A direct repeat of E-box-like elements is required for cell-autonomous circadian rhythm of clock genes

BMC Molecular Biology

Volumn 9, Issue , 2008, Pages

  Nakahata, Yasukazu ^a   Yoshida, Mayumi ^a,b   Takano, Atsuko ^a   Soma, Haruhiko ^c   Yamamoto, Takuro ^c   Yasuda, Akio ^c   Nakatsu, Toru ^d   Takumi, Toru ^a,e  

^a OSAKA BIOSCIENCE INSTITUTE   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c SONY CORPORATION   (Japan)

^d KYOTO UNIVERSITY   (Japan)

^e KYOTO UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; DNA; TRANSCRIPTION FACTOR CLOCK; BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; NUCLEAR PROTEIN; PER2 PROTEIN, HUMAN; PROTEIN BMAL1; TRANSACTIVATOR PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CIRCADIAN RHYTHM; COMPUTER ANALYSIS; CONTROLLED STUDY; DNA STRUCTURE; E BOX ELEMENT; E BOX LIKE ELEMENT; GENE SEQUENCE; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; NONHUMAN; PROMOTER REGION; REGULATORY MECHANISM; SEQUENCE ANALYSIS; TANDEM REPEAT; ANIMAL; BIOLOGICAL MODEL; CELL STRAIN 3T3; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; MACROMOLECULE; METABOLISM; MOUSE; MUTATION; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; TRANSACTIVATION;

MAMMALIA;

ANIMALS; BASE SEQUENCE; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; CIRCADIAN RHYTHM; DNA; E-BOX ELEMENTS; HUMANS; MACROMOLECULAR SUBSTANCES; MICE; MODELS, GENETIC; MODELS, MOLECULAR; MUTATION; NIH 3T3 CELLS; NUCLEAR PROTEINS; PROMOTER REGIONS (GENETICS); REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; TRANS-ACTIVATION (GENETICS); TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

EID: 39849084068     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-9-1     Document Type: Article

References (42)

1. Schibler U Sassone-Corsi P A web of circadian pacemakers Cell 2002, 111: 919-922 10.1016/S0092-8674(02)01225-4 12507418
2. HastingsMH Reddy AB Maywood ES A clockwork web: Circadian timing in brain and periphery, in health and disease Nat Rev Neurosci 2003, 4:649-661 10.1038/nrn1177 12894240
3. 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 535906 15473909 10.1186/1471-2199-5-18
4. Schibler U The daily rhythms of genes, cells and organs. Biological clocks and circadian timing in cells EMBO Rep 2005, 6 Spec No:S9-13 1369272 15995671 10.1038/sj.embor.7400424
5. Fu L Lee CC The circadian clock: Pacemaker and tumour suppressor Nat Rev Cancer 2003, 3:350-361 10.1038/nrc1072 12724733
6. Bell-Pedersen D Cassone VM Earnest DJ Golden SS Hardin PE Thomas TL Zoran MJ Circadian rhythms from multiple oscillators: Lessons from diverse organisms Nat Rev Genet 2005, 6:544-556 10.1038/nrg1633 15951747
7. Ko CH Takahashi JS Molecular components of the mammalian circadian clock Hum Mol Genet 2006, 15 Spec No 2:R271-7 10.1093/hmg/ddl207 16987893
8. Wijnen H Young MW Interplay of circadian clocks and metabolic rhythms Annu Rev Genet 2006, 40:409-448 10.1146/annurev.genet.40.110405.090603 17094740
9. Ueda HR 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 10.1038/ng1504 15665827
10. Gekakis N Staknis D Nguyen HB Davis FC Wilsbacher LD King DP Takahashi JS Weitz CJ Role of the CLOCK protein in the mammalian circadian mechanism Science 1998, 280:1564-1569 10.1126/science.280.5369.1564 9616112
11. Kume K Zylka MJ Sriram S Shearman LP Weaver DR Jin X Maywood ES Hastings MH Reppert SM mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop Cell 1999, 98:193-205 10.1016/ S0092-8674(00)81014-4 10428031
12. Hida A Koike N Hirose M Hattori M Sakaki Y Tei H The human and mouse Period1 genes: Five well-conserved E-boxes additively contribute to the enhancement of mPer1 transcription Genomics 2000, 65:224-233 10.1006/ geno.2000.6166 10857746
13. Jin X Shearman LP Weaver DR Zylka MJ de Vries GJ Reppert SM A molecular mechanism regulating rhythmic output from the suprachiasmatic circadian clock Cell 1999, 96:57-68 10.1016/S0092-8674(00)80959-9 9989497
14. Ripperger JA Shearman LP Reppert SM Schibler U CLOCK, an essential pacemaker component, controls expression of the circadian transcription factor DBP Genes Dev 2000, 14:679-689 316463 10733528
15. Etchegaray JP Lee C Wade PA Reppert SM Rhythmic histone acetylation underlies transcription in the mammalian circadian clock Nature 2003, 421:177-182 10.1038/nature01314 12483227
16. Triqueneaux G Thenot S Kakizawa T Antoch MP Safi R Takahashi JS Delaunay F Laudet V The orphan receptor Rev-erbalpha gene is a target of the circadian clock pacemaker J Mol Endocrinol 2004, 33:585-608 10.1677/ jme.1.01554 15591021
17. Ripperger JA Schibler U Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions Nat Genet 2006, 38:369-374 10.1038/ng1738 16474407
18. Preitner N Damiola F Lopez-Molina L Zakany J Duboule D Albrecht U Schibler U The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator Cell 2002, 110:251-260 10.1016/S0092-8674(02)00825-5 12150932
19. 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 10.1016/j.neuron.2004.07.018 15312651
20. Nakajima Y Ikeda M Kimura T Honma S Ohmiya Y Honma K Bidirectional role of orphan nuclear receptor RORalpha in clock gene transcriptions demonstrated by a novel reporter assay system FEBS Lett 2004, 565:122-126 10.1016/j.febslet.2004.03.083 15135064
21. Akashi M Takumi T The orphan nuclear receptor RORalpha regulates circadian transcription of the mammalian core-clock Bmal1 Nat Struct Mol Biol 2005, 12:441-448 10.1038/nsmb925 15821743
22. Albrecht U Sun ZS Eichele G Lee CC A differential response of two putative mammalian circadian regulators, mper1 and mper2, to light Cell 1997, 91:1055-1064 10.1016/S0092-8674(00)80495-X 9428527
23. Takumi T Matsubara C Shigeyoshi Y Taguchi K Yagita K Maebayashi Y Sakakida Y Okumura K Takashima N Okamura H A new mammalian period gene predominantly expressed in the suprachiasmatic nucleus Genes Cells 1998, 3:167-176 10.1046/j.1365-2443.1998.00178.x 9619629
24. Zheng B Larkin DW Albrecht U Sun ZS Sage M Eichele G Lee CC Bradley A The mPer2 gene encodes a functional component of the mammalian circadian clock Nature 1999, 400:169-173 10.1038/22659 10408444
25. Nakahata Y Akashi M Trcka D Yasuda A Takumi T The in vitro real-time oscillation monitoring system identifies potential entrainment factors for circadian clocks BMC Mol Biol 2006, 7:5 1386696 16483373 10.1186/ 1471-2199-7-5
26. Akashi M Ichise T Mamine T Takumi T Molecular mechanism of cell-autonomous circadian gene expression of Period2, a crucial regulator of the mammalian circadian clock Mol Biol Cell 2006, 17:555-565 1356568 16280364 10.1091/mbc.E05-05-0396
27. Yoo SH Ko CH Lowrey PL Buhr ED Song EJ Chang S Yoo OJ Yamazaki S Lee C Takahashi JS A noncanonical E-box enhancer drives mouse Period2 circadian oscillations in vivo Proc Natl Acad Sci U S A 2005, 102:2608-2613 548324 15699353 10.1073/pnas.0409763102
28. 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 10.1016/ S0092-8674(02)00722-5 12015981
29. 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 10.1038/nature744 11967526
30. Ueda HR Chen W Adachi A Wakamatsu H Hayashi S Takasugi T Nagano M Nakahama K Suzuki Y Sugano S Iino M Shigeyoshi Y Hashimoto S A transcription factor response element for gene expression during circadian night Nature 2002, 418:534-539 10.1038/nature00906 12152080
31. Coulson JM Fiskerstrand CE Woll PJ Quinn JP E-box motifs within the human vasopressin gene promoter contribute to a major enhancer in small-cell lung cancer Biochem J 1999, 344 Pt 3:961-970 1220722 10585887 10.1042/0264-6021:3440961
32. Kimura H Weisz A Ogura T Hitomi Y Kurashima Y Hashimoto K D'Acquisto F Makuuchi M Esumi H Identification of hypoxia-inducible factor 1 ancillary sequence and its function in vascular endothelial growth factor gene induction by hypoxia and nitric oxide J Biol Chem 2001, 276:2292-2298 11056166
33. McDonald MJ Rosbash M Emery P Wild-type circadian rhythmicity is dependent on closely spaced E boxes in the Drosophila timeless promoter Mol Cell Biol 2001, 21:1207-1217 99574 11158307 10.1128/ MCB.21.4.1207-1217.2001
34. Nair SK Burley SK X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors Cell 2003, 112:193-205 10.1016/S0092-8674(02)01284-9 12553908
35. Hogenesch JB Gu YZ Jain S Bradfield CA The basic-helix-loop-helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors Proc Natl Acad Sci U S A 1998, 95:5474-5479 20401 9576906 10.1073/pnas.95.10.5474
36. Ohno T Onishi Y Ishida N A novel E4BP4 element drives circadian expression of mPeriod2 Nucleic Acids Res 2007, 35:648-655 1802629 17182630 10.1093/nar/gkl868
37. Lee C Etchegaray JP Cagampang FR Loudon AS Reppert SM Posttranslational mechanisms regulate the mammalian circadian clock Cell 2001, 107:855-867 10.1016/S0092-8674(01)00610-9 11779462
38. Munoz E Brewer M Baler R Circadian Transcription. Thinking outside the E-Box J Biol Chem 2002, 277:36009-36017 10.1074/jbc.M203909200 12130638
39. Tamaru T Isojima Y van der Horst GT Takei K Nagai K Takamatsu K Nucleocytoplasmic shuttling and phosphorylation of BMAL1 are regulated by circadian clock in cultured fibroblasts Genes Cells 2003, 8:973-983 10.1046/j.1365-2443.2003.00686.x 14750952
40. Kuribara R Kinoshita T Miyajima A Shinjyo T Yoshihara T Inukai T Ozawa K Look AT Inaba T Two distinct interleukin-3-mediated signal pathways, Ras-NFIL3 (E4BP4) and Bcl-xL, regulate the survival of murine pro-B lymphocytes Mol Cell Biol 1999, 19:2754-2762 84068 10082541
41. VGB2 http://pipeline.lbl.gov/cgi-bin/gateway2
42. EMBOSS http://bioweb.pasteur.fr/docs/EMBOSS/fuzznuc.html