Mechanism for 12 Hr Rhythm Generation by the Circadian Clock

Cell Reports

Volumn 3, Issue 4, 2013, Pages 1228-1238

  Westermark, PålO ^a   Herzel, Hanspeter ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; MICROPHTHALMIA ASSOCIATED TRANSCRIPTION FACTOR; SMAD PROTEIN; TRANSCRIPTION FACTOR CLOCK;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CIRCADIAN RHYTHM; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION; INTRON; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; OSCILLATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN MOTIF;

ANIMALS; BINDING SITES; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; GENE EXPRESSION; LIVER; MICE; NUCLEOTIDE MOTIFS; PROMOTER REGIONS, GENETIC; TIME FACTORS; TRANSCRIPTION FACTORS;

ANIMALIA;

EID: 84876958516     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2013.03.013     Document Type: Article

References (39)

1. Balsalobre A. Clock genes in mammalian peripheral tissues. Cell Tissue Res. 2002, 309:193-199.
2. Bintu L., Buchler N.E., Garcia H.G., Gerland U., Hwa T., Kondev J., Phillips R. Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev. 2005, 15:116-124.
3. Cagampang F.R.A., Sheward W.J., Harmar A.J., Piggins H.D., Coen C.W. Circadian changes in the expression of vasoactive intestinal peptide 2 receptor mRNA in the rat suprachiasmatic nuclei. Brain Res. Mol. Brain Res. 1998, 54:108-112.
4. Chechik G., Oh E., Rando O., Weissman J., Regev A., Koller D. Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nat. Biotechnol. 2008, 26:1251-1259.
5. Chen Y.G., Mantalaris A., Bourne P., Keng P., Wu J.H.D. Expression of mPer1 and mPer2, two mammalian clock genes, in murine bone marrow. Biochem. Biophys. Res. Commun. 2000, 276:724-728.
6. Cornish-Bowden A. Fundamentals of Enzyme Kinetics 2004, Portland Press, Colchester, UK. Third Edition.
7. Cretenet G., Le Clech M., Gachon F. Circadian clock-coordinated 12 Hr period rhythmic activation of the IRE1α pathway controls lipid metabolism in mouse liver. Cell Metab. 2010, 11:47-57.
8. 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.
9. Dickmeis T. Glucocorticoids and the circadian clock. J.Endocrinol. 2009, 200:3-22.
10. Durinck S., Spellman P.T., Birney E., Huber W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protoc. 2009, 4:1184-1191.
11. Eckel-Mahan K.L., Patel V.R., Mohney R.P., Vignola K.S., Baldi P., Sassone-Corsi P. Coordination of the transcriptome and metabolome by the circadian clock. Proc. Natl. Acad. Sci. USA 2012, 109:5541-5546.
12. Frith M.C., Fu Y., Yu L., Chen J.F., Hansen U., Weng Z. Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res. 2004, 32:1372-1381.
13. Gachon F., Nagoshi E., Brown S.A., Ripperger J., Schibler U. The mammalian circadian timing system: from gene expression to physiology. Chromosoma 2004, 113:103-112.
14. Hogenesch J.B., Ueda H.R. Understanding systems-level properties: timely stories from the study of clocks. Nat. Rev. Genet. 2011, 12:407-416.
15. Hughes M.E., DiTacchio L., Hayes K.R., Vollmers C., Pulivarthy S., Baggs J.E., Panda S., Hogenesch J.B. Harmonics of circadian gene transcription in mammals. PLoS Genet. 2009, 5:e1000442.
16. Hughes M.E., Hong H.-K., Chong J.L., Indacochea A.A., Lee S.S., Han M., Takahashi J.S., Hogenesch J.B. Brain-specific rescue of Clock reveals system-driven transcriptional rhythms in peripheral tissue. PLoS Genet. 2012, 8:e1002835.
17. Jaworski A., Smith C.L., Burden S.J. GA-binding protein is dispensable for neuromuscular synapse formation and synapse-specific gene expression. Mol. Cell. Biol. 2007, 27:5040-5046.
18. Keller M., Mazuch J., Abraham U., Eom G.D., Herzog E.D., Volk H.D., Kramer A., Maier B. A circadian clock in macrophages controls inflammatory immune responses. Proc. Natl. Acad. Sci. USA 2009, 106:21407-21412.
19. Kohsaka A., Laposky A.D., Ramsey K.M., Estrada C., Joshu C., Kobayashi Y., Turek F.W., Bass J. High-fat diet disrupts behavioral and molecular circadian rhythms in mice. Cell Metab. 2007, 6:414-421.
20. Liu S., Cai Y., Sothern R.B., Guan Y., Chan P. Chronobiological analysis of circadian patterns in transcription of seven key clock genes in six peripheral tissues in mice. Chronobiol. Int. 2007, 24:793-820.
21. Mitsui S., Yamaguchi S., Matsuo T., Ishida Y., Okamura H. Antagonistic role of E4BP4 and PAR proteins in the circadian oscillatory mechanism. Genes Dev. 2001, 15:995-1006.
22. Pachkov M., Erb I., Molina N., van Nimwegen E. SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res. 2007, 35(Database issue):D127-D131.
23. Panda S., Antoch M.P., Miller B.H., Su A.I., Schook A.B., Straume M., Schultz P.G., Kay S.A., Takahashi J.S., Hogenesch J.B. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 2002, 109:307-320.
24. Perilhou A., Tourrel-Cuzin C., Kharroubi I., Henique C., Fauveau V., Kitamura T., Magnan C., Postic C., Prip-Buus C., Vasseur-Cognet M. The transcription factor COUP-TFII is negatively regulated by insulin and glucose via Foxo1- and ChREBP-controlled pathways. Mol. Cell. Biol. 2008, 28:6568-6579.
25. Ramsey K.M., Yoshino J., Brace C.S., Abrassart D., Kobayashi Y., Marcheva B., Hong H.K., Chong J.L., Buhr E.D., Lee C., et al. Circadian clock feedback cycle through NAMPT-mediated NAD+ biosynthesis. Science 2009, 324:651-654.
26. Sato T.K., Yamada R.G., Ukai H., Baggs J.E., Miraglia L.J., Kobayashi T.J., Welsh D.K., Kay S.A., Ueda H.R., Hogenesch J.B. Feedback repression is required for mammalian circadian clock function. Nat. Genet. 2006, 38:312-319.
27. Shea M.A., Ackers G.K. The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J.Mol. Biol. 1985, 181:211-230.
28. Storch K.F., Lipan O., Leykin I., Viswanathan N., Davis F.C., Wong W.H., Weitz C.J. Extensive and divergent circadian gene expression in liver and heart. Nature 2002, 417:78-83.
29. Sudarsanam P., Pilpel Y., Church G.M. Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res. 2002, 12:1723-1731.
30. Suzuki H., Forrest A.R., van Nimwegen E., Daub C.O., Balwierz P.J., Irvine K.M., Lassmann T., Ravasi T., Hasegawa Y., de Hoon M.J., et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet. 2009, 41:553-562. FANTOM Consortium, Riken Omics Science CenterRiken Omics Science Center.
31. Ueda H.R., Chen W., Adachi A., Wakamatsu H., Hayashi S., Takasugi T., Nagano M., Nakahama K.-i., Suzuki Y., Sugano S., et al. A transcription factor response element for gene expression during circadian night. Nature 2002, 418:534-539.
32. Ueda H.R., Hayashi S., Chen W., Sano M., Machida M., Shigeyoshi Y., Iino M., Hashimoto S. System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat. Genet. 2005, 37:187-192.
33. Ukai-Tadenuma M., Yamada R.G., Xu H., Ripperger J.A., Liu A.C., Ueda H.R. Delay in feedback repression by cryptochrome 1 is required for circadian clock function. Cell 2011, 144:268-281.
34. Vollmers C., Gill S., DiTacchio L., Pulivarthy S.R., Le H.D., Panda S. Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression. Proc. Natl. Acad. Sci. USA 2009, 106:21453-21458.
35. Wasserman W.W., Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 2004, 5:276-287.
36. Wilcockson D., Zhang L. Circatidal clocks. Curr. Biol. 2008, 18:R753-R755.
37. Yamamoto T., Nakahata Y., Soma H., Akashi M., Mamine T., Takumi T. Transcriptional oscillation of canonical clock genes in mouse peripheral tissues. BMC Mol. Biol. 2004, 5:18.
38. Youssef J.A., Badr M.Z. Hepatocarcinogenic potential of the glucocorticoid antagonist RU486 in B6C3F1 mice: effect on apoptosis, expression of oncogenes and the tumor suppressor gene p53. Mol. Cancer 2003, 2:3.
39. Zhang E.E., Kay S.A. Clocks not winding down: unravelling circadian networks. Nat. Rev. Mol. Cell Biol. 2010, 11:764-776.