The chemistries and consequences of DNA and RNA methylation and demethylation

References

• Breiling A, Lyko F. Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond. Epigenetics Chromatin 2015; 8:24; PMID:26195987; https://doi.org/10.1186/s13072-015-0016-6
   PubMed Web of Science ®Google Scholar
• Chen K, Zhao BS, He C. Nucleic acid modifications in regulation of gene expression. Cell Chem Biol 2016; 23:74-85; PMID:26933737; https://doi.org/10.1016/j.chembiol.2015.11.007
   PubMed Web of Science ®Google Scholar
• Duechler M, Leszczynska G, Sochacka E, Nawrot B. Nucleoside modifications in the regulation of gene expression: Focus on tRNA. Cell Mol Life Sci 2016; 73:3075-95; PMID:27094388; https://doi.org/10.1007/s00018-016-2217-y
   PubMed Web of Science ®Google Scholar
• Penzo M, Galbiati A, Trere D, Montanaro L. The importance of being (slightly) modified: The role of rRNA editing on gene expression control and its connections with cancer. Biochim Biophys Acta 2016; 1866:330-8; PMID:27815156; https://doi.org/10.1016/j.bbcan.2016.10.007
   PubMed Web of Science ®Google Scholar
• Sloan KE, Warda AS, Sharma S, Entian KD, Lafontaine DL, Bohnsack MT. Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function. RNA Biol 2016:1-16; PMID:27911188; https://doi.org/10.1080/15476286.2016.1259781
   PubMedGoogle Scholar
• El Yacoubi B, Bailly M, de Crecy-Lagard V. Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Annu Rev Genet 2012; 46:69-95; PMID:22905870; https://doi.org/10.1146/annurev-genet-110711-155641
   PubMed Web of Science ®Google Scholar
• Lioy VS, Goussard S, Guerineau V, Yoon E-J, Courvalin P, Galimand M, Grillot-Courvalin C. Aminoglycoside resistance 16S rRNA methyltransferases block endogenous methylation, affect translation efficiency and fitness of the host. RNA 2014; 20:382-91; PMID:24398977; https://doi.org/10.1261/rna.042572.113
   PubMed Web of Science ®Google Scholar
• Ehrlich M, Wang RY-H. 5-Methylcytosine in eukaryotic DNA. Science 1981; 212:1350-7; PMID:6262918; https://doi.org/10.1126/science.6262918
   PubMed Web of Science ®Google Scholar
• Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee AS. Genomics of DNA cytosine methylation in escherichia coli reveals its role in stationary phase transcription. Nat Commun 2012; 3:886; PMID:22673913; https://doi.org/10.1038/ncomms1878
   PubMed Web of Science ®Google Scholar
• Ehrlich M, Gama-Sosa MA, Carreira LH, Ljungdahl LG, Kuo KC, Gehrke CW. DNA methylation in thermophylic bacteria: N4-methylcytosine, 5-methylcytosine, and N6-methyladenine. Nucleic Acids Res 1985; 13:1399-412; PMID:4000939; https://doi.org/10.1093/nar/13.4.1399
   PubMed Web of Science ®Google Scholar
• Ehrlich M, Gama-Sosa MA, Huang L-H, Midgett RM, Kuo KC, McCune RA, Gehrke C. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues or cells. Nucleic Acids Res 1982; 10:2709-21; PMID:7079182; https://doi.org/10.1093/nar/10.8.2709
   PubMed Web of Science ®Google Scholar
• Globisch D, Münzel M, Müller M, Michalakis S, Wagner M, Koch S, Brückl T, Biel M, Carell T. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 2010; 5:e15367; PMID:21203455; https://doi.org/10.1371/journal.pone.0015367
   PubMed Web of Science ®Google Scholar
• Koziol MJ, Bradshaw CR, Allen GE, Costa AS, Frezza C, Gurdon JB. Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications. Nat Struct Mol Biol 2016; 23:24-30; PMID:26689968; https://doi.org/10.1038/nsmb.3145
   PubMed Web of Science ®Google Scholar
• Liu J, Zhu Y, Luo GZ, Wang X, Yue Y, Wang X, Zong X, Chen K, Yin H, Fu Y. Abundant DNA 6mA methylation during early embryogenesis of zebrafish and pig. Nat Commun 2016; 7:13052; PMID:27713410; https://doi.org/10.1038/ncomms13052
   PubMed Web of Science ®Google Scholar
• Greer EL, Blanco MA, Gu L, Sendinc E, Liu J, Aristizabal-Corrales D, Hsu CH, Aravind L, He C, Shi Y. DNA methylation on N6-Adenine in C. elegans. Cell 2015; 161:868-78; PMID:25936839; https://doi.org/10.1016/j.cell.2015.04.005
   PubMed Web of Science ®Google Scholar
• Zhang G, Huang H, Liu D, Cheng Y, Liu X, Zhang W, Yin R, Zhang D, Zhang P, Liu J, et al. N6-methyladenine DNA modification in drosophila. Cell 2015; 161:893-906; PMID:25936838; https://doi.org/10.1016/j.cell.2015.04.018
   PubMed Web of Science ®Google Scholar
• Fu Y, Luo GZ, Chen K, Deng X, Yu M, Han D, Hao Z, Liu J, Lu X, Doré LC, et al. N6-methyldeoxyadenosine marks active transcription start sites in chlamydomonas. Cell 2015; 161:879-92; PMID:25936837; https://doi.org/10.1016/j.cell.2015.04.010
   PubMed Web of Science ®Google Scholar
• Wu TP, Wang T, Seetin MG, Lai Y, Zhu S, Lin K, Liu Y, Byrum SD, Mackintosh SG, Zhong M, et al. DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature 2016; 532:329-33; PMID:27027282; https://doi.org/10.1038/nature17640
   PubMed Web of Science ®Google Scholar
• Koziol MJ, Bradshaw CR, Allen GE, Costa AS, Frezza C, Gurdon JB. Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications. Nat Struct Mol Biol 2016; 23:24-30; PMID:26689968; https://doi.org/10.1038/nsmb.3145
   PubMed Web of Science ®Google Scholar
• Schiffers S, Ebert C, Rahimoff R, Kosmatchev O, Steinbacher J, Bohne A-V, Spada F, Michalakis S, Nickelsen J, Müller M, et al. Quantitative LC–MS provides no evidence for m6da or m4dc in the genome of mouse embryonic stem cells and tissues. Angew Chem Int Ed 2017; PMID:28371147; https://doi.org/10.1002/anie.201700424
   PubMed Web of Science ®Google Scholar
• Kumar S, Cheng X, Klimasauskas S, Mi S, Postfai J, Roberts RJ, Wilson GG. The DNA (cytosine-5) methyltransferases. Nucleic Acids Res 1993; 22:1-10; PMID:8127644; https://doi.org/10.1093/nar/22.1.1
   PubMed Web of Science ®Google Scholar
• Smith SS, Kaplan BE, Sowers LC, Newman EM. Mechanism of human methyl-directed DNA methyltransferases and the fidelity of cytosine methylation. Proc Natl Acad Sci USA 1992; 89:4744-8; PMID:1584813; https://doi.org/10.1073/pnas.89.10.4744
   PubMed Web of Science ®Google Scholar
• Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014; 5:144; PMID:24904644; https://doi.org/10.3389/fgene.2014.00144
   PubMed Web of Science ®Google Scholar
• Bestor T, Laudano A, Mattaliano R, Ingram V. Cloning and sequencing of a cDNA encoding dna methyltransferase of mouse cells. J Mol Biol 1988; 203:971-83; PMID:3210246; https://doi.org/10.1016/0022-2836(88)90122-2
   PubMed Web of Science ®Google Scholar
• Okano M, Xie S, Li E. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat Genet 1998; 19:219-20; PMID:9662389; https://doi.org/10.1038/890
   PubMed Web of Science ®Google Scholar
• Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999; 99:247-57; PMID:10555141; https://doi.org/10.1016/S0092-8674(00)81656-6
   PubMed Web of Science ®Google Scholar
• Pradhan S, Bacolla A, Wells RD, Roberts RJ. Recombinant human DNA (Cytosine-5) methyltransferase. J Biol Chem 1999; 274:33002-10; PMID:10551868; https://doi.org/10.1074/jbc.274.46.33002
   PubMed Web of Science ®Google Scholar
• Klose RJ, Bird AP. Genomic DNA methylation: The mark and its mediators. Trends Biochem Sci 2006; 31:89-97; PMID:16403636; https://doi.org/10.1016/j.tibs.2005.12.008
   PubMed Web of Science ®Google Scholar
• Spada F, Haemmer A, Kuch D, Rothbauer U, Schermelleh L, Kremmer E, Carell T, Längst G, Leonhardt H. DNMT1 but not its interaction with the replication machinery is required for maintenance of DNA methylation in human cells. J Cell Biol 2007; 176:565-71; PMID:17312023; https://doi.org/10.1083/jcb.200610062
   PubMed Web of Science ®Google Scholar
• Li E, Bestor TH, Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 1992; 69:915-26; PMID:1606615; https://doi.org/10.1016/0092-8674(92)90611-F
   PubMed Web of Science ®Google Scholar
• Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Scholer A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 2011; 480:490-5; PMID:22170606; https://doi.org/10.1038/nature10716
   PubMed Web of Science ®Google Scholar
• Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, Jaenisch R. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA 2000; 97:5237-42; PMID:10805783; https://doi.org/10.1073/pnas.97.10.5237
   PubMed Web of Science ®Google Scholar
• Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009; 462:315-22; PMID:19829295; https://doi.org/10.1038/nature08514
   PubMed Web of Science ®Google Scholar
• Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, Dempster EL, Ren B. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 2012; 148:816-31; PMID:22341451; https://doi.org/10.1016/j.cell.2011.12.035
   PubMed Web of Science ®Google Scholar
• Suzuki MM, Bird A. DNA methylation landscapes: Provocative insights from epigenomics. Nat Rev Genet 2008; 9:465-76; PMID:18463664; https://doi.org/10.1038/nrg2341
   PubMed Web of Science ®Google Scholar
• Bird A, Taggart M, Frommer M, Miller OJ, Macleod D. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 1985; 40:91-9; PMID:2981636; https://doi.org/10.1016/0092-8674(85)90312-5
   PubMed Web of Science ®Google Scholar
• Bird AP. CpG-rich islands and the function of DNA methylation. Nature 1986; 321:209-13; PMID:2423876; https://doi.org/10.1038/321209a0
   PubMed Web of Science ®Google Scholar
• Antequera F, Bird A. Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci USA 1993; 90:11995-9; PMID:7505451; https://doi.org/10.1073/pnas.90.24.11995
   PubMed Web of Science ®Google Scholar
• Fatemi M, Pao MM, Jeong S, Gal-Yam EN, Egger G, Weisenberger DJ, Jones PA. Footprinting of mammalian promoters: Use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level. Nucleic Acids Res 2005; 33:e176; PMID:16314307; https://doi.org/10.1093/nar/gni180
   PubMed Web of Science ®Google Scholar
• Boyes J, Bird A. DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein. Cell 1991; 64:1123-34; PMID:2004419; https://doi.org/10.1016/0092-8674(91)90267-3
   PubMed Web of Science ®Google Scholar
• Siegfried Z, Eden S, Mendelsohn M, Feng X, Tsuberi B-Z, Cedar H. DNA methylation represses transcription in vivo. Nat Genet 1999; 22:203-6; PMID:10369268; https://doi.org/10.1038/9727
   PubMed Web of Science ®Google Scholar
• Zou S, Toh JDW, Wong KHQ, Gao Y-G, Hong W, Woon ECY. N(6)-methyladenosine: A conformational marker that regulates the substrate specificity of human demethylases FTO and ALKBH5. Sci Rep 2016; 6:25677; PMID:27156733; https://doi.org/10.1038/srep25677
   PubMed Web of Science ®Google Scholar
• Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, Yi C, Lindahl T, Pan T, Yang YG, et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 2011; 7:885-7; PMID:22002720; https://doi.org/10.1038/nchembio.687
   PubMed Web of Science ®Google Scholar
• Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, Vågbø CB, Shi Y, Wang WL, Song SH, et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell 2013; 49:18-29; PMID:23177736; https://doi.org/10.1016/j.molcel.2012.10.015
   PubMed Web of Science ®Google Scholar
• Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009; 324:930-5; PMID:19372391; https://doi.org/10.1126/science.1170116
   PubMed Web of Science ®Google Scholar
• 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; 333:1300-3; PMID:21778364; https://doi.org/10.1126/science.1210597
   PubMed Web of Science ®Google Scholar
• Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in purkinje neurons and the brain. Science 2009; 324:929-30; PMID:19372393; https://doi.org/10.1126/science.1169786
   PubMed Web of Science ®Google Scholar
• Bachman M, Uribe-Lewis S, Yang X, Williams M, Murrell A, Balasubramanian S. 5-Hydroxymethylcytosine is a predominantly stable DNA modification. Nat Chem 2014; 6:1049-55; PMID:25411882; https://doi.org/10.1038/nchem.2064
   PubMed Web of Science ®Google Scholar
• Wagner M, Steinbacher J, Kraus TF, Michalakis S, Hackner B, Pfaffeneder T, Perera A, Müller M, Giese A, Kretzschmar HA, et al. Age-dependent levels of 5-methyl-, 5-hydroxymethyl-, and 5-formylcytosine in human and mouse brain tissues. Angew Chem Int Ed Engl 2015; 54:12511-4; PMID:26137924; https://doi.org/10.1002/anie.201502722
   PubMed Web of Science ®Google Scholar
• Mellen M, Ayata P, Dewell S, Kriaucionis S, Heintz N. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 2012; 151:1417-30; PMID:23260135; https://doi.org/10.1016/j.cell.2012.11.022
   PubMed Web of Science ®Google Scholar
• Perera A, Eisen D, Wagner M, Laube SK, Künzel AF, Koch S, Steinbacher J, Schulze E, Splith V, Mittermeier N, et al. TET3 is recruited by REST for context-specific hydroxymethylation and induction of gene expression. Cell Rep 2015; 11:283-94; PMID:25843715; https://doi.org/10.1016/j.celrep.2015.03.020
   PubMed Web of Science ®Google Scholar
• Costa Y, Ding J, Theunissen TW, Faiola F, Hore TA, Shliaha PV, Fidalgo M, Saunders A, Lawrence M, Dietmann S, et al. NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature 2013; 495:370-4; PMID:23395962; https://doi.org/10.1038/nature11925
   PubMed Web of Science ®Google Scholar
• Koh KP, Yabuuchi A, Rao S, Huang Y, Cunniff K, Nardone J, Laiho A, Tahiliani M, Sommer CA, Mostoslavsky G, et al. Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 2011; 8:200-13; PMID:21295276; https://doi.org/10.1016/j.stem.2011.01.008
   PubMed Web of Science ®Google Scholar
• Szwagierczak A, Bultmann S, Schmidt CS, Spada F, Leonhardt H. Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res 2010; 38:e181; PMID:20685817; https://doi.org/10.1093/nar/gkq684
   PubMed Web of Science ®Google Scholar
• Gu TP, Guo F, Yang H, Wu HP, Xu GF, Liu W, Xie ZG, Shi L, He X, Jin SG, et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 2011; 477:606-10; PMID:21892189; https://doi.org/10.1038/nature10443
   PubMed Web of Science ®Google Scholar
• Penn NW, Suwalski R, O'Riley C, Bojanowski K, Yura R. The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem J 1972; 126:781-90; PMID:4538516; https://doi.org/10.1042/bj1260781
   PubMed Web of Science ®Google Scholar
• Globisch D, Münzel M, Müller M, Michalakis S, Wagner M, Koch S, Brückl T, Biel M, Carell T. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 2010; 5:e15367; PMID:21203455; https://doi.org/10.1371/journal.pone.0015367
   PubMed Web of Science ®Google Scholar
• Bachman M, Uribe-Lewis S, Yang X, Burgess HE, Iurlaro M, Reik W, Murrell A, Balasubramanian S. 5-Formylcytosine can be a stable DNA modification in mammals. Nat Chem Biol 2015; 11:555-7; PMID:26098680; https://doi.org/10.1038/nchembio.1848
   PubMed Web of Science ®Google Scholar
• Zhu C, Gao Y, Guo H, Xia B, Song J, Wu X, Zeng H, Kee K, Tang F, Yi C. Single-cell 5-formylcytosine landscapes of mammalian early embryos and escs at single-base resolution. Cell Stem Cell 2017; 20:720-731.e5; PMID:28343982; https://doi.org/10.1016/j.stem.2017.02.013
   PubMed Web of Science ®Google Scholar
• Mayer W, Niveleau A, Walter J, Fundele R, Haaf T. Embryogenesis: Demethylation of the zygotic paternal genome. Nature 2000; 403:501-2; PMID:10676950; https://doi.org/10.1038/35000656
   PubMed Web of Science ®Google Scholar
• Oswald J, Engemann S, Lane N, Mayer W, Olek A, Fundele R, Dean W, Reik W, Walter J. Active demethylation of the paternal genome in the mouse zygote. Curr Biol 2000; 10:475-8; PMID:10801417; https://doi.org/10.1016/S0960-9822(00)00448-6
   PubMed Web of Science ®Google Scholar
• Feng S, Jacobsen SE, Reik W. Epigenetic reprogramming in plant and animal development. Science 2010; 330:622-7; PMID:21030646; https://doi.org/10.1126/science.1190614
   PubMed Web of Science ®Google Scholar
• Sasaki H, Matsui Y. Epigenetic events in mammalian germ-cell development: Reprogramming and beyond. Nat Rev Genet 2008; 9:129-40; PMID:18197165; https://doi.org/10.1038/nrg2295
   PubMed Web of Science ®Google Scholar
• Guo JU, Ma DK, Mo H, Ball MP, Jang M-H, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, et al. Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci 2011; 14:1345-51; PMID:21874013; https://doi.org/10.1038/nn.2900
   PubMed Web of Science ®Google Scholar
• Morris MJ, Monteggia LM. Role of DNA methylation and the DNA methyltransferases in learning and memory. Dialogues Clin Neurosci 2014; 16:359-71; PMID:25364286
   PubMed Web of Science ®Google Scholar
• Ma DK, Jang M-H, Guo JU, Kitabatake Y, Chang M-l, Pow-anpongkul N, Flavell RA, Lu B, Ming GL, Song H. Neuronal activity–induced gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 2009; 323:1074-7; PMID:19119186; https://doi.org/10.1126/science.1166859
   PubMed Web of Science ®Google Scholar
• Seisenberger S, Peat JR, Reik W. Conceptual links between DNA methylation reprogramming in the early embryo and primordial germ cells. Curr Opin Cell Biol 2013; 25:281-8; PMID:23510682; https://doi.org/10.1016/j.ceb.2013.02.013
   PubMed Web of Science ®Google Scholar
• Schiesser S, Hackner B, Pfaffeneder T, Müller M, Hagemeier C, Truss M, Carell T. Mechanism and stem-cell activity of 5-carboxycytosine decarboxylation determined by isotope tracing. Angew Chem Int Ed Engl 2012; 51:6516-20; PMID:22644704; https://doi.org/10.1002/anie.201202583
   PubMed Web of Science ®Google Scholar
• Liutkevičiūtė Z, Lukinavičius G, Masevičius V, Daujotytė D, Klimaašauskas S. Cytosine-5-methyltransferases add aldehydes to DNA. Nat Chem Biol 2009; 5:400-2; PMID:19430486; https://doi.org/10.1038/nchembio.172
   PubMed Web of Science ®Google Scholar
• Haag S, Sloan KE, Ranjan N, Warda AS, Kretschmer J, Blessing C, Hübner B, Seikowski J, Dennerlein S, Rehling P, et al. NSUN3 and ABH1 modify the wobble position of mt-tRNA Met to expand codon recognition in mitochondrial translation. EMBO J 2016; 35:2104-19; PMID:27497299; https://doi.org/10.15252/embj.201694885
   PubMed Web of Science ®Google Scholar
• Liu F, Clark W, Luo G, Wang X, Fu Y, Wei J, Wang X, Hao Z, Dai Q, Zheng G, et al. ALKBH1-mediated tRNA demethylation regulates translation. Cell 2016; 167:816-28.e16; PMID:27745969; https://doi.org/10.1016/j.cell.2016.09.038
   PubMed Web of Science ®Google Scholar
• Delatte B, Wang F, Ngoc LV, Collignon E, Bonvin E, Deplus R, Calonne E, Hassabi B, Putmans P, Awe S, et al. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine. Science 2016; 351:282-5; PMID:26816380; https://doi.org/10.1126/science.aac5253
   PubMed Web of Science ®Google Scholar
• Fu L, Guerrero CR, Zhong N, Amato NJ, Liu Y, Liu S, Cai Q, Ji D, Jin SG, Niedernhofer LJ, et al. Tet-mediated formation of 5-hydroxymethylcytosine in RNA. J Am Chem Soc 2014; 136:11582-5; PMID:25073028; https://doi.org/10.1021/ja505305z
   PubMed Web of Science ®Google Scholar
• Zhang H-Y, Xiong J, Qi B-L, Feng Y-Q, Yuan B-F. The existence of 5-hydroxymethylcytosine and 5-formylcytosine in both DNA and RNA in mammals. Chem Commun 2016; 52:737-40; PMID:26562407; https://doi.org/10.1039/C5CC07354E
   PubMed Web of Science ®Google Scholar
• Maiti A, Drohat AC. Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: Potential implications for active demethylation of CpG sites. J Biol Chem 2011; 286:35334-8; PMID:21862836; https://doi.org/10.1074/jbc.C111.284620
   PubMed Web of Science ®Google Scholar
• He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 2011; 333:1303-7; PMID:21817016; https://doi.org/10.1126/science.1210944
   PubMed Web of Science ®Google Scholar
• Schomacher L, Han D, Musheev MU, Arab K, Kienhofer S, von Seggern A, Niehrs C. Neil DNA glycosylases promote substrate turnover by Tdg during DNA demethylation. Nat Struct Mol Biol 2016; 23:116-24; PMID:26751644; https://doi.org/10.1038/nsmb.3151
   PubMed Web of Science ®Google Scholar
• Cortellino S, Xu J, Sannai M, Moore R, Caretti E, Cigliano A, Le Coz M, Devarajan K, Wessels A, Soprano D, et al. Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell 2011; 146:67-79; PMID:21722948; https://doi.org/10.1016/j.cell.2011.06.020
   PubMed Web of Science ®Google Scholar
• Cortazar D, Kunz C, Selfridge J, Lettieri T, Saito Y, MacDougall E, Wirz A, Schuermann D, Jacobs AL, Siegrist F, et al. Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability. Nature 2011; 470:419-23; PMID:21278727; https://doi.org/10.1038/nature09672
   PubMed Web of Science ®Google Scholar
• Amouroux R, Nashun B, Shirane K, Nakagawa S, Hill PW, D'Souza Z, Nakayama M, Matsuda M, Turp A, Ndjetehe E, et al. De novo DNA methylation drives 5hmC accumulation in mouse zygotes. Nat Cell Biol 2016; 18:225-33; PMID:26751286; https://doi.org/10.1038/ncb3296
   PubMed Web of Science ®Google Scholar
• Santos F, Peat J, Burgess H, Rada C, Reik W, Dean W. Active demethylation in mouse zygotes involves cytosine deamination and base excision repair. Epigenetics Chromatin 2013; 6:39; PMID:24279473; https://doi.org/10.1186/1756-8935-6-39
   PubMed Web of Science ®Google Scholar
• Ko M, Huang Y, Jankowska AM, Pape UJ, Tahiliani M, Bandukwala HS, An J, Lamperti ED, Koh KP, Ganetzky R, et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 2010; 468:839-43; PMID:21057493; https://doi.org/10.1038/nature09586
   PubMed Web of Science ®Google Scholar
• Esteller M. Epigenetics in Cancer. N Engl J Med 2008; 358:1148-59; PMID:18337604; https://doi.org/10.1056/NEJMra072067
   PubMed Web of Science ®Google Scholar
• Jones PA, Baylin SB. The epigenomics of cancer. Cell 2007; 128:683-92; PMID:17320506; https://doi.org/10.1016/j.cell.2007.01.029
   PubMed Web of Science ®Google Scholar
• Chen WY, Wang DH, Yen RC, Luo J, Gu W, Baylin SB. Tumor suppressor HIC1 directly regulates SIRT1 to modulate p53-dependent DNA-damage responses. Cell 2005; 123:437-48; PMID:16269335; https://doi.org/10.1016/j.cell.2005.08.011
   PubMed Web of Science ®Google Scholar
• Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB. Issa J-PJ. CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci USA 1999; 96:8681-6; PMID:10411935; https://doi.org/10.1073/pnas.96.15.8681
   PubMed Web of Science ®Google Scholar
• Weisenberger DJ, Siegmund KD, Campan M, Young J, Long TI, Faasse MA, Kang GH, Widschwendter M, Weener D, Buchanan D, et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet 2006; 38:787-93; PMID:16804544; https://doi.org/10.1038/ng1834
   PubMed Web of Science ®Google Scholar
• Issa J-P. CpG island methylator phenotype in cancer. Nat Rev Cancer 2004; 4:988-93; PMID:15573120; https://doi.org/10.1038/nrc1507
   PubMed Web of Science ®Google Scholar
• Ono R, Taki T, Taketani T, Taniwaki M, Kobayashi H, Hayashi Y. LCX, leukemia-associated protein with a CXXC domain, is fused to MLL in acute myeloid leukemia with trilineage dysplasia having t(10;11)(q22;q23). Cancer Res 2002; 62:4075-80; PMID:12124344
   PubMed Web of Science ®Google Scholar
• Yang H, Liu Y, Bai F, Zhang JY, Ma SH, Liu J, Xu ZD, Zhu HG, Ling ZQ, Ye D, et al. Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene 2013; 32:663-9; PMID:22391558; https://doi.org/10.1038/onc.2012.67
   PubMed Web of Science ®Google Scholar
• Neri F, Dettori D, Incarnato D, Krepelova A, Rapelli S, Maldotti M, Parlato C, Paliogiannis P, Oliviero S. TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway. Oncogene 2015; 34:4168-76; PMID:25362856; https://doi.org/10.1038/onc.2014.356
   PubMed Web of Science ®Google Scholar
• Hsu C-H, Peng K-L, Kang M-L, Chen Y-R, Yang Y-C, Tsai C-H, Chu CS, Jeng YM, Chen YT, Lin FM, et al. TET1 suppresses cancer invasion by activating the tissue inhibitors of metalloproteinases. Cell Rep 2012; 2:568-79; PMID:22999938; https://doi.org/10.1016/j.celrep.2012.08.030
   PubMed Web of Science ®Google Scholar
• Liu C, Liu L, Chen X, Shen J, Shan J, Xu Y, Yang Z, Wu L, Xia F, Bie P, et al. Decrease of 5-hydroxymethylcytosine is associated with progression of hepatocellular carcinoma through downregulation of TET1. PLoS One 2013; 8:e62828; PMID:23671639; https://doi.org/10.1371/journal.pone.0062828
   PubMed Web of Science ®Google Scholar
• Langemeijer SMC, Kuiper RP, Berends M, Knops R, Aslanyan MG, Massop M, Stevens-Linders E, van Hoogen P, van Kessel AG, Raymakers RA, et al. Acquired mutations in TET2 are common in myelodysplastic syndromes. Nat Genet 2009; 41:838-42; PMID:19483684; https://doi.org/10.1038/ng.391
   PubMed Web of Science ®Google Scholar
• Lemonnier F, Couronné L, Parrens M, Jaïs J-P, Travert M, Lamant L, Tournillac O, Rousset T, Fabiani B, Cairns RA, et al. Recurrent TET2 mutations in peripheral T-cell lymphomas correlate with TFH-like features and adverse clinical parameters. Blood 2012; 120:1466-9; PMID:22760778; https://doi.org/10.1182/blood-2012-02-408542
   PubMed Web of Science ®Google Scholar
• Xu W, Yang H, Liu Y, Yang Y, Wang P, Kim S-H, Ito S, Yang C, Wang P, Xiao MT, et al. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases. Cancer Cell 2011; 19:17-30; PMID:21251613; https://doi.org/10.1016/j.ccr.2010.12.014
   PubMed Web of Science ®Google Scholar
• Inoue S, Lemonnier F, Mak TW. Roles of IDH1/2 and TET2 mutations in myeloid disorders. Int J Hematol 2016; 103:627-33; PMID:26980223; https://doi.org/10.1007/s12185-016-1973-7
   PubMed Web of Science ®Google Scholar
• Shih AH, Abdel-Wahab O, Patel JP, Levine RL. The role of mutations in epigenetic regulators in myeloid malignancies. Nat Rev Cancer 2012; 12:599-612; PMID:22898539; https://doi.org/10.1038/nrc3343
   PubMed Web of Science ®Google Scholar
• Thienpont B, Steinbacher J, Zhao H, D'Anna F, Kuchnio A, Ploumakis A, Ghesquière B, Van Dyck L, Boeckx B, Schoonjans L, et al. Tumour hypoxia causes DNA hypermethylation by reducing TET activity. Nature 2016; 537:63-8; PMID:27533040; https://doi.org/10.1038/nature19081
   PubMed Web of Science ®Google Scholar
• Yang H, Lin H, Xu H, Zhang L, Cheng L, Wen B, Shou J, Guan K, Xiong Y, Ye D. TET-catalyzed 5-methylcytosine hydroxylation is dynamically regulated by metabolites. Cell Res 2014; 24:1017-20; PMID:24971736; https://doi.org/10.1038/cr.2014.81
   PubMed Web of Science ®Google Scholar
• Sciacovelli M, Goncalves E, Johnson TI, Zecchini VR, da Costa AS, Gaude E, Drubbel AV, Theobald SJ, Abbo SR, Tran MG, et al. Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition. Nature 2016; 537:544-7; PMID:27580029; https://doi.org/10.1038/nature19353
   PubMed Web of Science ®Google Scholar
• Carey BW, Finley LW, Cross JR, Allis CD, Thompson CB. Intracellular alpha-ketoglutarate maintains the pluripotency of embryonic stem cells. Nature 2015; 518:413-6; PMID:25487152; https://doi.org/10.1038/nature13981
   PubMed Web of Science ®Google Scholar
• TeSlaa T, Chaikovsky AC, Lipchina I, Escobar SL, Hochedlinger K, Huang J, Graeber TG, Braas D, Teitell MA. alpha-ketoglutarate accelerates the initial differentiation of primed human pluripotent stem cells. Cell Metab 2016; 24:485-93; PMID:27476976; https://doi.org/10.1016/j.cmet.2016.07.002
   PubMed Web of Science ®Google Scholar
• Yang Q, Liang X, Sun X, Zhang L, Fu X, Rogers CJ, Berim A, Zhang S, Wang S, Wang B, et al. AMPK/alpha-ketoglutarate axis dynamically mediates dna demethylation in the prdm16 promoter and brown adipogenesis. Cell Metab 2016; 24:542-54; PMID:27641099; https://doi.org/10.1016/j.cmet.2016.08.010
   PubMed Web of Science ®Google Scholar
• Laukka T, Mariani CJ, Ihantola T, Cao JZ, Hokkanen J, Kaelin WG Jr., Godley LA, Koivunen P. Fumarate and succinate regulate expression of hypoxia-inducible genes via TET enzymes. J Biol Chem 2016; 291:4256-65; PMID:26703470; https://doi.org/10.1074/jbc.M115.688762
   PubMed Web of Science ®Google Scholar