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Light Control of Arabidopsis Development Entails Coordinated Regulation of Genome Expression and Cellular Pathways
Open accessAbstract
An expressed sequence tag-based microarray was used to profile genome expression underlying light control of Arabidopsis development. Qualitatively similar gene expression profiles were observed among seedlings grown in different light qualities, including far-red, red, and blue light, which are mediated primarily by phytochrome A, phytochrome B, and the cryptochromes, respectively. Furthermore, light/dark transitions also triggered similar differential genome expression profiles. Most light treatments also resulted in distinct expression profiles in small fractions of the expressed sequence tags examined. The similarly regulated genes in all light conditions were estimated to account for approximately one-third of the genome, with three-fifths upregulated and two-fifths downregulated by light. Analysis of those light-regulated genes revealed more than 26 cellular pathways that are regulated coordinately by light. Thus, light controls Arabidopsis development through coordinately regulating metabolic and regulatory pathways.
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Cites
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 16,184
Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray
Schena, M., Shalon, D., Davis, R. W., & Brown, P. O. (1995) · Science · doi:10.1126/science.270.5235.467 · Cited by 9,609
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock
Harmer, S. L., Hogenesch, J. B., Straume, M., Chang, H.-S., Han, B., Zhu, T., Wang, X., Kreps, J. A., & Kay, S. A. (2000) · Science · doi:10.1126/science.290.5499.2110 · Cited by 1,640
BRASSINOSTEROIDS: Essential Regulators of Plant Growth and Development
Clouse, S. D., & Sasse, J. M. (1998) · Annual Review of Plant Physiology and Plant Molecular Biology · doi:10.1146/annurev.arplant.49.1.427 · Cited by 1,462
Coordinated plant defense responses in Arabidopsis revealed by microarray analysis
Schenk, P. M., Kazan, K., Wilson, I., Anderson, J. P., Richmond, T., Somerville, S. C., & Manners, J. M. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.21.11655 · Cited by 1,370
Differential Gene Expression in Response to Mechanical Wounding and Insect Feeding in Arabidopsis
Reymond, P., Weber, H., Damond, M., & Farmer, E. E. (2000) · The Plant Cell · doi:10.1105/tpc.12.5.707 · Cited by 1,227
Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., Hayashizaki, Y., & Shinozaki, K. (2001) · The Plant Cell · doi:10.1105/tpc.13.1.61 · Cited by 1,096
Arabidopsis MAP Kinase 4 Negatively Regulates Systemic Acquired Resistance
Petersen, M., Brodersen, P., Naested, H., Andreasson, E., Lindhart, U., Johansen, B., Nielsen, H. B., Lacy, M., Austin, M. J., Parker, J. E., et al. (2000) · Cell · doi:10.1016/s0092-8674(00)00213-0 · Cited by 1,035
Reed, J. W., Nagpal, P., Poole, D. S., Furuya, M., & Chory, J. (1993) · The Plant Cell · doi:10.1105/tpc.5.2.147 · Cited by 943
THE MOLECULAR-GENETICS OF NITROGEN ASSIMILATION INTO AMINO ACIDS IN HIGHER PLANTS
Lam, H.-M., Coschigano, K. T., Oliveira, I. C., Melo-Oliveira, R., & Coruzzi, G. M. (1996) · Annual Review of Plant Physiology and Plant Molecular Biology · doi:10.1146/annurev.arplant.47.1.569 · Cited by 889
Lee, M.-L. T., Kuo, F. C., Whitmore, G. A., & Sklar, J. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.18.9834 · Cited by 861
A Role for Brassinosteroids in Light-Dependent Development of Arabidopsis
Li, J., Nagpal, P., Vitart, V., McMorris, T. C., & Chory, J. (1996) · Science · doi:10.1126/science.272.5260.398 · Cited by 858
Self-citationAnalysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana
The EU Arabidopsis Genome Project, Bevan, M., Bancroft, I., Bent, E., Love, K., Goodman, H., Dean, C., Bergkamp, R., Dirkse, W., Van Staveren, M., et al. (1998) · Nature · doi:10.1038/35140 · Cited by 825
Genetic Control of Light-inhibited Hypocotyl Elongation in Arabidopsis thaliana (L.) Heynh
Koornneef, M., Rolff, E., & Spruit, C. J. P. (1980) · Zeitschrift für Pflanzenphysiologie · doi:10.1016/s0044-328x(80)80208-x · Cited by 787
Phytochromes: Photosensory Perception and Signal Transduction
Quail, P. H., Boylan, M. T., Parks, B. M., Short, T. W., Xu, Y., & Wagner, D. (1995) · Science · doi:10.1126/science.7732376 · Cited by 751
P ATHWAYS AND R EGULATION OF S ULFUR M ETABOLISM R EVEALED T HROUGH M OLECULAR AND G ENETIC S TUDIES
Leustek, T., Martin, M. N., Bick, J.-A., & Davies, J. P. (2000) · Annual Review of Plant Physiology and Plant Molecular Biology · doi:10.1146/annurev.arplant.51.1.141 · Cited by 656
Arabidopsis NPL1: A Phototropin Homolog Controlling the Chloroplast High-Light Avoidance Response
Kagawa, T., Sakai, T., Suetsugu, N., Oikawa, K., Ishiguro, S., Kato, T., Tabata, S., Okada, K., & Wada, M. (2001) · Science · doi:10.1126/science.291.5511.2138 · Cited by 651
ENZYMES AND OTHER AGENTS THAT ENHANCE CELL WALL EXTENSIBILITY
Cosgrove, D. J. (1999) · Annual Review of Plant Physiology and Plant Molecular Biology · doi:10.1146/annurev.arplant.50.1.391 · Cited by 590
Wang, R., Guegler, K., LaBrie, S. T., & Crawford, N. M. (2000) · The Plant Cell · doi:10.1105/tpc.12.8.1491 · Cited by 578
A Global Profile of Germline Gene Expression in C. elegans
Reinke, V., Smith, H. E., Nance, J., Wang, J., Van Doren, C., Begley, R., Jones, S. J. M., Davis, E. B., Scherer, S., Ward, S., et al. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)00059-9 · Cited by 578
Nicol, F. (1998) · The EMBO Journal · doi:10.1093/emboj/17.19.5563 · Cited by 574
Terzaghi, W. B. (1995) · Annual Review of Plant Physiology and Plant Molecular Biology · doi:10.1146/annurev.arplant.46.1.445 · Cited by 539
Phytochrome A null mutants of Arabidopsis display a wild-type phenotype in white light.
Whitelam, G. C., Johnson, E., Peng, J., Carol, P., Anderson, M. L., Cowl, J. S., & Harberd, N. P. (1993) · The Plant Cell · doi:10.1105/tpc.5.7.757 · Cited by 532
Light: an indicator of time and place
Neff, M. M., Fankhauser, C., & Chory, J. (2000) · Genes & Development · doi:10.1101/gad.14.3.257 · Cited by 524
Direct Interaction of Arabidopsis Cryptochromes with COP1 in Light Control Development
Wang, H., Ma, L.-G., Li, J.-M., Zhao, H.-Y., & Deng, X. W. (2001) · Science · doi:10.1126/science.1063630 · Cited by 524
Self-citationLIGHT CONTROL OF PLANT DEVELOPMENT
Fankhauser, C., & Chory, J. (1997) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.13.1.203 · Cited by 485
Multiple transcription-factor genes are early targets of phytochrome A signaling
Tepperman, J. M., Zhu, T., Chang, H.-S., Wang, X., & Quail, P. H. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.161300998 · Cited by 481
Phototropin-related NPL1 controls chloroplast relocation induced by blue light
Jarillo, J. A., Gabrys, H., Capel, J., Alonso, J. M., Ecker, J. R., & Cashmore, A. R. (2001) · Nature · doi:10.1038/35073622 · Cited by 476
Microarray Analysis of Drosophila Development During Metamorphosis
White, K. P., Rifkin, S. A., Hurban, P., & Hogness, D. S. (1999) · Science · doi:10.1126/science.286.5447.2179 · Cited by 467
Microarray Analysis of Diurnal and Circadian-Regulated Genes in Arabidopsis
Schaffer, R., Landgraf, J., Accerbi, M., Simon, V., Larson, M., & Wisman, E. (2001) · The Plant Cell · doi:10.1105/tpc.13.1.113 · Cited by 457
LIGHT CONTROL OF SEEDLING DEVELOPMENT
von Arnim, A., & Deng, X.-W. (1996) · Annual Review of Plant Physiology and Plant Molecular Biology · doi:10.1146/annurev.arplant.47.1.215 · Cited by 363
Self-citationMockler, T. C., Guo, H., Yang, H., Duong, H., & Lin, C. (1999) · Development · doi:10.1242/dev.126.10.2073 · Cited by 353
Re-examining the role of the glyoxylate cycle in oilseeds
Eastmond, P. J., & Graham, I. A. (2001) · Trends in Plant Science · doi:10.1016/s1360-1385(00)01835-5 · Cited by 331
Somerville, C., & Somerville, S. (1999) · Science · doi:10.1126/science.285.5426.380 · Cited by 312
Wall Structure and Wall Loosening. A Look Backwards and Forwards
Cosgrove, D. J. (2001) · Plant Physiology · doi:10.1104/pp.125.1.131 · Cited by 309
The Arabidopsis DIMINUTO/DWARF1 Gene Encodes a Protein Involved in Steroid Synthesis
Klahre, U., Noguchi, T., Fujioka, S., Takatsuto, S., Yokota, T., Nomura, T., Yoshida, S., & Chua, N.-H. (1998) · The Plant Cell · doi:10.1105/tpc.10.10.1677 · Cited by 289
Aquaporins. A Molecular Entry into Plant Water Relations
Maurel, C., & Chrispeels, M. J. (2001) · Plant Physiology · doi:10.1104/pp.125.1.135 · Cited by 289
Briggs, W. R., & Olney, M. A. (2001) · Plant Physiology · doi:10.1104/pp.125.1.85 · Cited by 274
Xyloglucan endotransglycosylases: diversity of genes, enzymes and potential wall-modifying functions
Campbell, P. H. (1999) · Trends in Plant Science · doi:10.1016/s1360-1385(99)01468-5 · Cited by 268
Phytochrome control of RNA levels in developing pea and mung-bean leaves
Thompson, W. F., Everett, M., Polans, N. O., Jorgensen, R. A., & Palmer, J. D. (1983) · Planta · doi:10.1007/bf00397240 · Cited by 247
Ang, L. H., & Deng, X. W. (1994) · The Plant Cell · doi:10.1105/tpc.6.5.613 · Cited by 243
Self-citationZurek, D. M., & Clouse, S. D. (1994) · Plant Physiology · doi:10.1104/pp.104.1.161 · Cited by 218
Signalling in light-controlled development
Deng, X. W., & Quail, P. H. (1999) · Seminars in Cell and Developmental Biology · doi:10.1006/scdb.1999.0287 · Cited by 201
Self-citationChanges in cell wall architecture during cell elongation
McCann, M. C., & Roberts, K. (1994) · Journal of Experimental Botany · doi:10.1093/jxb/45.special_issue.1683 · Cited by 182
Phytochrome a overexpression inhibits hypocotyl elongation in transgenic Arabidopsis.
Boylan, M. T., & Quail, P. H. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.23.10806 · Cited by 178
Puente, P., Wei, N., & Deng, X. W. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00743.x · Cited by 160
Self-citationBrassinosteroid signal transduction: still casting the actors
Schumacher, K., & Chory, J. (2000) · Current Opinion in Plant Biology · doi:10.1016/s1369-5266(99)00038-2 · Cited by 122
Shi, L., Twary, S. N., Yoshioka, H., Gregerson, R. G., Miller, S. S., Samac, D. A., Gantt, J. S., Unkefer, P. J., & Vance, C. P. (1997) · The Plant Cell · doi:10.1105/tpc.9.8.1339 · Cited by 88
Batschauer, A., Ehmann, B., & Sch�fer, E. (1991) · Plant Molecular Biology · doi:10.1007/bf00020550 · Cited by 77
Sequence and analysis of the Arabidopsis genome
Bevan, M. W. (2001) · Current Opinion in Plant Biology · doi:10.1016/s1369-5266(00)00144-8 · Cited by 68
Phytochrome regulation of nuclear gene expression in plants
Kuno, N., & Furuya, M. (2000) · Seminars in Cell and Developmental Biology · doi:10.1006/scdb.2000.0205 · Cited by 52
Cited by
The cryptochromes: blue light photoreceptors in plants and animals
Chaves, I., Pokorny, R., Byrdin, M., Hoang, N., Ritz, T., Brettel, K., Essen, L.-O., van der Horst, G. T. J., Batschauer, A., & Ahmad, M. (2011) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042110-103759 · Cited by 845
Phytochrome Signaling Mechanisms
Li, J., Li, G., Wang, H., & Wang Deng, X. (2011) · The Arabidopsis Book · doi:10.1199/tab.0148 · Cited by 561
Self-citationHuché-Thélier, L., Crespel, L., Gourrierec, J. L., Morel, P., Sakr, S., & Leduc, N. (2016) · Environmental and Experimental Botany · doi:10.1016/j.envexpbot.2015.06.009 · Cited by 458
Shin, J., Park, E., & Choi, G. (2007) · The Plant Journal · doi:10.1111/j.1365-313x.2006.03021.x · Cited by 444
Qin, G., Gu, H., Ma, L., Peng, Y., Deng, X. W., Chen, Z., & Qu, L.-J. (2007) · Cell Research · doi:10.1038/cr.2007.40 · Cited by 411
Self-citation
Metadata
- Authors
- Ma, L., Li, J., Qu, L., Hager, J., Chen, Z., Zhao, H., & Deng, X. W.
- Venue
- The Plant Cell
- Publisher
- Oxford University Press (OUP)
- Published
- 2001-12
- Volume
- 13
- Issue
- 12
- Pages
- 2589-2607
- ISSN
- 1040-4651 (ISSN-L)
- 1532-298X
- OpenAlex
- W2130110013
- Cited by
- 561
- References
- 52
- FWCI
- 40.17
- Type
- journal article
- Language
- en
- Open access
- green
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