Detection of a circadian enhancer in the mDbp promoter using prokaryotic transposon vector-based strategy

Nucleic Acids Research

Volumn 36, Issue 4, 2008, Pages

  Kiyohara, Yota B ^a,b   Nishii, Keigo ^b   Ukai Tadenuma, Maki ^c   Ueda, Hiroki R ^c   Uchiyama, Yasuo ^a   Yagita, Kazuhiro ^a,b  

^a OSAKA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^b NAGOYA UNIVERSITY   (Japan)

^c RIKEN Center for Biosystems Dynamics Research   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PHTHALIC ACID DIBUTYL ESTER; TRANSCRIPTION FACTOR CLOCK; BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; DBP PROTEIN, MOUSE; DNA BINDING PROTEIN; LUCIFERASE; PROTEIN BMAL1; TRANSACTIVATOR PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CIRCADIAN RHYTHM; DNA FLANKING REGION; E BOX ELEMENT; ENHANCER REGION; EXPRESSION VECTOR; GENE EXPRESSION REGULATION; GENE SEQUENCE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROKARYOTIC CELL; PROMOTER REGION; PROTEIN STRUCTURE; TRANSPOSON; ANIMAL; CELL CULTURE; CELL STRAIN 3T3; GENE VECTOR; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RAT; REPORTER GENE; TRANSACTIVATION;

MAMMALIA; PROKARYOTA; RATTUS;

ANIMALS; BASE SEQUENCE; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; CELLS, CULTURED; CIRCADIAN RHYTHM; DNA TRANSPOSABLE ELEMENTS; DNA-BINDING PROTEINS; E-BOX ELEMENTS; GENE EXPRESSION REGULATION; GENES, REPORTER; GENETIC VECTORS; LUCIFERASES; MICE; MOLECULAR SEQUENCE DATA; NIH 3T3 CELLS; PROMOTER REGIONS (GENETICS); RATS; TRANS-ACTIVATION (GENETICS); TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

EID: 40249093080     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn018     Document Type: Article

References (27)

1. Lowrey,P.L. and Takahashi,J.S. (2004) Mammalian circadian biology: elucidating genome-wide levels of temporal organization. Annu. Rev. Gemonics Hum. Genet., 5, 407-441.
2. Reppert,S.M. and Weaver,D.R. (2002) Coordination of circadian timing in mammals. Nature, 418, 935-941.
3. Gachon,F., Nagoshi,E., Brown,S.A., Ripperger,J. and Schibler,U. (2004) The mammalian circadian timing system: From gene expression to physiology. Chromosoma, 113, 103-112.
4. Yamazaki,S., Numano,R., Abe,M., Hida,A., Takahashi,R., Ueda,M., Block,G.D., Sakaki,Y., Menaker,M. et al. (2000) Resetting central and peripheral circadian oscillators in transgenic rats. Science, 298, 682-685
5. Balsalobre,A., Damiola,F. and Schibler,U. (1998) A serum shock induces circadian gene expression in mammlian tissue culture cells. Cell, 93, 929-937.
6. Yagita,K., Tamanini,F., van der Horst,G. and Okamura,H. (2001) Molecular mechanisms of the biological clock in cultured fibroblasts. Science 292, 278-281.
7. Nagoshi,E., Saini,C., Bauer,C., Laroche,T., Naef,F. and Schibler,U. (2004) Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells. Cell, 119, 693-705.
8. Welsh,D.K., Yoo,S.-H., Liu,A.C., Takahashi,J.S. and Kay,S.A. (2004) Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression. Curr. Biol., 14, 2289-2295.
9. Young,M.W. and Kay,S.A. (2001) Time zones: A comparative genetics of circadian clocks. Nat. Rev. Genet., 2, 702-715.
10. Panda,S., Antoch,M., Miller,B., Su,A., Schook,A., Straume,M., Schultz,P., Kay,S., Takahashi,J. et al. (2002) Coordinated transcription of key pathways in the mouse by the circadian clock. Cell, 109, 307-320.
11. Storch,K.-F., Lipan,O., Leykin,I., Viswanathan,N., Davis,F.C., Wong,W.H. and Weitz,C.J. (2002) Extensive and divergent circadian gene expression in liver and heart. Nature, 417, 78-83.
12. Ueda,H., Chen,W., Adachi,A., Wakamatsu,H., Hayashi,S., Takasugi,T., Nagano,M., Nakahama,K., Suzuki,Y. et al. (2002) A transcription factor response element for gene,expression during circadian night. Nature, 418, 534-539.
13. Reddy,A.B., Wong,G.K.Y., O'Neill,J., Maywood,E.S. and Hastings,M.H. (2005) Circadian clocks: Neural and peripheral pacemakers that impact upon the cell division cycle. Mutat. Res., 574, 76-91.
14. Ripperger,J.A., Shearman,L.P., Reppert,S.M. and Schibler,U. (2000) CLOCK, an essential pacemaker component, controls expression of the circadian transcription factor DBP. Genes Develop., 14, 679-689.
15. Yamaguchi,S., Mitsui,S., Yan,L., Yagita,K., Miyake,S. and by Okamura,H. (2000) Role of DBP in the circadian oscillatory mechanism. Mol. Cell. Biol., 20, 4773-4781.
16. Ripperger,J. and Schibler,U. (2006) Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat. Genet., 38, 369-374.
17. Steiniger-White,M., Rayment,I. and Renznikoff,W.S. (2004) Structure/ function insights into Tn5 transposition. Curr. Opin. Struct. Biol. 14, 50-57.
18. Golden,S.S., Ishiura,M., Johnson,C.H. and Kondo,T. (1997) Cyanobacterial circadian rhythms. Annu. Rev. Plant Physiol. Plant Mol. Biol., 48, 327-354.
19. Schreiber,E., Matthias,P., Mueller,M. and Schaffner,W. (1989) Rapid detection of octamer binding proteins with "mini-extracts", prepared from a small number of cells. Nucleic Acids Res., 17, 6419.
20. Yamashita,M., Ukai-Tadenuma,M., Kimura,M., Omori,M., Inami,M., Taniguchi,M. and Nakayama,T. (2002) Identification of a conserved GATA3 reponse element upstream proximal from the interleukin-13 gene locus. J. Biol. Chem., 277, 42399-42408.
21. Matsumoto,A., Ukai-Tadenuma,M., Yamada,R.G., Houl,J., Uno,K., Kasukawa,T., Dauwalder,B., Itoh,T., Takahashi,K. et al. (2007) A functional genomics strategy reveals clockwork orange as a transcriptional regulator in the Drosophila circadian clock. Genes. Dev., 21, 1687-1700.
22. Lopez-Molina,L., Conquet,F., Dubois-Dauphin,M. and Schibler,U. (1997) The DBP gene is expressed according to a circadian rhythm in the suprachiasmatic nucleus and influences circadian behavior. EMBO J. 16, 6762-6771.
23. Yamaguchi,S., Mitsui,S., Miyake,S., Yan,L., Onishi,H., Yagita,K., Suzuki,M., Shibata,S., Kobayashi,M. et al. (2000) The 5′ upstream region of mPer1 gene contains two promoters and is responsible for circadian oscillation. Curr. Biol., 10, 873-876.
24. Preitner,N., Damiola,F., Lopes-Molina,L., Zakany,J., Duboule,D., Albrecht,U. and Schibler,U. (2002) The orphan nuclear receptor REV-ERB alpha controles circadian transcription within the positive limb of the mammalian circadian oscillator. Cell, 110, 251-260.
25. Yoo,S., Ko,C., Lowrey,P., Buhr,E., Song,E., Chang,S., Yoo,O., Yamazaki,S., Lee,C. et al. (2005) A noncanonical E-box enhancer drives mouse Period2 circadian oscillations in vivo. Proc. Natl Acad. Sci. USA, 102, 2608-2613.
26. Ueda,H.R., Hayashi,S., Chen,W., Sano,M., Machida,M., Shigeyoshi,Y., Iino,M. and Hashimoto,S. (2005) System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat. Genet., 37, 187-192.
27. Leclerc,G. and Boockfor,F. (2005) Pulses of prolactin promoter activity depend on a noncanonical E-box that can bind the circadian proteins CLOCK and BMAL1. Endocrinology, 146, 2782-2790.