System-level identification of transcriptional circuits underlying mammalian circadian clocks

Nature Genetics

Volumn 37, Issue 2, 2005, Pages 187-192

  Ueda, Hiroki R ^a,b,c   Hayashi, Satoko ^a   Chen, Wenbin ^a   Sano, Motoaki ^d   Machida, Masayuki ^d   Shigeyoshi, Yasufumi ^e   Iino, Masamitsu ^c   Hashimoto, Seiichi ^a  

^a ASTELLAS PHARMA INC   (Japan)

^b RIKEN Center for Biosystems Dynamics Research   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^e KINKI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS RECEPTOR; HELIX LOOP HELIX PROTEIN; HORMONE RECEPTOR; PROTEIN REVERBA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR DBP; UNCLASSIFIED DRUG; DBP PROTEIN, RAT; DNA BINDING PROTEIN; G BOX BINDING FACTOR; TRANSACTIVATOR PROTEIN;

ANIMAL CELL; ARTICLE; CIRCADIAN RHYTHM; CONTROLLED STUDY; E BOX ELEMENT; GENE ACTIVATION; GENE CONTROL; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; IN VITRO STUDY; MAMMAL; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RAT; REGULATORY MECHANISM; REPRESSOR GENE; TRANSCRIPTION REGULATION; ANIMAL; BIOLOGY; CELL CULTURE; GENE EXPRESSION REGULATION; GENETICS; PROTO ONCOGENE; REGULATOR GENE;

ANIMALIA; MAMMALIA;

ANIMALS; CELLS, CULTURED; CIRCADIAN RHYTHM; COMPUTATIONAL BIOLOGY; DNA-BINDING PROTEINS; G-BOX BINDING FACTORS; GENE EXPRESSION REGULATION; GENES, ERBA; GENES, REGULATOR; GENES, REV; RATS; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 13944254430     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1504     Document Type: Article

References (30)

1. Gekakis, N. et al. Role of the CLOCK protein in the mammalian circadian mechanism. Science 280, 1564-1569 (1998).
2. Kume, K. et al. mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell 98, 193-205 (1999).
3. Shearman, L.P. et al. Interacting molecular loops in the mammalian circadian clock. Science 288, 1013-1019 (2000).
4. Preitner, N. et al. The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110, 251-260 (2002).
5. Sato, T.K. et al. A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron 43, 527-537 (2004).
6. Kitano, H. Systems biology: a brief overview. Science 295, 1662-1664 (2002).
7. Falvey, E., Marcacci, L. & Schibler, U. DNA-binding specificity of PAR and C/EBP leucine zipper proteins: a single amino acid substitution in the C/EBP DNA-binding domain confers PAR-like specificity to C/EBP. Biol. Chem. 377, 797-809 (1996).
8. Harding, H.P. & Lazar, M.A. The orphan receptor Rev-ErbA alpha activates transcription via a novel response element. Mol. Cell. Biol. 13, 3113-3121 (1993).
9. Panda, S., Hogenesch, J.B. & Kay, S.A. Circadian rhythms from flies to human. Nature 417, 329-335 (2002).
10. Reppert, S.M. & Weaver, D.R. Coordination of circadian timing in mammals. Nature 418, 935-941 (2002).
11. King, D.P. et al. Positional cloning of the mouse circadian clock gene. Cell 89, 641-653 (1997).
12. Bunger, M.K. et al. Mop3 is an essential component of the master circadian pacemaker in mammals. Cell 103, 1009-1017 (2000).
13. Bae, K. et al. Differential functions of mPer1, mPer2, and mPer3 in the SCN circadian clock. Neuron 30, 525-536 (2001).
14. Zheng, B. et al. Nonredundant roles of the mPer1 and mPer2 genes in the mammalian circadian clock. Cell 105, 683-694 (2001).
15. van der Horst, G.T. et al. Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms. Nature 398, 627-630 (1999).
16. Lowrey, P.L. et al. Positional syntenic cloning and functional characterization of the mammalian circadian mutation tau. Science 288, 483-492 (2000).
17. Mitsui, S., Yamaguchi, S., Matsuo, T., Ishida, Y. & Okamura, H. Antagonistic role of E4BP4 and PAR proteins in the circadian oscillatory mechanism. Genes Dev. 15, 995-1006 (2001).
18. Wuarin, J. & Schibler, U. Expression of the liver-enriched transcriptional activator protein DBP follows a stringent circadian rhythm. Cell 63, 1257-1266 (1990).
19. Honma, S. et al. Dec1 and Dec2 are regulators of the mammalian molecular clock. Nature 419, 841-844 (2002).
20. Zylka, M.J., Shearman, L.P., Weaver, D.R. & Reppert, S.M. Three period homologs in mammals: differential light responses in the suprachiasmatic circadian clock and oscillating transcripts outside of brain. Neuron 20, 1103-1110 (1998).
21. Reick, M., Garcia, J.A., Dudley, C. & McKnight, S.L. NPAS2: an analog of clock operative in the mammalian forebrain. Science 293, 506-509 (2001).
22. Ueda, H.R. et al. A transcription factor response element for gene expression during circadian night. Nature 418, 534-539 (2002).
23. Honma, S. et al. Circadian oscillation of BMAL1, a partner of a mammalian clock gene Clock, in rat suprachiasmatic nucleus. Biochem. Biophys. Res. Commun. 250, 83-87 (1998).
24. Lee, C., Etchegaray, J.P., Cagampang, F.R., Loudon, A.S. & Reppert, S.M. Posttranslational mechanisms regulate the mammalian circadian clock. Cell 107, 855-867 (2001).
25. Tei, H. et al. Circadian oscillation of a mammalian homologue of the Drosophila period gene. Nature 389, 512-516 (1997).
26. Shearman, L.P., Zylka, M.J., Weaver, D.R., Kolakowski, L.F. Jr. & Reppert, S.M. Two period homologs: circadian expression and photic regulation in the suprachiasmatic nuclei. Neuron 19, 1261-1269 (1997).
27. Panda, S. et al. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109, 307-320 (2002).
28. Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824-827 (2002).
29. Albert, R., Jeong, H. & Barabasi, A.L. Error and attack tolerance of complex networks. Nature 406, 378-382 (2000).
30. Jeong, H., Mason, S.P., Barabasi, A.L. & Oltvai, Z.N. Lethality and centrality in protein networks. Nature 411, 41-42 (2001).