Oxidative demethylation of DNA

Rasmussen KD, Helin K. Role of TET enzymes in DNA methylation, development, and cancer. Genes Dev. 2016 Apr 01;30(7):733–50. PMID: 27036965; PMCID: PMC4826392.; Cadet J, Wagner JR. TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine. Mutation Research/Genetic Toxicology and Environmental Mutagenesis. 2014 Apr;764-765():18–35. doi: 10.1016/j.mrgentox.2013.09.001.; Kohli RM, Zhang Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature. 2013 Oct 24;502(7472):472–9. PMID: 24153300; PMCID: PMC4046508.; Kaas GA, Zhong C, Eason DE, Ross DL, Vachhani RV, Ming GL, King JR, Song H, Sweatt JD. TET1 controls CNS 5-methylcytosine hydroxylation, active DNA demethylation, gene transcription, and memory formation. Neuron. 2013 Sep 18;79(6):1086–93. PMID: 24050399; PMCID: PMC3816951.; Zhang RR, Cui QY, Murai K, Lim YC, Smith ZD, Jin S, Ye P, Rosa L, Lee YK, Wu HP, Liu W, Xu ZM, Yang L, Ding YQ, Tang F, Meissner A, Ding C, Shi Y, Xu GL. Tet1 regulates adult hippocampal neurogenesis and cognition. Cell Stem Cell. 2013 Aug 01;13(2):237–45. PMID: 23770080; PMCID: PMC4474382.; Ponnaluri VKC, Maciejewski JP, Mukherji M. A mechanistic overview of TET-mediated 5-methylcytosine oxidation. Biochemical and Biophysical Research Communications. 2013 Jun;436(2):115–20. doi: 10.1016/j.bbrc.2013.05.077.; Kinney SR, Pradhan S. Ten eleven translocation enzymes and 5-hydroxymethylation in mammalian development and cancer. Adv Exp Med Biol. 2013;754():57–79. doi: 10.1007/978-1-4419-9967-2_3. PMID: 22956496.; Franchini DM, Schmitz KM, Petersen-Mahrt SK. 5-Methylcytosine DNA demethylation: more than losing a methyl group. Annu Rev Genet. 2012;46():419–41. doi: 10.1146/annurev-genet-110711-155451. PMID: 22974304.; Wu H, Zhang Y. Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev. 2011 Dec 01;25(23):2436–52. PMID: 22156206; PMCID: PMC3243055.; He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, Sun Y, Li X, Dai Q, Song CX, Zhang K, He C, Xu GL. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science. 2011 Sep 02;333(6047):1303–7. PMID: 21817016; PMCID: PMC3462231.; Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. 2011 Sep 02;333(6047):1300–3. PMID: 21778364; PMCID: PMC3495246.; Guo JU, Su Y, Zhong C, Ming GL, Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell. 2011 Apr 29;145(3):423–34. PMID: 21496894; PMCID: PMC3088758.; Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S, Reik W. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature. 2011 May 19;473(7347):398–402. doi: 10.1038/nature10008. PMID: 21460836.; Wu H, D'Alessio AC, Ito S, Xia K, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature. 2011 May 19;473(7347):389–93. PMID: 21451524; PMCID: PMC3539771.; Iqbal K, Jin SG, Pfeifer GP, Szabó PE. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc Natl Acad Sci U S A. 2011 Mar 01;108(9):3642–7. PMID: 21321204; PMCID: PMC3048122.; Koh KP, Yabuuchi A, Rao S, Huang Y, Cunniff K, Nardone J, Laiho A, Tahiliani M, Sommer CA, Mostoslavsky G, Lahesmaa R, Orkin SH, Rodig SJ, Daley GQ, Rao A. Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell. 2011 Feb 04;8(2):200–13. PMID: 21295276; PMCID: PMC3134318.; Ito S, D'Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature. 2010 Aug 26;466(7310):1129–33. PMID: 20639862; PMCID: PMC3491567.; Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009 May 15;324(5929):930–5. PMID: 19372391; PMCID: PMC2715015.

Metabolites



Enzyme

EC Number name full name note


Proteins

Protein ID name full name