Identification of functional clock-controlled elements involved in differential timing of Per1 and Per2 transcription

Nucleic Acids Research

Volumn 38, Issue 22, 2010, Pages 7964-7973

  Yamajuku, Daisuke ^a   Shibata, Yasutaka ^a   Kitazawa, Masashi ^a   Katakura, Toshie ^a   Urata, Hiromi ^a   Kojima, Tomoko ^a   Nakata, Osamu ^a   Hashimoto, Seiichi ^a  

^a ASTELLAS PHARMA INC   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; MESSENGER RNA; PER1 PROTEIN; PER2 PROTEIN; PER3 PROTEIN; PROTEIN BMAL1; TRANSCRIPTION FACTOR CLOCK; UNCLASSIFIED DRUG;

AMPLITUDE MODULATION; ANIMAL TISSUE; ARTICLE; BIOASSAY; BIOLUMINESCENCE; CIRCADIAN RHYTHM; CONTROLLED STUDY; E BOX ELEMENT; FUNCTIONAL MORPHOLOGY; GENE ACTIVATION; GENE DOSAGE; GENE EXPRESSION REGULATION; GENETIC CONSERVATION; GENETIC TRANSFECTION; IN VITRO STUDY; MOLECULAR CLOCK; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

ANIMALS; BASE SEQUENCE; CELL LINE; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; CONSERVED SEQUENCE; E-BOX ELEMENTS; HUMANS; MICE; MOLECULAR SEQUENCE DATA; PERIOD CIRCADIAN PROTEINS; PROMOTER REGIONS, GENETIC; RNA, MESSENGER; SEQUENCE ALIGNMENT; TRANSCRIPTION, GENETIC;

EID: 78650482162     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq678     Document Type: Article

References (40)

1. Reppert, S.M. and Weaver, D.R. (2002) Coordination of circadian timing in mammals. Nature, 418, 935-941.
2. Balsalobre, A., Marcacci, L. and Schibler, U. (2000) Multiple signaling pathways elicit circadian gene expression in cultured Rat-1 fibroblasts. Curr. Biol., 10, 1291-1294.
3. 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.
4. 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.
5. Brown, S.A., Fleury-Olela, F., Nagoshi, E., Hauser, C., Juge, C., Meier, C.A., Chicheportiche, R., Dayer, J.M., Albrecht, U. and Schibler, U. (2005) The period length of fibroblast circadian gene expression varies widely among human individuals. PLoS Biol., 3, e338.
6. 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. and Hogenesch, J.B. (2006) Feedback repression is required for mammalian circadian clock function. Nat. Genet., 38, 312-319.
7. King, D.P., Zhao, Y., Sangoram, A.M., Wilsbacher, L.D., Tanaka, M., Antoch, M.P., Steeves, T.D., Vitaterna, M.H., Kornhauser, J.M., Lowrey, P.L. et al. (1997) Positional cloning of the mouse circadian clock gene. Cell, 89, 641-653.
8. Gekakis, N., Staknis, D., Nguyen, H.B., Davis, F.C., Wilsbacher, L.D., King, D.P., Takahashi, J.S. and Weitz, C.J. (1998) Role of the CLOCK protein in the mammalian circadian mechanism. Science, 280, 1564-1569.
9. Kume, K., Zylka, M.J., Sriram, S., Shearman, L.P., Weaver, D.R., Jin, X., Maywood, E.S., Hastings, M.H. and Reppert, S.M. (1999) mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell, 98, 193-205.
10. Bunger, M.K., Wilsbacher, L.D., Moran, S.M., Clendenin, C., Radcliffe, L.A., Hogenesch, J.B., Simon, M.C., Takahashi, J.S. and Bradfield, C.A. (2000) Mop3 is an essential component of the master circadian pacemaker in mammals. Cell, 103, 1009-1017.
11. Zheng, B., Albrecht, U., Kaasik, K., Sage, M., Lu, W., Vaishnav, S., Li, Q., Sun, Z.S., Eichele, G., Bradley, A. et al. (2001) Nonredundant roles of the mPer1 and mPer2 genes in the mammalian circadian clock. Cell, 105, 683-694. (Pubitemid 32524120)
12. Lee, C., Etchegaray, J.P., Cagampang, F.R., Loudon, A.S. and Reppert, S.M. (2001) Posttranslational mechanisms regulate the mammalian circadian clock. Cell, 107, 855-867. (Pubitemid 34084977)
13. Okamura, H., Miyake, S., Sumi, Y., Yamaguchi, S., Yasui, A., Muijtjens, M., Hoeijmakers, J.H. and Van der Horst, G.T. (1999) Photic induction of mPer1 and mPer2 in cry-deficient mice lacking a biological clock. Science, 286, 2531-2534.
14. Shearman, L.P., Sriram, S., Weaver, D.R., Maywood, E.S., Chaves, I., Zheng, B., Kume, K., Lee, C.C., Van der Horst, G.T., Hastings, M.H. et al. (2000) Interacting molecular loops in the mammalian circadian clock. Science, 288, 1013-1019.
15. Preitner, N., Damiola, F., Lopez-Molina, L., Zakany, J., Duboule, D., Albrecht, U. and Schibler, U. (2002) The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell, 110, 251-260. (Pubitemid 34876552)
16. Sato, T.K., Panda, S., Miraglia, L.J., Reyes, T.M., Rudic, R.D., McNamara, P., Naik, K.A., FitzGerald, G.A., Kay, S.A. and Hogenesch, J.B. (2004) A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron, 43, 527-537.
17. Triqueneaux, G., Thenot, S., Kakizawa, T., Antoch, M.P., Safi, R., Takahashi, J.S., Delaunay, F. and Laudet, V. (2004) The orphan receptor Rev-erbalpha gene is a target of the circadian clock pacemaker. J. Mol. Endocrinol., 33, 585-608.
18. Akashi, M. and Takumi, T. (2005) The orphan nuclear receptor RORalpha regulates circadian transcription of the mammalian core-clock Bmal1. Nat. Struct. Mol. Biol., 12, 441-448.
19. Ueda, H.R., Chen, W., Adachi, A., Wakamatsu, H., Hayashi, S., Takasugi, T., Nagano, M., Nakahama, K., Suzuki, Y., Sugano, S. et al. (2002) A transcription factor response element for gene expression during circadian night. Nature, 418, 534-539.
20. Mitsui, S., Yamaguchi, S., Matsuo, T., Ishida, Y. and Okamura, H. (2001) Antagonistic role of E4BP4 and PAR proteins in the circadian oscillatory mechanism. Genes. Dev., 15, 995-1006.
21. 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.
22. Ukai-Tadenuma, M., Kasukawa, T. and Ueda, H.R. (2008) Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks. Nat. Cell Biol., 10, 1154-1163.
23. Akashi, M., Ichise, T., Mamine, T. and Takumi, T. (2006) Molecular mechanism of cell-autonomous circadian gene expression of Period2, a crucial regulator of the mammalian circadian clock. Mol. Biol. Cell, 17, 555-565.
24. Yoo, S.H., Ko, C.H., Lowrey, P.L., Buhr, E.D., Song, E.J., Chang, S., Yoo, O.J., Yamazaki, S., Lee, C. and Takahashi, J.S. (2005) A noncanonical E-box enhancer drives mouse Period2 circadian oscillations in vivo. Proc. Natl Acad. Sci. USA, 102, 2608-2613.
25. Ohno, T., Onishi, Y. and Ishida, N. (2007) A novel E4BP4 element drives circadian expression of mPeriod2. Nucleic Acids Res., 35, 648-655.
26. Hida, A., Koike, N., Hirose, M., Hattori, M., Sakaki, Y. and Tei, H. (2000) The human and mouse Period1 genes: five well-conserved E-boxes additively contribute to the enhancement of mPer1 transcription. Genomics, 65, 224-233.
27. Yamaguchi, S., Mitsui, S., Yan, L., Yagita, K., Miyake, S. and Okamura, H. (2000) Role of DBP in the circadian oscillatory mechanism. Mol. Cell. Biol., 20, 4773-4781.
28. Yamazaki, S., Straume, M., Tei, H., Sakaki, Y., Menaker, M. and Block, G.D. (2002) Effects of aging on central and peripheral mammalian clocks. Proc. Natl Acad. Sci. USA, 99, 10801-10806.
29. Abe, M., Herzog, E.D., Yamazaki, S., Straume, M., Tei, H., Sakaki, Y., Menaker, M. and Block, G.D. (2002) Circadian rhythms in isolated brain regions. J. Neurosci., 22, 350-356.
30. Yoo, S.H., Yamazaki, S., Lowrey, P.L., Shimomura, K., Ko, C.H., Buhr, E.D., Siepka, S.M., Hong, H.K., Oh, W.J., Yoo, O.J. et al. (2004) PERIOD2::LUCIFERASE real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues. Proc. Natl Acad. Sci. USA, 101, 5339-5346.
31. Kawaguchi, S., Shinozaki, A., Obinata, M., Saigo, K., Sakaki, Y. and Tei, H. (2007) Establishment of cell lines derived from the rat suprachiasmatic nucleus. Biochem. Biophys. Res. Commun., 355, 555-561.
32. Honma, S., Kawamoto, T., Takagi, Y., Fujimoto, K., Sato, F., Noshiro, M., Kato, Y. and Honma, K. (2002) Dec1 and Dec2 are regulators of the mammalian molecular clock. Nature, 419, 841-844.
33. Ueda, H.R., Chen, W., Minami, Y., Honma, S., Honma, K., Iino, M. and Hashimoto, S. (2004) Molecular-timetable methods for detection of body time and rhythm disorders from single-time-point genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 101, 11227-11232.
34. Yamazaki, S., Numano, R., Abe, M., Hida, A., Takahashi, R., Ueda, M., Block, G.D., Sakaki, Y., Menaker, M. and Tei, H. (2000) Resetting central and peripheral circadian oscillators in transgenic rats. Science, 288, 682-685.
35. He, P.J., Hirata, M., Yamauchi, N., Hashimoto, S. and Hattori, M.A. (2007) The disruption of circadian clockwork in differentiating cells from rat reproductive tissues as identified by in vitro real-time monitoring system. J. Endocrinol., 193, 413-420.
36. Yoshida, K., He, P.J., Yamauchi, N., Hashimoto, S. and Hattori, M.A. (2010) Up-regulation of circadian clock gene Period 2 in the prostate mesenchymal cells during flutamide-induced apoptosis. Mol. Cell. Biochem., 335, 37-45.
37. Nakashima, A., Kawamoto, T., Honda, K.K., Ueshima, T., Noshiro, M., Iwata, T., Fujimoto, K., Kubo, H., Honma, S., Yorioka, N. et al. (2008) DEC1 modulates the circadian phase of clock gene expression. Mol. Cell. Biol., 28, 4080-4092.
38. Leclerc, G.M. and Boockfor, F.R. (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.
39. Nakahata, Y., Yoshida, M., Takano, A., Soma, H., Yamamoto, T., Yasuda, A., Nakatsu, T. and Takumi, T. (2008) A direct repeat of E-box-like elements is required for cell-autonomous circadian rhythm of clock genes. BMC Mol. Biol., 9, 1.
40. Kumaki, Y., Ukai-Tadenuma, M., Uno, K.D., Nishio, J., Masumoto, K.H., Nagano, M., Komori, T., Shigeyoshi, Y., Hogenesch, J.B. and Ueda, H.R. (2008) Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock. Proc. Natl Acad. Sci. USA, 105, 14946-14951.