The Interplay of cis-Regulatory Elements Rules Circadian Rhythms in Mouse Liver

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Korenčič, Anja ^a   Bordyugov, Grigory ^b   Košir, Rok ^a   Rozman, Damjana ^a   Goličnik, Marko ^a   Herzel, Hanspeter ^b  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS RECEPTOR; CRYPTOCHROME 1; NUCLEAR RECEPTOR NR1D1; PROTEIN BMAL1;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BMAL1 GENE; CIRCADIAN RHYTHM; CIS REGULATORY ELEMENT; CLOCK GENE; CONTROLLED STUDY; CRY1 GENE; DARKNESS; DNA STRUCTURE; E BOX ELEMENT; GENE; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; LIGHT DARK CYCLE; LIVER; MOUSE; NEGATIVE FEEDBACK; NONHUMAN; REV ERBA GENE; TRANSCRIPTION REGULATION;

ANIMALS; ARNTL TRANSCRIPTION FACTORS; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; CIRCADIAN RHYTHM SIGNALING PEPTIDES AND PROTEINS; CRYPTOCHROMES; DNA-BINDING PROTEINS; E-BOX ELEMENTS; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; LIVER; MICE; MICE, INBRED C57BL; MODELS, GENETIC; PERIOD CIRCADIAN PROTEINS; PHOTOPERIOD; TRANSCRIPTION FACTORS;

MAMMALIA;

EID: 84868384122     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046835     Document Type: Article

References (57)

1. Levi F, Schibler U, (2007) Circadian rhythms: mechanisms and therapeutic implications. Annu Rev Pharmacol Toxicol 47: 593-628.
2. Storch KF, Lipan O, Leykin I, Viswanathan N, Davis FC, et al. (2002) Extensive and divergent circadian gene expression in liver and heart. Nature 417: 78-83.
3. Yamamoto T, Nakahata Y, Soma H, Akashi M, Mamine T, et al. (2004) Transcriptional oscillation of canonical clock genes in mouse peripheral tissues. BMC Mol Biol 5: 18.
4. Reppert SM, Weaver DR, (2002) Coordination of circadian timing in mammals. Nature 418: 935-941.
5. Ukai H, Ueda HR, (2010) Systems biology of mammalian circadian clocks. Annu Rev Physiol 72: 579-603.
6. Ukai-Tadenuma M, Kasukawa T, Ueda HR, (2008) Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks. Nat Cell Biol 10: 1154-1163.
7. Ueda HR, Hayashi S, Chen W, Sano M, Machida M, et al. (2005) System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat Genet 37: 187-192.
8. Rey G, Cesbron F, Rougemont J, Reinke H, Brunner M, et al. (2011) Genome-wide and phase-specific dna-binding rhythms of bmal1 control circadian output functions in mouse liver. PLoS Biol 9: e1000595.
9. Wuarin J, Schibler U, (1990) Expression of the liver-enriched transcriptional activator protein DBP follows a stringent circadian rhythm. Cell 63: 1257-1266.
10. Mitsui S, Yamaguchi S, Matsuo T, Ishida Y, Okamura H, (2001) Antagonistic role of E4BP4 and PAR proteins in the circadian oscillatory mechanism. Genes Dev 15: 995-1006.
11. Preitner N, Damiola F, Lopez-Molina L, Zakany J, Duboule D, et al. (2002) The orphan nuclear receptor REV-ERBα controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110: 251-260.
12. Yamazaki S, Numano R, Abe M, Hida A, Takahashi R, et al. (2000) Resetting central and peripheral circadian oscillators in transgenic rats. Science 288: 682-685.
13. Relógio A, Westermark PO, Wallach T, Schellenberg K, Kramer A, et al. (2011) Tuning the mam-malian circadian clock: robust synergy of two loops. PLoS Comput Biol 7: e1002309.
14. Atwood A, DeConde R, Wang S, Mockler T, Sabir J, et al. (2011) Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. Proc Natl Acad Sci U S A 108: 18560-18565.
15. Kornmann B, Schaad O, Bujard H, Takahashi JS, Schibler U, (2007) System-driven and oscillator-dependent circadian transcription in mice with a conditionally active liver clock. PLoS Biol 5: e34.
16. Mackey MC, Glass L, (1977) Oscillation and chaos in physiological control systems. Science 197: 287-289.
17. Scheper T, Klinkenberg D, Pennartz C, van Pelt J, (1999) A mathematical model for the intracellular circadian rhythm generator. J Neurosci 19: 40-47.
18. Smolen P, Baxter DA, Byrne JH, (2001) Modeling circadian oscillations with interlocking positive and negative feedback loops. J Neurosci 21: 6644-6656.
19. Forger DB, Peskin CS, (2003) A detailed predictive model of the mammalian circadian clock. Proc Natl Acad Sci U S A 100: 14806-14811.
20. Leloup J, Goldbeter A, (2003) Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci U S A 100: 7051-7056.
21. Liu S, Cai Y, Sothern RB, Guan Y, Chan P, (2007) Chronobiological analysis of circadian patterns in transcription of seven key clock genes in six peripheral tissues in mice. Chronobiol Int 24: 793-820.
22. Hughes ME, DiTacchio L, Hayes KR, Vollmers C, Pulivarthy S, et al. (2009) Harmonics of circadian gene transcription in mammals. PLoS Genet 5: e1000442.
23. Kosir R, Acimovic J, Golicnik M, Perse M, Majdic G, et al. (2010) Determination of reference genes for circadian studies in different tissues and mouse strains. BMC Mol Biol 11: 60.
24. Yamajuku D, Shibata Y, Kitazawa M, Katakura T, Urata H, et al. (2010) Identification of func-tional clock-controlled elements involved in differential timing of Per1 and Per2 transcription. Nucleic Acids Res 38: 7964-7973.
25. Liu AC, Tran HG, Zhang EE, Priest AA, Welsh DK, et al. (2008) Redundant function of REV-ERBα and β and non-essential role for Bmal1 cycling in transcriptional regulation of intracellular circadian rhythms. PLoS Genet 4: e1000023.
26. Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, et al. (2005) Transcriptional regulation by the numbers: Models. Curr Opin Genet Dev 15: 116-124.
27. Sharova LV, Sharov AA, Nedorezov T, Piao Y, Shaik N, et al. (2009) Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res 16: 45-58.
28. Lee C, Etchegaray JP, Cagampang FR, Loudon AS, Reppert SM, (2001) Posttranslational mechanisms regulate the mammalian circadian clock. Cell 107: 855-867.
29. Kurosawa G, Mochizuki A, Iwasa Y, (2002) Comparative study of circadian clock models, in search of processes promoting oscillation. J theor Biol 216: 193-208.
30. Legewie S, Herzel H, Westerhoff HV, Bluthgen N, (2008) Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol Syst Biol 4: 190.
31. Bernard S, Cajavec B, Pujo-Menjouet L, Mackey MC, Herzel H, (2006) Modelling transcriptional feedback loops: the role of gro/tle1 in hes1 oscillations. Philos Transact A Math Phys Eng Sci 364: 1155-1170.
32. Ueda HR, Chen W, Adachi A, Wakamatsu H, Hayashi S, et al. (2002) A transcription factor response element for gene expression during circadian night. Nature 418: 534-539.
33. Friedel CC, Doelken L, Ruzsics Z, Koszinowski UH, Zimmer R, (2009) Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res 37: e115.
34. Jacobshagen S, Kessler B, Rinehart CA, (2008) At least four distinct circadian regulatory mecha-nisms are required for all phases of rhythms in mRNA amount. J Biol Rhythms 23: 511-524.
35. Sato TK, Panda S, Miraglia LJ, Reyes TM, Rudic RD, et al. (2004) A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron 43: 527-537.
36. Honma S, Kawamoto T, Takagi Y, Fujimoto K, Sato F, et al. (2002) Dec1 and Dec2 are regulators of the mammalian molecular clock. Nature 419: 841-844.
37. Bozek K, Relogio A, Kielbasa SM, Heine M, Dame C, et al. (2009) Regulation of clock-controlled genes in mammals. PLoS One 4: e4882.
38. Ukai-Tadenuma M, Yamada RG, Xu H, Ripperger JA, Liu AC, et al. (2011) Delay in feedback repression by Cryptochrome 1 is required for circadian clock function. Cell 144: 268-281.
39. Wilkins AK, Barton PI, Tidor B, (2007) The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. PLoS Comput Biol 3: e242.
40. Vanselow K, Vanselow JT, Westermark PO, Reischl S, Maier B, et al. (2006) Differential effects of PER2 phosphorylation: molecular basis for the human familial advanced sleep phase syndrome (FASPS). Genes Dev 20: 2660-2672.
41. Etchegaray JP, Machida KK, Noton E, Constance CM, Dallmann R, et al. (2009) Casein kinase 1 delta regulates the pace of the mammalian circadian clock. Mol Cell Biol 29: 3853-3866.
42. Meng QJ, Maywood ES, Bechtold DA, Lu WQ, Li J, et al. (2010) Entrainment of disrupted circadian behavior through inhibition of casein kinase 1 (CK1) enzymes. Proc Natl Acad Sci U S A 107: 15240-15245.
43. Dibner C, Sage D, Unser M, Bauer C, d'Eysmond T, et al. (2009) Circadian gene expression is resilient to large uctuations in overall transcription rates. EMBO J 28: 123-134.
44. Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, et al. (2009) A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell 139: 199-210.
45. Ramsey KM, Marcheva B, Kohsaka A, Bass J, (2007) The clockwork of metabolism. Annu Rev Nutr 27: 219-240.
46. Ko CH, Takahashi JS, (2006) Molecular components of the mammalian circadian clock. Hum Mol Genet 15 Spec No 2: R271-R277.
47. Gallego M, Virshup DM, (2007) Post-translational modifications regulate the ticking of the circadian clock. Nat Rev Mol Cell Biol 8: 139-148.
48. Suter DM, Molina N, Gatfield D, Schneider K, Schibler U, et al. (2011) Mammalian genes are transcribed with widely different bursting kinetics. Science 332: 472-474.
49. Xu Y, Toh KL, Jones CR, Shin JY, Fu YH, et al. (2007) Modeling of a human circadian mutation yields insights into clock regulation by PER2. Cell 128: 59-70.
50. Chen R, Schirmer A, Lee Y, Lee H, Kumar V, et al. (2009) Rhythmic PER abundance defines a critical nodal point for negative feedback within the circadian clock mechanism. Mol Cell 36: 417-430.
51. Lee H, Chen R, Kim H, Etchegaray JP, Weaver DR, et al. (2011) The period of the circadian oscillator is primarily determined by the balance between casein kinase 1 and protein phosphatase 1. Proc Natl Acad Sci U S A 108: 16451-16456.
52. Gachon F, Fonjallaz P, Damiola F, Gos P, Kodama T, et al. (2004) The loss of circadian PAR bZip transcription factors results in epilepsy. Genes Dev 18: 1397-1412.
53. Vollmers C, Gill S, DiTacchio L, Pulivarthy S, Le H, et al. (2009) Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression. Proc Natl Acad Sci USA 106: 21453-21458.
54. Scheer FAJL, Wright KP, Kronauer RE, Czeisler CA, (2007) Plasticity of the intrinsic period of the human circadian timing system. PLoS One 2: e721.
55. Brown SA, Kunz D, Dumas A, Westermark PO, Vanselow K, et al. (2008) Molecular insights into human daily behavior. Proc Natl Acad Sci U S A 105: 1602-1607.
56. Aase SO, Ruoff P, (2008) Semi-algebraic optimization of temperature compensation in a general switch-type negative feedback model of circadian clocks. J Math Biol 56: 279-292.
57. Abraham U, Granada AE, Westermark PO, Heine M, Kramer A, et al. (2010) Coupling governs entrainment range of circadian clocks. Mol Syst Biol 6: 438.