Punctual transcriptional regulation by the rice circadian clock under fluctuating field conditions

Plant Cell

Volumn 27, Issue 3, 2015, Pages 633-648

  Matsuzaki, Jun ^a   Kawahar, Yoshihiro ^a   Izawa, Takeshi ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ORYZA SATIVA;

BAYES THEOREM; BIOLOGICAL MODEL; CIRCADIAN RHYTHM; ENVIRONMENT; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; LIGHT; MUTATION; ORYZA; PHYSIOLOGY; PLANT GENE; RADIATION RESPONSE; TEMPERATURE; TIME FACTOR;

BAYES THEOREM; CIRCADIAN CLOCKS; ENVIRONMENT; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; LIGHT; MODELS, BIOLOGICAL; MUTATION; ORYZA; TEMPERATURE; TIME FACTORS; TRANSCRIPTION, GENETIC;

EID: 84927771923     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.114.135582     Document Type: Article

References (45)

1. Alabadí, D., Yanovsky, M.J., Más, P., Harmer, S.L., and Kay, S.A. (2002). Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis. Curr. Biol. 12: 757-761.
2. Baggs, J.E., Price, T.S., DiTacchio, L., Panda, S., Fitzgerald, G.A., and Hogenesch, J.B. (2009). Network features of the mammalian circadian clock. PLoS Biol. 7: e52.
3. Batschelet, E. (1965). Statistical Methods for the Analysis of Problems in Animal Orientation and Certain Biological Rhythms. (Washington, DC: American Institute of Biological Sciences).
4. Covington, M.F., Panda, S., Liu, X.L., Strayer, C.A., Wagner, D.R., and Kay, S.A. (2001). ELF3 modulates resetting of the circadian clock in Arabidopsis. Plant Cell 13: 1305-1315.
5. Dodd, A.N., Salathia, N., Hall, A., Kévei, E., Tóth, R., Nagy, F., Hibberd, J.M., Millar, A.J., and Webb, A.A.R. (2005). Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309: 630-633.
6. Franklin, K.A., Toledo-Ortiz, G., Pyott, D.E., and Halliday, K.J. (2014). Interaction of light and temperature signalling. J. Exp. Bot. 65: 2859-2871.
7. Geier, F., Becker-Weimann, S., Kramer, A., and Herzel, H. (2005). Entrainment in a model of the mammalian circadian oscillator. J. Biol. Rhythms 20: 83-93.
8. Hicks, K.A., Millar, A.J., Carré, I.A., Somers, D.E., Straume, M., Meeks-Wagner, D.R., and Kay, S.A. (1996). Conditional circadian dysfunction of the Arabidopsis early-flowering 3 mutant. Science 274: 790-792.
9. Itoh, H., and Izawa, T. (2013). The coincidence of critical day length recognition for florigen gene expression and floral transition under long-day conditions in rice. Mol. Plant 6: 635-649.
10. Itoh, H., Nonoue, Y., Yano, M., and Izawa, T. (2010). A pair of floral regulators sets critical day length for Hd3a florigen expression in rice. Nat. Genet. 42: 635-638.
11. Izawa, T. (2012). Physiological significance of the plant circadian clock in natural field conditions. Plant Cell Environ. 35: 1729-1741.
12. Izawa, T., Mihara, M., Suzuki, Y., Gupta, M., Itoh, H., Nagano, A.J., Motoyama, R., Sawada, Y., Yano, M., Hirai, M.Y., Makino, A., and Nagamura, Y. (2011). Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field. Plant Cell 23: 1741-1755.
13. Kasukawa, T., Sugimoto, M., Hida, A., Minami, Y., Mori, M., Honma, S., Honma, K., Mishima, K., Soga, T., and Ueda, H.R. (2012). Human blood metabolite timetable indicates internal body time. Proc. Natl. Acad. Sci. USA 109: 15036-15041.
14. Kennedy, J., and Eberhart, R. (1995). Particle swarm optimization. Proc. IEEE Internat. Conf. Neural Networks 4: 1942-1948.
15. Kerwin, R.E., Jimenez-Gomez, J.M., Fulop, D., Harmer, S.L., Maloof, J.N., and Kliebenstein, D.J. (2011). Network quantitative trait loci mapping of circadian clock outputs identifies metabolic pathway-to-clock linkages in Arabidopsis. Plant Cell 23: 471-485.
16. Laud, P., and Ibrahim, J. (1995). Predictive model selection. J. R. Stat. Soc. B 57: 247-262.
17. Michael, T.P., Breton, G., Hazen, S.P., Priest, H., Mockler, T.C., Kay, S.A., and Chory, J. (2008). A morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biol. 6: e225.
18. Minami, Y., Kasukawa, T., Kakazu, Y., Iigo, M., Sugimoto, M., Ikeda, S., Yasui, A., van der Horst, G.T.J., Soga, T., and Ueda, H.R. (2009). Measurement of internal body time by blood metabolomics. Proc. Natl. Acad. Sci. USA 106: 9890-9895.
19. Mizoguchi, T., Wheatley, K., Hanzawa, Y., Wright, L., Mizoguchi, M., Song, H.-R., Carré, I.A., and Coupland, G. (2002). LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Dev. Cell 2: 629-641.
20. Murakami, M., Tago, Y., Yamashino, T., and Mizuno, T. (2007). Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa. Plant Cell Physiol. 48: 110-121.
21. Nagano, A.J., Sato, Y., Mihara, M., Antonio, B.A., Motoyama, R., Itoh, H., Nagamura, Y., and Izawa, T. (2012). Deciphering and prediction of transcriptome dynamics under fluctuating field conditions. Cell 151: 1358-1369.
22. Nagel, D.H., and Kay, S.A. (2012). Complexity in the wiring and regulation of plant circadian networks. Curr. Biol. 22: R648-R657.
23. Nozue, K., Covington, M.F., Duek, P.D., Lorrain, S., Fankhauser, C., Harmer, S.L., and Maloof, J.N. (2007). Rhythmic growth explained by coincidence between internal and external cues. Nature 448: 358-361.
24. Nusinow, D.A., Helfer, A., Hamilton, E.E., King, J.J., Imaizumi, T., Schultz, T.F., Farré, E.M., and Kay, S.A. (2011). The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature 475: 398-402.
25. Ohyanagi, H., et al. (2006). The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res. 34: D741-D744.
26. Pfeuty, B., Thommen, Q., and Lefranc, M. (2011). Robust entrainment of circadian oscillators requires specific phase response curves. Biophys. J. 100: 2557-2565.
27. Pittendrigh, C., and Daan, S. (1976). A functional analysis of circadian pacemakers in nocturnal rodents, IV. Entrainment: pacemaker as clock. J. Comp. Physiol. 106: 291-331.
28. Pittendrigh, C.S. (1972). Circadian surfaces and the diversity of possible roles of circadian organization in photoperiodic induction. Proc. Natl. Acad. Sci. USA 69: 2734-2737.
29. Pittendrigh, C.S., and Minis, D.H. (1964). The entrainment of circadian oscillations by light and their role as photoperiodic clocks. Am. Nat. 98: 261-294.
30. Pokhilko, A., Mas, P., and Millar, A.J. (2013). Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. BMC Syst. Biol. 7: 23.
31. R Core Team (2013). R: A language and environment for statistical computing. (Vienna, Austria: R Foundation for Statistical Computing). Roenneberg, T., Rémi, J., and Merrow, M. (2010). Modeling a circadian surface. J. Biol. Rhythms 25: 340-349.
32. Sakai, H., et al. (2013). Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 54: e6.
33. Sato, Y., Antonio, B., Namiki, N., Motoyama, R., Sugimoto, K., Takehisa, H., Minami, H., Kamatsuki, K., Kusaba, M., Hirochika, H., and Nagamura, Y. (2011). Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice. BMC Plant Biol. 11: 10.
34. Soetaert, K., Petzoldt, T., and Setzer, R.W. (2010). Solving differential equations in R: Package deSolve. J. Stat. Softw. 33: 1-25.
35. Suárez-López, P., Wheatley, K., Robson, F., Onouchi, H., Valverde, F., and Coupland, G. (2001). CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410: 1116-1120.
36. Sugiyama, N., Izawa, T., Oikawa, T., and Shimamoto, K. (2001). Light regulation of circadian clock-controlled gene expression in rice. Plant J. 26: 607-615.
37. Tagkopoulos, I., Liu, Y.-C., and Tavazoie, S. (2008). Predictive behavior within microbial genetic networks. Science 320: 1313-1317.
38. 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.
39. Wood, S.N. (2011). Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. J. R. Stat. Soc. B 73: 3-36.
40. Workman, C., Jensen, L.J., Jarmer, H., Berka, R., Gautier, L., Nielser, H.B., Saxild, H.H., Nielsen, C., Brunak, S., and Knudsen S. (2002). A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol. 3: 0048.
41. Yamashino, T., Ito, S., Niwa, Y., Kunihiro, A., Nakamichi, N., and Mizuno, T. (2008). Involvement of Arabidopsis clock-associated pseudo-response regulators in diurnal oscillations of gene expression in the presence of environmental time cues. Plant Cell Physiol. 49: 1839-1850.
42. Yano, M., Katayose, Y., Ashikari, M., Yamanouchi, U., Monna, L., Fuse, T., Baba, T., Yamamoto, K., Umehara, Y., Nagamura, Y., and Sasaki, T. (2000). Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12: 2473-2484.
43. Yeang, H.-Y. (2013). Solar rhythm in the regulation of photoperiodic flowering of long-day and short-day plants. J. Exp. Bot. 64: 2643-2652.
44. Yerushalmi, S., and Green, R.M. (2009). Evidence for the adaptive significance of circadian rhythms. Ecol. Lett. 12: 970-981.
45. Zar, J.H. (1999). Biostatistical Analysis. (Upper Saddle River, NJ: Prentice-Hall).