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한국생명정보학회 (Korean Society for Bioinformatics)
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Overview of Arabidopsis Resource Project in Japan

  • 투고 : 2011.01.01
  • 심사 : 2011.01.15
  • 발행 : 2011.03.31
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초록

Arabidopsis is well-known to the world's plant research community as a model plant. Many significant resources and innovative research tools, as well as large bodies of genomic information, have been created and shared by the research community, partly explaining why so many researchers use this small plant for their research. The genome sequence of Arabidopsis was fully characterized by the end of the $20^{th}$ century. Soon afterwards, the Arabidopsis research community began a 10-year international project on the functional genomics of the species. In 2001, at the beginning of the project, the RIKEN BioResource Center (BRC) started its Arabidopsis resource project. The following year, the National BioResource Project was launched, funded by the Japanese government, and the RIKEN BRC was chosen as a core facility for Arabidopsis resource. Seeds of RIKEN Arabidopsis transposon-tagged mutant lines, activation-tagged lines, full-length cDNA over-expresser lines, and natural accessions, as well as RIKEN Arabidopsis full-length cDNA clones and T87 cells, are preserved at RIKEN BRC and distributed around the world. The major resources provided to the research community have been full-length cDNA clones and insertion mutants that are suitable for use in reverse-genetics studies. This paper provides an overview of the Arabidopsis resources made available by RIKEN BRC and examples of research that has been done by users and developers of these resources.

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참고문헌

  1. Ito, T., Motohashi, R., Kuromori, T., Mizukado, S., Sakurai, T., Kanahara, H., Seki, M., and Shinozaki, K. (2002). A new resource of locally transposed Dissociation elements for screening gene-knockout lines in silico on the Arabidopsis genome. Plant Physiol 129, 1695-1699. https://doi.org/10.1104/pp.002774
  2. Ito, T., Motohashi, R., Kuromori, T., Noutoshi, Y., Seki, M., Kamiya, A., Mizukado, S., Sakurai, T., and Shinozaki, K. (2005). A resource of 5,814 dissociation transposon-tagged and sequence-indexed lines of Arabidopsis transposed from start loci on chromosome 5. Plant Cell Physiol 46, 1149-1153. https://doi.org/10.1093/pcp/pci112
  3. Kuromori, T., Hirayama, T., Kiyosue, Y., Takabe, H., Mizukado, S., Sakurai, T., Akiyama, K., Kamiya, A., Ito, T., and Shinozaki, K. (2004). A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis. Plant J 37, 897-905. https://doi.org/10.1111/j.1365.313X.2004.02009.x
  4. Smith, D., Yanai, Y., Liu, Y.G., Ishiguro, S., Okada, K., Shibata, D., Whittier, R.F., and Fedoroff, N.V. (1996). Characterization and mapping of Ds-GUS-T-DNA lines for targeted insertional mutagenesis. Plant J 10, 721-732. https://doi.org/10.1046/j.1365-313X.1996.10040721.x
  5. Hayashi, H., Czaja, I., Lubenow, H., Schell, J., and Walden, R. (1992). Activation of a plant gene by T-DNA tagging: auxin-independent growth in vitro. Science 258, 1350-1353. https://doi.org/10.1126/science.1455228
  6. Nakazawa, M., Ichikawa, T., Ishikawa, A., Kobayashi, H., Tsuhara, Y., Kawashima, M., Suzuki, K., Muto, S., and Matsui, M. (2003). Activation tagging, a novel tool to dissect the functions of a gene family. Plant J 34, 741-750. https://doi.org/10.1046/j.1365-313X.2003.01758.x
  7. Takase, T., Nakazawa, M., Ishikawa, A., Kawashima, M., Ichikawa, T., Takahashi, N., Shimada, H., Manabe, K., and Matsui, M. (2004). ydk1-D, an auxin-responsive GH3 mutant that is involved in hypocotyl and root elongation. Plant J 37, 471-483. https://doi.org/10.1046/j.1365-313X.2003.01973.x
  8. Takase, T., Nakazawa, M., Ishikawa, A., Manabe, K., and Matsui, M. (2003). DFL2, a new member of the Arabidopsis GH3 gene family, is involved in red light-specific hypocotyl elongation. Plant Cell Physiol 44, 1071-1080. https://doi.org/10.1093/pcp/pcg130
  9. Zhao, L., Nakazawa, M., Takase, T., Manabe, K., Kobayashi, M., Seki, M., Shinozaki, K., and Matsui, M. (2004). Overexpression of LSH1, a member of an uncharacterised gene family, causes enhanced light regulation of seedling development. Plant J 37, 694-706. https://doi.org/10.1111/j.1365-313X.2003.01993.x
  10. Ichikawa, T., Nakazawa, M., Kawashima, M., Muto, S., Gohda, K., Suzuki, K., Ishikawa, A., Kobayashi, H., Yoshizumi, T., Tsumoto, Y., et al. (2003). Sequence database of 1172 T-DNA insertion sites in Arabidopsis activation-tagging lines that showed phenotypes in T1 generation. Plant J 36, 421-429. https://doi.org/10.1046/j.1365-313X.2003.01876.x
  11. Ichikawa, T., Nakazawa, M., Kawashima, M., Iizumi, H., Kuroda, H., Kondou, Y., Tsuhara, Y., Suzuki, K., Ishikawa, A., Seki, M., et al. (2006). The FOX hunting system: an alternative gain-of-function gene hunting technique. Plant J 48, 974-985. https://doi.org/10.1111/j.1365-313X.2006.02924.x
  12. Kobayashi, Y., Kuroda, K., Kimura, K., Southron-Francis, J.L., Furuzawa, A., Iuchi, S., Kobayashi, M., Taylor, G.J., and Koyama, H. (2008). Amino acid polymorphisms in strictly conserved domains of a P-type ATPase HMA5 are involved in the mechanism of copper tolerance variation in Arabidopsis. Plant Physiol 148, 969-980. https://doi.org/10.1104/pp.108.119933
  13. Sakurai, T., Satou, M., Akiyama, K., Iida, K., Seki, M., Kuromori, T., Ito, T., Konagaya, A., Toyoda, T., and Shinozaki, K. (2005). RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. Nucleic Acids Res 33, D647-650.
  14. Seki, M., Carninci, P., Nishiyama, Y., Hayashizaki, Y., and Shinozaki, K. (1998). High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper. Plant J 15, 707-720. https://doi.org/10.1046/j.1365-313x.1998.00237.x
  15. Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama, K., Oono, Y., et al. (2002). Functional annotation of a full-length Arabidopsis cDNA collection. Science 296, 141-145. https://doi.org/10.1126/science.1071006
  16. Seki, M., Narusaka, M., Ishida, J., Nanjo, T., Fujita, M., Oono, Y., Kamiya, A., Nakajima, M., Enju, A., Sakurai, T., et al. (2002). Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31, 279-292. https://doi.org/10.1046/j.1365-313X.2002.01359.x
  17. Seki, M., Ishida, J., Narusaka, M., Fujita, M., Nanjo, T., Umezawa, T., Kamiya, A., Nakajima, M., Enju, A., Sakurai, T., et al. (2002). Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Funct Integr Genomics 2, 282-291. https://doi.org/10.1007/s10142-002-0070-6
  18. Ogawa, Y., Suzuki, H., Sakurai, N., Aoki, K., Saito, K., and Shibata, D. (2008). Cryopreservation and metabolic profiling analysis of Arabidopsis T87 suspension-cultured cells. Cryo Letters 29, 427-436.
  19. Axelos, M., Curie, C., Mazzolini, L., C., B., and Lescure, B. (1992). A protocol for transient gene expression in Arabidopsis thaliana protoplasts isolated from cell suspension cultures. Plant Physiol Biochem 30, 123-128.
  20. Nakamichi, N., Matsushika, A., Yamashino, T., and Mizuno, T. (2003). Cell autonomous circadian waves of the APRR1/TOC1 quintet in an established cell line of Arabidopsis thaliana. Plant Cell Physiol 44, 360-365. https://doi.org/10.1093/pcp/pcg039
  21. Shinozaki, K. (2010). The ICAR2010 for development of Arabidopsis research beyond 2010. J Plant Res 123, 265-266. https://doi.org/10.1007/s10265-010-0335-4