Analysis of RNA regulation mechanisms in environmental stress adaptation and acclimation.

Publications

Manavella, P., Herz, M.G., Kornblihtt, A., Sorenson, R., Sieburth, L., Nakaminami, K., Seki, M., Ding, Y., Sun, Q., Kang, H., Ariel, F., Crespi, M., Giudicatti , A., Cai, Q., Jin, H., Feng, X., Qi, Y., and Pikaard, C. (2023) Beyond transcription: compelling open questions in plant RNA biology. Plant Cell 35:1626-1653.

Matsui, A. and Seki, M. (2022) Plant Non-coding Transcriptomics. In “Plant Omics: Advances in Big Data Biology” (Edited by Drs. Hajime Ohyanagi, Eiji Yamamoto, Kentaro Yano)". CABI, Nosworthy Way, Wallingford OX10 8DE, UK. 79-96.

Zhang, R., Kuo, R., Coulter, M., Calixto, C.P.G., Entizne, J.C., Guo, W., Marquez, Y., Milne, L., Riegler, S., Matsui, A., Tanaka, M., Harvey, S., Gao, Y., Wießner-Kroh, T., Paniagua, A., Crespi, M., Denby, K., Hur, A.B., Huq, E., Jantsch, M.F., Jarmolowski, A., Koester, T., Laubinger, S., Li, Q.Q., Gu, L., Seki, M., Staiger, D., Sunkar, R., Szweykowska-Kulinska, Z., Tu, S.L., Wachter, A., Waugh, R., Xiong, L., Zhang, X.N., Conesa, A., Reddy, A.S.N., Barta, A., Kalyna, M., Brown, J.W.S. (2022) A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biol. 23:149. doi: 10.1186/s13059-022-02711-0.

Akter, M.A., Mehraj, H., Miyaji, N., Takahashi, S., Takasaki-Yasuda, T., Seki, M., Dennis, E.S., Fujimoto, R. and Osabe, K. (2022) Transcriptional association between mRNAs and their paired natural antisense transcripts following Fusarium oxysporum inoculation in Brassica rapa L. Horticulturae 8, 17.

Bailey-Serres, J., Zhai, J. and Seki, M. (2020) The dynamic kaleidoscope of RNAs in plants. Plant Physiol. 182:1-9.

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.

Bashir, K., Matsui, A., Rasheed, S. and Seki, M. (2019) Recent advances in the characterization of plant transcriptomes in response to drought, salinity, heat and cold stress. F1000 Faculty Reviews　Rev-658. doi: 10.12688/f1000research.18424.1.

Matsui, A., Nakaminami, K. and Seki, M. (2019) Biological function of changes in RNA metabolism in plant adaptation to abiotic stress. Plant Cell Physiol. 60:1897-1905.

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.

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.

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.

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.

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.
Abstract

Nguyen, 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.
Abstract

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.
Abstract

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.
Abstract

Nguyen, A.H., Matsui, A., Tanaka, M., Mizunashi, K., Nakaminami, K., Hayashi, M., Iida, K., Toyoda, T., Nguyen, D.V. and Seki, M. (2015) Loss of Arabidopsis 5'-3' exoribonuclease AtXRN4 function enhances heat stress tolerance of plants subjected to severe heat stress. Plant Cell Physiol. 56:1762-1772.
Abstract

Matsui, A., Mizunashi, K., Tanaka, M., Kaminuma, E., Nguyem, A.H., Nakajima, M., Kim, J.M., Nguyen, D.V., Toyoda, T. and Seki, M. (2014) tasiRNA-ARF pathway moderates floral architecture in Arabidopsis plants subjected to drought stress. BioMed Research International. Special Issue "Plants Coping Abiotic and Biotic Stresses: A Tale of Diligent Management" 2014:303451.
Abstract

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. (2014) Analysis of differential expression patterns of mRNA and protein during cold- and de-acclimation in Arabidopsis. Mol Cell Proteomics 13:3602-3611.
Abstract  Press Release

Hirayama, T., Matsuura, T., Ushiyama, S., Narusaka, M., Kurihara, Y., Yasuda, M., Ohtani, M., Seki, M., Demura, T., Nakashita, H., Narusaka, Y., Hayashi, S. (2013) Poly(A)-specific ribonuclease directly regulates the poly(A) status of mitochondrial mRNA in Arabidopsis. Nature Commun. 4:2247.
Abstract

Kurihara, Y., Schmitz, R.J., Nery, J.R., Schultz, M.D., Okubo-Kurihara, E., Morosawa, T., Tanaka, M., Toyoda, T., Seki, M. and Ecker, J.R. (2012) Surveillance of 3' non-coding transcripts requires FIERY1 and XRN3 in Arabidopsis. G3 2:487-498.
Abstract

Okamoto, M. and Seki, M. (2011) Expression profile and 5'-terminal structure of Arabidopsis antisense transcripts expressed in seeds. Plant Signaling Behavior 6:691-693.
Abstract

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. (2010) Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays. Plant J. 62:39-51.
Abstract

Kurihara, Y., Kaminuma, E., Matsui, A., Kawashima, M., Tanaka, M., Morosawa, T., Ishida, J., Mochizuki, Y., Shinozaki, K., Toyoda, T. and Seki, M. (2009) Transcriptome analyses revealed diverse expression changes in ago1 and hyl1 Arabidopsis mutants. Plant Cell Physiol. 50:1715-1720.
Abstract

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. (2009) Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc. Natl. Acad. Sci. USA 106:2453-2458.
Abstract;  Press Release

Kurihara, Y., Matsui, A., Kawashima, M., Kaminuma, E., Ishida, J., Morosawa, T., Mochizuki, Y., Kobayashi, N., Toyoda, T., Shinozaki, K. and Seki, M. (2008) Identification of the candidate genes regulated by RNA-directed DNA methylation. Biochem. Biophys. Res. Commun. 376:553-557.
Abstract

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. (2008) Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array. Plant Cell Physiol. 49: 1135-1149.
Abstract  Press Release  RIKEN Research