Krebs cycle intermediates regulate DNA and histone methylation: Epigenetic impact on the aging process

Ageing Research Reviews

Volumn 16, Issue 1, 2014, Pages 45-65

  Salminen, Antero ^a,b   Kauppinen, Anu ^a,b   Hiltunen, Mikko ^a,b   Kaarniranta, Kai ^a,b  

^a UNIVERSITY OF EASTERN FINLAND   (Finland)

^b KUOPIO UNIVERSITY HOSPITAL   (Finland)

Author keywords

Aging; Energy metabolism; Epigenetics; Krebs cycle; Methylation; Mitochondria

Indexed keywords

2 HYDROXYGLUTARIC ACID; 2 OXOGLUTARATE DEPENDENT DIOXYGENASE; 2 OXOGLUTARIC ACID; DIOXYGENASE; FUMARIC ACID; HISTONE DEMETHYLASE; KDM 2 PROTEIN; KDM 3 PROTEIN; KDM 4 PROTEIN; KDM 5 PROTEIN; KDM 6 PROTEIN; KDM 7 PROTEIN; OXOGLUTARATE DEHYDROGENASE; SUCCINATE DEHYDROGENASE; SUCCINIC ACID; UNCLASSIFIED DRUG; HISTONE;

AGING; CHROMATIN STRUCTURE; CITRIC ACID CYCLE; COLLAGEN SYNTHESIS; DNA METHYLATION; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; HISTONE METHYLATION; HUMAN; HYPOXIA; PROTEIN FAMILY; REVIEW; ANIMAL; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENETIC EPIGENESIS; GENETICS; METABOLISM; METHYLATION; MITOCHONDRION; SIGNAL TRANSDUCTION;

AGING; ANIMALS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CITRIC ACID CYCLE; DNA METHYLATION; EPIGENESIS, GENETIC; HISTONES; HUMANS; METHYLATION; MITOCHONDRIA; SIGNAL TRANSDUCTION;

EID: 84902685602     PISSN: 15681637     EISSN: 18729649     Source Type: Journal    
DOI: 10.1016/j.arr.2014.05.004     Document Type: Review

References (347)

1. Aas P.A., Otterlei M., Falnes P.O., Vagbo C.B., Skorpen F., Akbari M., Sundheim O., Bjoras M., Slupphaug G., Seeberg E., Krokan H.E. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature 2003, 421:859-863.
2. Adam J., Hatipoglu E., O'Flaherty L., Ternette N., Sahgal N., Lockstone H., Baban D., Nye E., Stamp G.W., Wolhuter K., Stevens M., Fischer R., Carmeliet P., Maxwell P.H., Pugh C.W., Frizzell N., Soga T., Kessler B.M., El-Bahrawy M., Ratcliffe P.J., Pollard P.J. Renal cyst formation in Fh1-deficient mice is independent of the Hif/Phd pathway: roles for fumarate in KEAP1 succination and Nrf2 signaling. Cancer Cell 2011, 20:524-537.
3. Agger K., Cloos P.A., Christensen J., Pasini D., Rose S., Rappsilber J., Issaeva I., Canaani E., Salcini A.E., Helin K. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 2007, 449:731-734.
4. Agger K., Cloos P.A., Rudkjaer L., Williams K., Andersen G., Christensen J., Helin K. The H3K27me3 demethylase JMJD3 contributes to the activation of the INK4A-ARF locus in response to oncogene- and stress-induced senescence. Genes Dev. 2009, 23:1171-1176.
5. Aguilo F., Zhou M.M., Walsh M.J. Long noncoding RNA, polycomb, and the ghosts haunting INK4b-ARF-INK4a expression. Cancer Res. 2011, 71:5365-5369.
6. Aik W., McDonough M.A., Thalhammer A., Chowdhury R., Schofield C.J. Role of the jelly-roll fold in substrate binding by 2-oxoglutarate oxygenases. Curr. Opin. Struct. Biol. 2012, 22:691-700.
7. Aragones J., Fraisl P., Baes M., Carmeliet P. Oxygen sensors at the crossroad of metabolism. Cell Metab. 2009, 9:11-22.
8. Arivazhagan P., Ramanathan K., Panneerselvam C. Effect of dl-α-lipoic acid on mitochondrial enzymes in aged rats. Chem. Biol. Interact. 2001, 138:189-198.
9. Arjamaa O., Nikinmaa M., Salminen A., Kaarniranta K. Regulatory role of HIF-1α in the pathogenesis of age-related macular degeneration (AMD). Ageing Res. Rev. 2009, 8:349-358.
10. Asensio-Juan E., Gallego C., Martinez-Balbas M.A. The histone demethylase PHF8 is essential for cytoskeleton dynamics. Nucleic Acids Res. 2012, 40:9429-9440.
11. Ashrafi G., Schwarz T.L. The pathways of mitophagy for quality control and clearance of mitochondria. Cell Death Differ. 2013, 20:31-42.
12. Badeaux A.I., Shi Y. Emerging roles for chromatin as a signal integration and storage platform. Nat. Rev. Mol. Cell Biol. 2013, 14:211-224.
13. Baker M.J., Tatsuta T., Langer T. Quality control of mitochondrial proteostasis. Cold Spring Harb. Perspect. Biol. 2011, 3:7.
14. Baker D.J., Wijshake T., Tchkonia T., LeBrasseur N.K., Childs B.G., van de Sluis B., Kirkland J.L., van Deursen J.M. Clearance of p16Ink4a-positive senescent cells delays ageing-associated disorders. Nature 2011, 479:232-236.
15. Bailey A.J. Molecular mechanisms of ageing in connective tissues. Mech. Ageing Dev. 2001, 122:735-755.
16. Balietti M., Fattoretti P., Giorgetti B., Casoli T., Di Stefano G., Solazzi M., Platano D., Aicardi G., Bertoni-Freddari C. A ketogenic diet increases succinic dehydrogenase activity in aging cardiomyocytes. Ann. N. Y. Acad. Sci. 2009, 1171:377-384.
17. Balietti M., Giorgetti B., Di Stefano G., Casoli T., Platano D., Solazzi M., Bertoni-Freddari C., Aicardi G., Lattanzio F., Fattoretti P. A ketogenic diet increases succinic dehydrogenase (SDH) activity and recovers age-related decrease in numeric density of SDH-positive mitochondria in cerebellar Purkinje cells of late-adult rats. Micron 2010, 41:143-148.
18. Band M., Joel A., Hernandez A., Avivi A. Hypoxia-induced BNIP3 expression and mitophagy: in vivo comparison of the rat and the hypoxia-tolerant mole rat, Spalax ehrenbergi. FASEB J. 2009, 23:2327-2335.
19. Bantignies F., Cavalli G. Polycomb group proteins: repression in 3D. Trends Genet. 2011, 27:454-464.
20. Barbieri M., Bonafe M., Franceschi C., Paolisso G. Insulin/IGF-I-signaling pathway: an evolutionarily conserved mechanism of longevity from yeast to humans. Am. J. Physiol. Endocrinol. Metab. 2003, 285:E1064-E1071.
21. Barradas M., Anderton E., Acosta J.C., Li S., Banito A., Rodriguez-Niedenfuhr M., Maertens G., Banck M., Zhou M.M., Walsh M.J., Peters G., Gil J. Histone demethylase JMJD3 contributes to epigenetic control of INK4a/ARF by oncogenic RAS. Genes Dev. 2009, 23:1177-1182.
22. Beerman I., Bock C., Garrison B.S., Smith Z.D., Gu H., Meissner A., Rossi D.J. Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging. Cell Stem Cell 2013, 12:413-425.
23. Bell J.T., Tsai P.C., Yang T.P., Pidsley R., Nisbet J., Glass D., Mangino M., Zhai G., Zhang F., Valdes A., Shin S.Y., Dempster E.L., Murray R.M., Grundberg E., Hedman A.K., Nica A., Small K.S., MuTHER Consortium, Dermitzakis E.T., McCarthy M.I., Mill J., Spector T.D., Deloukas P. Epigenome-wide scans identify differentially methylated regions for age andage-related phenotypes in a healthy ageing population. PLoS Genet. 2012, 8:e1002629.
24. Benderro G.F., Lamanna J.C. Hypoxia-induced angiogenesis is delayed in aging mouse brain. Brain Res. 2011, 1389:50-60.
25. Bertoni-Freddari C., Fattoretti P., Caselli U., Paoloni R., Meier-Ruge W. Age-dependent decrease in the activity of succinic dehydrogenase in rat CA1 pyramidal cells: a quantitative cytochemical study. Mech. Ageing Dev. 1996, 90:53-62.
26. Beyer S., Kristensen M.M., Jensen K.S., Johansen J.V., Staller P. The histone demethylases JMJD1A and JMJD2B are transcriptional targets of hypoxia-inducible factor HIF. J. Biol. Chem. 2008, 283:36542-36552.
27. Black J.C., Van Rechem C., Whetstine J.R. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Mol. Cell 2012, 48:491-507.
28. Blagosklonny M.V. Answering the ultimate question what is the proximal cause of aging?. Aging (Albany, NY) 2012, 4:861-877.
29. Bradley-Whitman M.A., Lovell M.A. Epigenetic changes in the progression of Alzheimer's disease. Mech. Ageing Dev. 2013, 134:486-495.
30. + metabolism oxidative stress and Sirt1 activity in Wistar rats. PLoS ONE 2011, 6:e19194.
31. Brauchle M., Yao Z., Arora R., Thigale S., Clay I., Inverardi B., Fletcher J., Taslimi P., Acker M.G., Gerrits B., Voshol J., Bauer A., Schubeler D., Bouwmeester T., Ruffner H. Protein complex interactor analysis and differential activity of KDM3 subfamily members towards H3K9 methylation. PLoS ONE 2013, 8:e60549.
32. Brinckmann J., Notbohm H., Tronnier M., Acil Y., Fietzek P.P., Schmeller W., Muller P.K., Bätge B. Overhydroxylation of lysyl residues is the initial step for altered collagen cross-links and fibril architecture in fibrotic skin. J. Invest. Dermatol. 1999, 113:617-621.
33. Brown J.C., Chung D.J., Cooper A.N., Staples J.F. Regulation of succinate-fuelled mitochondrial respiration in liver and skeletal muscle of hibernating thirteen-lined ground squirrels. J. Exp. Biol. 2013, 216:1736-1743.
34. Brusslan J.A., Rus Alvarez-Canterbury A.M., Nair N.U., Rice J.C., Hitchler M.J., Pellegrini M. Genome-wide evaluation of histone methylation changes associated with leaf senescence in Arabidopsis. PLoS ONE 2012, 7:e33151.
35. Bunik V.I., Sievers C. Inactivation of the 2-oxo acid dehydrogenase complexes upon generation of intrinsic radical species. Eur. J. Biochem. 2002, 269:5004-5015.
36. Bunik V.I. 2-Oxo acid dehydrogenase complexes in redox regulation. Role of the lipoate residues and thioredoxin. Eur. J. Biochem. 2003, 270:1036-1042.
37. Bunik V.I., Fernie A.R. Metabolic control exerted by the 2-oxoglutarate dehydrogenase reaction: a cross-kingdom comparison of the crossroad between energy production and nitrogen assimilation. Biochem. J 2009, 422:405-421.
38. Burtner C.R., Kennedy B.K. Progeria syndromes and ageing: what is the connection? Nat. Rev. Mol. Cell. Biol. 2010, 11:567-578.
39. Calvanese V., Lara E., Kahn A., Fraga M.F. The role of epigenetics in aging and age-related diseases. Ageing Res. Rev. 2009, 8:268-276.
40. Casadesus J., Low D. Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev. 2006, 70:830-856.
41. Cascella B., Mirica L.M. Kinetic analysis of iron-dependent histone demethylases: α-ketoglutarate substrate inhibition and potential relevance to the regulation of histone demethylation in cancer cells. Biochemistry 2012, 51:8699-8701.
42. Cedar H., Bergman Y. Programming of DNA methylation patterns. Annu. Rev. Biochem. 2012, 81:97-117.
43. Cervera A.M., Bayley J.P., Devilee P., McCreath K.J. Inhibition of succinate dehydrogenase dysregulates histone modification in mammalian cells. Mol. Cancer 2009, 8:89.
44. Chandwaney R., Leichtweis S., Leeuwenburgh C., Ji L.L. Oxidative stress and mitochondrial function in skeletal muscle: effects of aging and exercise training. Age (Omaha) 1998, 21:109-117.
45. Chen H., Dzitoyeva S., Manev H. Effect of aging on 5-hydroxymethylcytosine in the mouse hippocampus. Restor. Neurol. Neurosci. 2012, 30:237-245.
46. Chen S., Ma J., Wu F., Xiong L.J., Ma H., Xu W., Lv R., Li X., Villen J., Gygi S.P., Liu X.S., Shi Y. The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation. Genes Dev. 2012, 26:1364-1375.
47. Chen Q., Chen Y., Bian C., Fujiki R., Yu X. TET2 promotes histone O-GlcNAcylation during gene transcription. Nature 2013, 493:561-564.
48. Cheung I., Shulha H.P., Jiang Y., Matevossian A., Wang J., Weng Z., Akbarian S. Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:8824-8829.
49. Chicas A., Kapoor A., Wang X., Aksoy O., Evertts A.G., Zhang M.Q., Garcia B.A., Bernstein E., Lowe S.W. H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:8971-8976.
50. Chinopoulos C. Which way does the citric acid cycle turn during hypoxia? The critical role of α-ketoglutarate dehydrogenase complex. J. Neurosci. Res. 2013, 91:1030-1043.
51. Chouliaras L., van den Hove D.L., Kenis G., Keitel S., Hof P.R., van Os J., Steinbusch H.W., Schmitz C., Rutten B.P. Age-related increase in levels of 5-hydroxymethylcytosine in mouse hippocampus is prevented by caloric restriction. Curr. Alzheimer Res. 2012, 9:536-544.
52. Chouliaras L., van den Hove D.L., Kenis G., Keitel S., Hof P.R., van Os J., Steinbusch H.W., Schmitz C., Rutten B.P. Prevention of age-related changes in hippocampal levels of 5-methylcytidine by caloric restriction. Neurobiol. Aging 2012, 33:1672-1681.
53. Chouliaras L., Mastroeni D., Delvaux E., Grover A., Kenis G., Hof P.R., Steinbusch H.W., Coleman P.D., Rutten B.P., van den Hove D.L. Consistent decrease in global DNA methylation and hydroxymethylation in the hippocampus of Alzheimer's disease patients. Neurobiol. Aging 2013, 34:2091-2099.
54. Christensen B.C., Houseman E.A., Marsit C.J., Zheng S., Wrensch M.R., Wiemels J.L., Nelson H.H., Karagas M.R., Padbury J.F., Bueno R., Sugarbaker D.J., Yeh R.F., Wiencke J.K., Kelsey K.T. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet. 2009, 5:e1000602.
55. Chypre M., Zaidi N., Smans K. ATP-citrate lyase: a mini-review. Biochem. Biophys. Res. Commun. 2012, 422:1-4.
56. Clissold P.M., Ponting C.P. JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2β. Trends Biochem. Sci. 2001, 26:7-9.
57. Cloos P.A., Christensen J., Agger K., Helin K. Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev. 2008, 22:1115-1140.
58. Collado M., Blasco M.A., Serrano M. Cellular senescence in cancer and aging. Cell 2007, 130:223-233.
59. Couture J.F., Collazo E., Ortiz-Tello P.A., Brunzelle J.S., Trievel R.C. Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat. Struct. Mol. Biol. 2007, 14:689-695.
60. Cimen H., Han M.J., Yang Y., Tong Q., Koc H., Koc E.C. Regulation of succinate dehydrogenase activity by SIRT3 in mammalian mitochondria. Biochemistry 2010, 49:304-311.
61. Clifton I.J., McDonough M.A., Ehrismann D., Kershaw N.J., Granatino N., Schofield C.J. Structural studies on 2-oxoglutarate oxygenases and related double-stranded β-helix fold proteins. J. Inorg. Biochem. 2006, 100:644-669.
62. Dabek M., Kruszewska D., Filip R., Hotowy A., Pierzynowski L., Wojtasz-Pajak A., Szymanczyk S., Valverde Piedra J.L., Werpachowska E., Pierzynowski S.G. α-Ketoglutarate (AKG) absorption from pig intestine and plasma pharmacokinetics. J. Anim. Physiol. Anim. Nutr. (Berl.) 2005, 89:419-426.
63. Dang L., White D.W., Gross S., Bennett B.D., Bittinger M.A., Driggers E.M., Fantin V.R., Jang H.G., Jin S., Keenan M.C., Marks K.M., Prins R.M., Ward P.S., Yen K.E., Liau L.M., Rabinowitz J.D., Cantley L.C., Thompson C.B., Vander Heiden M.G., Su S.M. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 2009, 462:739-744.
64. D'Aquila P., Rose G., Bellizzi D., Passarino G. Epigenetics and aging. Maturitas 2013, 74:130-136.
65. Das N.D., Jung K.H., Choi M.R., Yoon H.S., Kim S.H., Chai Y.G. Gene networking and inflammatory pathway analysis in a JMJD3 knockdown human monocytic cell line. Cell Biochem. Funct. 2012, 30:224-232.
66. Davidov Y., Jurkevitch E. Predation between prokaryotes and the origin of eukaryotes. Bioessays 2009, 31:748-757.
67. Deaton A.M., Bird A. CpG islands and the regulation of transcription. Genes Dev. 2011, 25:1010-1022.
68. De Carolis E., De Luca V. 2-oxoglutarate-dependent dioxygenase and related enzymes: biochemical characterization. Phytochemistry 1994, 36:1093-1107.
69. Dechat T., Pfleghaar K., Sengupta K., Shimi T., Shumaker D.K., Solimando L., Goldman R.D. Nuclear lamins: major factors in the structural organization and function of the nucleus and chromatin. Genes Dev. 2008, 22:832-853.
70. Denton R.M. Regulation of mitochondrial dehydrogenases by calcium ions. Biochim. Biophys. Acta 2009, 1787:1309-1316.
71. Deplus R., Delatte B., Schwinn M.K., Defrance M., Mendez J., Murphy N., Dawson M.A., Volkmar M., Putmans P., Calonne E., Shih A.H., Levine R.L., Bernard O., Mercher T., Solary E., Urh M., Daniels D.L., Fuks F. TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS. EMBO J. 2013, 32:645-655.
72. De Santa F., Totaro M.G., Prosperini E., Notarbartolo S., Testa G., Natoli G. The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. Cell 2007, 130:1083-1094.
73. De Santa F., Narang V., Yap Z.H., Tusi B.K., Burgold T., Austenaa L., Bucci G., Caganova M., Notarbartolo S., Casola S., Testa G., Sung W.K., Wei C.L., Natoli G. Jmjd3 contributes to the control of gene expression in LPS-activated macrophages. EMBO J. 2009, 28:3341-3352.
74. Detmer S.A., Chan D.C. Functions and dysfunctions of mitochondrial dynamics. Nat. Rev. Mol. Cell Biol. 2007, 8:870-879.
75. DiTacchio L., Le H.D., Vollmers C., Hatori M., Witcher M., Secombe J., Panda S. Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and influences the circadian clock. Science 2011, 333:1881-1885.
76. Edrey Y.H., Hanes M., Pinto M., Mele J., Buffenstein R. Successful aging and sustained good health in the naked mole rat: a long-lived mammalian model for biogerontology and biomedical research. ILAR J. 2011, 52:41-53.
77. Eng C., Kiuru M., Fernandez M.J., Aaltonen L.A. A role for mitochondrial enzymes in inherited neoplasia and beyond. Nat. Rev. Cancer 2003, 3:193-202.
78. Esser C., Ahmadinejad N., Wiegand C., Rotte C., Sebastiani F., Gelius-Dietrich G., Henze K., Kretschmann E., Richly E., Leister D., Bryant D., Steel M.A., Lockhart P.J., Penny D., Martin W. A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol. Biol. Evol. 2004, 21:1643-1660.
79. Estaras C., Fueyo R., Akizu N., Beltran S., Martinez-Balbas M.A. RNA polymerase II progression through H3K27me3-enriched gene bodies requires JMJD3 histone demethylase. Mol. Biol. Cell 2013, 24:351-360.
80. Fattoretti P., Bertoni-Freddari C., Caselli U., Paoloni R., Meier-Ruge W. Impaired succinic dehydrogenase activity of rat Purkinje cell mitochondria during aging. Mech. Ageing Dev. 1998, 101:175-182.
81. Feng W., Yonezawa M., Ye J., Jenuwein T., Grummt I. PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. Nat. Struct. Mol. Biol. 2010, 17:445-450.
82. Fernandez A.F., Fraga M.F. The effects of the dietary polyphenol resveratrol on human healthy aging and lifespan. Epigenetics 2011, 6:870-874.
83. Feser J., Tyler J. Chromatin structure as a mediator of aging. FEBS Lett. 2011, 585:2041-2048.
84. Finkel T., Holbrook N.J. Oxidants, oxidative stress and the biology of ageing. Nature 2000, 408:239-247.
85. Finley L.W., Haas W., Desquiret-Dumas V., Wallace D.C., Procaccio V., Gygi S.P., Haigis M.C. Succinate dehydrogenase is a direct target of sirtuin 3 deacetylase activity. PLoS ONE 2011, 6:e23295.
86. Fleming J.E., Miquel J., Cottrell S.F., Yengoyan L.S., Economos A.C. Is cell aging caused by respiration-dependent injury to the mitochondrial genome?. Gerontology 1982, 28:44-53.
87. Fortschegger K., de Graaf P., Outchkourov N.S., van Schaik F.M., Timmers H.T., Shiekhattar R. PHF8 targets histone methylation and RNA polymerase II to activate transcription. Mol. Cell. Biol. 2010, 30:3286-3298.
88. Franceschi C., Capri M., Monti D., Giunta S., Olivieri F., Sevini F., Panourgia M.P., Invidia L., Celani L., Scurti M., Cevenini E., Castellani G.C., Salvioli S. Inflammaging and anti-inflammaging: a systemic perspective on aging and longevity emerged from studies in humans. Mech. Ageing Dev. 2007, 128:92-105.
89. Franchini D.M., Schmitz K.M., Petersen-Mahrt S.K. 5-Methylcytosine DNA demethylation: more than losing a methyl group. Annu. Rev. Genet. 2012, 46:419-441.
90. Frankel S., Rogina B. Indy mutants: live long and prosper. Front. Genet. 2012, 3:13.
91. Frescas D., Guardavaccaro D., Bassermann F., Koyama-Nasu R., Pagano M. JHDM1B/FBXL10 is a nucleolar protein that represses transcription of ribosomal RNA genes. Nature 2007, 450:309-313.
92. Friguet B., Bulteau A.L., Petropoulos I. Mitochondrial protein quality control: implications in ageing. Biotechnol. J. 2008, 3:757-764.
93. Fujiki R., Hashiba W., Sekine H., Yokoyama A., Chikanishi T., Ito S., Imai Y., Kim J., He H.H., Igarashi K., Kanno J., Ohtake F., Kitagawa H., Roeder R.G., Brown M., Kato S. GlcNAcylation of histone H2B facilitates its monoubiquitination. Nature 2011, 480:557-560.
94. Ganan-Gomez I., Wei Y., Yang H., Boyano-Adanez M.C., Garcia-Manero G. Oncogenic functions of the transcription factor Nrf2. Free Radic. Biol. Med. 2013, 65C:750-764.
95. Giacco F., Brownlee M. Oxidative stress and diabetic complications. Circ. Res. 2010, 107:1058-1070.
96. Gibson G.E., Park L.C., Sheu K.F., Blass J.P., Calingasan N.Y. The α-ketoglutarate dehydrogenase complex in neurodegeneration. Neurochem. Int. 2000, 36:97-112.
97. Gibson G.E., Starkov A., Blass J.P., Ratan R.R., Beal M.F. Cause and consequence: mitochondrial dysfunction initiates and propagates neuronal dysfunction, neuronal death and behavioral abnormalities in age-associated neurodegenerative diseases. Biochim. Biophys. Acta 2010, 1802:122-134.
98. Gil J., Peters G. Regulation of the INK4b-ARF-INK4a tumour suppressor locus: all for one or one for all. Nat. Rev. Mol. Cell Biol. 2006, 7:667-677.
99. 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.
100. Gonzalo S. Epigenetic alterations in aging. J. Appl. Physiol. 2010, 109:586-597.
101. Gouspillou G., Hepple R.T. Facts and controversies in our understanding of how caloric restriction impacts the mitochondrion. Exp. Gerontol. 2013, 48:1075-1084.
102. Gravina S., Vijg J. Epigenetic factors in aging and longevity. Pflugers Arch. 2010, 459:247-258.
103. Gray M.W., Burger G., Lang B.F. Mitochondrial evolution. Science 1999, 283:1476-1481.
104. Greer E.L., Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat. Rev. Genet. 2012, 13:343-357.
105. Greer E.L., Maures T.J., Hauswirth A.G., Green E.M., Leeman D.S., Maro G.S., Han S., Banko M.R., Gozani O., Brunet A. Members of the H3K4 trimethylation complex regulate lifespan in a germline-dependent manner in C. elegans. Nature 2010, 466:383-387.
106. Greer E.L., Maures T.J., Ucar D., Hauswirth A.G., Mancini E., Lim J.P., Benayoun B.A., Shi Y., Brunet A. Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature 2011, 479:365-371.
107. Guarente L. Mitochondria - a nexus for aging, calorie restriction, and sirtuins?. Cell 2008, 132:171-176.
108. Guarente L., Kenyon C. Genetic pathways that regulate ageing in model organisms. Nature 2000, 408:255-262.
109. Guo J.U., Su Y., Zhong C., Ming G.L., Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 2011, 145:423-434.
110. Hagopian K., Ramsey J.J., Weindruch R. Krebs cycle enzymes from livers of old mice are differentially regulated by caloric restriction. Exp. Gerontol. 2004, 39:1145-1154.
111. Haithcock E., Dayani Y., Neufeld E., Zahand A.J., Feinstein N., Mattout A., Gruenbaum Y., Liu J. Age-related changes of nuclear architecture in Caenorhabditis elegans. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:16690-16695.
112. Han S., Brunet A. Histone methylation makes its mark on longevity. Trends Cell Biol. 2012, 22:42-49.
113. Han Y., Han D., Yan Z., Boyd-Kirkup J.D., Green C.D., Khaitovich P., Han J.D. Stress-associated H3K4 methylation accumulates during postnatal development and aging of rhesus macaque brain. Aging Cell 2012, 11:1055-1064.
114. Hannum G., Guinney J., Zhao L., Zhang L., Hughes G., Sadda S., Klotzle B., Bibikova M., Fan J.B., Gao Y., Deconde R., Chen M., Rajapakse I., Friend S., Ideker T., Zhang K. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol. Cell 2013, 49:359-367.
115. Haripriya D., Devi M.A., Kokilavani V., Sangeetha P., Panneerselvam C. Age-dependent alterations in mitochondrial enzymes in cortex, striatum and hippocampus of rat brain - potential role of l-carnitine. Biogerontology 2004, 5:355-364.
116. Harman D. Aging: a theory based on free radical and radiation chemistry. J. Gerontol. 1956, 11:298-300.
117. Harrison A.P., Pierzynowski S.G. Biological effects of 2-oxoglutarate with particular emphasis on the regulation of protein, mineral and lipid absorption/metabolism, muscle performance, kidney function, bone formation and cancerogenesis, all viewed from a healthy ageing perspective state of the art - review article. J. Physiol. Pharmacol. 2008, 59(Suppl. 1):91-106.
118. Hausinger R.P. Fe(II)/α-ketoglutarate-dependent hydroxylases and related enzymes. Crit. Rev. Biochem. Mol. Biol. 2004, 39:21-68.
119. Hautala T., Byers M.G., Eddy R.L., Shows T.B., Kivirikko K.I., Myllylä R. Cloning of human lysyl hydroxylase: complete cDNA-derived amino acid sequence and assignment of the gene (PLOD) to chromosome 1p36.3-p36.2. Genomics 1992, 13:62-69.
120. He J., Kallin E.M., Tsukada Y., Zhang Y. The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15(Ink4b). Nat. Struct. Mol. Biol. 2008, 15:1169-1175.
121. He W., Newman J.C., Wang M.Z., Ho L., Verdin E. Mitochondrial sirtuins: regulators of protein acylation and metabolism. Trends Endocrinol. Metab. 2012, 23:467-476.
122. Henikoff S., Shilatifard A. Histone modification: cause or cog?. Trends Genet. 2011, 27:389-396.
123. Hernandez D.G., Nalls M.A., Gibbs J.R., Arepalli S., van der Brug M., Chong S., Moore M., Longo D.L., Cookson M.R., Traynor B.J., Singleton A.B. Distinct DNA methylation changes highly correlated with chronological age in the human brain. Hum. Mol. Genet. 2011, 20:1164-1172.
124. Hewitson K.S., Lienard B.M., McDonough M.A., Clifton I.J., Butler D., Soares A.S., Oldham N.J., McNeill L.A., Schofield C.J. Structural and mechanistic studies on the inhibition of the hypoxia-inducible transcription factor hydroxylases by tricarboxylic acid cycle intermediates. J. Biol. Chem. 2007, 282:3293-3301.
125. Heyn H., Li N., Ferreira H.J., Moran S., Pisano D.G., Gomez A., Diez J., Sanchez-Mut J.V., Setien F., Carmona F.J., Puca A.A., Sayols S., Pujana M.A., Serra-Musach J., Iglesias-Platas I., Formiga F., Fernandez A.F., Fraga M.F., Heath S.C., Valencia A., Gut I.G., Wang J., Esteller M. Distinct DNA methylomes of newborns and centenarians. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:10522-10527.
126. Heyn H., Moran S., Esteller M. Aberrant DNA methylation profiles in the premature aging disorders Hutchinson-Gilford progeria and Werner syndrome. Epigenetics 2013, 8:28-33.
127. Hillringhaus L., Yue W.W., Rose N.R., Ng S.S., Gileadi C., Loenarz C., Bello S.H., Bray J.E., Schofield C.J., Oppermann U. Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family. J. Biol. Chem. 2011, 286:41616-41625.
128. Hirschey M.D., Shimazu T., Huang J.Y., Schwer B., Verdin E. SIRT3 regulates mitochondrial protein acetylation and intermediary metabolism. Cold Spring Harb. Symp. Quant. Biol. 2011, 76:267-277.
129. Hoekstra A.S., Bayley J.P. The role of complex II in disease. Biochim. Biophys. Acta 2013, 1827:543-551.
130. Hong S., Cho Y.W., Yu L.R., Yu H., Veenstra T.D., Ge K. Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:18439-18444.
131. Horton J.R., Upadhyay A.K., Qi H.H., Zhang X., Shi Y., Cheng X. Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat. Struct. Mol. Biol. 2010, 17:38-43.
132. Houtkooper R.H., Pirinen E., Auwerx J. Sirtuins as regulators of metabolism and healthspan. Nat. Rev. Mol. Cell Biol. 2012, 13:225-238.
133. Houtkooper R.H., Mouchiroud L., Ryu D., Moullan N., Katsyuba E., Knott G., Williams R.W., Auwerx J. Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 2013, 497:451-457.
134. Hudson R.C., Daniel R.M. l-Glutamate dehydrogenases: distribution, properties and mechanism. Comp. Biochem. Physiol. B 1993, 106:767-792.
135. Hudson D.M., Eyre D.R. Collagen prolyl 3-hydroxylation: a major role for a minor post-translational modification? Connect. Tissue Res. 2013, 54:245-251.
136. Huidobro C., Fernandez A.F., Fraga M.F. Aging epigenetics: causes and consequences. Mol. Aspects Med. 2013, 34:765-781.
137. Huidobro C., Fernandez A.F., Fraga M.F. The role of genetics in the establishment and maintenance of the epigenome. Cell. Mol. Life Sci. 2013, 70:1543-1573.
138. Hulbert A.J., Pamplona R., Buffenstein R., Buttemer W.A. Life and death: metabolic rate, membrane composition, and life span of animals. Physiol. Rev. 2007, 87:1175-1213.
139. Huynen M.A., Dandekar T., Bork P. Variation and evolution of the citric-acid cycle: a genomic perspective. Trends Microbiol. 1999, 7:281-291.
140. Hwang E.S., Yoon G., Kang H.T. A comparative analysis of the cell biology of senescence and aging. Cell. Mol. Life Sci. 2009, 66:2503-2524.
141. Iglesias-Bartolome R., Callejas-Valera J.L., Gutkind J.S. Control of the epithelial stem cell epigenome: the shaping of epithelial stem cell identity. Curr. Opin. Cell Biol. 2013, 25:162-169.
142. Imai S., Guarente L. Ten years of NAD-dependent SIR2 family deacetylases: implications for metabolic diseases. Trends Pharmacol. Sci. 2010, 31:212-220.
143. Inagaki T., Tachibana M., Magoori K., Kudo H., Tanaka T., Okamura M., Naito M., Kodama T., Shinkai Y., Sakai J. Obesity and metabolic syndrome in histone demethylase JHDM2a-deficient mice. Genes Cells 2009, 14:991-1001.
144. Ipenberg I., Guttmann-Raviv N., Khoury H.P., Kupershmit I., Ayoub N. Heat shock protein 90 (Hsp90) selectively regulates the stability of KDM4B/JMJD2B histone demethylase. J. Biol. Chem. 2013, 288:14681-14687.
145. Ishii M., Wen H., Corsa C.A., Liu T., Coelho A.L., Allen R.M., Carson W.F., Cavassani K.A., Li X., Lukacs N.W., Hogaboam C.M., Dou Y., Kunkel S.L. Epigenetic regulation of the alternatively activated macrophage phenotype. Blood 2009, 114:3244-3254.
146. Issa J.P. Aging and epigenetic drift: a vicious cycle. J. Clin. Invest. 2014, 124:24-29.
147. Iwase S., Lan F., Bayliss P., de la Torre-Ubieta L., Huarte M., Qi H.H., Whetstine J.R., Bonni A., Roberts T.M., Shi Y. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 2007, 128:1077-1088.
148. 2-regulated prolyl hydroxylation. Science 2001, 292:468-472.
149. Jaakkola P.M., Rantanen K. The regulation, localization, and functions of oxygen-sensing prolyl hydroxylase PHD3. Biol. Chem. 2013, 394:449-457.
150. Jacobs H.T. The mitochondrial theory of aging: dead or alive?. Aging Cell 2003, 2:11-17.
151. James A.M., Collins Y., Logan A., Murphy M.P. Mitochondrial oxidative stress and the metabolic syndrome. Trends Endocrinol. Metab. 2012, 23:234-429.
152. Jeck W.R., Siebold A.P., Sharpless N.E. Review: a meta-analysis of GWAS and age-associated diseases. Aging Cell 2012, 11:727-731.
153. Jenkins T.G., Aston K.I., Cairns B.R., Carrell D.T. Paternal aging and associated intraindividual alterations of global sperm 5-methylcytosine and 5-hydroxymethylcytosine levels. Fertil. Steril. 2013, 100:945-951.
154. Jensen L.R., Amende M., Gurok U., Moser B., Gimmel V., Tzschach A., Janecke A.R., Tariverdian G., Chelly J., Fryns J.P., Van Esch H., Kleefstra T., Hamel B., Moraine C., Gecz J., Turner G., Reinhardt R., Kalscheuer V.M., Ropers H.H., Lenzner S. Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. Am. J. Hum. Genet. 2005, 76:227-236.
155. Jenuwein T., Allis C.D. Translating the histone code. Science 2001, 293:1074-1080.
156. Jin C., Li J., Green C.D., Yu X., Tang X., Han D., Xian B., Wang D., Huang X., Cao X., Yan Z., Hou L., Liu J., Shukeir N., Khaitovich P., Chen C.D., Zhang H., Jenuwein T., Han J.D. Histone demethylase UTX-1 regulates C. elegans life span by targeting the insulin/IGF-1 signaling pathway. Cell Metab. 2011, 14:161-172.
157. Johansson A., Enroth S., Gyllensten U. Continuous aging of the human DNA methylome throughout the human lifespan. PLoS ONE 2013, 8:e67378.
158. Johansson C., Tumber A., Che K., Cain P., Nowak R., Gileadi C., Oppermann U. The roles of Jumonji-type oxygenases in human disease. Epigenomics 2014, 6:89-120.
159. Johnson A.A., Akman K., Calimport S.R., Wuttke D., Stolzing A., de Magalhaes J.P. The role of DNA methylation in aging, rejuvenation, and age-related disease. Rejuvenation Res. 2012, 15:483-494.
160. Jones D.L., Rando T.A. Emerging models and paradigms for stem cell ageing. Nat. Cell Biol. 2011, 13:506-512.
161. Jorgensen S., Schotta G., Sorensen C.S. Histone H4 lysine 20 methylation: key player in epigenetic regulation of genomic integrity. Nucleic Acids Res. 2013, 41:2797-2806.
162. Jung J.W., Lee S., Seo M.S., Park S.B., Kurtz A., Kang S.K., Kang K.S. Histone deacetylase controls adult stem cell aging by balancing the expression of polycomb genes and jumonji domain containing 3. Cell. Mol. Life Sci. 2010, 67:1165-1176.
163. Kaas G.A., Zhong C., Eason D.E., Ross D.L., Vachhani R.V., Ming G.L., King J.R., Song H., Sweatt J.D. TET1 controls CNS 5-methylcytosine hydroxylation, active DNA demethylation, gene transcription, and memory formation. Neuron 2013, 79:1086-1093.
164. Kaelin W.G., McKnight S.L. Influence of metabolism on epigenetics and disease. Cell 2013, 153:56-69.
165. Katschinski D.M. Is there a molecular connection between hypoxia and aging?. Exp. Gerontol. 2006, 41:482-484.
166. Killian J.K., Kim S.Y., Miettinen M., Smith C., Merino M., Tsokos M., Quezado M., Smith W.I., Jahromi M.S., Xekouki P., Szarek E., Walker R.L., Lasota J., Raffeld M., Klotzle B., Wang Z., Jones L., Zhu Y., Wang Y., Waterfall J.J., O'Sullivan M.J., Bibikova M., Pacak K., Stratakis C., Janeway K.A., Schiffman J.D., Fan J.B., Helman L., Meltzer P.S. Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor. Cancer Discov. 2013, 3:648-657.
167. Kim W.Y., Sharpless N.E. The regulation of INK4/ARF in cancer and aging. Cell 2006, 127:265-275.
168. King A., Selak M.A., Gottlieb E. Succinate dehydrogenase and fumarate hydratase: linking mitochondrial dysfunction and cancer. Oncogene 2006, 25:4675-4682.
169. Kivirikko K.I., Myllylä R., Pihlajaniemi T. Protein hydroxylation: prolyl 4-hydroxylase, an enzyme with four cosubstrates and a multifunctional subunit. FASEB J. 1989, 3:1609-1617.
170. Kivirikko K.I., Myllyharju J. Prolyl 4-hydroxylases and their protein disulfide isomerase subunit. Matrix Biol. 1998, 16:357-368.
171. Klose R.J., Kallin E.M., Zhang Y. JmjC-domain-containing proteins and histone demethylation. Nat. Rev. Genet. 2006, 7:715-727.
172. Kobayashi T.A. A new role of the rDNA and nucleolus in the nucleus - rDNA instability maintains genome integrity. Bioessays 2008, 30:267-272.
173. Koike K., Matsuo S. Functional characterization of the 5'-flanking region of the gene encoding human 2-oxoglutarate dehydrogenase. Gene 1997, 186:45-53.
174. Koivunen P., Hirsilä M., Remes A.M., Hassinen I.E., Kivirikko K.I., Myllyharju J. Inhibition of hypoxia-inducible factor (HIF) hydroxylases by citric acid cycle intermediates: possible links between cell metabolism and stabilization of HIF. J. Biol. Chem. 2007, 282:4524-4532.
175. Koturbash I., Simpson N.E., Beland F.A., Pogribny I.P. Alterations in histone H4 lysine 20 methylation: implications for cancer detection and prevention. Antioxid. Redox Signal. 2012, 17:365-374.
176. Kriaucionis S., Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009, 324:929-930.
177. Krieg A.J., Rankin E.B., Chan D., Razorenova O., Fernandez S., Giaccia A.J. Regulation of the histone demethylase JMJD1A by hypoxia-inducible factor 1α enhances hypoxic gene expression and tumor growth. Membr. Cell Biol. 2010, 30:344-353.
178. Krishnamurthy J., Torrice C., Ramsey M.R., Kovalev G.I., Al-Regaiey K., Su L., Sharpless N.E. Ink4a/Arf expression is a biomarker of aging. J. Clin. Invest. 2004, 114:1299-1307.
179. Kruidenier L., Chung C.W., Cheng Z., Liddle J., Che K., Joberty G., Bantscheff M., Bountra C., Bridges A., Diallo H., Eberhard D., Hutchinson S., Jones E., Katso R., Leveridge M., Mander P.K., Mosley J., Ramirez-Molina C., Rowland P., Schofield C.J., Sheppard R.J., Smith J.E., Swales C., Tanner R., Thomas P., Tumber A., Drewes G., Oppermann U., Patel D.J., Lee K., Wilson D.M. A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Nature 2012, 488:404-408.
180. Kugler P., Vogel S., Gehm M. Quantitative succinate dehydrogenase histochemistry in the hippocampus of aged rats. Histochemistry 1988, 88:299-307.
181. Kumar A., Takada Y., Boriek A.M., Aggarwal B.B. Nuclear factor-κB: its role in health and disease. J. Mol. Med. (Berl.) 2004, 82:434-448.
182. Kumaran S., Subathra M., Balu M., Panneerselvam C. Supplementation of l-carnitine improves mitochondrial enzymes in heart and skeletal muscle of aged rats. Exp. Aging Res. 2005, 31:55-67.
183. Landan G., Cohen N.M., Mukamel Z., Bar A., Molchadsky A., Brosh R., Horn-Saban S., Zalcenstein D.A., Goldfinger N., Zundelevich A., Gal-Yam E.N., Rotter V., Tanay A. Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat. Genet. 2012, 44:1207-1214.
184. Lapointe J., Hekimi S. Early mitochondrial dysfunction in long-lived Mclk1+/- mice. J. Biol. Chem. 2008, 283:26217-26227.
185. Larson K., Yan S.J., Tsurumi A., Liu J., Zhou J., Gaur K., Guo D., Eickbush T.H., Li W.X. Heterochromatin formation promotes longevity and represses ribosomal RNA synthesis. PLoS Genet. 2012, 8:e1002473.
186. Lee C.T., Duerre J.A. Changes in histone methylase activity of rat brain and liver with ageing. Nature 1974, 251:240-242.
187. Lee M.G., Villa R., Trojer P., Norman J., Yan K.P., Reinberg D., Di Croce L., Shiekhattar R. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science 2007, 318:447-450.
188. Lee S.H., Kim J., Kim W.H., Lee Y.M. Hypoxic silencing of tumor suppressor RUNX3 by histone modification in gastric cancer cells. Oncogene 2009, 28:184-194.
189. Leigh J.A., Dodsworth J.A. Nitrogen regulation in bacteria and archaea. Annu. Rev. Microbiol. 2007, 61:349-377.
190. Letouze E., Martinelli C., Loriot C., Burnichon N., Abermil N., Ottolenghi C., Janin M., Menara M., Nguyen A.T., Benit P., Buffet A., Marcaillou C., Bertherat J., Amar L., Rustin P., De Reynies A., Gimenez-Roqueplo A.P., Favier J. SDH mutations establish a hypermethylator phenotype in paraganglioma. Cancer Cell 2013, 23:739-752.
191. Li Y., Daniel M., Tollefsbol T.O. Epigenetic regulation of caloric restriction in aging. BMC Med. 2011, 9:98.
192. Li M., Li C., Allen A., Stanley C.A., Smith T.J. The structure and allosteric regulation of mammalian glutamate dehydrogenase. Arch. Biochem. Biophys. 2012, 519:69-80.
193. Lionaki E., Tavernarakis N. Oxidative stress and mitochondrial protein quality control in aging. J. Proteomics 2013, 92:181-194.
194. Liu L., Rando T.A. Manifestations and mechanisms of stem cell aging. J. Cell Biol. 2011, 193:257-266.
195. Liu L., van Groen T., Kadish I., Tollefsbol T.O. DNA methylation impacts on learning and memory in aging. Neurobiol. Aging 2009, 30:549-560.
196. Liu L., Cheung T.H., Charville G.W., Hurgo B.M., Leavitt T., Shih J., Brunet A., Rando T.A. Chromatin modifications as determinants of muscle stem cell quiescence and chronological aging. Cell Rep. 2013, 4:189-204.
197. Liu B., Wang Z., Zhang L., Ghosh S., Zheng H., Zhou Z. Depleting the methyltransferase Suv39h1 improves DNA repair and extends lifespan in a progeria mouse model. Nat. Commun. 2013, 4:1868.
198. Loenarz C., Schofield C.J. Physiological and biochemical aspects of hydroxylations and demethylations catalyzed by human 2-oxoglutarate oxygenases. Trends Biochem. Sci. 2011, 36:7-18.
199. Londono Gentile T., Lu C., Lodato P.M., Tse S., Olejniczak S.H., Witze E.S., Thompson C.B., Wellen K.E. DNMT1 is regulated by ATP-citrate lyase and maintains methylation patterns during adipocyte differentiation. Mol. Cell. Biol. 2013, 33:3864-3878.
200. Lu R., Wang G.G. Tudor: a versatile family of histone methylation 'readers'. Trends Biochem. Sci. 2013, 10.1016/j.tibs.2013.08.002.
201. MacKenzie E.D., Selak M.A., Tennant D.A., Payne L.J., Crosby S., Frederiksen C.M., Watson D.G., Gottlieb E. Cell-permeating α-ketoglutarate derivatives alleviate pseudohypoxia in succinate dehydrogenase-deficient cells. Mol. Cell. Biol. 2007, 27:3282-3289.
202. Maegawa S., Hinkal G., Kim H.S., Shen L., Zhang L., Zhang J., Zhang N., Liang S., Donehower L.A., Issa J.P. Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res. 2010, 20:332-340.
203. Mallette F.A., Richard S. JMJD2A promotes cellular transformation by blocking cellular senescence through transcriptional repression of the tumor suppressor CHD5. Cell Rep. 2012, 2:1233-1243.
204. Mallette F.A., Mattiroli F., Cui G., Young L.C., Hendzel M.J., Mer G., Sixma T.K., Richard S. RNF8- and RNF168-dependent degradation of KDM4A/JMJD2A triggers 53BP1 recruitment to DNA damage sites. EMBO J. 2012, 31:1865-1878.
205. Martin G.M. Stochastic modulations of the pace and patterns of ageing: impacts on quasi-stochastic distributions of multiple geriatric pathologies. Mech. Ageing Dev. 2012, 133:107-111.
206. Martin S.L., Hardy T.M., Tollefsbol T.O. Medicinal chemistry of the epigenetic diet and caloric restriction. Curr. Med. Chem. 2013, 20:4050-4059.
207. + metabolism in human tissue. PLoS ONE 2012, 7:e42357.
208. Maures T.J., Greer E.L., Hauswirth A.G., Brunet A. The H3K27 demethylase UTX-1 regulates C. elegans lifespan in a germline-independent, insulin-dependent manner. Aging Cell 2011, 10:980-990.
209. McBride H.M., Neuspiel M., Wasiak S. Mitochondria: more than just a powerhouse. Curr. Biol. 2006, 16:R551-R560.
210. McClay J.L., Aberg K.A., Clark S.L., Nerella S., Kumar G., Xie L.Y., Hudson A.D., Harada A., Hultman C.M., Magnusson P.K., Sullivan P.F., Van Den Oord E.J. A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects. Hum. Mol. Genet. 2013, 23:1175-1185.
211. McClintock D., Ratner D., Lokuge M., Owens D.M., Gordon L.B., Collins F.S., Djabali K. The mutant form of lamin A that causes Hutchinson-Gilford progeria is a biomarker of cellular aging in human skin. PLoS ONE 2007, 2:e1269.
212. McCord R.P., Nazario-Toole A., Zhang H., Chines P.S., Zhan Y., Erdos M.R., Collins F.S., Dekker J., Cao K. Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome. Genome Res. 2013, 23:260-269.
213. McDonough M.A., Loenarz C., Chowdhury R., Clifton I.J., Schofield C.J. Structural studies on human 2-oxoglutarate dependent oxygenases. Curr. Opin. Struct. Biol. 2010, 20:659-672.
214. Medvedev Z.A., Medvedeva M.N. Age changes in chromatin: accumulative or programmed?. Ann. N. Y. Acad. Sci. 1991, 621:40-52.
215. Merkley E.D., Metz T.O., Smith R.D., Baynes J.W., Frizzell N. The succinated proteome. Mass Spectrom. Rev. 2013, 10.1002/mas.21382.
216. Minocherhomji S., Tollefsbol T.O., Singh K.K. Mitochondrial regulation of epigenetics and its role in human diseases. Epigenetics 2012, 7:326-334.
217. Miyake N., Mizuno S., Okamoto N., Ohashi H., Shiina M., Ogata K., Tsurusaki Y., Nakashima M., Saitsu H., Niikawa N., Matsumoto N. KDM6A point mutations cause Kabuki syndrome. Hum. Mutat. 2013, 34:108-110.
218. Monfort A., Wutz A. Breathing-in epigenetic change with vitamin C. EMBO Rep. 2013, 14:337-346.
219. Monne M., Miniero D.V., Iacobazzi V., Bisaccia F., Fiermonte G. The mitochondrial oxoglutarate carrier: from identification to mechanism. J. Bioenerg. Biomembr. 2013, 45:1-13.
220. Moreau R., Heath S.H., Doneanu C.E., Lindsay J.G., Hagen T.M. Age-related increase in 4-hydroxynonenal adduction to rat heart α-ketoglutarate dehydrogenase does not cause loss of its catalytic activity. Antioxid. Redox Signal. 2003, 5:517-527.
221. Morin P., Storey K.B. Mammalian hibernation: differential gene expression and novel application of epigenetic controls. Int. J. Dev. Biol. 2009, 53:433-442.
222. Moser M.D., Matsuzaki S., Humphries K.M. Inhibition of succinate-linked respiration and complex II activity by hydrogen peroxide. Arch. Biochem. Biophys. 2009, 488:69-75.
223. +/Sirtuin pathway modulates longevity through activation of mitochondrial UPR and FOXO signaling. Cell 2013, 154:430-441.
224. Murayama A., Ohmori K., Fujimura A., Minami H., Yasuzawa-Tanaka K., Kuroda T., Oie S., Daitoku H., Okuwaki M., Nagata K., Fukamizu A., Kimura K., Shimizu T., Yanagisawa J. Epigenetic control of rDNA loci in response to intracellular energy status. Cell 2008, 133:627-639.
225. Myllyharju J. Prolyl 4-hydroxylases, master regulators of the hypoxia response. Acta Physiol. (Oxf.) 2013, 208:148-165.
226. Nagai R., Brock J.W., Blatnik M., Baatz J.E., Bethard J., Walla M.D., Thorpe S.R., Baynes J.W., Frizzell N. Succination of protein thiols during adipocyte maturation: a biomarker of mitochondrial stress. J. Biol. Chem. 2007, 282:34219-34228.
227. Ndubuizu O.I., Chavez J.C., LaManna J.C. Increased prolyl 4-hydroxylase expression and differential regulation of hypoxia-inducible factors in the aged rat brain. Am. J. Physiol. Regul. Integr. Comp. Physiol. 2009, 297:R158-R165.
228. Nguyen S., Meletis K., Fu D., Jhaveri S., Jaenisch R. Ablation of de novo DNA methyltransferase Dnmt3a in the nervous system leads to neuromuscular defects and shortened lifespan. Dev. Dyn. 2007, 236:1663-1676.
229. Noon A.T., Goodarzi A.A. 53BP1-mediated DNA double strand break repair: insert bad pun here. DNA Repair (Amst.) 2011, 10:1071-1076.
230. Oakes C.C., Smiraglia D.J., Plass C., Trasler J.M., Robaire B. Aging results in hypermethylation of ribosomal DNA in sperm and liver of male rats. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:1775-1780.
231. Ogunshola O.O., Antoniou X. Contribution of hypoxia to Alzheimer's disease: is HIF-1α a mediator of neurodegeneration?. Cell. Mol. Life Sci. 2009, 66:3555-3563.
232. Olive M., Harten I., Mitchell R., Beers J.K., Djabali K., Cao K., Erdos M.R., Blair C., Funke B., Smoot L., Gerhard-Herman M., Machan J.T., Kutys R., Virmani R., Collins F.S., Wight T.N., Nabel E.G., Gordon L.B. Cardiovascular pathology in Hutchinson-Gilford progeria: correlation with the vascular pathology of aging. Arterioscler. Thromb. Vasc. Biol. 2010, 30:2301-2309.
233. Oliveira A.M., Hemstedt T.J., Bading H. Rescue of aging-associated decline in Dnmt3a2 expression restores cognitive abilities. Nat. Neurosci. 2012, 15:1111-1113.
234. O'Sullivan R.J., Karlseder J. The great unravelling: chromatin as a modulator of the aging process. Trends Biochem. Sci. 2012, 37:466-476.
235. Otto C., Yovkova V., Barth G. Overproduction and secretion of α-ketoglutaric acid by microorganisms. Appl. Microbiol. Biotechnol. 2011, 92:689-695.
236. 2. Free Radic. Biol. Med. 2012, 52:160-166.
237. Pasmant E., Sabbagh A., Vidaud M., Bieche I. ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J. 2011, 25:444-448.
238. Pastor W.A., Aravind L., Rao A. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat. Rev. Mol. Cell Biol. 2013, 14:341-356.
239. Pegoraro G., Kubben N., Wickert U., Göhler H., Hoffmann K., Misteli T. Ageing-related chromatin defects through loss of the NURD complex. Nat. Cell Biol. 2009, 11:1261-1267.
240. Plank M., Wuttke D., van Dam S., Clarke S.A., de Magalhaes J.P. A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms. Mol. Biosyst. 2012, 8:1339-1349.
241. Pollard P.J., Loenarz C., Mole D.R., McDonough M.A., Gleadle J.M., Schofield C.J., Ratcliffe P.J. Regulation of Jumonji-domain-containing histone demethylases by hypoxia-inducible factor (HIF)-1α. Biochem. J 2008, 416:387-394.
242. Popov N., Gil J. Epigenetic regulation of the INK4b-ARF-INK4a locus: in sickness and in health. Epigenetics 2010, 5:685-690.
243. Qiu J., Shi G., Jia Y., Li J., Wu M., Li J., Dong S., Wong J. The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation. Cell Res. 2010, 20:908-918.
244. Rabie T., Kunze R., Marti H.H. Impaired hypoxic response in senescent mouse brain. Int. J. Dev. Neurosci. 2011, 29:655-661.
245. Raimundo N., Baysal B.E., Shadel G.S. Revisiting the TCA cycle: signaling to tumor formation. Trends Mol. Med. 2011, 17:641-649.
246. Rakyan V.K., Down T.A., Maslau S., Andrew T., Yang T.P., Beyan H., Whittaker P., McCann O.T., Finer S., Valdes A.M., Leslie R.D., Deloukas P., Spector T.D. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res. 2010, 20:434-439.
247. Rando T.A. Stem cells, ageing and the quest for immortality. Nature 2006, 441:1080-1086.
248. Rando T.A., Chang H.Y. Aging, rejuvenation, and epigenetic reprogramming: resetting the aging clock. Cell 2012, 148:46-57.
249. Reddy S., Comai L. Lamin A farnesylation and aging. Exp. Cell Res. 2012, 318:1-7.
250. Richardson B. Impact of aging on DNA methylation. Ageing Res. Rev. 2003, 2:245-261.
251. Rivard A., Berthou-Soulie L., Principe N., Kearney M., Curry C., Branellec D., Semenza G.L., Isner J.M. Age-dependent defect in vascular endothelial growth factor expression is associated with reduced hypoxia-inducible factor 1 activity. J. Biol. Chem. 2000, 275:29643-29647.
252. Robinson C.M., Neary R., Levendale A., Watson C.J., Baugh J.A. Hypoxia-induced DNA hypermethylation in human pulmonary fibroblasts is associated with Thy-1 promoter methylation and the development of a pro-fibrotic phenotype. Respir. Res. 2012, 13:74.
253. Rodriguez J., Munoz M., Vives L., Frangou C.G., Groudine M., Peinado M.A. Bivalent domains enforce transcriptional memory of DNA methylated genes in cancer cells. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:19809-19814.
254. Rohrbach S., Simm A., Pregla R., Franke C., Katschinski D.M. Age-dependent increase of prolyl-4-hydroxylase domain (PHD) 3 expression in human and mouse heart. Biogerontology 2005, 6:165-171.
255. Rohrbach S., Teichert S., Niemann B., Franke C., Katschinski D.M. Caloric restriction counteracts age-dependent changes in prolyl-4-hydroxylase domain (PHD) 3 expression. Biogerontology 2008, 9:169-176.
256. Ruotsalainen H., Sipilä L., Vapola M., Sormunen R., Salo A.M., Uitto L., Mercer D.K., Robins S.P., Risteli M., Aszodi A., Fässler R., Myllylä R. Glycosylation catalyzed by lysyl hydroxylase 3 is essential for basement membranes. J. Cell Sci. 2006, 119:625-635.
257. Rutter J., Winge D.R., Schiffman J.D. Succinate dehydrogenase - assembly, regulation and role in human disease. Mitochondrion 2010, 10:393-401.
258. Sack M.N., Finkel T. Mitochondrial metabolism, sirtuins, and aging. Cold Spring Harb. Perspect. Biol. 2012, 4:a013102.
259. Sahin E., DePinho R.A. Axis of ageing: telomeres, p53 and mitochondria. Nat. Rev. Mol. Cell Biol. 2012, 13:397-404.
260. Salminen A., Kaarniranta K. SIRT1 regulates the ribosomal DNA locus: epigenetic candles twinkle longevity in the Christmas tree. Biochem. Biophys. Res. Commun. 2009, 378:6-9.
261. Salminen A., Kaarniranta K. Insulin/IGF-1 paradox of aging: regulation via AKT/IKK/NF-κB signaling. Cell. Signal. 2010, 22:573-577.
262. Salminen A., Huuskonen J., Ojala J., Kauppinen A., Kaarniranta K., Suuronen T. Activation of innate immunity system during aging: NF-κB signaling is the molecular culprit of inflamm-aging. Ageing Res. Rev. 2008, 7:83-105.
263. Salminen A., Kauppinen A., Kaarniranta K. Emerging role of NF-κB signaling in the induction of senescence-associated secretory phenotype (SASP). Cell. Signal. 2012, 24:835-845.
264. Samokhvalov V., Ignatov V., Kondrashova M. Inhibition of Krebs cycle and activation of glyoxylate cycle in the course of chronological aging of Saccharomyces cerevisiae. Compensatory role of succinate oxidation. Biochimie 2004, 86:39-46.
265. Sarg B., Koutzamani E., Helliger W., Rundquist I., Lindner H.H. Postsynthetic trimethylation of histone H4 at lysine 20 in mammalian tissues is associated with aging. J. Biol. Chem. 2002, 277:39195-39201.
266. Sastre J., Pallardo F.V., Vina J. The role of mitochondrial oxidative stress in aging. Free Radic. Biol. Med. 2003, 35:1-8.
267. Satoh T., Takeuchi O., Vandenbon A., Yasuda K., Tanaka Y., Kumagai Y., Miyake T., Matsushita K., Okazaki T., Saitoh T., Honma K., Matsuyama T., Yui K., Tsujimura T., Standley D.M., Nakanishi K., Nakai K., Akira S. The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nat. Immunol. 2010, 11:936-944.
268. Savitha S., Sivarajan K., Haripriya D., Kokilavani V., Panneerselvam C. Efficacy of levo carnitine and alpha lipoic acid in ameliorating the decline in mitochondrial enzymes during aging. Clin. Nutr. 2005, 24:794-800.
269. Scaffidi P., Misteli T. Lamin A-dependent nuclear defects in human aging. Science 2006, 312:1059-1063.
270. Schofield C.J., Zhang Z. Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes. Curr. Opin. Struct. Biol. 1999, 9:722-731.
271. Sedgwick B. Repairing DNA-methylation damage. Nat. Rev. Mol. Cell Biol. 2004, 5:148-157.
272. Sekirnik R., Rose N.R., Mecinovic J., Schofield C.J. 2-Oxoglutarate oxygenases are inhibited by a range of transition metals. Metallomics 2010, 2:397-399.
273. Selak M.A., Armour S.M., MacKenzie E.D., Boulahbel H., Watson D.G., Mansfield K.D., Pan Y., Simon M.C., Thompson C.B., Gottlieb E. Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-α prolyl hydroxylase. Cancer Cell 2005, 7:77-85.
274. Seo A.Y., Joseph A.M., Dutta D., Hwang J.C., Aris J.P., Leeuwenburgh C. New insights into the role of mitochondria in aging: mitochondrial dynamics and more. J. Cell Sci. 2010, 123:2533-2542.
275. Seward D.J., Cubberley G., Kim S., Schonewald M., Zhang L., Tripet B., Bentley D.L. Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat. Struct. Mol. Biol. 2007, 14:240-242.
276. Shams I., Avivi A., Nevo E. Hypoxic stress tolerance of the blind subterranean mole rat: expression of erythropoietin and hypoxia-inducible factor 1α. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:9698-9703.
277. Shapiro H., Lutaty A., Ariel A. Macrophages, meta-inflammation, and immuno-metabolism. ScientificWorldJournal 2011, 11:2509-2529.
278. Sharpless N.E., DePinho R.A. How stem cells age and why this makes us grow old. Nat. Rev. Mol. Cell Biol. 2007, 8:703-713.
279. Shen L., Zhang Y. 5-Hydroxymethylcytosine: generation, fate, and genomic distribution. Curr. Opin. Cell Biol. 2013, 25:289-296.
280. Sheu K.F., Blass J.P. The α-ketoglutarate dehydrogenase complex. Ann. N. Y. Acad. Sci. 1999, 893:61-78.
281. Shi F.T., Kim H., Lu W., He Q., Liu D., Goodell M.A., Wan M., Songyang Z. Ten-eleven translocation 1 (Tet1) is regulated by O-linked N-acetylglucosamine transferase (Ogt) for target gene repression in mouse embryonic stem cells. J. Biol. Chem. 2013, 288:20776-20784.
282. Shilatifard A. The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. Annu. Rev. Biochem 2012, 81:65-95.
283. Shumaker D.K., Dechat T., Kohlmaier A., Adam S.A., Bozovsky M.R., Erdos M.R., Eriksson M., Goldman A.E., Khuon S., Collins F.S., Jenuwein T., Goldman R.D. Mutant nuclear lamin A leads to progressive alterations of epigenetic control in premature aging. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:8703-8708.
284. Signer R.A., Morrison S.J. Mechanisms that regulate stem cell aging and life span. Cell Stem Cell 2013, 12:152-165.
285. Simon J.A., Kingston R.E. Occupying chromatin: polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol. Cell 2013, 49:808-824.
286. Smith Z.D., Meissner A. DNA methylation: roles in mammalian development. Nat. Rev. Genet. 2013, 14:204-220.
287. So A.Y., Jung J.W., Lee S., Kim H.S., Kang K.S. DNA methyltransferase controls stem cell aging by regulating BMI1 and EZH2 through microRNAs. PLoS ONE 2011, 6:e19503.
288. Sohal R.S., Weindruch R. Oxidative stress, caloric restriction, and aging. Science 1996, 273:59-63.
289. Sonenshein A.L. Control of key metabolic intersections in Bacillus subtilis. Nat. Rev. Microbiol. 2007, 5:917-927.
290. Song C.X., He C. Potential functional roles of DNA demethylation intermediates. Trends Biochem. Sci. 2013, 10.1016/j.tibs.2013.07.003.
291. Staples J.F., Brown J.C. Mitochondrial metabolism in hibernation and daily torpor: a review. J. Comp. Physiol. B 2008, 178:811-827.
292. Stender J.D., Pascual G., Liu W., Kaikkonen M.U., Do K., Spann N.J., Boutros M., Perrimon N., Rosenfeld M.G., Glass C.K. Control of proinflammatory gene programs by regulated trimethylation and demethylation of histone H4K20. Mol. Cell 2012, 48:28-38.
293. Swindell W.R. Genes and gene expression modules associated with caloric restriction and aging in the laboratory mouse. BMC Genomics 2009, 10:585.
294. Tahiliani M., Koh K.P., Shen Y., Pastor W.A., Bandukwala H., Brudno Y., Agarwal S., Iyer L.M., Liu D.R., Aravind L., Rao A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009, 324:930-935.
295. Tanaka Y., Okamoto K., Teye K., Umata T., Yamagiwa N., Suto Y., Zhang Y., Tsuneoka M. JmjC enzyme KDM2A is a regulator of rRNA transcription in response to starvation. EMBO J. 2010, 29:1510-1522.
296. Tateishi K., Okada Y., Kallin E.M., Zhang Y. Role of Jhdm2a in regulating metabolic gene expression and obesity resistance. Nature 2009, 458:757-761.
297. Tausendschön M., Dehne N., Brune B. Hypoxia causes epigenetic gene regulation in macrophages by attenuating Jumonji histone demethylase activity. Cytokine 2011, 53:256-262.
298. Terman A., Kurz T., Navratil M., Arriaga E.A., Brunk U.T. Mitochondrial turnover and aging of long-lived postmitotic cells: the mitochondrial-lysosomal axis theory of aging. Antioxid. Redox Signal. 2010, 12:503-535.
299. Ternette N., Yang M., Laroyia M., Kitagawa M., O'Flaherty L., Wolhulter K., Igarashi K., Saito K., Kato K., Fischer R., Berquand A., Kessler B.M., Lappin T., Frizzell N., Soga T., Adam J., Pollard P.J. Inhibition of mitochondrial aconitase by succination in fumarate hydratase deficiency. Cell Rep. 2013, 3:689-700.
300. Teschendorff A.E., West J., Beck S. Age-associated epigenetic drift: implications, and a case of epigenetic thrift?. Hum. Mol. Genet. 2013, 22:R7-R15.
301. Thakur M.K. Age-related changes in the structure and function of chromatin: a review. Mech. Ageing Dev. 1984, 27:263-286.
302. Thompson R.F., Atzmon G., Gheorghe C., Liang H.Q., Lowes C., Greally J.M., Barzilai N. Tissue-specific dysregulation of DNA methylation in aging. Aging Cell 2010, 9:506-518.
303. Tobi E.W., Slagboom P.E., van Dongen J., Kremer D., Stein A.D., Putter H., Heijmans B.T., Lumey L.H. Prenatal famine and genetic variation are independently and additively associated with DNA methylation at regulatory loci within IGF2/H19. PLoS ONE 2012, 7:e37933.
304. Tokonami N., Morla L., Centeno G., Mordasini D., Ramakrishnan S.K., Nikolaeva S., Wagner C.A., Bonny O., Houillier P., Doucet A., Firsov D. α-Ketoglutarate regulates acid-base balance through an intrarenal paracrine mechanism. J. Clin. Invest. 2013, 123:3166-3171.
305. Tretter L., Adam-Vizi V. Alpha-ketoglutarate dehydrogenase: a target and generator of oxidative stress. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2005, 360:2335-2345.
306. Trifunovic A., Larsson N.G. Mitochondrial dysfunction as a cause of ageing. J. Intern. Med. 2008, 263:167-178.
307. Trofimova L.K., Araujo W.L., Strokina A.A., Fernie A.R., Bettendorff L., Bunik V.I. Consequences of the α-ketoglutarate dehydrogenase inhibition for neuronal metabolism and survival: implications for neurodegenerative diseases. Curr. Med. Chem. 2012, 19:5895-5906.
308. Tsukada Y., Fang J., Erdjument-Bromage H., Warren M.E., Borchers C.H., Tempst P., Zhang Y. Histone demethylation by a family of JmjC domain-containing proteins. Nature 2006, 439:811-816.
309. Tsukada Y., Ishitani T., Nakayama K.I. KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions in brain development. Genes Dev. 2010, 24:432-437.
310. Tsurumi A., Li W.X. Global heterochromatin loss: a unifying theory of aging?. Epigenetics 2012, 7:680-688.
311. Tzatsos A., Pfau R., Kampranis S.C., Tsichlis P.N. Ndy1/KDM2B immortalizes mouse embryonic fibroblasts by repressing the Ink4a/Arf locus. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:2641-2646.
312. Tzatsos A., Paskaleva P., Lymperi S., Contino G., Stoykova S., Chen Z., Wong K.K., Bardeesy N. Lysine-specific demethylase 2B (KDM2B)-let-7-enhancer of zester homolog 2 (EZH2) pathway regulates cell cycle progression and senescence in primary cells. J. Biol. Chem. 2011, 286:33061-33069.
313. Unoki M., Masuda A., Dohmae N., Arita K., Yoshimatsu M., Iwai Y., Fukui Y., Ueda K., Hamamoto R., Shirakawa M., Sasaki H., Nakamura Y. Lysyl 5-hydroxylation, a novel histone modification, by Jumonji domain containing 6 (JMJD6). J. Biol. Chem. 2013, 288:6053-6062.
314. Upadhyay A.K., Horton J.R., Zhang X., Cheng X. Coordinated methyl-lysine erasure: structural and functional linkage of a Jumonji demethylase domain and a reader domain. Curr. Opin. Struct. Biol. 2011, 21:750-760.
315. Uzawa K., Grzesik W.J., Nishiura T., Kuznetsov S.A., Robey P.G., Brenner D.A., Yamauchi M. Differential expression of human lysyl hydroxylase genes, lysine hydroxylation, and cross-linking of type I collagen during osteoblastic differentiation in vitro. J. Bone Miner. Res. 1999, 14:1272-1280.
316. Vanyushin B.F., Nemirovsky L.E., Klimenko V.V., Vasiliev V.K., Belozersky A.N. The 5-methylcytosine in DNA of rats. Tissue and age specificity and the changes induced by hydrocortisone and other agents. Gerontologia 1973, 19:138-152.
317. Varani J., Dame M.K., Rittie L., Fligiel S.E., Kang S., Fisher G.J., Voorhees J.J. Decreased collagen production in chronologically aged skin: roles of age-dependent alteration in fibroblast function and defective mechanical stimulation. Am. J. Pathol. 2006, 168:1861-1868.
318. Vijg J., Suh Y. Genome instability and aging. Annu. Rev. Physiol. 2013, 75:645-668.
319. Vranka J.A., Sakai L.Y., Bächinger H.P. Prolyl 3-hydroxylase 1, enzyme characterization and identification of a novel family of enzymes. J. Biol. Chem. 2004, 279:23615-23621.
320. Wagner G.R., Payne R.M. Mitochondrial acetylation and diseases of aging. J. Aging Res. 2011, ID 234875.
321. Ward P.S., Patel J., Wise D.R., Abdel-Wahab O., Bennett B.D., Coller H.A., Cross J.R., Fantin V.R., Hedvat C.V., Perl A.E., Rabinowitz J.D., Carroll M., Su S.M., Sharp K.A., Levine R.L., Thompson C.B. The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting α-ketoglutarate to 2-hydroxyglutarate. Cancer Cell 2010, 17:225-234.
322. Ward P.S., Thompson C.B. Metabolic reprogramming: a cancer hallmark even Warburg did not anticipate. Cancer Cell 2012, 21:297-308.
323. Wellen K.E., Hatzivassiliou G., Sachdeva U.M., Bui T.V., Cross J.R., Thompson C.B. ATP-citrate lyase links cellular metabolism to histone acetylation. Science 2009, 324:1076-1080.
324. Wellmann S., Bettkober M., Zelmer A., Seeger K., Faigle M., Eltzschig H.K., Buhrer C. Hypoxia upregulates the histone demethylase JMJD1A via HIF-1. Biochem. Biophys. Res. Commun. 2008, 372:892-897.
325. Wen H., Li J., Song T., Lu M., Kan P.Y., Lee M.G., Sha B., Shi X. Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation. J. Biol. Chem. 2010, 285:9322-9326.
326. Widmer H.R., Hoppeler H., Nevo E., Taylor C.R., Weibel E.R. Working underground: respiratory adaptations in the blind mole rat. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:2062-2067.
327. Wilson V.L., Smith R.A., Ma S., Cutler R.G. Genomic 5-methyldeoxycytidine decreases with age. J. Biol. Chem. 1987, 262:9948-9951.
328. Winder W.W., Holmes B.F., Rubink D.S., Jensen E.B., Chen M., Holloszy J.O. Activation of AMP-activated protein kinase increases mitochondrial enzymes in skeletal muscle. J. Appl. Physiol. 2000, 88:2219-2226.
329. Wise D.R., Ward P.S., Shay J.E., Cross J.R., Gruber J.J., Sachdeva U.M., Platt J.M., DeMatteo R.G., Simon M.C., Thompson C.B. Hypoxia promotes isocitrate dehydrogenase-dependent carboxylation of α-ketoglutarate to citrate to support cell growth and viability. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:19611-19616.
330. Wittenberger T., Hellebrand S., Munck A., Kreienkamp H.J., Schaller H.C., Hampe W. GPR99, a new G protein-coupled receptor with homology to a new subgroup of nucleotide receptors. BMC Genomics 2002, 3:17.
331. Wojtovich A.P., Smith C.O., Haynes C.M., Nehrke K.W., Brookes P.S. Physiological consequences of complex II inhibition for aging, disease, and the mKATP channel. Biochim. Biophys. Acta 2013, 1827:598-611.
332. Wood J.G., Hillenmeyer S., Lawrence C., Chang C., Hosier S., Lightfoot W., Mukherjee E., Jiang N., Schorl C., Brodsky A.S., Neretti N., Helfand S.L. Chromatin remodeling in the aging genome of Drosophila. Aging Cell 2010, 9:971-978.
333. Wu X., Johansen J.V., Helin K. Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. Mol. Cell 2013, 49:1134-1146.
334. Xiao M., Yang H., Xu W., Ma S., Lin H., Zhu H., Liu L., Liu Y., Yang C., Xu Y., Zhao S., Ye D., Xiong Y., Guan K.L. 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. 2012, 26:1326-1338.
335. Xu W., Yang H., Liu Y., Yang Y., Wang P., Kim S.H., Ito S., Yang C., Wang P., Xiao M.T., Liu L.X., Jiang W.Q., Liu J., Zhang J.Y., Wang B., Frye S., Zhang Y., Xu Y.H., Lei Q.Y., Guan K.L., Zhao S.M., Xiong Y. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases. Cancer Cell 2011, 19:17-30.
336. Yamane K., Toumazou C., Tsukada Y., Erdjument-Bromage H., Tempst P., Wong J., Zhang Y. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 2006, 125:483-495.
337. Yan H., Parsons D.W., Jin G., McLendon R., Rasheed B.A., Yuan W., Kos I., Batinic-Haberle I., Jones S., Riggins G.J., Friedman H., Friedman A., Reardon D., Herndon J., Kinzler K.W., Velculescu V.E., Vogelstein B., Bigner D.D. IDH1 and IDH2 mutations in gliomas. N. Engl. J. Med. 2009, 360:765-773.
338. Yang M., Soga T., Pollard P.J. Oncometabolites: linking altered metabolism with cancer. J. Clin. Invest. 2013, 123:3652-3658.
339. Yarian C.S., Sohal R.S. In the aging housefly aconitase is the only citric acid cycle enzyme to decline significantly. J. Bioenerg. Biomembr. 2005, 37:91-96.
340. Yarian C.S., Toroser D., Sohal R.S. Aconitase is the main functional target of aging in the citric acid cycle of kidney mitochondria from mice. Mech. Ageing Dev. 2006, 127:79-84.
341. Yeaman S.J. The 2-oxo acid dehydrogenase complexes: recent advances. Biochem. J 1989, 257:625-632.
342. Yee Koh M., Spivak-Kroizman T.R., Powis G. HIF-1 regulation: not so easy come easy go. Trends Biochem. Sci. 2008, 33:526-534.
343. Youn M.Y., Yokoyama A., Fujiyama-Nakamura S., Ohtake F., Minehata K., Yasuda H., Suzuki T., Kato S., Imai Y. JMJD5, a Jumonji C (JmjC) domain-containing protein, negatively regulates osteoclastogenesis by facilitating NFATc1 protein degradation. J. Biol. Chem. 2012, 287:12994-13004.
344. Yu K.R., Kang K.S. Aging-related genes in mesenchymal stem cells: a mini-review. Gerontology 2013, 59:557-563.
345. Yu C., Li Y., Holmes A., Szafranski K., Faulkes C.G., Coen C.W., Buffenstein R., Platzer M., de Magalhaes J.P., Church G.M. RNA sequencing reveals differential expression of mitochondrial and oxidation reduction genes in the long-lived naked mole-rat when compared to mice. PLoS ONE 2011, 6:e26729.
346. Zhou X., Sun H., Chen H., Zavadil J., Kluz T., Arita A., Costa M. Hypoxia induces trimethylated H3 lysine 4 by inhibition of JARID1A demethylase. Cancer Res. 2010, 70:4214-4221.
347. Zhu Z., Wang Y., Li X., Wang Y., Xu L., Wang X., Sun T., Dong X., Chen L., Mao H., Yu Y., Li J., Chen P.A., Chen C.D. PHF8 is a histone H3K9me2 demethylase regulating rRNA synthesis. Cell Res. 2010, 20:794-801.