Network news: prime time for systems biology of the plant circadian clock

Gutierrez, 2005, Systems biology for the virtual plant, Plant Physiol, 138, 550, 10.1104/pp.104.900150 McClung, 2006, Plant circadian rhythms, Plant Cell, 18, 792, 10.1105/tpc.106.040980 Harmer, 2009, The circadian system in higher plants, Annu Rev Plant Biol, 60, 357, 10.1146/annurev.arplant.043008.092054 Pruneda-Paz, 2010, An expanding universe of circadian networks in higher plants, Trends Plant Sci, 15, 259, 10.1016/j.tplants.2010.03.003 Zhong, 1998, Imbibition, but not release from stratification, sets the circadian clock in Arabidopsis seedlings, Plant Cell, 10, 2005, 10.1105/tpc.10.12.2005 Oliverio, 2007, GIGANTEA regulates phytochrome A-mediated photomorphogenesis independently of Its role in the circadian clock, Plant Physiol, 144, 495, 10.1104/pp.107.097048 Salomé, 2008, Circadian timekeeping during early Arabidopsis development, Plant Physiol, 147, 1110, 10.1104/pp.108.117622 Penfield, 2009, A role for multiple circadian clock genes in the response to signals that break seed dormancy in Arabidopsis, Plant Cell, 21, 1722, 10.1105/tpc.108.064022 Para, 2007, PRR3 is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock, Plant Cell, 19, 3462, 10.1105/tpc.107.054775 Michael, 2003, Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity, Proc Natl Acad Sci U S A, 100, 6878, 10.1073/pnas.1131995100 Thain, 2002, The circadian clock that controls gene expression in Arabidopsis is tissue specific, Plant Physiol, 130, 102, 10.1104/pp.005405 James, 2008, The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots, Science, 322, 1832, 10.1126/science.1161403 Salomé, 2005, What makes Arabidopsis tick: light and temperature entrainment of the circadian clock, Plant Cell Environ, 28, 21, 10.1111/j.1365-3040.2004.01261.x Gutiérrez, 2008, Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1, Proc Natl Acad Sci U S A, 105, 4939, 10.1073/pnas.0800211105 Hanano, 2006, Multiple phytohormones influence distinct parameters of the plant circadian clock, Genes to Cells, 11, 1381, 10.1111/j.1365-2443.2006.01026.x Salomé, 2006, Arabidopsis response regulators ARR3 and ARR4 play cytokinin-independent roles in the control of circadian period, Plant Cell, 18, 55, 10.1105/tpc.105.037994 Legnaioli, 2009, TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought, EMBO J, 28, 3745, 10.1038/emboj.2009.297 Alabadí, 2001, Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock, Science, 293, 880, 10.1126/science.1061320 Pruneda-Paz, 2009, A functional genomics approach reveals CHE as a novel component of the Arabidopsis circadian clock, Science, 323, 1481, 10.1126/science.1167206 Más, 2003, Dual role of TOC1 in the control of circadian and photomorphogenic responses in Arabidopsis, Plant Cell, 15, 223, 10.1105/tpc.006734 Hazen, 2005, LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms, Proc Natl Acad Sci U S A, 102, 10387, 10.1073/pnas.0503029102 Onai, 2005, PHYTOCLOCK1 encoding a novel GARP protein essential for the Arabidopsis circadian clock, Genes Cells, 10, 963, 10.1111/j.1365-2443.2005.00892.x Kikis, 2005, ELF4 is a phytochrome-regulated component of a negative-feedback loop involving the central oscillator components CCA1 and LHY, Plant J, 44, 300, 10.1111/j.1365-313X.2005.02531.x McWatters, 2007, ELF4 Is required for oscillatory properties of the circadian clock, Plant Physiol, 144, 391, 10.1104/pp.107.096206 Gould, 2006, The molecular basis of temperature compensation in the Arabidopsis circadian clock, Plant Cell, 18, 1177, 10.1105/tpc.105.039990 Spensley, 2009, Evolutionarily conserved regulatory motifs in the promoter of the Arabidopsis clock gene late elongated hypocotyl, Plant Cell, 21, 2606, 10.1105/tpc.109.069898 Salathia, 2006, FLOWERING LOCUS C-dependent and -independent regulation of the circadian clock by the autonomous and vernalization pathways, BMC Plant Biol, 6, 10, 10.1186/1471-2229-6-10 Farré, 2005, Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock, Curr Biol, 15, 47, 10.1016/j.cub.2004.12.067 Nakamichi, 2010, Sakakibara H: PSEUDO-RESPONSE REGULATORS 9, 7 and 5 are transcriptional repressors in the Arabidopsis circadian clock, Plant Cell, 22, 594, 10.1105/tpc.109.072892 Salomé, 2005, PRR7 and PRR9 are partially redundant genes essential for the temperature responsiveness of the Arabidopsis circadian clock, Plant Cell, 17, 791, 10.1105/tpc.104.029504 Nakamichi, 2005, The Arabidopsis Pseudo-Response Regulators, PRR5 and PRR7, coordinately play essential roles for circadian clock function, Plant Cell Physiol, 46, 609, 10.1093/pcp/pci061 Nakamichi, 2005, PSEUDO-RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together play essential roles close to the circadian clock of Arabidopsis thaliana, Plant Cell Physiol, 46, 686, 10.1093/pcp/pci086 Nakamichi, 2007, Arabidopsis clock-associated pseudo-response regulators PRR9, PRR7 and PRR5 coordinately and positively regulate flowering time through the canonical CONSTANS-dependent photoperiodic pathway, Plant Cell Physiol, 48, 822, 10.1093/pcp/pcm056 Tiwari, 2010, The flowering time regulator CONSTANS is recruited to the FLOWERING LOCUS T promoter via a unique cis-element, New Phytol, 187, 57, 10.1111/j.1469-8137.2010.03251.x Gutiérrez, 2002, Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes, Proc Natl Acad Sci U S A, 99, 11513, 10.1073/pnas.152204099 Lidder, 2005, Circadian control of mRNA stability: association with DST-mediated mRNA decay, Plant Physiol, 138, 2374, 10.1104/pp.105.060368 Yakir, 2007, CIRCADIAN CLOCK ASSOCIATED1 transcript stability and the entrainment of the circadian clock in Arabidopsis, Plant Physiol, 145, 925, 10.1104/pp.107.103812 Nilsen, 2010, Expansion of the eukaryotic proteome by alternative splicing, Nature, 463, 457, 10.1038/nature08909 Hazen, 2009, Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays, Genome Biol, 10, R17, 10.1186/gb-2009-10-2-r17 Filichkin, 2010, Genome-wide mapping of alternative splicing in Arabidopsis thaliana, Genome Res, 20, 45, 10.1101/gr.093302.109 Staiger, 2003, The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA, Plant J, 33, 361, 10.1046/j.1365-313X.2003.01629.x Schöning, 2008, Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis, Nucl Acids Res, 36, 6977, 10.1093/nar/gkn847 Streitner, 2008, The small glycine-rich RNA binding protein AtGRP7 promotes floral transition in Arabidopsis thaliana, Plant J, 56, 239, 10.1111/j.1365-313X.2008.03591.x Gallego, 2007, Post-translational modifications regulate the ticking of the circadian clock, Nature Rev Mol Cell Biol, 8, 139, 10.1038/nrm2106 Daniel, 2004, CK2 phosphorylation of CCA1 is necessary for its circadian oscillator function in Arabidopsis, Proc Natl Acad Sci U S A, 101, 3292, 10.1073/pnas.0400163101 Fujiwara, 2008, Post-translational regulation of the circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins, J Biol Chem, 283, 23073, 10.1074/jbc.M803471200 Más, 2003, Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana, Nature, 426, 567, 10.1038/nature02163 Kiba, 2007, Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by a SCFZTL complex regulates clock function and photomorphogenesis in Arabidopsis thaliana, Plant Cell, 19, 2516, 10.1105/tpc.107.053033 Wang, 2010, PRR5 regulates phosphorylation, nuclear import and subnuclear localization of TOC1 in the Arabidopsis circadian clock, EMBO J, 29, 1903, 10.1038/emboj.2010.76 Baudry, 2010, F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression, Plant Cell, 22, 606, 10.1105/tpc.109.072843 Locke, 2005, Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana, J Theor Biol, 234, 383, 10.1016/j.jtbi.2004.11.038 Locke, 2006, Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana, Mol Syst Biol, 2, 59, 10.1038/msb4100102 Hubbard, 2009, Systems analyses of circadian networks, Mol Biosyst, 5, 1502, 10.1039/b907714f Salazar, 2009, Prediction of photoperiodic regulators from quantitative gene circuit models, Cell, 139, 1170, 10.1016/j.cell.2009.11.029 Gutiérrez, 2007, Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis, Genome Biol, 8, R7, 10.1186/gb-2007-8-1-r7 Hermans, 2010, Early transcriptomic changes induced by magnesium deficiency in Arabidopsis thaliana reveal the alteration of circadian clock gene expression in roots and the triggering of abscisic acid-responsive genes, New Phytol, 187, 119, 10.1111/j.1469-8137.2010.03258.x Harmer, 2000, Orchestrated transcription of key pathways in Arabidopsis by the circadian clock, Science, 290, 2110, 10.1126/science.290.5499.2110 Schaffer, 2001, Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis, Plant Cell, 13, 113, 10.1105/tpc.13.1.113 Edwards, 2006, FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock, Plant Cell, 18, 639, 10.1105/tpc.105.038315 Michael, 2008, Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules PLoS, Genet, 4, e14 Covington, 2008, Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development, Genome Biol, 9, R130, 10.1186/gb-2008-9-8-r130 Michael, 2008, A morning-specific phytohormone gene expression program underlying rhythmic plant growth, Plos Biol, 6, 1887, 10.1371/journal.pbio.0060225 Fowler, 2005, Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock, Plant Physiol, 137, 961, 10.1104/pp.104.058354 Nakamichi, 2009, Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response, Plant Cell Physiol, 50, 447, 10.1093/pcp/pcp004 Mikkelsen, 2009, A role for circadian evening elements in cold-regulated gene expression in Arabidopsis, Plant J, 60, 328, 10.1111/j.1365-313X.2009.03957.x Wilkins, 2009, Genotype and time of day shape the Populus drought response, Plant J, 60, 703, 10.1111/j.1365-313X.2009.03993.x Wilkins, 2010, Time of day shapes Arabidopsis drought transcriptomes, Plant J., 67 Zdepski, 2008, Conserved daily transcriptional programs in Carica papaya, Trop Plant Biol, 1, 236, 10.1007/s12042-008-9020-3 Green, 2002, Circadian rhythms confer a higher level of fitness to Arabidopsis plants, Plant Physiol, 129, 576, 10.1104/pp.004374 Dodd, 2005, Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage, Science, 309, 630, 10.1126/science.1115581 Ni, 2009, Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids, Nature, 457, 327, 10.1038/nature07523 Graf, 2010, Circadian control of carbohydrate availability for growth in Arabidopsis plants at night, Proc Natl Acad Sci U S A, 107, 9458, 10.1073/pnas.0914299107