain development from fetus to young adult involve dynamic changes of 5mC into oxidative marks, and that these modified cytosine residues in DNA are recognized by specific protein readers with distinct roles in the maintenance of epigenetic memory. A detailed biochemical and structural analyses of generation, recognition and erasure of these marks should shed light on this issue.
|Valente, Sergio; Liu, Yiwei; Schnekenburger, Michael et al. (2014) Selective non-nucleoside inhibitors of human DNA methyltransferases active in cancer including in cancer stem cells. J Med Chem 57:701-13|
|Horton, John R; Wang, Hua; Mabuchi, Megumu Yamada et al. (2014) Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix. Nucleic Acids Res 42:12092-101|
|Hong, Samuel; Hashimoto, Hideharu; Kow, Yoke Wah et al. (2014) The carboxy-terminal domain of ROS1 is essential for 5-methylcytosine DNA glycosylase activity. J Mol Biol 426:3703-12|
|Cheng, Xiaodong (2014) Structural and functional coordination of DNA and histone methylation. Cold Spring Harb Perspect Biol 6:|
|Liu, Yiwei; Olanrewaju, Yusuf Olatunde; Zheng, Yu et al. (2014) Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Res 42:4859-67|
|Hashimoto, Hideharu; Pais, June E; Zhang, Xing et al. (2014) Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. Nature 506:391-5|
|Horton, John R; Nugent, Rebecca L; Li, Andrew et al. (2014) Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI. Sci Rep 4:4246|
|Hashimoto, Hideharu; Olanrewaju, Yusuf Olatunde; Zheng, Yu et al. (2014) Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence. Genes Dev 28:2304-13|
|Rotili, Dante; Tarantino, Domenico; Marrocco, Biagina et al. (2014) Properly substituted analogues of BIX-01294 lose inhibition of G9a histone methyltransferase and gain selective anti-DNA methyltransferase 3A activity. PLoS One 9:e96941|
|Liu, Yiwei; Olanrewaju, Yusuf Olatunde; Zhang, Xing et al. (2013) DNA recognition of 5-carboxylcytosine by a Zfp57 mutant at an atomic resolution of 0.97 A. Biochemistry 52:9310-7|
Showing the most recent 10 out of 77 publications