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Plant Cell, Vol. 13, 61-72, January 2001, Copyright © 2001, American Society of Plant Physiologists

Monitoring the Expression Pattern of 1300 Arabidopsis Genes under Drought and Cold Stresses by Using a Full-Length cDNA Microarray

Motoaki Sekia,b, Mari Narusakaa, Hiroshi Abec, Mie Kasugac, Kazuko Yamaguchi-Shinozakic, Piero Carnincid, Yoshihide Hayashizakid, and Kazuo Shinozakia,b
a Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 3-1-1 Koyadai, Tsukuba 305-0074, Japan
b Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba 305-0074, Japan
c Biological Resources Division, Japan International Research Center for Agricultural Sciences, Ministry of Agriculture, Forestry, and Fisheries, 2-1 Ohwashi, Tsukuba, Ibaraki 305-0851, Japan
d Genome Science Laboratory, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba 305-0074, Japan

Correspondence to: Kazuo Shinozaki, shinozaki{at}rtc.riken.go.jp (E-mail), 81-298-36-9060 (fax)

Full-length cDNAs are essential for functional analysis of plant genes. Using the biotinylated CAP trapper method, we constructed full-length Arabidopsis cDNA libraries from plants in different conditions, such as drought-treated, cold-treated, or unstressed plants, and at various developmental stages from germination to mature seed. We prepared a cDNA microarray using ~1300 full-length Arabidopsis cDNAs to identify drought- and cold-inducible genes and target genes of DREB1A/CBF3, a transcription factor that controls stress-inducible gene expression. In total, 44 and 19 cDNAs for drought- and cold-inducible genes, respectively, were isolated, 30 and 10 of which were novel stress-inducible genes that have not been reported as drought- or cold-inducible genes previously. Twelve stress-inducible genes were identified as target stress-inducible genes of DREB1A, and six of them were novel. On the basis of RNA gel blot and microarray analyses, the six genes were identified as novel drought- and cold-inducible genes that are controlled by DREB1A. Eleven DREB1A target genes whose genomic sequences have been registered in the GenBank database contained the dehydration-responsive element (DRE) or DRE-related CCGAC core motif in their promoter regions. These results show that our full-length cDNA microarray is a useful material with which to analyze the expression pattern of Arabidopsis genes under drought and cold stresses, to identify target genes of stress-related transcription factors, and to identify potential cis-acting DNA elements by combining the expression data with the genomic sequence data.




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 Plant Cell PhysiolHome page
Y. Narusaka, M. Narusaka, M. Seki, M. Fujita, J. Ishida, M. Nakashima, A. Enju, T. Sakurai, M. Satou, A. Kamiya, et al.
Expression Profiles of Arabidopsis Phospholipase A IIA Gene in Response to Biotic and Abiotic Stresses
Plant Cell Physiol., November 15, 2003; 44(11): 1246 - 1252.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
E. J. Campbell, P. M. Schenk, K. Kazan, I. A.M.A. Penninckx, J. P. Anderson, D. J. Maclean, B. P.A. Cammue, P. R. Ebert, and J. M. Manners
Pathogen-Responsive Expression of a Putative ATP-Binding Cassette Transporter Gene Conferring Resistance to the Diterpenoid Sclareol Is Regulated by Multiple Defense Signaling Pathways in Arabidopsis
Plant Physiology, November 1, 2003; 133(3): 1272 - 1284.
[Abstract] [Full Text] [PDF]

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 J Exp BotHome page
N. Tuteja
Plant DNA helicases: the long unwinding road
J. Exp. Bot., October 1, 2003; 54(391): 2201 - 2214.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
Y. H. Cheong, K.-N. Kim, G. K. Pandey, R. Gupta, J. J. Grant, and S. Luan
CBL1, a Calcium Sensor That Differentially Regulates Salt, Drought, and Cold Responses in Arabidopsis
PLANT CELL, August 1, 2003; 15(8): 1833 - 1845.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
P. Casati and V. Walbot
Gene Expression Profiling in Response to Ultraviolet Radiation in Maize Genotypes with Varying Flavonoid Content
Plant Physiology, August 1, 2003; 132(4): 1739 - 1754.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
A. K. Singh, L. M. McIntyre, and L. A. Sherman
Microarray Analysis of the Genome-Wide Response to Iron Deficiency and Iron Reconstitution in the Cyanobacterium Synechocystis sp. PCC 6803
Plant Physiology, August 1, 2003; 132(4): 1825 - 1839.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
F. T.S. Nogueira, V. E. De Rosa Jr., M. Menossi, E. C. Ulian, and P. Arruda
RNA Expression Profiles and Data Mining of Sugarcane Response to Low Temperature
Plant Physiology, August 1, 2003; 132(4): 1811 - 1824.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
P. Wu, L. Ma, X. Hou, M. Wang, Y. Wu, F. Liu, and X. W. Deng
Phosphate Starvation Triggers Distinct Alterations of Genome Expression in Arabidopsis Roots and Leaves
Plant Physiology, July 1, 2003; 132(3): 1260 - 1271.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
J.-Y. Lee and D.-H. Lee
Use of Serial Analysis of Gene Expression Technology to Reveal Changes in Gene Expression in Arabidopsis Pollen Undergoing Cold Stress
Plant Physiology, June 1, 2003; 132(2): 517 - 529.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
G. Breton, J. Danyluk, J.-B. F. Charron, and F. Sarhan
Expression Profiling and Bioinformatic Analyses of a Novel Stress-Regulated Multispanning Transmembrane Protein Family from Cereals and Arabidopsis
Plant Physiology, May 1, 2003; 132(1): 64 - 74.
[Abstract] [Full Text] [PDF]

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 Plant Cell PhysiolHome page
Y. Narusaka, M. Narusaka, M. Seki, J. Ishida, M. Nakashima, A. Kamiya, A. Enju, T. Sakurai, M. Satoh, M. Kobayashi, et al.
The cDNA Microarray Analysis Using an Arabidopsis pad3 Mutant Reveals the Expression Profiles and Classification of Genes Induced by Alternaria brassicicola Attack
Plant Cell Physiol., April 15, 2003; 44(4): 377 - 387.
[Abstract] [Full Text] [PDF]

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 ANN BOT (LOND)Home page
M. TESTER and R. DAVENPORT
Na+ Tolerance and Na+ Transport in Higher Plants
Ann. Bot., April 1, 2003; 91(5): 503 - 527.
[Abstract] [Full Text] [PDF]

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 J. Cell Sci.Home page
S. Hoth, M. Morgante, J.-P. Sanchez, M. K. Hanafey, S. V. Tingey, and N.-H. Chua
Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant
J. Cell Sci., March 14, 2003; 115(24): 4891 - 4900.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
K.-N. Kim, Y. H. Cheong, J. J. Grant, G. K. Pandey, and S. Luan
CIPK3, a Calcium Sensor-Associated Protein Kinase That Regulates Abscisic Acid and Cold Signal Transduction in Arabidopsis
PLANT CELL, February 1, 2003; 15(2): 411 - 423.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
L.-X. Yu and T. L. Setter
Comparative Transcriptional Profiling of Placenta and Endosperm in Developing Maize Kernels in Response to Water Deficit
Plant Physiology, February 1, 2003; 131(2): 568 - 582.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
M. Reymond, B. Muller, A. Leonardi, A. Charcosset, and F. Tardieu
Combining Quantitative Trait Loci Analysis and an Ecophysiological Model to Analyze the Genetic Variability of the Responses of Maize Leaf Growth to Temperature and Water Deficit
Plant Physiology, February 1, 2003; 131(2): 664 - 675.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
H. Abe, T. Urao, T. Ito, M. Seki, K. Shinozaki, and K. Yamaguchi-Shinozaki
Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) Function as Transcriptional Activators in Abscisic Acid Signaling
PLANT CELL, January 1, 2003; 15(1): 63 - 78.
[Abstract] [Full Text] [PDF]

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 J Exp BotHome page
S. Brandt, S. Kloska, T. Altmann, and J. Kehr
Using array hybridization to monitor gene expression at the single cell level
J. Exp. Bot., December 1, 2002; 53(379): 2315 - 2323.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
J. A. Kreps, Y. Wu, H.-S. Chang, T. Zhu, X. Wang, and J. F. Harper
Transcriptome Changes for Arabidopsis in Response to Salt, Osmotic, and Cold Stress
Plant Physiology, December 1, 2002; 130(4): 2129 - 2141.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
Y.-L. Xiao, M. Malik, C. A. Whitelaw, and C. D. Town
Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis
Plant Physiology, December 1, 2002; 130(4): 2118 - 2128.
[Abstract] [Full Text] [PDF]

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 Plant Cell PhysiolHome page
R. Inatsugi, M. Nakamura, and I. Nishida
Phosphatidylcholine Biosynthesis at Low Temperature: Differential Expression of CTP:Phosphorylcholine Cytidylyltransferase Isogenes in Arabidopsis thaliana
Plant Cell Physiol., November 15, 2002; 43(11): 1342 - 1350.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
L. Rizhsky, H. Liang, and R. Mittler
The Combined Effect of Drought Stress and Heat Shock on Gene Expression in Tobacco
Plant Physiology, November 1, 2002; 130(3): 1143 - 1151.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
H. Goda, Y. Shimada, T. Asami, S. Fujioka, and S. Yoshida
Microarray Analysis of Brassinosteroid-Regulated Genes in Arabidopsis
Plant Physiology, November 1, 2002; 130(3): 1319 - 1334.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
M. Menges, L. Hennig, W. Gruissem, and J. A. H. Murray
Cell Cycle-regulated Gene Expression in Arabidopsis
J. Biol. Chem., October 25, 2002; 277(44): 41987 - 42002.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
E. J. Klok, I. W. Wilson, D. Wilson, S. C. Chapman, R. M. Ewing, S. C. Somerville, W. J. Peacock, R. Dolferus, and E. S. Dennis
Expression Profile Analysis of the Low-Oxygen Response in Arabidopsis Root Cultures
PLANT CELL, October 1, 2002; 14(10): 2481 - 2494.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
M. Fedorova, J. van de Mortel, P. A. Matsumoto, J. Cho, C. D. Town, K. A. VandenBosch, J. S. Gantt, and C. P. Vance
Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula
Plant Physiology, October 1, 2002; 130(2): 519 - 537.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
V. Haake, D. Cook, J. L. Riechmann, O. Pineda, M. F. Thomashow, and J. Z. Zhang
Transcription Factor CBF4 Is a Regulator of Drought Adaptation in Arabidopsis
Plant Physiology, October 1, 2002; 130(2): 639 - 648.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
R. Satoh, K. Nakashima, M. Seki, K. Shinozaki, and K. Yamaguchi-Shinozaki
ACTCAT, a Novel cis-Acting Element for Proline- and Hypoosmolarity-Responsive Expression of the ProDH Gene Encoding Proline Dehydrogenase in Arabidopsis
Plant Physiology, October 1, 2002; 130(2): 709 - 719.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
E. Ruelland, C. Cantrel, M. Gawer, J.-C. Kader, and A. Zachowski
Activation of Phospholipases C and D Is an Early Response to a Cold Exposure in Arabidopsis Suspension Cells
Plant Physiology, October 1, 2002; 130(2): 999 - 1007.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
I. Lacourt, S. Duplessis, S. Abba, P. Bonfante, and F. Martin
Isolation and Characterization of Differentially Expressed Genes in the Mycelium and Fruit Body of Tuber borchii
Appl. Envir. Microbiol., September 1, 2002; 68(9): 4574 - 4582.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
G.-P. Xue
Characterisation of the DNA-binding profile of barley HvCBF1 using an enzymatic method for rapid, quantitative and high-throughput analysis of the DNA-binding activity
Nucleic Acids Res., August 1, 2002; 30(15): e77 - e77.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
S. Fowler and M. F. Thomashow
Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway
PLANT CELL, August 1, 2002; 14(8): 1675 - 1690.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
K. P. Kollipara, I. N. Saab, R. D. Wych, M. J. Lauer, and G. W. Singletary
Expression Profiling of Reciprocal Maize Hybrids Divergent for Cold Germination and Desiccation Tolerance
Plant Physiology, July 1, 2002; 129(3): 974 - 992.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
T.-H. Hsieh, J.-T. Lee, P.-T. Yang, L.-H. Chiu, Y.-y. Charng, Y.-C. Wang, and M.-T. Chan
Heterology Expression of the Arabidopsis C-Repeat/Dehydration Response Element Binding Factor 1 Gene Confers Elevated Tolerance to Chilling and Oxidative Stresses in Transgenic Tomato
Plant Physiology, July 1, 2002; 129(3): 1086 - 1094.
[Abstract] [Full Text] [PDF]


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