Plant Genomic Network Research Team

Laboratories

Publications

2019

Original Papers

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.

Takahashi, N., Ogita, N., Takahashi, T., Taniguchi, S., Tanaka, M., Seki, M. and Umeda, M. (2019) A regulatory module controlling stress-induced cell cycle arrest in Arabidopsis. eLife 8:e43944.

Utsumi, Y., Ha, C.V., Utsumi, C., Tanaka, M., Takahashi, S., Matsui, A., Matsunaga, M.T., Matsunaga, S., Kanno, Y., Seo, M., Okamoto, Y., Moriya, E. and Seki, M. (2019) Acetic Acid Treatment Enhances the Drought Avoidance in Cassava (Manihot esculenta Crantz). Front. Plant Sci. (in press).

Patanun, O., Viboonjun, U., Punyasuk, N., Thitamadee, S., Seki, M. and Narangajavana, J. (2019) Cassava microRNAs and storage root development. Biologia Plantarum 63:193-199.

Review Papers

Matsui, A., Nakaminami, K. and Seki, M. (2019) Biological function of changes in RNA metabolism in plant adaptation to abiotic stress. Plant Cell Physiol. (in press)

Seki, M. (2019) Editorial. Plant Mol. Biol. (in press).

Matsui, A.* and Seki, M.* (2019) The involvement of long non-coding RNAs in response to plant stress, In "Methods in Molecular Biology - Plant lncRNAs –” 1933:151-171.

2018

Original Papers

Watanabe, S., Sato, M., Sawada, Y., Tanaka, M., Matsui, A., Kanno, Y., Yokota-Hirai, M., Seki, M., Sakamoto, A. and Seo, M. (2018) Arabidopsis molybdenum cofactor sulfurase ABA3 contributes to anthocyanin accumulation and oxidative stress tolerance in ABA-dependent and independent manners. Scientific Rep. 8:16592.

Liu, B., Zhang, J., Yang, Z., Matsui, A., Seki, M., Li, S., Yan, X., Kohnen, M.V., Gu, L., Prasad, K., Tuskan, G.A., Lu, M. and Oka, Y. (2018) PtWOX11 acts as master regulator conducting the expression of key transcription factors to induce de novo shoot organogenesis in poplar. Plant Mol. Biol. 98:389-406.

Takaoka, Y., Iwahashi, M., Chini, A., Saito, H., Ishimaru, Y., Egoshi, S., Kato, N., Tanaka, M., Bashir, K., Seki, M., Solano, R. and Ueda, M. (2018) A rationally designed JAZ subtype-selective agonist of jasmonate perception. Nature Commun. 9:3654.

Sako, K., Sunaoshi, Y., Tanaka, M., Matsui, A. and Seki, M. (2018) The duration of high-salinity stress tolerance by ethanol in Arabidopsis thaliana. Plant Signal. Behav. 13:e1500065.

Takahashi, S., Osabe, K., Fukushima, N., Takuno, S., Itabashi, E., Miyaji, N., Shimizu, M., Takasaki-Yasuda, T., Suzuki, Y., Dennis, E.S., Seki, M. and Fujimoto, R. (2018) Genome wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L. DNA Res. 25:511-520.

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. 13:e1475808.

Rasheed, S.#, Bashir, K.#, Kim, J.M., Ando, M., Tanaka, M. and Seki, M. (2018) The modulation of acetic acid pathway genes in Arabidopsis produces drought-stress tolerant plants. Scientific Rep. 8:7831.

Nakaminami, K., Okamoto, M., Higuchi-Takeuchi, M., Yoshizumi, T., Yamaguchi, Y., Fukao, Y., Shimizu, M., Ohashi, C., Tanaka, M., Matsui, M., Shinozaki, K., Seki, M.* and Hanada, K.* (2018) AtPep3 is a hormone-like peptide that plays a role in salinity stress tolerance of plants. Proc. Natl. Acad. Sci. USA 115:5810-5815. (*Co-corresponding Authors).

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.

Ogita, N., Okushima, Y., Tokizawa, M., Yamamoto, Y.Y., Tanaka, M., Seki, M., Makita, Y., Matsui, M., Okamoto-Yoshiyama, K., Sakamoto, T., Kurata, T., Hiruma, K., Saijo, Y., Takahashi, N. and Umeda, M. (2018) Identifying the target genes of SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor controlling DNA damage response in Arabidopsis. Plant J. 94:439-453.

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 using Methylated DNA immunoprecipitation sequencing in Brassica rapa L. Crop and Pasture Science 69:107-120.

Review Papers

Seki, M., Tokunaga, H., Utsumi, C., Okamoto, Y., Moriya, E., Vu, T.A., Sakamoto, A., Takei, Y., Sakurai, T., Endo, M., Mikami, M., Toki, S., Tsuji, H., Jarunya Narangajavana, J., Triwitayakorn, K., Sojikul, P., Nguyen, A.H., Do, Q.T.N., Nguyen D.V., Nguyen, V.A., Le,H.H., Pham, N.T., Nguyen, H.H., Touch, B., Srean, P., Wongtiem, P., Ishitani, M. and Utsumi, Y. (2018) Advancement of Asian Cassava Molecular Breeding towards SDGs. Proceedings of the 18th Science Council of Asia (SCA) Conference "Role of Science for Society: Strategies towards SDGs in Asia", Dec. 5-7, 2018, Tokyo, Japan, Theme 10, 6.

Nakaminami, K. and Seki, M. (2018) RNA regulation in plant cold stress response. In: "Survival Strategies in Extreme Cold and Desiccation: Adaptation Mechanisms and their Applications. Advances in Experimental Medicine and Biology (Edited by Iwaya-Inoue M, Sakurai M, Uemura M)", Springer Japan, 1081:23-44.

Bashir, K., Rasheed, S., Matsui, A., Iida, K., Tanaka, M. and Seki, M. (2018) Monitoring transcriptomic changes in soil-grown roots and shoots of Arabidopsis thaliana subjected to a progressive drought stress, In "Methods in Molecular Biology - Root Development - (Edited by Drs. Elke Barbez and Daniela Ristova)". Vol. 1761. Humana Press, New York, NY. pp. 223-230.

Tokunaga, H., Baba, T., Ishitani, M., Ito, K., Kim, O.K., Le, H.H., Le, H.K., Maejima, K., Namba, S., Natsuaki, K.T., Nguyen, D.V., Nguyen, H.H., Nguyen, N.C., Nguyen, V.A., Nomura, H., Seki, M., Srean, P., Tanaka, H., Touch, B., Trinh, H.X., Ugaki, M., Uke, A., Utsumi, Y., Wongtiem, P. and Takasu, K. (2018) Sustainable Management of Invasive Pests of Cassava in Vietnam, Cambodia and Thailand. In "Crop Production under Stressful Conditions: Application of Cutting-edge Science and Technology in Developing Countries (Edited by Drs. Makie Kokubun and Shuichi Asanuma)", Springer, pp. 131-157.

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.

2017

Original Papers

Li, W., Nguyen, K., Chu, D.H., Ha, C.V., Watanabe, Y., Osakabe, Y., Leyva-González, M., Sato, M., Toyooka, K., Voges, L., Tanaka, M., Seki, M., Seo, M., Yamaguchi, S., Nelson, D., Herrera-Estrella, L. and Tran, L.S. (2017) The Karrikin Receptor KAI2 Promotes Drought Resistance in Arabidopsis thaliana. PLoS Genet. 13:e1007076.

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.

Shirai, K., Matsuda, F., Nakabayashi, R., Okamoto, M., Tanaka, M., Fujimoto, A., Shimizu, M., Shinozaki, K., Seki, M., Saito, K. and Hanada, K. (2017) A highly specific genome-wide association study integrated with transcriptome data reveals the contribution of copy number variations to specialized metabolites in Arabidopsis thaliana. Mol. Biol. Evol. 34: 3111–3122.

Utsumi, Y., Utsumi, C., Tanaka, M., Ha, T.V., Matsui, A., Takahashi, S. and Seki, M. (2017) Formation of Friable Embryogenic Callus in Cassava is Enhanced under Conditions of Reduced Nitrate, Potassium and Phosphate. PLoS ONE. 12:e0180736.

Matsui, A., Iida, K., Tanaka, M., Yamaguchi, K., Mizunashi, K., Kim, J.M., Takahashi, S., Kobayashi, N., Shigenobu, S., Shinozaki, K. and Seki, M. (2017) Novel stress-inducible antisense RNAs of protein-coding loci are synthesized by Arabidopsis RDRs. Plant Physiol.175: 457-472.

Nguyen, H.M., Sako, K., Matsui, A., Suzuki, Y., Mostofa, M.G., Ha, C.V., Tanaka, M., Tran, L.S.P., Habu, Y. and Seki, M. (2017) Ethanol Enhances High-salinity Stress Tolerance by Detoxifying Reactive Oxygen Species in Arabidopsis thaliana and Rice. Front. Plant Sci. 8: 1001.

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.

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.

Bashir, K., Nozoye, T., Nagasaka, S., Seki, M., Nakanishi, H. and Nishizawa, N.K. (2017) Paralogs and mutants show that one DMA synthase functions in Fe homeostasis in rice. J. Exp. Bot. 68:1785-1795.

Nguyen, T.C.C, Nakaminami, K., Matsui, A., Watanabe, S., Kanno, Y., Seo, M. and Seki, M. (2017) Overexpression of oligouridylate binding protein 1b results in ABA hypersensitivity. Plant Signaling & Behavior, 12:e1282591.

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.

Review Papers

Seki, M. (2017) Trying to Solve Global Food Problems Using Ethanol. Highlighting JAPAN, Sep. Vol. 112, p. 22-23.

2016

Original Papers

Kamiya, M., Higashio, S., Isomoto, A., Kim, J.M., Seki, M., Miyashima, S. and Nakajima, K. (2016) Control of root cap maturation and cell detachment by the BEARSKIN transcription factors in Arabidopsis. Development, 143:4063-4072.

Hoshino, A., Jayakumar, V., Nitasaka, E., Toyoda, A., Noguchi, H., Itoh, T., Shin-I, T., Minakuchi, Y., Koda, Y., Nagano, A.J., Yasugi, M., Honjo, M.N., Kudoh, H., Seki, M., Kamiya, A., Shiraki, T., Carninci, P., Asamizu, E., Nishide, H., Tanaka, S., Park, K., Morita, Y., Yokoyama, K., Uchiyama, I., Tanaka, Y., Tabata, S., Shinozaki, K., Hayashizaki, Y., Kohara, Y., Suzuki, Y., Sugano, S., Fujiyama, A., Iida, S. and Sakakibara, Y. (2016) Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nature Commun.7:13295.

Rasheed, S., Bashir, K., Nakaminami, K., Hanada, K., Matsui, A. and Seki, M. (2016) Drought stress differentially regulates the expression of small open reading frames (sORFs) in Arabidopsis roots and shoots. Plant Signaling Behavior 11 (8) e1215792.

Okamoto, M., Matsui, A., Tanaka, M., Morosawa, T., Ishida, J., Iida, K., Mochizuki, Y., Toyoda, T. and Seki, M. (2016) Sm-like protein-mediated RNA metabolism is required for heat stress tolerance in Arabidopsis. Front. Plant Sci. 7:1079.

Nguyen, T.C.C, Nakaminami, K., Matsui, A., Kobayashi, S., Kurihara, Y., Toyooka, K., Tanaka, M. and Seki, M. (2016) Oligouridylate binding protein 1b plays an integral role in plant heat stress tolerance. Front. Plant Sci. 7:853.

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.

Utsumi, Y., Tanaka, M., Kurotani, A., Yoshida, T., Mochida, K., Matsui, A., Ishitani, M., Sraphet, S., Whankaew, S., Asvarak, T., Narangajavana, J., Triwitayakorn, K., Sakurai, T. and Seki, M. (2016) Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide–DNA microarray. J. Plant Res. 129: 711-726.

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.

Nguyen, K.H., Ha, C.V., Nishiyama, R., Watanabe, Y., Leyva-González, M.A., Fujita, Y., Tran, U.T., Li, W., Tanaka, M., Seki, M., Schaller, G.E., Herrera-Estrella, L. and Tran, L.S.P. (2016) The Arabidopsis type-B cytokinin response regulators ARR1, ARR10 and ARR12 negatively regulate plant responses to drought. Proc. Natl. Acad. Sci. USA, 113: 3090-3095.

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

Vigani, G., Bashir, K., Ishimaru,Y., Lehmann, M., Casiraghi, F.M., Nakanishi, H., Seki, M., Geigenberger, P., Zocchi, G. and Nishizawa, N.K. (2016) Knocking down mitochondrial iron transporter (MIT) reprograms primary and secondary metabolism in rice plants. J. Exp. Bot. 67:1357-1368.

Review Papers

Bashir, K., Rasheed, S., Kobayashi, T., Seki, M. and Nishizawa, N.K. (2016) Regulating Subcellular Metal Homeostasis, the Key to Crop Improvement. Front. Plant Sci. 7: 1192