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Functional genomics using RIKEN Arabidopsis thaliana full-length cDNAs

  • Current Topics in Plant Research
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Abstract

Full-length cDNAs are essential for the correct annotation of genomic sequences as well as for the functional analysis of genes and their products. We have isolated about 240,000 RIKEN Arabidopsis full-length (RAFL) cDNA clones. These clones were clustered into about 17,000 non-redundant cDNA groups, i.e., about 60% of all Arabidopsis predicted genes. The sequence information of the RAFL cDNAs is useful for promoter analysis, and for the correct annotation of predicted transcriptional units and gene products. We prepared cDNA microarrays containing independent full-length cDNA groups and studied the expression profiles of genes under various stress- and hormone-treatment conditions, and in various mutants and transgenic plants. These expression profiling studies have shown the expression levels of many genes as a detailed snapshot describing the state of a biological system in planta under various conditions. We have applied RAFL cDNAs to the functional analysis of proteins using the full-length cDNA over-expressing (FOX) gene hunting system and the wheat germ cell-free protein synthesis system. The RAFL cDNA collection was also used for determination of the domain structure of proteins by NMR. In this review, we summarize the present state and perspectives of functional genomics using RAFL cDNAs.

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Acknowledgments

We would like to thank our many collaborators for their valuable participation in this work. This work was supported 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 to K.S. It was also supported by a Grant-in-Aid for Scientific Research on Priority Areas (C) “Genome Science” from the Ministry of Education, Culture, Sports, Science and Technology of Japan to M.S.

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Authors and Affiliations

  1. Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center (PSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan

    Motoaki Seki

  2. Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, 244-0813, Japan

    Motoaki Seki

  3. Gene Discovery Research Team, RIKEN Plant Science Center (PSC), RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan

    Kazuo Shinozaki

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  1. Motoaki Seki
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  2. Kazuo Shinozaki
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Correspondence to Motoaki Seki.

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Motoaki Seki is the recipient of the BSJ Award for Young Scientists, 2005.

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Seki, M., Shinozaki, K. Functional genomics using RIKEN Arabidopsis thaliana full-length cDNAs. J Plant Res 122, 355–366 (2009). https://doi.org/10.1007/s10265-009-0239-3

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