Plant Genomic Network Research Team

We are analyzing novel epigenetic and RNA regulation mechanisms in environmental stress adaptation and acclimation by cutting-edge genomic approaches. We aim to develop useful plant resources, such as stress-tolerant plants by use of chemical compounds. We are analyzing regulatory networks of starch biosynthesis by integrated omics analyses and aim to develop useful plant resources, such as improved plant productivity. We also collaborate with other research teams inside and outside the center on the transcriptome and epigenome analysis using cutting-edge genome technologies.

Research Fields

Biology & Biochemistry / Molecular Biology & Genetics / Agricultural Sciences / Plant & Animal Science

• Analysis of epigenetic regulation mechanisms in environmental stress adaptation and acclimation
• Analysis of RNA regulation mechanisms in environmental stress adaptation and acclimation
• Development of useful plant resources, such as stress-tolerant plants by use of chemical compounds
• Analysis of regulatory networks of starch biosynthesis by integrated omics analyses and development of useful plant resources, such as improved plant productivity
• Advancement of plant transcriptome and epigenome analyses (Cutting-edge Plant Science Research Network in Japan etc.)

Publications

1. Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., Hayashizaki, Y. and Shinozaki, K.:
   "Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses using a full-length cDNA microarray."
   Plant Cell 13, 61-72 (2001).
2. Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama, K., Oono, Y., Muramatsu, M., Hayashizaki, Y., Kawai, J., Carninci, P., Itoh, M., Ishii, Y., Arakawa, T., Shibata, K., Shinagawa, A. and Shinozaki, K.:
   "Functional annotation of a full-length Arabidopsis cDNA collection."
   Science 296, 141-145 (2002).
3. Seki, M., Narusaka, M., Ishida, J., Nanjo, T., Fujita, M., Oono, Y., Kamiya, A., Nakajima, M., Enju, A., Sakurai, T., Satou, M., Akiyama, K., Taji, T., Yamaguchi-Shinozaki, K., Carninci, P., Kawai, J., Hayashizaki, Y. and Shinozaki, K.:
   "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 (2002).
4. Yamada, K., Lim, J., Dale, J.M., Chen, H., Shinn, P., Palm, C.J., Southwick, A.M., Wu, H.C., Kim, C., Nguyen, M., Pham, P., Cheuk, R., Karlin-Neumann, G., Liu, S.X., Lam, B., Sakano, H., Wu, T., Yu, G., Miranda, M., Quach, H.L., Tripp, M., Chang, C.H., Lee, J.M., Toriumi, M., Chan, M.M.H., Tang, C.C., Onodera, C.S., Deng, J.M., Akiyama, K., Ansari, Y., Arakawa, T., Banh, J., Banno, F., Bowser, L., Brooks, S., Carninci, P., Chao, Q., Choy, N., Enju, A., Goldsmith, A.D., Gurjal, M., Hansen, N.F., Hayashizaki, Y., Johnson-Hopson, C., Hsuan, V.W., Iida, K., Karnes, M., Khan, S., Koesema, E., Ishida, J., Jiang, P.X., Jones, T., Kawai, J., Kamiya, A., Meyers, C., Nakajima, M., Narusaka, M., Seki, M., Sakurai, T., Satou, M., Tamse, R., Vaysberg, M., Wallender, E.K., Wong, C., Yamamura, Y., Yuan, S., Shinozaki, K., Davis, R.W., Theologis, A. and Ecker, J.R.:
   "Empirical analysis of transcriptional activity in the Arabidopsis genome.
   Science 302, 842-846 (2003)."
5. Seki, M., Kamei, A., Yamaguchi-Shinozaki, K. and Shinozaki, K.:
   "Molecular responses to drought, salinity and frost: common and different paths for plant protection."
   Curr. Opin. Biotechnol. 4,194-199 (2003).
6. Matsui, A., Ishida, J., Morosawa, T., Mochizuki, Y., Kaminuma, E., Endo, T.A., Okamoto, M., Nambara, E., Nakajima, M., Kawashima, M., Satou, M., Kim, J.M., Kobayashi, N., Toyoda, T., Shinozaki, K. and Seki, M:
   "Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array."
   Plant Cell Physiol. 49, 1135-1149 (2008).
7. Kurihara, Y., Matsui, A., Hanada, K., Kawashima, M., Ishida, J., Morosawa, T., Tanaka, M., Kaminuma, E., Mochizuki, Y., Matsushima, A., Toyoda, T., Shinozaki, K. and Seki, M.:
   "Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis."
   Proc. Natl. Acad. Sci. USA 106, 2453-2458 (2009).
8. Okamoto, M., Tatematsu, K., Matsui, A., Morosawa, T., Ishida, J., Tanaka, M., Endo, A.T., Mochizuki, Y., Toyoda, T., Kamiya, Y., Shinozaki, K., Nambara, E. and Seki, M.:
   "Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays."
   Plant J. 62, 39-51 (2010).
9. To, T.K., Kim, J.M., Matsui, A., Kurihara, Y., Morosawa, T., Ishida, J., Tanaka, M., Endo, T., Kakutani, T., Toyoda, T., Kimura, H., Yokoyama, S., Shinozaki, K. and Seki, M.:
   "Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1. PLoS Genet. 7, e1002055 (2011)."
10. Kim, J.M., To, T.K., Ishida, J., Matsui, A., Kimura, H. and Seki, M.:
    "Transition of chromatin status during the recovery process from drought stress in Arabidopsis thaliana."
    Plant Cell Physiol. 53, 847-856 (2012).