1932

Abstract

Epigenetic mechanisms by which cells inherit information are, to a large extent, enabled by DNA methylation and posttranslational modifications of histone proteins. These modifications operate both to influence the structure of chromatin per se and to serve as recognition elements for proteins with motifs dedicated to binding particular modifications. Each of these modifications results from an enzyme that consumes one of several important metabolites during catalysis. Likewise, the removal of these marks often results in the consumption of a different metabolite. Therefore, these so-called epigenetic marks have the capacity to integrate the expression state of chromatin with the metabolic state of the cell. This review focuses on the central roles played by acetyl-CoA, S-adenosyl methionine, NAD+, and a growing list of other acyl-CoA derivatives in epigenetic processes. We also review how metabolites that accumulate as a result of oncogenic mutations are thought to subvert the epigenetic program.

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2015-11-13
2024-12-11
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Literature Cited

  1. Adam J, Yang M, Soga T, Pollard PJ. 2014. Rare insights into cancer biology. Oncogene 33:202547–56 [Google Scholar]
  2. Allfrey VG, Faulkner R, Mirsky AE. 1964. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. PNAS 51:5786–94 [Google Scholar]
  3. Anderson RM, Bitterman KJ, Wood JG, Medvedik O, Cohen H. et al. 2002. Manipulation of a nuclear NAD+ salvage pathway delays aging without altering steady-state NAD+ levels. J. Biol. Chem. 277:2118881–90 [Google Scholar]
  4. Anderson RM, Bitterman KJ, Wood JG, Medvedik O, Sinclair DA. 2003. Nicotinamide and PNC1 govern lifespan extension by calorie restriction in Saccharomyces cerevisiae. Nature 423:6936181–85 [Google Scholar]
  5. Apostolou E, Hochedlinger K. 2013. Chromatin dynamics during cellular reprogramming. Nature 502:7472462–71 [Google Scholar]
  6. Asher G, Gatfield D, Stratmann M, Reinke H, Dibner C. et al. 2015. SIRT1 regulates circadian clock gene expression through PER2 deacetylation. Cell 134:2317–28 [Google Scholar]
  7. Avalos JL, Bever KM, Wolberger C. 2005. Mechanism of sirtuin inhibition by nicotinamide: altering the NAD+ cosubstrate specificity of a Sir2 enzyme. Mol. Cell 17:6855–68 [Google Scholar]
  8. Balan V, Miller GS, Kaplun L, Balan K, Chong Z-Z. et al. 2008. Life span extension and neuronal cell protection by Drosophila nicotinamidase. J. Biol. Chem. 283:4127810–19 [Google Scholar]
  9. Baubec T, Dinh HQ, Pecinka A, Rakic B, Rozhon W. et al. 2010. Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic states in Arabidopsis. Plant Cell 22:34–47 [Google Scholar]
  10. Bitterman KJ, Anderson RM, Cohen HY, Latorre-Esteves M, Sinclair DA. 2002. Inhibition of silencing and accelerated aging by nicotinamide, a putative negative regulator of yeast Sir2 and human SIRT1. J. Biol. Chem. 277:4745099–107 [Google Scholar]
  11. Blaschke K, Ebata KT, Karimi MM, Zepeda-Martínez JA, Goyal P. et al. 2013. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature 500:7461222–26 [Google Scholar]
  12. Blewitt ME, Vickaryous NK, Paldi A, Koseki H, Whitelaw E. 2006. Dynamic reprogramming of DNA methylation at an epigenetically sensitive allele in mice. PLOS Genet. 2:e49 [Google Scholar]
  13. Borra MT, O'Neill FJ, Jackson MD, Marshall B, Verdin E. et al. 2002. Conserved enzymatic production and biological effect of O-acetyl-ADP-ribose by silent information regulator 2-like NAD+-dependent deacetylases. J. Biol. Chem. 277:1512632–41 [Google Scholar]
  14. Cai L, Sutter BM, Li B, Tu BP. 2011. Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Mol. Cell 42:4426–37 [Google Scholar]
  15. Carey BW, Finley LWS, Cross JR, Allis CD, Thompson CB. 2015. Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells. Nature 518:413–16 [Google Scholar]
  16. Cervera AM, Bayley J-P, Devilee P, McCreath KJ. 2009. Inhibition of succinate dehydrogenase dysregulates histone modification in mammalian cells. Mol. Cancer 8:89 [Google Scholar]
  17. Chang B, Chen Y, Zhao Y, Bruick RK. 2007. JMJD6 is a histone arginine demethylase. Science 318:444–47 [Google Scholar]
  18. Chen J, Guo L, Zhang L, Wu HH, Yang J. et al. 2013a. Vitamin C modulates TET1 function during somatic cell reprogramming. Nat. Genet. 45:121504–9 [Google Scholar]
  19. Chen JJ, Liu H, Liu J, Qi J, Wei B. et al. 2013b. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat. Genet. 45:134–42 [Google Scholar]
  20. Chen Q, Chen Y, Bian C, Fujiki R, Yu X. 2013c. TET2 promotes histone O-GlcNAcylation during gene transcription. Nature 493:561–64 [Google Scholar]
  21. Chou C-C, Li Y-C, Gartenberg MR. 2008. Bypassing Sir2 and O-acetyl-ADP-ribose in transcriptional silencing. Mol. Cell 31:5650–59 [Google Scholar]
  22. Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M. et al. 2009. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325:5942834–40 [Google Scholar]
  23. Chowdhury R, Yeoh KK, Tian Y-M, Hillringhaus L, Bagg EA. et al. 2011. The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep. 12:5463–69 [Google Scholar]
  24. Chung TL, Brena RM, Kolle G, Grimmond SM, Berman BP. et al. 2010. Vitamin C promotes widespread yet specific DNA demethylation of the epigenome in human embryonic stem cells. Stem Cells 28:1848–55 [Google Scholar]
  25. Cloos PAC, Christensen J, Agger K, Maiolica A, Rappsilber J. et al. 2006. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442:307–11 [Google Scholar]
  26. Cropley JE, Suter CM, Beckman KB, Martin DI. 2006. Germ-line epigenetic modification of the murine Avy allele by nutritional supplementation. PNAS 1103:17308–12 [Google Scholar]
  27. Cropley JE, Suter CM, Beckman KB, Martin DI. 2010. CpG methylation of a silent controlling element in the murine Avy allele is incomplete and unresponsive to methyl donor supplementation. PLOS ONE 5:2e9055 [Google Scholar]
  28. Dang L, White DW, Gross S, Bennett BD, Bittinger MA. et al. 2009. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462:739–44 [Google Scholar]
  29. De Jong L, Albracht SP, Kemp A. 1982. Prolyl 4-hydroxylase activity in relation to the oxidation state of enzyme-bound iron. The role of ascorbate in peptidyl proline hydroxylation. Biochim. Biophys. Acta 704:326–32 [Google Scholar]
  30. Deplus R, Delatte B, Schwinn MK, Defrance M, Méndez J. et al. 2013. TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS. EMBO J. 32:645–55 [Google Scholar]
  31. Dhalluin C, Carlson JE, Zeng L, He C, Aggarwal AK. et al. 1999. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399:6735491–96 [Google Scholar]
  32. Dickson KM, Gustafson CB, Young JI, Züchner S, Wang G. 2013. Ascorbate-induced generation of 5-hydroxymethylcytosine is unaffected by varying levels of iron and 2-oxoglutarate. Biochem. Biophys. Res. Commun. 439:522–27 [Google Scholar]
  33. Dolinoy DC, Weinhouse C, Jones TR, Rozek LS, Jirtle RL. 2010. Variable histone modifications at the A(vy) metastable epiallele. Epigenetics 5:637–44 [Google Scholar]
  34. Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL. et al. 2015. Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, Gcn5, and Esa1. Mol. Cell. Proteomics 14:1162–76 [Google Scholar]
  35. Downey M, Knight B, Vashisht AA, Seller CA, Wohlschlegel JA. et al. 2013. Gcn5 and sirtuins regulate acetylation of the ribosomal protein transcription factor Ifh1. Curr. Biol. 23:171638–48 [Google Scholar]
  36. Duncan CG, Barwick BG, Jin G, Rago C, Kapoor-Vazirani P. et al. 2012. A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation. Genome Res. 22:2339–55 [Google Scholar]
  37. Edgar AJ. 2002. The human L-threonine 3-dehydrogenase gene is an expressed pseudogene. BMC Genet. 3:18 [Google Scholar]
  38. Esteban MA, Wang T, Qin B, Yang J, Qin D. et al. 2010. Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Stem Cell 6:71–79 [Google Scholar]
  39. Fang EF, Scheibye-Knudsen M, Brace LE, Kassahun H, SenGupta T. et al. 2014. Defective mitophagy in XPA via PARP-1 hyperactivation and NAD+/SIRT1 reduction. Cell 157:4882–96 [Google Scholar]
  40. Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J. et al. 2010. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18:6553–67 [Google Scholar]
  41. Fischle W, Tseng BS, Dormann HL, Ueberheide BM, Garcia BA. et al. 2005. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438:70711116–22 [Google Scholar]
  42. Friis RMN, Wu BP, Reinke SN, Hockman DJ, Sykes BD, Schultz MC. 2009. A glycolytic burst drives glucose induction of global histone acetylation by picNuA4 and SAGA. Nucleic Acids Res. 37:123969–80 [Google Scholar]
  43. Friso S, Choi SW, Girelli D, Mason JB, Dolnikowski GG. et al. 2002. A common mutation in the 5,10-methylenetetrahydrofolate reductase gene affects genomic DNA methylation through an interaction with folate status. PNAS 99:5606–11 [Google Scholar]
  44. Fulco M, Cen Y, Zhao P, Hoffman EP, McBurney MW. et al. 2008. Glucose restriction inhibits skeletal myoblast differentiation by activating SIRT1 through AMPK-mediated regulation of Nampt. Dev. Cell 14:5661–73 [Google Scholar]
  45. Gaidzik VI, Paschka P, Späth D, Habdank M, Köhne CH. et al. 2012. TET2 mutations in acute myeloid leukemia (AML): results from a comprehensive genetic and clinical analysis of the AML study group. J. Clin. Oncol. 30:1350–57 [Google Scholar]
  46. Galdieri L, Vancura A. 2012. Acetyl-CoA carboxylase regulates global histone acetylation. J. Biol. Chem. 287:2823865–76 [Google Scholar]
  47. Gallo CM, Smith DL, Smith JS. 2004. Nicotinamide clearance by Pnc1 directly regulates Sir2-mediated silencing and longevity. Mol. Cell. Biol. 24:31301–12 [Google Scholar]
  48. Ghislain M, Talla E, François JM. 2002. Identification and functional analysis of the Saccharomyces cerevisiae nicotinamidase gene, PNC1. Yeast 19:3215–24 [Google Scholar]
  49. Gross S, Cairns RA, Minden MD, Driggers EM, Bittinger MA. et al. 2010. Cancer-associated metabolite 2-hydroxyglutarate accumulates in acute myelogenous leukemia with isocitrate dehydrogenase 1 and 2 mutations. J. Exp. Med. 207:339–44 [Google Scholar]
  50. Guse AH. 2015. Calcium mobilizing second messengers derived from NAD. Biochim. Biophys. Acta 1854:91132–37 [Google Scholar]
  51. Hahn MA, Szabó PE, Pfeifer GP. 2014. 5-Hydroxymethylcytosine: a stable or transient DNA modification?. Genomics 104:5314–23 [Google Scholar]
  52. Hales CN, Barker DJ. 2001. The thrifty phenotype hypothesis. Br. Med. Bull. 60:5–20 [Google Scholar]
  53. Hassan AH, Prochasson P, Neely KE, Galasinski SC, Chandy M. et al. 2002. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111:3369–79 [Google Scholar]
  54. He J, Kallin EM, Tsukada Y-I, Zhang Y. 2008. The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15(Ink4b). Nat. Struct. Mol. Biol. 15:111169–75 [Google Scholar]
  55. He Y-F, Li B-Z, Li Z, Liu P, Wang Y. et al. 2011. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333:60471303–7 [Google Scholar]
  56. Hecht A, Laroche T, Strahl-Bolsinger S, Gasser SM, Grunstein M. 2015. Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell 80:4583–92 [Google Scholar]
  57. Hong L, Schroth GP, Matthews HR, Yau P, Bradbury EM. 1993. Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 “tail” to DNA. J. Biol. Chem. 268:1305–14 [Google Scholar]
  58. Honjo T, Nishizuka Y, Hayaishi O, Kato I. 1968. Diphtheria toxin-dependent adenosine diphosphate ribosylation of aminoacyl transferase II and inhibition of protein synthesis. J. Biol. Chem. 243:123553–55 [Google Scholar]
  59. Hornig D. 1975. Distribution of ascorbic acid, metabolites and analogues in man and animals. Ann. N. Y. Acad. Sci. 258:103–18 [Google Scholar]
  60. Imai S, Armstrong CM, Kaeberlein M, Guarente L. 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403:6771795–800 [Google Scholar]
  61. Imai S, Guarente L. 2010. Ten years of NAD-dependent SIR2 family deacetylases: implications for metabolic diseases. Trends Pharmacol. Sci. 31:212–20 [Google Scholar]
  62. Ito S, Shen L, Dai Q, Wu SC, Collins LB. et al. 2011. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333:1300–3 [Google Scholar]
  63. Jackson MD, Denu JM. 2002. Structural identification of 2′- and 3′-O-acetyl-ADP-ribose as novel metabolites derived from the Sir2 family of β-NAD+-dependent histone/protein deacetylases. J. Biol. Chem. 277:2118535–44 [Google Scholar]
  64. Jacobson RH, Ladurner AG, King DS, Tjian R. 2000. Structure and function of a human TAFII250 double bromodomain module. Science 288:54701422–25 [Google Scholar]
  65. Kaelin WG. 2011. Cancer and altered metabolism: potential importance of hypoxia-inducible factor and 2-oxoglutarate–dependent dioxygenases. Cold Spring Harb. Symp. Quant. Biol. 76:335–45 [Google Scholar]
  66. Killian JK, Kim SY, Miettinen M, Smith C, Merino M. et al. 2013. Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor. Cancer Discov. 3:6648–57 [Google Scholar]
  67. Kohli RM, Zhang Y. 2013. TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502:472–79 [Google Scholar]
  68. Landry J, Sutton A, Tafrov ST, Heller RC, Stebbins J. et al. 2000. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. PNAS 97:115807–11 [Google Scholar]
  69. Letouzé E, Martinelli C, Loriot C, Burnichon N, Abermil N. et al. 2013. SDH mutations establish a hypermethylator phenotype in paraganglioma. Cancer Cell 23:739–52 [Google Scholar]
  70. Lewis BA, Hanover JA. 2014. O-GlcNAc and the epigenetic regulation of gene expression. J. Biol. Chem. 289:3440–8 [Google Scholar]
  71. Liang G, He J, Zhang Y. 2012. Kdm2b promotes induced pluripotent stem cell generation by facilitating gene activation early in reprogramming. Nat. Cell Biol. 14:5457–66 [Google Scholar]
  72. Liou G-G, Tanny JC, Kruger RG, Walz T, Moazed D. 2005. Assembly of the SIR complex and its regulation by O-acetyl-ADP-ribose, a product of NAD-dependent histone deacetylation. Cell 121:4515–27 [Google Scholar]
  73. Losman J-A, Kaelin WG. 2013. What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer. Genes Dev. 27:836–52 [Google Scholar]
  74. Losman J-A, Looper RE, Koivunen P, Lee S, Schneider RK. et al. 2013. (R)-2-hydroxyglutarate is sufficient to promote leukemogenesis and its effects are reversible. Science 339:61271621–5 [Google Scholar]
  75. Lu C, Ward PS, Kapoor GS, Rohle D, Turcan S. et al. 2012. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature 483:7390474–78 [Google Scholar]
  76. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:6648251–60 [Google Scholar]
  77. Ma Z, Vosseller K. 2014. Cancer metabolism and elevated O-GlcNAc in oncogenic signaling. J. Biol. Chem. 289:34457–65 [Google Scholar]
  78. Majamaa K, Gunzler V, Hanauske-Abel HM, Myllylä R, Kivirikko KI. 1986. Partial identity of the 2-oxoglutarate and ascorbate binding sites of prolyl 4-hydroxylase. J. Biol. Chem. 261:7819–23 [Google Scholar]
  79. Mantri M, Loik ND, Hamed RB, Claridge TDW, McCullagh JSO, Schofield CJ. 2011. The 2-oxoglutarate-dependent oxygenase JMJD6 catalyses oxidation of lysine residues to give 5S-hydroxylysine residues. ChemBioChem 12:531–34 [Google Scholar]
  80. Marcotte PA, Richardson PR, Guo J, Barrett LW, Xu N. et al. 2004. Fluorescence assay of SIRT protein deacetylases using an acetylated peptide substrate and a secondary trypsin reaction. Anal. Biochem. 332:190–99 [Google Scholar]
  81. Martino F, Kueng S, Robinson P, Tsai-Pflugfelder M, van Leeuwen F. et al. 2009. Reconstitution of yeast silent chromatin: multiple contact sites and O-AADPR binding load SIR complexes onto nucleosomes in vitro. Mol. Cell 33:3323–34 [Google Scholar]
  82. Masri S, Sassone-Corsi P. 2014. Sirtuins and the circadian clock: bridging chromatin and metabolism. Sci. Signal. 7:342re6 [Google Scholar]
  83. Minor EA, Court BL, Young JI, Wang G. 2013. Ascorbate induces ten-eleven translocation (Tet) methylcytosine dioxygenase–mediated generation of 5-hydroxymethylcytosine. J. Biol. Chem. 288:13669–74 [Google Scholar]
  84. Morgan HD, Sutherland HG, Martin DI, Whitelaw E. 1999. Epigenetic inheritance at the agouti locus in the mouse. Nat. Genet. 23:314–18 [Google Scholar]
  85. Myllylä R, Kuutti-Savolainen ER, Kivirikko KI. 1978. The role of ascorbate in the prolyl hydroxylase reaction. Biochem. Biophys. Res. Commun. 83:2441–48 [Google Scholar]
  86. Myllylä R, Majamaa K, Günzler V, Hanauske-Abel HM, Kivirikko KI. 1984. Ascorbate is consumed stoichiometrically in the uncoupled reactions catalyzed by prolyl 4-hydroxylase and lysyl hydroxylase. J. Biol. Chem. 259:5403–5 [Google Scholar]
  87. Nakahata Y, Sahar S, Astarita G, Kaluzova M, Sassone-Corsi P. 2009. Circadian control of the NAD+ salvage pathway by CLOCK-SIRT1. Science 324:5927654–57 [Google Scholar]
  88. Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K. et al. 2010. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell 17:510–22 [Google Scholar]
  89. Ono T, Kasamatsu A, Oka S, Moss J. 2006. The 39-kDa poly(ADP-ribose) glycohydrolase ARH3 hydrolyzes O-acetyl-ADP-ribose, a product of the Sir2 family of acetyl-histone deacetylases. PNAS 103:4516687–91 [Google Scholar]
  90. Papanicolaou KN, O'Rourke B, Foster DB. 2014. Metabolism leaves its mark on the powerhouse: recent progress in post-translational modifications of lysine in mitochondria. Front. Physiol. 5:301 [Google Scholar]
  91. Pollard PJ, Brière JJ, Alam NA, Barwell J, Barclay E. et al. 2005. Accumulation of Krebs cycle intermediates and over-expression of HIF1α in tumours which result from germline FH and SDH mutations. Hum. Mol. Genet. 14:152231–39 [Google Scholar]
  92. Puistola U, Turpeenniemi-Hujanen TM, Myllylä R, Kivirikko KI. 1980. Studies on the lysyl hydroxylase reaction. II. Inhibition kinetics and the reaction mechanism. Biochim. Biophys. Acta 611:51–60 [Google Scholar]
  93. Ramsey KM, Yoshino J, Brace CS, Abrassart D, Kobayashi Y. et al. 2009. Circadian clock feedback cycle through NAMPT-mediated NAD+ biosynthesis. Science 324:5927651–54 [Google Scholar]
  94. Rando OJ. 2012. Daddy issues: paternal effects on phenotype. Cell 151:702–8 [Google Scholar]
  95. Revollo JR, Grimm AA, Imai S. 2004. The NAD biosynthesis pathway mediated by nicotinamide phosphoribosyltransferase regulates Sir2 activity in mammalian cells. J. Biol. Chem. 279:4950754–63 [Google Scholar]
  96. Rice ME, Russo-Menna I. 1997. Differential compartmentalization of brain ascorbate and glutathione between neurons and glia. Neuroscience 82:1213–23 [Google Scholar]
  97. Rine J, Herskowitz I. 1987. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics 116:19–22 [Google Scholar]
  98. Roberts CJ, Selker EU. 1995. Mutations affecting the biosynthesis of S-adenosylmethionine cause reduction of DNA methylation in Neurospora crassa. Nucleic Acids Res. 23:4818–26 [Google Scholar]
  99. Rohle D, Popovici-Muller J, Palaskas N, Turcan S, Grommes C. et al. 2013. An inhibitor of mutant IDH1 delays growth and promotes differentiation of glioma cells. Science 340:6132626–30 [Google Scholar]
  100. Rose NR, Klose RJ. 2014. Understanding the relationship between DNA and histone lysine methylation. BBA Gene Regul. Mech. 1839:1362–72 [Google Scholar]
  101. Rose NR, McDonough MA, King ON, Kawamura A, Schofield CJ. 2011. Inhibition of 2-oxoglutarate dependent oxygenases. Chem. Soc. Rev. 40:84364–97 [Google Scholar]
  102. Rose NR, Ng SS, Mecinović J, Liénard BMR, Bello SH. et al. 2008. Inhibitor scaffolds for 2-oxoglutarate–dependent histone lysine demethylases. J. Med. Chem. 51:7053–56 [Google Scholar]
  103. Sadhu MJ, Guan Q, Li F, Sales-Lee J, Iavarone AT. et al. 2013. Nutritional control of epigenetic processes in yeast and human cells. Genetics 195:831–44 [Google Scholar]
  104. Sandmeier JJ, Celic I, Boeke JD, Smith JS. 2002. Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD+ salvage pathway. Genetics 160:3877–89 [Google Scholar]
  105. Scheibye-Knudsen M, Mitchell SJ, Fang EF, Iyama T, Ward T. et al. 2014. A high-fat diet and NAD+ activate Sirt1 to rescue premature aging in Cockayne syndrome. Cell Metab. 20:5840–55 [Google Scholar]
  106. Schreiber V, Dantzer F, Ame J-C, de Murcia G. 2006. Poly(ADP-ribose): novel functions for an old molecule. Nat. Rev. Mol. Cell Biol. 7:7517–28 [Google Scholar]
  107. Sharma P, Azebi S, England P, Christensen T, Møller-Larsen A. et al. 2012. Citrullination of histone H3 interferes with HP1-mediated transcriptional repression. PLOS Genet. 8:9e1002934 [Google Scholar]
  108. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR. et al. 2004. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941–53 [Google Scholar]
  109. Shyh-Chang N, Locasale JW, Lyssiotis CA, Zheng Y, Teo RY. et al. 2013. Influence of threonine metabolism on S-adenosylmethionine and histone methylation. Science 339:222–6 [Google Scholar]
  110. Smith EH, Janknecht R, Maher LJ. 2007. Succinate inhibition of α-ketoglutarate–dependent enzymes in a yeast model of paraganglioma. Hum. Mol. Genet. 16:243136–48 [Google Scholar]
  111. Smith JS, Brachmann CB, Celic I, Kenna MA, Muhammad S. et al. 2000. A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. PNAS 97:126658–63 [Google Scholar]
  112. Sotiriou S, Gispert S, Cheng J, Wang Y, Chen A. et al. 2002. Ascorbic-acid transporter Slc23a1 is essential for vitamin C transport into the brain and for perinatal survival. Nat. Med. 8:514–17 [Google Scholar]
  113. Soufi A, Donahue G, Zaret K. 2012. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 151:5994–1004 [Google Scholar]
  114. Sridharan R, Tchieu J, Mason MJ, Yachechko R, Kuoy E. et al. 2009. Role of the murine reprogramming factors in the induction of pluripotency. Cell 136:364–77 [Google Scholar]
  115. Stadtfeld M, Apostolou E, Ferrari F, Choi J, Walsh RM. et al. 2012. Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nat. Genet. 44:4398–405 [Google Scholar]
  116. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H. et al. 2009. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930–35 [Google Scholar]
  117. Takahashi H, McCaffery JM, Irizarry RA, Boeke JD. 2006. Nucleocytosolic acetyl-coenzyme A synthetase is required for histone acetylation and global transcription. Mol. Cell 23:2207–17 [Google Scholar]
  118. Takeuchi T, Yamazaki Y, Katoh-Fukui Y, Tsuchiya R, Kondo S. et al. 1995. Gene trap capture of a novel mouse gene, jumonji, required for neural tube formation. Genes Dev. 9:1211–22 [Google Scholar]
  119. Tanner KG, Landry J, Sternglanz R, Denu JM. 2000. Silent information regulator 2 family of NAD-dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose. PNAS 97:2614178–82 [Google Scholar]
  120. Trickey M, Grimaldi M, Yamano H. 2008. The anaphase-promoting complex/cyclosome controls repair and recombination by ubiquitylating Rhp54 in fission yeast. Mol. Cell. Biol. 28:123905–16 [Google Scholar]
  121. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH. et al. 2006. Histone demethylation by a family of JmjC domain–containing proteins. Nature 439:7078811–16 [Google Scholar]
  122. Tu BP, Kudlicki A, Rowicka M, McKnight SL. 2005. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310:57511152–58 [Google Scholar]
  123. Tu BP, Mohler RE, Liu JC, Dombek KM, Young ET. et al. 2007. Cyclic changes in metabolic state during the life of a yeast cell. PNAS 104:4316886–91 [Google Scholar]
  124. Tuderman L, Myllylä R, Kivirikko KI. 1977. Mechanism of the prolyl hydroxylase reaction. Eur. J. Biochem. 348:341–48 [Google Scholar]
  125. Turcan S, Rohle D, Goenka A, Walsh LA, Fang F. et al. 2012. IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype. Nature 483:7390479–83 [Google Scholar]
  126. Van der Veer E, Ho C, O'Neil C, Barbosa N, Scott R. et al. 2007. Extension of human cell lifespan by nicotinamide phosphoribosyltransferase. J. Biol. Chem. 282:1510841–45 [Google Scholar]
  127. Venneti S, Thompson CB. 2013. Metabolic modulation of epigenetics in gliomas. Brain Pathol. 23:217–21 [Google Scholar]
  128. Verdin E, Ott M. 2015. 50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond. Nat. Rev. Mol. Cell Biol. 16:258–64 [Google Scholar]
  129. Vrablik TL, Huang L, Lange SE, Hanna-Rose W. 2009. Nicotinamidase modulation of NAD+ biosynthesis and nicotinamide levels separately affect reproductive development and cell survival in C. elegans. Development 136:213637–46 [Google Scholar]
  130. Wang J, Alexander P, Wu L, Hammer R, Cleaver O, McKnight SL. 2009. Dependence of mouse embryonic stem cell on threonine catabolism. Science 325:435–39 [Google Scholar]
  131. Wang G, Pichersky E. 2007. Nicotinamidase participates in the salvage pathway of NAD biosynthesis in Arabidopsis. Plant J. 49:61020–29 [Google Scholar]
  132. Wang T, Chen K, Zeng X, Yang J, Wu Y. et al. 2011. The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C–dependent manner. Cell Stem Cell 9:6575–87 [Google Scholar]
  133. Ward PS, Patel J, Wise DR, Abdel-Wahab O, Bennett BD. et al. 2010. The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting α-ketoglutarate to 2-hydroxyglutarate. Cancer Cell 17:225–34 [Google Scholar]
  134. Webby CJ, Wolf A, Gromak N, Dreger M, Kramer H. et al. 2009. Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing. Science 325:593690–93 [Google Scholar]
  135. Weissmann S, Alpermann T, Grossmann V, Kowarsch A, Nadarajah N. et al. 2012. Landscape of TET2 mutations in acute myeloid leukemia. Leukemia 26:5934–42 [Google Scholar]
  136. Wellen KE, Hatzivassiliou G, Sachdeva UM, Bui TV, Cross JR, Thompson CB. 2009. ATP-citrate lyase links cellular metabolism to histone acetylation. Science 324:59301076–80 [Google Scholar]
  137. Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S. et al. 2006. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125:467–81 [Google Scholar]
  138. Wolff GL, Kodell RL, Moore SR, Cooney CA. 1998. Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice. FASEB J. 12:949–57 [Google Scholar]
  139. Wolffe AP, Hayes JJ. 1999. Chromatin disruption and modification. Nucleic Acids Res. 27:3711–20 [Google Scholar]
  140. Wu H, D'Alessio AC, Ito S, Xia K, Wang Z. et al. 2011. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473:389–93 [Google Scholar]
  141. Xiao M, Yang H, Xu W, Ma S, Lin H. et al. 2012. Inhibition of α-KG–dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors. Genes Dev. 26:121326–38 [Google Scholar]
  142. Xie Z, Dai J, Dai L, Tan M, Cheng Z. et al. 2012. Lysine succinylation and lysine malonylation in histones. Mol. Cell. Proteomics 11:100–7 [Google Scholar]
  143. Xu W, Yang H, Liu Y, Yang Y, Wang PP. et al. 2011. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate–dependent dioxygenases. Cancer Cell 19:117–30 [Google Scholar]
  144. Yamada K, Chen Z, Rozen R, Matthews RG. 2001. Effects of common polymorphisms on the properties of recombinant human methylenetetrahydrofolate reductase. PNAS 98:2614853–58 [Google Scholar]
  145. Yang H, Lin H, Xu H, Zhang L, Cheng L. et al. 2014. TET-catalyzed 5-methylcytosine hydroxylation is dynamically regulated by metabolites. Cell Res. 24:1017–20 [Google Scholar]
  146. Yin R, Mao SQ, Zhao B, Chong Z, Yang Y. et al. 2013. Ascorbic acid enhances Tet-mediated 5-methylcytosine oxidation and promotes DNA demethylation in mammals. J. Am. Chem. Soc. 135:10396–403 [Google Scholar]
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