Analysis of epigenetic regulation mechanisms in environmental stress adaptation and acclimation

Publications

Temman, H., Sakamoto, T., Ueda, M, Sugimoto, K., Migihashi, M., Yamamoto, K., Tsujimoto-Inui, Y., Sato, H., Shibuta, M. K., Nishino, N., Nakamura, T., Shimada, H., Taniguchi, Y. Y., Takeda, S., Aida, M., Suzuki, T., Seki, M. and Matsunaga, S. (2023) Histone deacetylation regulates de novo shoot regeneration. PNAS Nexus 2:pgad002.

Onosato, H., Fujimoto, G., Higami, T., Sakamoto, T., Yamada, A., Suzuki, T., Ozawa, R., Matsunaga, S., Seki, M., Ueda, M., Sako, K., Galis, I. and Arimura, G. (2022) Sustained defense response via volatile signaling and its epigenetic transcriptional regulation. Plant Physiol. 189:922-933.

Vincent, S., Kim, J.M., Pérez-Salamó, I., To, T.K., Torii, C., Ishida, J., Tanaka, M., Endo, T.A., Bhat, P., Devlin, P., *Seki, M., and *Devoto, A. (2022) Jasmonates and histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response. BMC Biol. 20: 83.

Mehraj, H., Takahashi, S., Miyaji, N., Akter, A., Suzuki, Y., Seki, M., Dennis, E. and Fujimoto, R. (2021) Characterization of histone H3 lysine 4 and 36 tri-methylation in Brassica rapa L. Front. Plant Sci. 12:659634.

Mehraj, H., Shea, D.J., Takahashi, S., Miyaji, N., Akter, A., Seki, M., Dennis, E.S., Fujimoto R. and Osabe, K. (2021) Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa. PLOS ONE 16: e0242530.

Ueda, M. and Seki, M. (2020) Histone modifications form epigenetic regulatory networks to regulate abiotic stress response. Plant Physiol. 182: 15-26.

Shea, D., Nishida, N., Takada, S., Itabashi, E., Takahashi, S., Akter, A., Miyaji, N., Osabe, K., Mehraj, H., Shimizu, M., Seki, M., Kakizaki, T.,Okazaki, K., Dennis, E. and Fujimoto, R. (2019) Long noncoding RNAs in Brassica rapa L. following vernalization. Scientific Rep., 9:9302.

Kurita, K.#, Sakamoto, Y.#, Naruse, S., Matsunaga, T.M., Arata, H., Higashiyama, T., Habu, Y., Utsumi, Y., Utsumi, C., Tanaka, M., Takahashi, S., Kim, J.M., Seki, M., Sakamoto, T. and Matsunaga, S. (2019) Intracellular localization of histone deacetylase HDA6 in plants. J. Plant Res. 132: 629-640.

Akter, A. #, Takahashi, S. #, Deng, W. #, Shea, D.J., Itabashi, E., Shimizu, M., Miyaji, N., Osabe, K., Nishida, N., Suzuki, Y., Helliwell, C.A., Seki, M., Peacock, W.J., Dennis, E.S. and Fujimoto, R. (2019) The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L. DNA Res. 26: 433-443.

Ueda, M., Matsui, A., Watanabe, S., Kobayashi, M., Saito, K., Tanaka, M., Ishida, J., Kusano, M., Seo, M. and Seki, M. (2019) Transcriptome analysis of the hierarchical response of histone deacetylase proteins that respond in an antagonistic manner to salinity stress. Front. Plant Sci. 10: 1323.

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. and Matsunaga, S.* (2019) Primed histone demethylation regulates shoot regenerative competency. Nature Commun. 10:1786.

Rymen, B., Kawamura, A., Lambolez, A., Inagaki, S., Takebayashi, A., Iwase, A., Sakamoto, Y., Sako, K., Favero, D. S., Ikeuchi, M., Suzuki, T., Seki, M., Kakutani, T., Roudier, F. and Sugimoto, K. (2019) Histone acetylation orchestrates wound-induced transcriptional activation and cellular reprogramming in Arabidopsis. Commun. Biol. 2: 404.

Ueda, M., Matsui, A., Watanabe, S., Kobayashi, M., Saito, K., Tanaka, M., Ishida, J., Kusano, M., Seo, M. and Seki, M. (2019) Transcriptome analysis of the hierarchical response of HDAC proteins that respond in an antagonistic manner to salinity stress. Front. Plant Sci. 10: 1323.

Kurita, K.#, Sakamoto, Y.#, Naruse, S., Matsunaga, T.M., Arata, H., Higashiyama, T., Habu, Y., Utsumi, Y., Utsumi, C., Tanaka, M., Takahashi, S., Kim, J.M., Seki, M., Sakamoto, T. and Matsunaga, S. (2019) Intracellular localization of histone deacetylase HDA6 in plants. J. Plant Res. 132: 629-640.

Ueda, M., Sako, K. and Seki, M. (2018) Regulation and Modification of the Epigenome for Enhanced Salinity Tolerance in Crop Plants. In “Salinity Responses and Tolerance in Plants, Volume 2: Exploring RNAi, Genome Editing and Systems Biology (Edited by Drs. Vinay Kumar, Shabir Hussain Wani, Lam-Son Phan Tran and Penna Suprasanna)", Springer, pp. 77-91.

Ueda, M., Matsui, A., Nakamura, T., Abe, T., Sunaoshi, Y., Shimada, H. and Seki, M. (2018) Versatility of HDA19-deficiency for increasing tolerance to environmental stresses in Arabidopsis. Plant Signal. Behav. (in press).

Takahashi, S., Fukushima, N., Osabe, K., Itabashi, E., Shimizu, M., Miyaji, N., Takasaki-Yasuda, T., Suzuki, Y., Seki, M. and Fujimoto, R. (2018) Identification of DNA methylated regions by using methylated DNAimmunoprecipitation sequencing in Brassica rapa Crop and Pasture Science 69:107-120.
Abstract

Nguyen, H.M., Sako, K., Matsui, A., Ueda, M., Tanaka, M., Ito, A., Nishino, N., Yoshida, M. and Seki, M. (2018) Transcriptomic analysis of Arabidopsis thaliana plants treated with the Ky-9 and Ky-72 histone deacetylase inhibitors. Plant Signaling and Behavior 13:e1448333.
Abstract

Ueda, M., Matsui, A., Tanaka, M., Nakamura, T., Abe, T., Sako, K., Sasaki, T., Kim, J.M., Ito, A., Nishino, N., Shimada, H., Yoshida, M. and Seki, M. (2017) The distinct role of RPD3-like histone deacetylases between class I and II in salinity stress response. Plant Physiol. 175:1760-1773.
Abstract

Patanun, O., Ueda, M., Itouga, M., Kato, Y., Utsumi, Y., Matsui, A., Tanaka, M., Utsumi, C., Sakakibara, H., Yoshida, M., Narangajavana, J., and Seki, M. (2017) The histone deacetylase inhibitor suberoylanilide hydroxamic acid alleviates salinity stress in cassava. Front. Plant Sci. 7:2039.
Abstract

Kurita, K., Sakamoto, T., Yagi, N., Sakomoto, Y., Ito, A., Nishino, N., Sako, K., Yoshida, M., Kimura, H., Seki, M. and Matsunaga, S. (2017) Live imaging of H3K9 acetylation in plant cells. Scientific Reports 7: 45894.
Abstract

Kim, J.M., To, K.T., Matsui, A., Tanoi, K., Kobayashi, N.I., Matsuda, F., Habu, Y., Ogawa, D., Sakamoto, T., Matsunaga, S., Bashir, K., Rasheed, S., Ando, M., Takeda, H., Kawaura, K., Kusano, M., Fukushima, A., Endo, A.T., Kuromori, T., Ishida, J., Morosawa, T., Tanaka, M., Torii, C., Takebayashi, Y., Sakakibara, H., Ogihara, Y., Saito, K., Shinozaki, K., Devoto, A. and Seki, M. (2017) Acetate-mediated novel survival strategy against drought in plants. Nature Plants 3: 17097.
Abstract

Ito, H., Kim, J.M., Matsunaga, W., Saze, H., Matsui, A., Endo, T.A., Harukawa, Y., Takagi, H., Hiroki, Y., Masuta, Y., Masuda, S., Ishida, J., Tanaka, M., Takahashi, S., Morosawa, T., Toyoda, T., Kakutani, T., Kato, A. and Seki, M. (2016) A Stress-activated transposon in Arabidopsis induces transgenerational abscisic acid insensitivity. Scientific Reports 6:23181.
Abstract

Rasheed, S., Bashir, K., Matsui, A., Tanaka, M. and Seki, M. (2016) Transcriptomic analysis of soil-grown Arabidopsis thaliana roots and shoots in response to a drought stress. Front. Plant Sci. 7: 180.
Abstract

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. (2016) Ky-2, a histone deacetylase inhibitor, enhances high-salinity stress tolerance in Arabidopsis thaliana. Plant Cell Physiol. 57:776-783.
Abstract

Kim, J.M., To, T.K., Ishida, J., Matsui, A., Kimura, H. and Seki, M. (2012) Transition of Chromatin Status During The Recovery Process from Drought Stress in Arabidopsis thaliana. Plant Cell Physiol. 53:847-856.
Abstract

To, T.K., Nakaminami, K., Kim, J.M., Morosawa, T., Ishida, J., Tanaka, M., Yokoyama, S., Shinozaki, K. and Seki, M. (2011) Arabidopsis HDA6 is required for freezing tolerance. Biochem. Biophys. Res. Commun. 406:414-419.
Abstract

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. (2011) Arabidopsis HDA6 Regulates Locus-Directed Heterochromatin Silencing in Cooperation with MET1. PLoS Genet. 7:e1002055.
Abstract;  Press Release

Numa, H., Kim, J.M., Matsui, A., Kurihara, Y., Morosawa, T., Ishida, J., Mochizuki, Y., Kimura, H., Shinozaki, K., Toyoda, T., Seki, M., Yoshikawa, M. and Habu, Y. (2010) Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana. EMBO J. 29:352-362.
Abstract  Press Release

Kim, J.M., Kim-To, T., Ishida, J., Morosawa, T., Kawashima, M., Matsui, A., Toyoda, T., Kimura, H., Shinozaki, K. and Seki, M. (2008) Alterations of lysine modifications on histone H3 N-tail under drought stress conditions in Arabidopsis thaliana. Plant Cell Physiol. 49:1580-1588.
Abstract  Press Release  RIKEN Research