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.

Public Health Relevance

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.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Macromolecular Structure and Function C Study Section (MSFC)
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Preusch, Peter
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Emory University
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Ren, Ren; Horton, John R; Zhang, Xing et al. (2018) Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 53:88-99
Patel, Anamika; Yang, Peng; Tinkham, Matthew et al. (2018) DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins. Cell 173:221-233.e12
Hashimoto, Hideharu; Wang, Dongxue; Horton, John R et al. (2017) Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA. Mol Cell 66:711-720.e3
Patel, Anamika; Zhang, Xing; Blumenthal, Robert M et al. (2017) Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence. J Biol Chem 292:15994-16002
Lee, Chen-Cheng; Peng, Shih-Huan; Shen, Li et al. (2017) The Role of N-?-acetyltransferase 10 Protein in DNA Methylation and Genomic Imprinting. Mol Cell 68:89-103.e7
Yang, Peng; Wang, Yixuan; Hoang, Don et al. (2017) A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568. Science 356:757-759
Estève, Pierre-Olivier; Zhang, Guoqiang; Ponnaluri, V K Chaithanya et al. (2016) Binding of 14-3-3 reader proteins to phosphorylated DNMT1 facilitates aberrant DNA methylation and gene expression. Nucleic Acids Res 44:1642-56
Patel, A; Hashimoto, H; Zhang, X et al. (2016) Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins. Methods Enzymol 573:387-401
Patel, Anamika; Horton, John R; Wilson, Geoffrey G et al. (2016) Structural basis for human PRDM9 action at recombination hot spots. Genes Dev 30:257-65
Zeng, Yaxue; Yao, Bing; Shin, Jaehoon et al. (2016) Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression. Mol Cell 61:153-60

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