Complexity in the wiring and regulation of plant circadian networks

Current Biology

Volumn 22, Issue 16, 2012, Pages

  Nagel, Dawn H ^a,b   Kay, Steve A ^a,b  

^a SECTION OF CELL AND DEVELOPMENTAL BIOLOGY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; CIRCADIAN RHYTHM; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; PHYSIOLOGY; REVIEW;

ARABIDOPSIS; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS;

EID: 84865204375     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2012.07.025     Document Type: Review

References (117)

1. D. Bell-Pedersen, V.M. Cassone, D.J. Earnest, S.S. Golden, P.E. Hardin, T.L. Thomas, and M.J. Zoran Circadian rhythms from multiple oscillators: lessons from diverse organisms Nat. Rev. Genet. 6 2005 544 556 (Pubitemid 40910431)
2. S. Yerushalmi, and R.M. Green Evidence for the adaptive significance of circadian rhythms Ecol. Lett. 12 2009 970 981
3. C.T. Hotta, M.J. Gardner, K.E. Hubbard, S.J. Baek, N. Dalchau, D. Suhita, A.N. Dodd, and A.A.R. Webb Modulation of environmental responses of plants by circadian clocks Plant Cell Environ. 30 2007 333 349 (Pubitemid 46184434)
4. A.N. Dodd, N. Salathia, A. Hall, E. Kévei, R. Tóth, F. Nagy, J.M. Hibberd, A.J. Millar, and A.A.R. Webb Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage Science 309 2005 630 633 (Pubitemid 41033650)
5. Y. Ouyang, C.R. Andersson, T. Kondo, S.S. Golden, and C.H. Johnson Resonating circadian clocks enhance fitness in cyanobacteria Proc. Natl. Acad. Sci. USA 95 1998 8660 8664 (Pubitemid 28350544)
6. R.M. Green, S. Tingay, Z.-Y. Wang, and E.M. Tobin Circadian rhythms confer a higher level of fitness to Arabidopsis plants Plant Physiol. 129 2002 576 584 (Pubitemid 34689146)
7. F. Corellou, C. Schwartz, J.-P. Motta, E.B. Djouani-Tahri, F. Sanchez, and F.-Y. Bouget Clocks in the green lineage: comparative functional analysis of the circadian architecture of the picoeukaryote ostreococcus Plant Cell 21 2009 3436 3449
8. S.L. Harmer The circadian system in higher plants Annu. Rev. Plant Biol. 60 2009 357 377
9. H. Wijnen, F. Naef, C. Boothroyd, A. Claridge-Chang, and M.W. Young Control of daily transcript oscillations in Drosophila by light and the circadian clock PLoS Genet. 2 2006 e39
10. T. Stratmann, and P. Más Chromatin, photoperiod and the Arabidopsis circadian clock: a question of time Semin. Cell Dev. Biol. 19 2008 554 559
11. Y. Nakahata, B. Grimaldi, S. Sahar, J. Hirayama, and P. Sassone-Corsi Signaling to the circadian clock: plasticity by chromatin remodeling Curr. Opin. Cell Biol. 19 2007 230 237 (Pubitemid 46386412)
12. A. Fukushima, M. Kusano, N. Nakamichi, M. Kobayashi, N. Hayashi, H. Sakakibara, T. Mizuno, and K. Saito Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination Proc. Natl. Acad. Sci. USA 106 2009 7251 7256
13. K. Nozue, M.F. Covington, P.D. Duek, S. Lorrain, C. Fankhauser, S.L. Harmer, and J.N. Maloof Rhythmic growth explained by coincidence between internal and external cues Nature 448 2007 358 361 (Pubitemid 47080338)
14. T. Mizuno, and T. Yamashino Comparative transcriptome of diurnally oscillating genes and hormone-responsive genes in Arabidopsis thaliana: insight into circadian clock-controlled daily responses to common ambient stresses in plants Plant Cell Physiol. 49 2008 481 487 (Pubitemid 351398304)
15. W. Wang, J.Y. Barnaby, Y. Tada, H. Li, M. Tör, D. Caldelari, D. Lee, X.-D. Fu, and X. Dong Timing of plant immune responses by a central circadian regulator Nature 470 2011 110 114
16. M.F. Covington, J.N. Maloof, M. Straume, S.A. Kay, and S.L. Harmer Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development Genome Biol. 9 2008 R130
17. T.P. Michael, T.C. Mockler, G. Breton, C. McEntee, A. Byer, J.D. Trout, S.P. Hazen, R. Shen, H.D. Priest, and C.M. Sullivan Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules PLoS Genet. 4 2008 e14
18. D. Alabadí, T. Oyama, M.J. Yanovsky, F.G. Harmon, P. Más, and S.A. Kay Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock Science 293 2001 880 883 (Pubitemid 32743980)
19. C. Strayer, T. Oyama, T.F. Schultz, R. Raman, D.E. Somers, P. Más, S. Panda, J.A. Kreps, and S.A. Kay Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog Science 289 2000 768 771 (Pubitemid 30650195)
20. Z.Y. Wang, and E.M. Tobin Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression Cell 93 1998 1207 1217 (Pubitemid 28307425)
21. R. Schaffer, N. Ramsay, A. Samach, S. Corden, J. Putterill, I.A. Carré, and G. Coupland The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering Cell 93 1998 1219 1229 (Pubitemid 28307426)
22. A.J. Millar, I.A. Carré, C.A. Strayer, N.H. Chua, and S.A. Kay Circadian clock mutants in Arabidopsis identified by luciferase imaging Science 267 1995 1161 1163
23. S.L. Harmer, and S.A. Kay Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis Plant Cell 17 2005 1926 1940
24. J.C.W. Locke, A.J. Millar, and M.S. Turner Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana J. Theor. Biol. 234 2005 383 393 (Pubitemid 40387462)
25. J.L. Pruneda-Paz, and S.A. Kay An expanding universe of circadian networks in higher plants Trends Plant Sci. 15 2010 259 265
26. J.M. Gendron, J.L. Pruneda-Paz, C.J. Doherty, A.M. Gross, S.E. Kang, and S.A. Kay Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor Proc. Natl. Acad. Sci. USA 109 2012 3167 3172
27. W. Huang, P. Pérez-García, A. Pokhilko, A.J. Millar, I. Antoshechkin, J.L. Riechmann, and P. Mas Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator Science 336 2012 75 79
28. A. Pokhilko, S.K. Hodge, K. Stratford, K. Knox, K.D. Edwards, A.W. Thomson, T. Mizuno, and A.J. Millar Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model Mol. Syst. Biol. 6 2010 416
29. A. Pokhilko, A.P. Fernández, K.D. Edwards, M.M. Southern, K.J. Halliday, and A.J. Millar The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops Mol. Syst. Biol. 8 2012 574
30. N. Takata, S. Saito, C.T. Saito, T. Nanjo, K. Shinohara, and M. Uemura Molecular phylogeny and expression of poplar circadian clock genes, LHY1 and LHY2 New Phytol. 181 2009 808 819
31. N. Takata, S. Saito, C.T. Saito, and M. Uemura Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of pseudo-response regulators BMC Evol. Biol. 10 2010 126
32. K. Holm, T. Källman, N. Gyllenstrand, H. Hedman, and U. Lagercrantz Does the core circadian clock in the moss Physcomitrella patens (Bryophyta) comprise a single loop? BMC Plant Biol. 10 2010 109
33. M. Murakami, M. Ashikari, K. Miura, T. Yamashino, and T. Mizuno The evolutionarily conserved OsPRR quintet: rice pseudo-response regulators implicated in circadian rhythm Plant Cell Physiol. 44 2003 1229 1236 (Pubitemid 37519082)
34. J.A. Kim, T.-J. Yang, J.S. Kim, J.Y. Park, S.-J. Kwon, M.-H. Lim, M. Jin, S.C. Lee, S.I. Lee, and B.-S. Choi Isolation of circadian-associated genes in Brassica rapa by comparative genomics with Arabidopsis thaliana Mol. Cell 23 2007 145 153 (Pubitemid 46711675)
35. E.M. Farré, S.L. Harmer, F.G. Harmon, M.J. Yanovsky, and S.A. Kay Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock Curr. Biol. 15 2005 47 54 (Pubitemid 40084701)
36. S. Portolés, and P. Más The functional interplay between protein kinase CK2 and CCA1 transcriptional activity is essential for clock temperature compensation in Arabidopsis PLoS Genet. 6 2010 e1001201
37. N. Nakamichi, T. Kiba, R. Henriques, T. Mizuno, N.-H. Chua, and H. Sakakibara PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock Plant Cell 22 2010 594 605
38. S.M. Knowles, S.X. Lu, and E.M. Tobin Testing time: can ethanol-induced pulses of proposed oscillator components phase shift rhythms in Arabidopsis? J. Biol. Rhythms 23 2008 463 471
39. Y. Wang, J.-F. Wu, N. Nakamichi, H. Sakakibara, H.-G. Nam, and S.-H. Wu LIGHT-REGULATED WD1 and PSEUDO-RESPONSE REGULATOR9 form a positive feedback regulatory loop in the Arabidopsis circadian clock Plant Cell 23 2011 486 498
40. J.-F. Wu, Y. Wang, and S.-H. Wu Two new clock proteins, LWD1 and LWD2, regulate Arabidopsis photoperiodic flowering Plant Physiol. 148 2008 948 959 (Pubitemid 352847551)
41. Z. Ding, M.R. Doyle, R.M. Amasino, and S.J. Davis A complex genetic interaction between Arabidopsis thaliana TOC1 and CCA1/LHY in driving the circadian clock and in output regulation Genetics 176 2007 1501 1510 (Pubitemid 47105213)
42. S.P. Hazen, T.F. Schultz, J.L. Pruneda-Paz, J.O. Borevitz, J.R. Ecker, and S.A. Kay LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms Proc. Natl. Acad. Sci. USA 102 2005 10387 10392 (Pubitemid 41023380)
43. K. Onai, and M. Ishiura PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock Genes Cells 10 2005 963 972 (Pubitemid 41404006)
44. L.E. Dixon, K. Knox, L. Kozma-Bognar, M.M. Southern, A. Pokhilko, and A.J. Millar Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis Curr. Biol. 21 2011 120 125
45. A. Helfer, D.A. Nusinow, B.Y. Chow, A.R. Gehrke, M.L. Bulyk, and S.A. Kay LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock Curr. Biol. 21 2011 126 133
46. Chow, B. Y., Helfer, A., Nusinow, D. A., and Kay, S. A. (2012). ELF3 recruitment to the PRR9 promoter requires other Evening Complex members in the Arabidopsis circadian clock. Plant Signal. Behav. 7. Available at: http://www.ncbi.nlm.nih.gov/pubmed/22307044 [Accessed April 27, 2012é.
47. S. Dai, X. Wei, L. Pei, R.L. Thompson, Y. Liu, J.E. Heard, T.G. Ruff, and R.N. Beachy BROTHER OF LUX ARRHYTHMO is a component of the Arabidopsis circadian clock Plant Cell 23 2011 961 972
48. J.L. Pruneda-Paz, G. Breton, A. Para, and S.A. Kay A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock Science 323 2009 1481 1485
49. O.S. Lau, X. Huang, J.-B. Charron, J.-H. Lee, G. Li, and X.W. Deng Interaction of Arabidopsis DET1 with CCA1 and LHY in mediating transcriptional repression in the plant circadian clock Mol. Cell 43 2011 703 712
50. D.A. Nusinow, A. Helfer, E.E. Hamilton, J.J. King, T. Imaizumi, T.F. Schultz, E.M. Farré, and S.A. Kay The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth Nature 475 2011 398 402
51. E. Herrero, E. Kolmos, N. Bujdoso, Y. Yuan, M. Wang, M.C. Berns, H. Uhlworm, G. Coupland, R. Saini, and M. Jaskolski EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock Plant Cell 24 2012 428 443
52. K.A. Hicks, T.M. Albertson, and D.R. Wagner EARLY FLOWERING3 encodes a novel protein that regulates circadian clock function and flowering in Arabidopsis Plant Cell 13 2001 1281 1292 (Pubitemid 32592903)
53. E.A. Kikis, R. Khanna, and P.H. Quail ELF4 is a phytochrome-regulated component of a negative-feedback loop involving the central oscillator components CCA1 and LHY Plant J. 44 2005 300 313
54. M.R. Doyle, S.J. Davis, R.M. Bastow, H.G. McWatters, L. Kozma-Bognár, F. Nagy, A.J. Millar, and R.M. Amasino The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana Nature 419 2002 74 77 (Pubitemid 34987872)
55. G. Li, H. Siddiqui, Y. Teng, R. Lin, X. Wan, J. Li, O.-S. Lau, X. Ouyang, M. Dai, and J. Wan Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis Nat. Cell Biol. 13 2011 616 622
56. S.X. Lu, S.M. Knowles, C. Andronis, M.S. Ong, and E.M. Tobin CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis Plant Physiol. 150 2009 834 843
57. T.P. Michael, and C.R. McClung Phase-specific circadian clock regulatory elements in Arabidopsis Plant Physiol. 130 2002 627 638 (Pubitemid 35224770)
58. Z.Y. Wang, D. Kenigsbuch, L. Sun, E. Harel, M.S. Ong, and E.M. Tobin A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene Plant Cell 9 1997 491 507 (Pubitemid 27218748)
59. R. Rawat, N. Takahashi, P.Y. Hsu, M.A. Jones, J. Schwartz, M.R. Salemi, B.S. Phinney, and S.L. Harmer REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock PLoS Genet. 7 2011 e1001350
60. B. Farinas, and P. Mas Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation Plant J. 66 2011 318 329
61. C. Hervé, P. Dabos, C. Bardet, A. Jauneau, M.C. Auriac, A. Ramboer, F. Lacout, and D. Tremousaygue In vivo interference with AtTCP20 function induces severe plant growth alterations and deregulates the expression of many genes important for development Plant Physiol. 149 2009 1462 1477
62. E. Giraud, S. Ng, C. Carrie, O. Duncan, J. Low, C.P. Lee, O. Van Aken, A.H. Millar, M. Murcha, and J. Whelan TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana Plant Cell 22 2010 3921 3934
63. Braun, P., Carvunis, A. R., Charloteaux, B., Dreze, M., Ecker, J. R., Hill, D. E., Roth, F. P., Vidal, M., Galli, M., Balumuri, P., et al. (2011). Evidence for network evolution in an Arabidopsis interactome map. Science 333, 601-607.
64. T.C. Mockler, T.P. Michael, H.D. Priest, R. Shen, C.M. Sullivan, S.A. Givan, C. McEntee, S.A. Kay, and J. Chory The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis Cold Spring Harb. Symp. Quant. Biol. 72 2007 353 363
65. T.W. Nilsen, and B.R. Graveley Expansion of the eukaryotic proteome by alternative splicing Nature 463 2010 457 463
66. A. Diernfellner, H.V. Colot, O. Dintsis, J.J. Loros, J.C. Dunlap, and M. Brunner Long and short isoforms of Neurospora clock protein FRQ support temperature-compensated circadian rhythms FEBS Lett. 581 2007 5759 5764 (Pubitemid 50007778)
67. H.V. Colot, J.J. Loros, and J.C. Dunlap Temperature-modulated alternative splicing and promoter use in the Circadian clock gene frequency Mol. Biol. Cell 16 2005 5563 5571 (Pubitemid 41752207)
68. S.A. Filichkin, H.D. Priest, S.A. Givan, R. Shen, D.W. Bryant, S.E. Fox, W.-K. Wong, and T.C. Mockler Genome-wide mapping of alternative splicing in Arabidopsis thaliana Genome Res. 20 2010 45 58
69. A.B. James, N.H. Syed, S. Bordage, J. Marshall, G.A. Nimmo, G.I. Jenkins, P. Herzyk, J.W.S. Brown, and H.G. Nimmo Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes Plant Cell 24 2012 961 981
70. X. Deng, L. Gu, C. Liu, T. Lu, F. Lu, Z. Lu, P. Cui, Y. Pei, B. Wang, and S. Hu Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing Proc. Natl. Acad. Sci. USA 107 2010 19114 19119
71. S. Hong, H.-R. Song, K. Lutz, R.A. Kerstetter, T.P. Michael, and C.R. McClung Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana Proc. Natl. Acad. Sci. USA 107 2010 21211 21216
72. S.E. Sanchez, E. Petrillo, E.J. Beckwith, X. Zhang, M.L. Rugnone, C.E. Hernando, J.C. Cuevas, M.A. Godoy Herz, A. Depetris-Chauvin, and C.G. Simpson A methyl transferase links the circadian clock to the regulation of alternative splicing Nature 468 2010 112 116
73. P. Más Circadian clock function in Arabidopsis thaliana: time beyond transcription Trends Cell Biol. 18 2008 273 281
74. A. Mehra, C.L. Baker, J.J. Loros, and J.C. Dunlap Post-translational modifications in circadian rhythms Trends Biochem. Sci. 34 2009 483 490
75. T. Mizoguchi, J. Putterill, and Y. Ohkoshi Kinase and phosphatase: the cog and spring of the circadian clock Int. Rev. Cytol. 250 2006 47 72 (Pubitemid 44067203)
76. Y. Tsuchiya, M. Akashi, M. Matsuda, K. Goto, Y. Miyata, K. Node, and E. Nishida Involvement of the protein kinase CK2 in the regulation of mammalian circadian rhythms Sci. Signal. 2 2009 ra26
77. J.-M. Lin, V.L. Kilman, K. Keegan, B. Paddock, M. Emery-Le, M. Rosbash, and R. Allada A role for casein kinase 2alpha in the Drosophila circadian clock Nature 420 2002 816 820 (Pubitemid 36019629)
78. A. Mehra, M. Shi, C.L. Baker, H.V. Colot, J.J. Loros, and J.C. Dunlap A role for casein kinase 2 in the mechanism underlying circadian temperature compensation Cell 137 2009 749 760
79. S. Sugano, C. Andronis, M.S. Ong, R.M. Green, and E.M. Tobin The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis Proc. Natl. Acad. Sci. USA 96 1999 12362 12366 (Pubitemid 29513507)
80. X. Daniel, S. Sugano, and E.M. Tobin CK2 phosphorylation of CCA1 is necessary for its circadian oscillator function in Arabidopsis Proc. Natl. Acad. Sci. USA 101 2004 3292 3297 (Pubitemid 38327774)
81. S.X. Lu, H. Liu, S.M. Knowles, J. Li, L. Ma, E.M. Tobin, and C. Lin A role for protein kinase casein kinase2 α-subunits in the Arabidopsis circadian clock Plant Physiol. 157 2011 1537 1545
82. H.-R. Song, and I.A. Carré DET1 regulates the proteasomal degradation of LHY, a component of the Arabidopsis circadian clock Plant Mol. Biol. 57 2005 761 771 (Pubitemid 40938361)
83. B.S. Park, H.J. Eo, I.-C. Jang, H.-G. Kang, J.T. Song, and H.S. Seo Ubiquitination of LHY by SINAT5 regulates flowering time and is inhibited by DET1 Biochem. Biophys. Res. Commun. 398 2010 242 246
84. S. Fujiwara, L. Wang, L. Han, S.-S. Suh, P.A. Salomé, C.R. McClung, and D.E. Somers Post-translational regulation of the Arabidopsis circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins J. Biol. Chem. 283 2008 23073 23083
85. K.M. David, U. Armbruster, N. Tama, and J. Putterill Arabidopsis GIGANTEA protein is post-transcriptionally regulated by light and dark FEBS Lett. 580 2006 1193 1197 (Pubitemid 43221978)
86. P. Más, W.-Y. Kim, D.E. Somers, and S.A. Kay Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana Nature 426 2003 567 570 (Pubitemid 37522643)
87. A. Baudry, S. Ito, Y.H. Song, A.A. Strait, T. Kiba, S. Lu, R. Henriques, J.L. Pruneda-Paz, N.-H. Chua, and E.M. Tobin F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression Plant Cell 22 2010 606 622
88. L. Wang, S. Fujiwara, and D.E. Somers PRR5 regulates phosphorylation, nuclear import and subnuclear localization of TOC1 in the Arabidopsis circadian clock EMBO J. 29 2010 1903 1915
89. A. Para, E.M. Farré, T. Imaizumi, J.L. Pruneda-Paz, F.G. Harmon, and S.A. Kay PRR3 Is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock Plant Cell 19 2007 3462 3473
90. T. Kiba, R. Henriques, H. Sakakibara, and N.-H. Chua Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by an SCFZTL complex regulates clock function and photomorphogenesis in Arabidopsis thaliana Plant Cell 19 2007 2516 2530 (Pubitemid 47583841)
91. W.-Y. Kim, S. Fujiwara, S.-S. Suh, J. Kim, Y. Kim, L. Han, K. David, J. Putterill, H.G. Nam, and D.E. Somers ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light Nature 449 2007 356 360 (Pubitemid 47443478)
92. M. Perales, and P. Más A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock Plant Cell 19 2007 2111 2123 (Pubitemid 47347456)
93. Z. Ni, E.-D. Kim, M. Ha, E. Lackey, J. Liu, Y. Zhang, Q. Sun, and Z.J. Chen Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids Nature 457 2009 327 331
94. M.A. Jones, M.F. Covington, L. DiTacchio, C. Vollmers, S. Panda, and S.L. Harmer Jumonji domain protein JMJD5 functions in both the plant and human circadian systems Proc. Natl. Acad. Sci. USA 107 2010 21623 21628
95. S.X. Lu, S.M. Knowles, C.J. Webb, R.B. Celaya, C. Cha, J.P. Siu, and E.M. Tobin The Jumonji C domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock Plant Physiol. 155 2011 906 915
96. D.A. Hsia, C.G. Tepper, M.R. Pochampalli, E.Y.C. Hsia, C. Izumiya, S.B. Huerta, M.E. Wright, H.-W. Chen, H.-J. Kung, and Y. Izumiya KDM8, a H3K36me2 histone demethylase that acts in the cyclin A1 coding region to regulate cancer cell proliferation Proc. Natl. Acad. Sci. USA 107 2010 9671 9676
97. M.A. Jones, and S. Harmer JMJD5 Functions in concert with TOC1 in the Arabidopsis circadian system Plant Signal. Behav. 6 2011 445 448
98. E. Yakir, D. Hilman, Y. Harir, and R.M. Green Regulation of output from the plant circadian clock FEBS J. 274 2007 335 345 (Pubitemid 46046644)
99. M.J. Dowson-Day, and A.J. Millar Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis Plant J. 17 1999 63 71
100. S. Lorrain, T. Allen, P.D. Duek, G.C. Whitelam, and C. Fankhauser Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors Plant J. 53 2008 312 323
101. E. Huq, and P.H. Quail PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis EMBO J. 21 2002 2441 2450 (Pubitemid 34546716)
102. R. Khanna, E. Huq, E.A. Kikis, B. Al-Sady, C. Lanzatella, and P.H. Quail A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors Plant Cell 16 2004 3033 3044 (Pubitemid 41075750)
103. T. Fujimori, T. Yamashino, T. Kato, and T. Mizuno Circadian-controlled basic/helix-loop-helix factor, PIL6, implicated in light-signal transduction in Arabidopsis thaliana Plant Cell Physiol. 45 2004 1078 1086 (Pubitemid 39260285)
104. K. Nozue, S.L. Harmer, and J.N. Maloof Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis Plant Physiol. 156 2011 357 372
105. A. Kunihiro, T. Yamashino, N. Nakamichi, Y. Niwa, H. Nakanishi, and T. Mizuno Phytochrome-interacting factor 4 and 5 (PIF4 and PIF5) activate the homeobox ATHB2 and auxin-inducible IAA29 genes in the coincidence mechanism underlying photoperiodic control of plant growth of Arabidopsis thaliana Plant Cell Physiol. 52 2011 1315 1329
106. T. Imaizumi, and S.A. Kay Photoperiodic control of flowering: not only by coincidence Trends Plant Sci. 11 2006 550 558 (Pubitemid 44636297)
107. M. Koornneef, C. Alonso-Blanco, H. Blankestijn-de Vries, C.J. Hanhart, and A.J. Peeters Genetic interactions among late-flowering mutants of Arabidopsis Genetics 148 1998 885 892 (Pubitemid 28087636)
108. D.E. Somers, A.A. Webb, M. Pearson, and S.A. Kay The short-period mutant, toc1-1, alters circadian clock regulation of multiple outputs throughout development in Arabidopsis thaliana Development 125 1998 485 494 (Pubitemid 28102655)
109. S. Fowler, K. Lee, H. Onouchi, A. Samach, K. Richardson, B. Morris, G. Coupland, and J. Putterill GIGANTEA: a circadian clock-controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membrane-spanning domains EMBO J. 18 1999 4679 4688 (Pubitemid 29415522)
110. P. Suárez-López, K. Wheatley, F. Robson, H. Onouchi, F. Valverde, and G. Coupland CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis Nature 410 2001 1116 1120 (Pubitemid 32391045)
111. F. Valverde, A. Mouradov, W. Soppe, D. Ravenscroft, A. Samach, and G. Coupland Photoreceptor regulation of CONSTANS protein in photoperiodic flowering Science 303 2004 1003 1006 (Pubitemid 38209702)
112. M. Sawa, and S.A. Kay GIGANTEA directly activates Flowering Locus T in Arabidopsis thaliana Proc. Natl. Acad. Sci. USA 108 2011 11698 11703
113. S.C. Thain, G. Murtas, J.R. Lynn, R.B. McGrath, and A.J. Millar The circadian clock that controls gene expression in Arabidopsis is tissue specific Plant Physiol. 130 2002 102 110
114. A.B. James, J.A. Monreal, G.A. Nimmo, C.L. Kelly, P. Herzyk, G.I. Jenkins, and H.G. Nimmo The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots Science 322 2008 1832 1835
115. E. Yakir, M. Hassidim, N. Melamed-Book, D. Hilman, I. Kron, and R.M. Green Cell autonomous and cell-type specific circadian rhythms in Arabidopsis Plant J. 68 2011 520 531
116. B. Wenden, D.L.K. Toner, S.K. Hodge, R. Grima, and A.J. Millar Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf Proc. Natl. Acad. Sci. USA 109 2012 6757 6762
117. N. Dalchau, S.J. Baek, H.M. Briggs, F.C. Robertson, A.N. Dodd, M.J. Gardner, M.A. Stancombe, M.J. Haydon, G.-B. Stan, and J.M. Gonalves The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose Proc. Natl. Acad. Sci. USA 108 2011 5104 5109