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Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays

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Abstract

A comparative analysis of gene expression profiles during cold acclimation and deacclimation is necessary to elucidate the molecular mechanisms of cold stress responses in higher plants. We analyzed gene expression profiles in the process of cold acclimation and deacclimation (recovery from cold stress) using two microarray systems, the 7K RAFL cDNA microarray and the Agilent 22K oligonucleotide array. By both microarray analyses, we identified 292 genes up-regulated and 320 genes down-regulated during deacclimation, and 445 cold up-regulated genes and 341 cold down-regulated genes during cold acclimation. Many genes up-regulated during deacclimation were found to be down-regulated during cold acclimation, and vice versa. The genes up-regulated during deacclimation were classified into (1) regulatory proteins involved in further regulation of signal transduction and gene expression and (2) functional proteins involved in the recovery process from cold-stress-induced damages and plant growth. We also applied expression profiling studies to identify the key genes involved in the biosynthesis of carbohydrates and amino acids that are known to play important roles in cold acclimation. We compared genes that are regulated during deacclimation with those regulated during rehydration after dehydration to discuss the similarity and difference of each recovery process.

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Abbreviations

GM:

Germination medium

LEA:

Late-embryogenesis-abundant

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Acknowledgements

We thank Dr. Matuo Uemura, Dr. Riichiro Yoshida, and Dr. Fumiyoshi Myouga for their helpful discussion and advices. We thank all the members of RIKEN Plant Functional Genomics Research Team and Plant Molecular Biology Laboratory for their help. This work was supported in part by a grant for Genome Research from RIKEN, the Program for Promotion of Basic Research Activities for Innovative Biosciences, the Special Coordination Fund of the Science and Technology Agency, and a Grant-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MECSST) to K.S. It was also supported in part by a Grant-in-Aid for Scientific Research on Priority Areas (C) ‘Genome Science’ from MECSST to M.S.

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Authors and Affiliations

  1. Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan

    Youko Oono, Motoaki Seki, Masakazu Satou, Kei Iida, Kenji Akiyama, Tetsuya Sakurai, Miki Fujita & Kazuo Shinozaki

  2. Graduate School of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-0074, Japan

    Youko Oono & Kazuo Shinozaki

  3. Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan

    Youko Oono, Motoaki Seki & Kazuo Shinozaki

  4. Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 2-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan

    Kazuko Yamaguchi-Shinozaki

  5. CREST, Japan Science and Technology Corporation (JST), Tokyo, Japan

    Miki Fujita, Kazuko Yamaguchi-Shinozaki & Kazuo Shinozaki

  6. Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyou-ku, Tokyo, 113-8657, Japan

    Kazuko Yamaguchi-Shinozaki

  7. RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan

    Masakazu Satou, Kenji Akiyama, Tetsuya Sakurai & Kazuo Shinozaki

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  1. Youko Oono
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  2. Motoaki Seki
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  3. Masakazu Satou
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Correspondence to Kazuo Shinozaki.

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Oono, Y., Seki, M., Satou, M. et al. Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays. Funct Integr Genomics 6, 212–234 (2006). https://doi.org/10.1007/s10142-005-0014-z

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