Educational Activities

Eukaryotic Cell Biology

Research Activities

1. Approaching the mystery of the robust regeneration in plants to save the food hunger
3500-year-old cedars exhibit that plant live longer than animals. One of the causes of longevity is the robust regeneration. Roots and leaves can regenerate immediately after grafting and pruning. We study the molecular mechanism from the view point of epigenetics without the alternation in DNA sequence itself. The histone modification is examined by chromatin immunoprecipitation and biochemically transparent plants are analyzed by three-dimensional deep imaging. We are also developing the application that contributes to food and biomass production, such as by irradiating plants with radiation in advance to enhance their regeneration capacity.

2. Unraveling the secrets of chromatin dynamics in plant nuclei to develop the novel gene regulation techniques for enhancement in the environmental tolerance
The nucleus likened to intracellular microcosmos is a dynamic organelle in which chromatin expands four-dimensionally and controls gene expression. In plants, it is not known how the chromatin changes and responds to the environment in response to environmental stimuli such as light or temperature changes. Because we found plant-specific subnuclear structures in flowering plants, we have a chance to develop new technologies to regulate the gene expression of crop species based on chromatin dynamics. We study the chromatin and nuclear dynamics through live imaging and Hi-C techniques.

3. Studying the integrated system beyond kingdoms with synthetic biology
Approximately 1.6 billion years ago, a primitive eukaryotic cell took up a cyanobacterium in the first endosymbiosis and evolved into algae with plastids derived from the endosymbiotic cyanobacterium. Several algae have become nested within secondary host cells through secondary endosymbiosis. Secondary endosymbiosis has occurred individually and horizontally at different times in different lineages in the animal, fungi and plant kingdoms, resulting in a great diversity of eukaryotes. Evolutional insights from secondary endosymbiosis and extant photosynthetic animals imply that heterotrophic organisms have the potential to uptake algae and convert to autotrophic organisms. Inspired by such endosymbiosis and photosynthetic animals, we have attempted to experimentally create animal cells including plant genome known as planimal cells. Transcriptomic, proteomic and epigenetic analyses of planimal cells will give us new insights into the universality and specificity of molecular mechanisms between plants and animals. Planimal cells have the potential to induce an energy revolution and solve the global food problem by reducing energy consumption by heterotrophic species.

Literature

Selected publication(*Corresponding authors、#Equally contributed authors)
1) Shibuta, M. K., Sakamoto, T., Yamaoka, T., Yoshikawa, M., Kasamatsu, S., Yagi, N., Fujimoto, S., Suzuki, T., Uchino, S., Sato, Y., Kimura, H. and Matsunaga, S.*(2021) A live imaging system to analyze spatiotemporal dynamics of RNA polymerase II modification in Arabidopsis thaliana. Commun. Biol., 4, 580 (10 pages).
2) Sakamoto, Y., Sato, M., Sato, Y., Harada, A., Suzuki, T., Goto, C., Tamura, K., Toyooka, K., Kimura, H., Ohkawa, Y., Hara-Nishimura, I., Takagi, S. and Matsunaga, S.*(2020) Subnuclear gene positioning through lamina association affects copper tolerance. Nature Commun., 11, 5914 (12 pages).
3) Ishihara, H.#, Sugimoto, K.*#, Tarr, P. T., Temman, H., Kadokura, S., Inui, Y., Sakamoto, T., Sasaki, T., Aida, M., Suzuki, T., Inagaki, S., Morohashi, K., Seki, M., Kakutani, T., Meyerowitz, E. M., and Matsunaga, S.* (2019) Primed histone demethylation regulates shoot regenerative competency. Nature Commun., 10, 1786 (15 pages).
4) Kato, S., Okamura, E., Matsunaga, T. M., Nakayama, M., Kawanishi, Y., Ichinose, T., Iwane, A. H., Sakamoto, T., Imoto, Y., Ohnuma, M., Nomura, Y., Nakagami, H., Kuroiwa, H., Kuroiwa, T., and Matsunaga, S.* (2019) Cyanidioschyzon merolae aurora kinase phosphorylates evolutionarily conserved sites on its target to regulate mitochondrial division. Commun. Biol., 2, 477 (9 pages).
5) Sugimoto, K., Temman, H.#, Kadokura, S.#, and Matsunaga, S.* (2019) To regenerate or not to regenerate: factors that drive plant regeneration. Curr. Opin. Plant Biol., 47, 138-150.
6) Sakamoto, T., Tsujimoto-Inui, Y., Sotta, N., Hirakawa, T., Matsunaga, T. M., Fukao, Y., Matsunaga, S.*, and Fujiwara, T.* (2018) Proteasomal degradation of BRAHMA promotes Boron tolerance in Arabidopsis. Nature Commun., 9, 5285 (16 pages).
7) Katagiri, Y., Hasegawa, J., Fujikura, U., Hoshino, R., Matsunaga, S.*, and Tsukaya, H.* (2016) The coordination of ploidy and cell size differs between cell layers in leaves. Development, 143, 1120-1125.
8)Kutsuna, N.#, Higaki, T.#, Matsunaga, S.*#, Otsuki, T., Yamaguchi, M., Fujii, H., and Hasezawa, S. (2012) Active learning framework with iterative clustering for bioimage classification. Nature Commun., 3, 1032 (10 pages).

Other Activities

2019-present Vice President The Union of Japanese Societies for Biological Sciences
2019-present Director The Botanical Society of Japan
2017-2019 Managing Director The Botanical Society of Japan
2012-2017 Director The Japanese Society of Plant Physiologists
2011-present Director Japan Mendel Society

Future Plan

Costruction of planimal cells
Analyses of molecular mechanism of 4D dynamics of chromatin
Analyses of molecular mechanism of plant regeneration

Messages to Students

"The best way to predict your future is to create it."
Where is life science headed in this omics era based on genome information? According to the above quote from President Lincoln, our laboratory will pioneer the frontier of life science by ourselves. We will work on find a novel biological mechanism and develop original techniques to contribute to advances in life science.
Laboratory policy
(1) Be Serious: Do your best to achieve your goal.
(2) Be Enthusiastic: Focus on the research which you really have much interest.
(3) Have your strengths: Rediscover yourself and find your own strengths for the future.
(4) Keep your professional sprits: Spare no effort to raise your level.

URL

http://park.itc.u-tokyo.ac.jp/matsunaga_lab/english/index.html