Centers & Labs

RIKEN Center for Sustainable Resource Science

Plant Genomic Network Research Team

Team Leader: Motoaki Seki (Ph.D.)
Motoaki  Seki(Ph.D.)

We are analyzing novel epigenetic, RNA and peptide 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 etc. We are analyzing regulatory networks of tuber root development in cassava by integrated omics analyses and aim to develop useful cassava plants, 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.

Main Research Field

Plant & Animal Science

Related Research Fields

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

Research Subjects

  • 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 etc.
  • Analysis of regulatory networks of tuber root development in cassava by integrated omics analyses and development of useful cassava plants, such as improved plant productivity
  • Advancement of plant transcriptome and epigenome analyses (Cutting-edge Plant Science Research Network in Japan etc.)

Selected 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. 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).
  6. 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).
  7. 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).
  8. 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).
  9. Nakaminami, K.,Matsui,A, Nakagami, H.,Minami, A., Nomura, Y., Tanaka, M., Morosawa, T., Ishida, J., Takahashi, S., Umemura, M., Shirasu, K. and Seki, M.:
    "Analysis of differential expression patterns of mRNA and protein during cold- and de-acclimation in Arabidopsis."
    Mol. Cell. Proteomics 13, 3602-3611 (2014).
  10. Sako, K., Kim, J.M., Matsui, A., Nakamura, K., Tanaka, M., Kobayashi, M., Saito, K., Nishino, N., Kusano, M., Taji, T., Yoshida, M. and Seki, M.:
    "Ky-2, a histone deacetylase inhibitor, enhances high-salinity stress tolerance in Arabidopsis thaliana."
    Plant Cell Physiol. (in press).

Lab Members

Principal Investigator

Motoaki Seki
Team Leader

Core Members

Jong Myong Kim
Research Scientist
Akihiro Matsui
Research Scientist
Kentaro Nakaminami
Research Scientist
Yoshinori Utsumi
Research Scientist
Khurram Bashir
Research Scientist
Minoru Ueda
Research Scientist
Hiroki Tokunaga
Postdoctoral Researcher
Kaori Sako
Postdoctoral Researcher
Sultana Rasheed
Junior Research Associate
Onsaya Patanun
International Program Associate
Maho Tanaka
Technical Staff I
Junko Ishida
Technical Staff I
Satoshi Takahashi
Technical Staff I
Seiko Nomura
Technical Staff II
Chikako Utsumi
Technical Staff II