The circadian epigenome: How metabolism talks to chromatin remodeling

Current Opinion in Cell Biology

Volumn 25, Issue 2, 2013, Pages 170-176

  Aguilar Arnal, Lorena ^a   Sassone Corsi, Paolo ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE DEACETYLASE 3; HISTONE DEMETHYLASE; MULTIPROTEIN COMPLEX; NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE; TRANSCRIPTION FACTOR CLOCK;

ACETYLATION; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHRONOTHERAPY; CIRCADIAN RHYTHM; ENERGY METABOLISM; FEEDBACK SYSTEM; GENE EXPRESSION; GENETIC TRANSCRIPTION; GLUCOSE HOMEOSTASIS; HISTONE ACETYLATION; HUMAN; LIVER FUNCTION; LIVER METABOLISM; METABOLIC REGULATION; METABOLISM; METHYLATION; MOLECULAR CLOCK; NERVE EXCITABILITY; NONHUMAN; OSCILLATION; OXIDATION REDUCTION STATE; PERIODICITY; PERSONALIZED MEDICINE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; SLEEP DISORDER; TRANSCRIPTION INITIATION; ANIMAL; EPIGENETICS; GENETIC EPIGENESIS; GENETICS; METABOLIC DISORDER; PHYSIOLOGY; REVIEW;

ANIMALS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; ENERGY METABOLISM; EPIGENESIS, GENETIC; EPIGENOMICS; HUMANS; METABOLIC DISEASES; SLEEP DISORDERS; TRANSCRIPTION, GENETIC;

MLCS; MLOWN;

EID: 84877929035     PISSN: 09550674     EISSN: 18790410     Source Type: Journal    
DOI: 10.1016/j.ceb.2013.01.003     Document Type: Review

References (66)

1. Schibler U, Sassone-Corsi P: A web of circadian pacemakers. Cell 2002, 111:919-922.
2. Ralph MR, Foster RG, Davis FC, Menaker M: Transplanted suprachiasmatic nucleus determines circadian period. Science 1990, 247:975-978.
3. Freedman MS, Lucas RJ, Soni B, von Schantz M, Munoz M, David-Gray Z, Foster R: Regulation of mammalian circadian behavior by non-rod, non-cone, ocular photoreceptors. Science 1999, 284:502-504.
4. Cermakian N, Sassone-Corsi P: Environmental stimulus perception and control of circadian clocks. Curr Opin Neurobiol 2002, 12:359-365.
5. Quintero JE, Kuhlman SJ, McMahon DG: The biological clock nucleus: a multiphasic oscillator network regulated by light. J Neurosci 2003, 23:8070-8076.
6. Bellet MM, Sassone-Corsi P: Mammalian circadian clock and metabolism-the epigenetic link. J Cell Sci 2010, 123(Pt 22):3837-3848.
7. Damiola F, Le Minh N, Preitner N, Kornmann B, Fleury-Olela F, Schibler U: Restricted feeding uncouples circadian oscillators in peripheral tissues from the central pacemaker in the suprachiasmatic nucleus. Genes Dev 2000, 14:2950-2961.
8. Cermakian N, Sassone-Corsi P: Multilevel regulation of the circadian clock. Nat Rev Mol Cell Biol 2000, 1:59-67.
9. King DP, Takahashi JS: Molecular genetics of circadian rhythms in mammals. Annu Rev Neurosci 2000, 23:713-742.
10. Reppert SM, Weaver DR: Coordination of circadian timing in mammals. Nature 2002, 418:935-941.
11. Young MW, Kay SA: Time zones: a comparative genetics of circadian clocks. Nat Rev Genet 2001, 2:702-715.
12. Wuarin J, Schibler U: Expression of the liver-enriched transcriptional activator protein DBP follows a stringent circadian rhythm. Cell 1990, 63:1257-1266.
13. Gachon F, Olela FF, Schaad O, Descombes P, Schibler U: The circadian PAR-domain basic leucine zipper transcription factors DBP, TEF, and HLF modulate basal and inducible xenobiotic detoxification. Cell Metab 2006, 4:25-36.
14. Preitner N, Damiola F, Lopez-Molina L, Zakany J, Duboule D, Albrecht U, Schibler U: The orphan nuclear receptor Rev-Erb alpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 2002, 110:251-260.
15. Sato TK, Panda S, Miraglia LJ, Reyes TM, Rudic RD, McNamara P, Naik KA, FitzGerald GA, Kay SA, Hogenesch JB: A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron 2004, 43:527-537.
16. Mehra A, Baker CL, Loros JJ, Dunlap JC: Post-translational modifications in circadian rhythms. Trends Biochem Sci 2009, 34:483-490.
17. Duffield GE, Best JD, Meurers BH, Bittner A, Loros JJ, Dunlap JC: Circadian programs of transcriptional activation, signaling, and protein turnover revealed by microarray analysis of mammalian cells. Curr Biol 2002, 12:551-557.
18. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, Schultz PG, Kay SA, Takahashi JS, Hogenesch JB: Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 2002, 109:307-320.
19. Storch KF, Lipan O, Leykin I, Viswanathan N, Davis FC, Wong WH, Weitz CJ: Extensive and divergent circadian gene expression in liver and heart. Nature 2002, 417:78-83.
20. Ueda HR, Chen W, Adachi A, Wakamatsu H, Hayashi S, Takasugi T, Nagano M, Nakahama K, Suzuki Y, Sugano S et al.: A transcription factor response element for gene expression during circadian night. Nature 2002, 418:534-539.
21. Borrelli E, Nestler EJ, Allis CD, Sassone-Corsi P: Decoding the epigenetic language of neuronal plasticity. Neuron 2008, 60:961-974.
22. Masri S, Sassone-Corsi P: Plasticity and specificity of the circadian epigenome. Nat Neurosci 2010, 13:1324-1329.
23. Doi M, Hirayama J, Sassone-Corsi P: Circadian regulator clock is a histone acetyltransferase. Cell 2006, 125:497-508.
24. Nakahata Y, Grimaldi B, Sahar S, Hirayama J, Sassone-Corsi P: Signaling to the circadian clock: plasticity by chromatin remodeling. Curr Opin Cell Biol 2007, 19:230-237.
25. Etchegaray JP, Lee C, Wade PA, Reppert SM: Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature 2003, 421:177-182.
26. Koike N, Yoo SH, Huang HC, Kumar V, Lee C, Kim TK, Takahashi JS: Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 2012.
27. Hirayama J, Sahar S, Grimaldi B, Tamaru T, Takamatsu K, Nakahata Y, Sassone-Corsi P: CLOCK-mediated acetylation of BMAL1 controls circadian function. Nature 2007, 450: 1086-1090.
28. Katada S, Sassone-Corsi P: The histone methyltransferase MLL1 permits the oscillation of circadian gene expression. Nat Struct Mol Biol 2010, 17:1414-1421.
29. Etchegaray JP, Yang X, DeBruyne JP, Peters AH, Weaver DR, Jenuwein T, Reppert SM: The polycomb group protein EZH2 is required for mammalian circadian clock function. J Biol Chem 2006, 281:21209-21215.
30. DiTacchio L, Le HD, 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.
31. Jones MA, Covington MF, DiTacchio L, Vollmers C, Panda S, Harmer SL: Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proc Natl Acad Sci U S A 2010, 107:21623-21628.
32. Alenghat T, Meyers K, Mullican SE, Leitner K, Adeniji-Adele A, Avila J, Bucan M, Ahima RS, Kaestner KH, Lazar MA: Nuclear receptor corepressor and histone deacetylase 3 govern circadian metabolic physiology. Nature 2008, 456:997-1000.
33. Feng D, Liu T, Sun Z, Bugge A, Mullican SE, Alenghat T, Liu XS, Lazar MA: A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science 2011, 331:1315-1319.
34. Cho H, Zhao X, Hatori M, Yu RT, Barish GD, Lam MT, Chong LW, DiTacchio L, Atkins AR, Glass CK et al.: Regulation of circadian behaviour and metabolism by Rev-Erb-alpha and Rev-Erbbeta. Nature 2012, 485:123-127.
35. Katada S, Imhof A, Sassone-Corsi P: Connecting threads: epigenetics and metabolism. Cell 2012, 148:24-28.
36. Asher G, Gatfield D, Stratmann M, Reinke H, Dibner C, Kreppel F, Mostoslavsky R, Alt FW, Schibler U: SIRT1 regulates circadian clock gene expression through PER2 deacetylation. Cell 2008, 134:317-328.
37. Asher G, Reinke H, Altmeyer M, Gutierrez-Arcelus M, Hottiger MO, Schibler U: Poly(adp-ribose) polymerase 1 participates in the phase entrainment of circadian clocks to feeding. Cell 2010, 142:943-953.
38. Nakahata Y, Kaluzova M, Grimaldi B, Sahar S, Hirayama J, Chen D, Guarente LP, Sassone-Corsi P: The NAD+-dependent deacetylase SIRT1 modulates clock-mediated chromatin remodeling and circadian control. Cell 2008, 134:329-340.
39. Krishnakumar R, Kraus WL: PARP-1 regulates chromatin structure and transcription through a KDM5b-dependent pathway. Mol Cell 2010, 39:736-749.
40. Nakahata Y, Sahar S, Astarita G, Kaluzova M, Sassone-Corsi P: Circadian control of the NAD+ salvage pathway by clock-SIRT1. Science 2009, 324:654-657.
41. Ramsey KM, Yoshino J, Brace CS, Abrassart D, Kobayashi Y, Marcheva B, Hong HK, Chong JL, Buhr ED, Lee C et al.: Circadian clock feedback cycle through NAMPT-mediated NAD+ biosynthesis. Science 2009, 324:651-654.
42. Sahar S, Nin V, Barbosa MT, Chini EN, Sassone-Corsi P: Altered behavioral and metabolic circadian rhythms in mice with disrupted NAD+ oscillation. Aging (Albany NY) 2011, 3:794-802.
43. Bai P, Canto C, Oudart H, Brunyanszki A, Cen Y, Thomas C, Yamamoto H, Huber A, Kiss B, Houtkooper RH et al.: PARP-1 inhibition increases mitochondrial metabolism through SIRT1 activation. Cell Metab 2011, 13:461-468.
44. Pang J, Gong H, Xi C, Fan W, Dai Y, Zhang TM: Poly(adp-ribose) polymerase 1 is involved in glucose toxicity through SIRT1 modulation in Hepg2 hepatocytes. J Cell Biochem 2011, 112:299-306.
45. Kolthur-Seetharam U, Dantzer F, McBurney MW, de Murcia G, Sassone-Corsi P: Control of AIF-mediated cell death by the functional interplay of SIRT1 and PARP-1 in response to DNA damage. Cell Cycle 2006, 5:873-877.
46. Droge W: Free radicals in the physiological control of cell function. Physiol Rev 2002, 82:47-95.
47. Rutter J, Reick M, Wu LC, McKnight SL: Regulation of CLOCK and NPAS2 DNA binding by the redox state of NAD+ cofactors. Science 2001, 293:510-514.
48. O'Neill J.S., Reddy AB: Circadian clocks in human red blood cells. Nature 2011, 469:498-503.
49. EdgarRS,GreenEW,ZhaoY,vanOoijenG,OlmedoM,QinX,XuY,PanM, Valekunja UK, Feeney KA et al.: Peroxiredoxins are conserved markers of circadian rhythms. Nature 2012, 485:459-464.
50. Wang TA, Yu YV, Govindaiah G, Ye X, Artinian L, Coleman TP, Sweedler JV, Cox CL, Gillette MU: Circadian rhythm of redox state regulates excitability in suprachiasmatic nucleus neurons. Science 2012, 337:839-842.
51. Mizrak D, Ruben M, Myers GN, Rhrissorrakrai K, Gunsalus KC, Blau J: Electrical activity can impose time of day on the circadian transcriptome of pacemaker neurons. Curr Biol 2012, 22:1871-1880.
52. Sahar S, Sassone-Corsi P: Regulation of metabolism: the circadian clock dictates the time. Trends Endocrinol Metab 2012, 23:1-8.
53. Buxton OM, Cain SW, O'Connor SP, Porter JH, Duffy JF, Wang W, Czeisler CA, Shea SA: Adverse metabolic consequences in humans of prolonged sleep restriction combined with circadian disruption. Sci Transl Med 2012, 4:129-143.
54. Marcheva B, Ramsey KM, Buhr ED, Kobayashi Y, Su H, Ko CH, Ivanova G, Omura C, Mo S, Vitaterna MH et al.: Disruption of the clock components CLOCK and BMAL1 leads to hypoinsulinaemia and diabetes. Nature 2010, 466:627-631.
55. Scott EM, Carter AM, Grant PJ: Association between polymorphisms in the clock gene, obesity and the metabolic syndrome in man. Int J Obes (Lond) 2008, 32:658-662.
56. Turek FW, Joshu C, Kohsaka A, Lin E, Ivanova G, McDearmon E, Laposky A, Losee-Olson S, Easton A, Jensen DR et al.: Obesity and metabolic syndrome in circadian clock mutant mice. Science 2005, 308:1043-1045.
57. Hatori M, Vollmers C, Zarrinpar A, DiTacchio L, Bushong EA, Gill S, Leblanc M, Chaix A, Joens M, Fitzpatrick JA et al.: Timerestricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet. Cell Metab 2012, 15:848-860.
58. Sherman H, Genzer Y, Cohen R, Chapnik N, Madar Z, Froy O: Timed high-fat diet resets circadian metabolism and prevents obesity. Faseb J 2012, 26:3493-3502.
59. Eckel-Mahan K, Sassone-Corsi P: Metabolism control by the circadian clock and vice versa. Nat Struct Mol Biol 2009, 16:462-467.
60. Eckel-Mahan KL, Patel VR, Mohney RP, Vignola KS, Baldi P, Sassone-Corsi P: Coordination of the transcriptome and metabolome by the circadian clock. Proc Natl Acad Sci U S A 2012, 109:5541-5546.
61. Braissant O: Current concepts in the pathogenesis of urea cycle disorders. Mol Genet Metab 2010, 100(Suppl 1):S3-S12.
62. Patel VR, Eckel-Mahan K, Sassone-Corsi P, Baldi P: Circadiomics: integrating circadian genomics, transcriptomics, proteomics and metabolomics. Nat Methods 2012, 9:772-773.
63. Dallmann R, Viola AU, Tarokh L, Cajochen C, Brown SA: The human circadian metabolome. Proc Natl Acad Sci U S A 2012, 109:2625-2629.
64. Kasukawa T, Sugimoto M, Hida A, Minami Y, Mori M, Honma S, Honma K, Mishima K, Soga T, Ueda HR: Human blood metabolite timetable indicates internal body time. Proc Natl Acad Sci U S A 2012, 109:15036-15041.
65. Solt LA, Wang Y, Banerjee S, Hughes T, Kojetin DJ, Lundasen T, Shin Y, Liu J, Cameron MD, Noel R et al.: Regulation of circadian behaviour and metabolism by synthetic Rev-Erb agonists. Nature 2012, 485:62-68.
66. Hirota T, Lee JW, St John PC, Sawa M, Iwaisako K, Noguchi T, Pongsawakul PY, Sonntag T, Welsh DK, Brenner DA et al.: Identification of small molecule activators of cryptochrome. Science 2012, 337:1094.