Publications

2015

Original Papers

Ramadan, A., Nemoto, K., Seki, M., Shinozaki, K., Takeda, H., Takahashi, H. and Sawasaki, T. (2015) Wheat germ-based protein libraries for the functional characterisation of the Arabidopsis E2 ubiquitin conjugating enzymes and the RING-type E3 ubiquitin ligase enzymes. BMC Plant Biol. 15:275.

Takahashi, F., Tilbrook, J., Trittermann, C., Berger, B., Roy, S.J., Seki, M., Shinozaki, K. and Tester, M. (2015) Correlation of leaf sheath transcriptome profiles with physiological traits of bread wheat cultivars under salinity stress. PLOS ONE 10:e0133322.

Ha, C.V., Watanabe, Y., Tran, U.T., Le, D.T., Tanaka, M., Nguyen, K.H., Seki, M., Nguyen, D.V. and Tran, L.S. (2015) Comparative analysis of root transcriptomes from two contrasting drought-responsive Williams 82 and DT2008 soybean cultivars under normal and dehydration conditions. Frontiers in Plant Science 6: 551.

Sojikul, P., Saithong, T., Kalapanulak, S., Pisuttinusart, N., Limsirichaikul, S., Tanaka, M., Utsumi, Y., Sakurai, T., Seki, M. and Narangajavana, J. (2015) Genome-wide analysis: unraveling the puzzle of phytohormone acting in concert during storage root initiation of cassava. Plant Mol. Biol. 88:531-543.

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.

Nemoto, K., Takemori, N., Seki, M., Shinozaki, K., and Sawasaki, T. (2015)　Members of the Plant CRK-superfamily are Capable of trans-/auto-Phosphorylation of Tyrosine Residues. J. Biol. Chem. 290:16665-16677.

Cartagena, J.A., Seki, M., Tanaka, M., Yamauchi, T., Sato, S., Hirakawa, H. and Tsuge, T. (2015) Gene expression profiles in Jatropha under drought stress and during recovery. Plant Mol. Biol. Rep. 33, 1075-1087.

Review Papers

Utsumi, Y., Sakurai, T., Utsumi, C., Vu, H.T., Takei, Y., Matsui, A., Hirano, T., Abe, T., Fernando, A.E.J, J León-Sánchez, J.E., Lopez, H.D., Duitama, J., Ayling, S., Ishitani, M., Nguyen, D.V., Nguyen, V.A., Tien, L.D., Triwitayakorn, K., Sojikul, P., Narangajavana, J., Le, H.H. and Seki, M. (2015) An Integrated Platform for the Advancement of Molecular Breeding of Cassava. Proceedings of the 9th Regional Workshop "Sustainable Cassava Production in Asia for Multiple Uses and for Multiple Markets" held in Nanning, Guangxi, China PR, pp. 116-123.

Kim, J.M., Sasaki, T., Ueda, M., Sako, K. and Seki, M. (2015) Chromatin changes in response to drought, salinity, heat, and cold stresses in plants. Frontiers in Plant Science (Research Topic title: "Epigenetic Mechanisms of Plant Responses to the Environment", hosted by Drs. Keqiang Wu and Yuhai Cui) 6:114.

2014

Original Papers

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.

Bashir, K., Hanada, K., Shimizu, M., Seki, M., Nakanishi, H. and Nishizawa, N.K. (2014) Transcriptomic analysis of rice in response to iron deficiency and excess. Rice 7:18.

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.

Sako, K, Yanagawa, Y., Kanai, T., Sato, T., Seki, M., Fujiwara, M., Fukao, Y. and Yamaguchi, J. (2014) Proteomic analysis of 26S proteasome reveals direct interaction with transit peptides of plastid protein precursors for degradation. J. Proteome Res. 13:3223-3230.

Ha, C.V., Leyva-González, M.A., Osakabe, Y., Tran, U.T., Nishiyama, R., Watanabe, Y., Tanaka, M., Seki, M., Yamaguchi, S., Dong, N.V., Yamaguchi-Shinozaki, K., Shinozaki, K., Herrera-Estrella, L., Tran, L.S.P. (2014) Strigolactone: a positive regulator of plant responses to drought and salt stress. Proc. Natl. Acad. Sci. USA 111:851-856.

Review Papers

Kinoshita, T. and Seki, M. (2014) Epigenetic memory for stress response and adaptation in plants. Plant Cell Physiol. 55:1859-1863.

Kim, J.M., To, T.K., Tanaka, M., Endo, T.A., Matsui, A., Ishida, J., Robertson, F.C., Toyoda, T. and Seki, M. (2014) Highly-reproducible ChIP-on-chip analysis to identify genome-wide protein binding and chromatin status in Arabidopsis. In "Methods in Molecular Biology- A third edition of the Arabidopsis Protocols (Edited by Drs. Jose J. Sanchez-Serrano and Julio Salinas)". Humana Press Inc., NJ, 1062:405-426.

2013

Original Papers

Jung, J.H., Park, J.H., Lee, S., To, T.K., Kim, J.M., Seki, M. and Park, C.M. (2013) The Cold Signaling Attenuator High Expression of Osmotically Responsive Gene1 Activates Flowering Locus C Transcription via Chromatin Remodeling under Short-Term Cold Stress in Arabidopsis. Plant Cell 25: 4378-4390.

Sakurai, T., Mochida, K., Yoshida, T., Akiyama, K., Ishitani, M., Seki, M. and Shinozaki, K. (2013) Genome-wide discovery and information resource development of DNA polymorphisms in cassava. PLOS ONE, 8(9) e74056.

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.

Komatsu, K., Suzuki, N., Kuwamura, M.,Nishikawa, Y., Nakatani, M., Ohtawa, H., Takezawa, D., Seki, M., Tanaka, M., Taji, T., Hayashi, T. and Sakata, Y. (2013) Group A PP2Cs evolved in land plants as key regulators of intrinsic desiccation tolerance. Nature Commun. 4:2219.

Nishiyama, R., Watanabe, Y., Leyva-Gonzalez, M.A., Ha, C.V., Fujita, Y., Tanaka, M., Seki, M., Yamaguchi-Shinozaki, K., Shinozaki, K., Herrera-Estrellab, L. and Tran, L.S. (2013) Arabidopsis AHP2, AHP3 and AHP5 histidine phosphotransfer proteins function as redundant regulators of drought stress response. Proc. Natl. Acad. Sci. USA 110: 4840–4845.

Higashi, Y., Ohhama, N., Ishikawa, T., Katori, T., Shimura, A., Kusakabe, K. Yamaguchi-Shinozaki, K., Ishida, J., Tanaka, M., Seki, M., Shinozaki, K., Sakata, Y., Hayashi, T. and Taji, T. (2013) HsfA1d, a protein identified via FOX hunting using Thellungiella salsuginea cDNAs, improves heat tolerance by regulating heat stress–responsive gene expression. Molecular Plant 6:411-422.

Hanada, K., Higuchia, M., Okamoto, M., Yoshizumi, T., Shimizu, M., Nakaminami, K., Nishi, R., Ohashi, C., Iida, K., Tanaka, M., Horii, Y., Kawashima, M., Matsui, K.,Toyoda, T., Shinozaki, K., Seki, M. and Minami, M. (2013) Small open reading frames associated with morphogenesis are hidden in plant genomes. Proc. Natl. Acad. Sci. USA 110: 2395-2400.

Review Papers

Matsui, A., Nguyen, A.H., Nakaminami, K. and Seki, M. (2013) Arabidopsis Non-coding RNA Regulation in Abiotic Stress Responses. In Special Issue "Regulation by non-coding RNAs". International Journal of Molecular Sciences. 14: 22642-22654.

Yamasaki, K., Kigawa, T., Seki, M., Shinozaki, K. and Yokoyama, S. (2013) DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. Trends Plant Sci. 18:267-276.

2012

Original Papers

Le, D.T., Nishiyama, R., Watanabe, Y., Tanaka, M., Seki, M., Ham, L.H., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. (2012) Differential gene expression in soybean leaf tissues at late developmental stages under drought stress revealed by genome-wide transcriptome analysis. PLoS One. 7:e49522.

Takahashi, H., Ozawa, A., Nemoto, K., Nozawa, A., Seki, M., Shinozaki, K., Takeda, H., Endo, Y. and Sawasaki, T. (2012) Genome-wide biochemical analysis of Arabidopsis protein phosphatase using a wheat cell-free system. FEBS Lett. 586:3134-3141.

Le, D.T., Nishiyama, R., Watanabe, Y., Vankova, R., Tanaka, M., Seki, M., Ham, L. H., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. (2012) Identification and Expression Analysis of Cytokinin Metabolic Genes in Soybean under Normal and Drought Conditions in Relation to Cytokinin Levels. PLoS One. 7:e42411.

Utsumi, Y., Tanaka, M., Morosawa, T., Kurotani, A., Yoshida, T., Mochida, K., Matsui, A., Umemura, Y., Ishitani, M., Shinozaki, K., Sakurai, T. and Seki, M. (2012) Transcriptome analysis using a high-density oligo microarray under drought stress in various genotypes of cassava, an important tropical crop. DNA Res. 19:335-345.

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.

Yamasaki, K., Kigawa, T., Watanabe, S., Inoue, M., Yamasaki, T., Seki, M., Shinozaki, K. and Yokoyama, S. (2012) Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor. J. Biol. Chem. 287: 7683-7691.

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.

Kawaguchi, S., Iida, K., Harada, E., Hanada, K., Matsui, A.,Okamoto, M., Shinozaki, K., Seki, M. and Toyoda, T. (2012) Positional correlation analysis improves reconstruction of full-length transcript and alternative isoform from noisy array signals or short reads. Bioinformatics 28:929-937.

Nishiyama, R., Le, D.T., Watanabe, Y., Seki, M., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. (2012) Transcriptome analyses of a salt-tolerant cytokinin-deficient mutant reveals differential regulation of salt stress response by cytokinin deficiency. PLoS ONE 7:e32124.

Blair, M.W., Fernandez, A.C., Ishitani, M., Moreta, D., Seki, M. and Shinozaki, K. (2012) Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.). BMC Plant Biol. 11:171.

Endo, A., Tatematsu, K., Hanada, K., Duermeyer, L., Okamoto, M., Yonekura-Sakakibara, K., Saito, K., Toyoda, T., Kawakami, N., Kamiya, Y., Seki, M. and Nambara, E. (2012) Tissue-specific transcriptome analysis reveals cell wall metabolism, flavonol biosynthesis, and defense responses are activated in the endosperm of germinating Arabidopsis thaliana seeds. Plant Cell Physiol. 53:16-27.

Review Papers

Yamasaki, K., Kigawa, T., Seki, M., Shinozaki, K. and Yokoyama, S. (2012) DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. Trends Plant Sci. (in press).

Utsumi. Y., Sakurai, T., Umemura, Y., Ayling, S., Ishitani, M., Narangajavana, J., Sojikul, P., Triwitayakorn, K., Matsui, M., Manabe, R., Shinozaki, K. and Seki, M. (2012) RIKEN Cassava Initiative: Establishment of a cassava functional genomics platform. Tropical Plant Biol. 5:110-116.

Kim, J.M., To, T.K., Tanaka, M., Endo, T.A., Matsui, A., Ishida, J., Robertson, F.C., Toyoda, T. and Seki, M. (2012) Highly-reproducible ChIP-on-chip analysis to identify genome-wide protein binding and chromatin status in Arabidopsis. In “Methods in Molecular Biology- A third edition of the Arabidopsis Protocols (Edited by Drs. Jose J. Sanchez-Serrano and Julio Salinas)”. Humana Press Inc., NJ. (in press).

Kim, J.M., To, T. and Seki, M. (2012) An Epigenetic Integrator: New Insights into Genome Regulation, Environmental Stress Responses and Developmental Controls by HISTONE DEACETYLASE 6. Plant Cell Physiol. 53:794-800.

Nakaminami, K., Matsui, A., Shinozaki, K. and Seki, M. (2012) RNA regulation in plant abiotic stress responses. BBA - Gene Regulatory Mechanisms. 1819:149-153.

2011

Original Papers

Yoshida, T., Ohama, N., Nakajima, J., Kidokoro, S., Mizoi, J., Nakashima, K., Maruyama, K., Kim, J.-M., Seki, M., Todaka, D., Osakabe, Y., Sakuma, Y., Schöffl, F., Shinozaki, K., Yamaguchi- Shinozaki, K. (2011) Arabidopsis HsfA1 transcription factors function as the main positive regulators in heat shock-responsive gene expression. Mol. Genet. Genomics 286:321-332.

Zhu Z, An F, Feng Y, Li P, Xue L, A M, Jiang Z, Kim JM, To TK, Li W, Zhang X, Yu Q, Dong Z, Chen WQ, Seki M, Zhou JM, Guo H. (2011) Derepression of ethylene-stabilized transcription factors (EIN3/EIL1) mediates jasmonate and ethylene signaling synergy in Arabidopsis. Proc. Natl. Acad. Sci. USA 108:12539-12544.

Ueda, M., Matsui, K., Ishiguro, S., Kato, T., Tabata, S., Kobayashi, M., Seki, M.,Shinozaki, K., and Okada, K. (2011) The Arabidopsis RPT2a encoding the 26S proteasome subunit is required for various cellular processes in the root meristem, and regulates gametogenesis redundantly with its homolog, RPT2b. Plant Cell Physiol. 52: 1628–1640.

Nemoto, K., Seto, T., Takahashi, H., Nozawa, A., Seki, M., Shinozaki, K., Endo, Y. and Sawasaki, T. (2011) Autophosphorylation profiling of Arabidopsis protein kinases using the cell-free system. Phytochemistry 72:1136-1144.

Iwase, A., Mitsuda, N., Koyama, T., Hiratsu, K., Kojima, M., Arai, T., Inoue, Y., Seki, M., Sakakibara, H., Sugimoto, K. and Ohme-Takagi, M. (2011) The AP2/ERF transcription factor WIND1 controls cell dedifferentiation in Arabidopsis. Curr Biol. 21:508-514.

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.

Okamoto, M., Kushiro, T., Jikumaru, Y., Abrams, S.R., Kamiya, Y.,Seki, M. and Nambara, E. (2011) ABA 9'-hydroxylation is catalyzed by CYP707A in Arabidopsis. Phytochemistry. 72:717-722.

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.

Mito, T., Seki, M., Shinozaki, K., Ohme-Takagi, M. and Matsui, K. (2011) Generation of chimeric repressors that confer salt tolerance in Arabidopsis and rice. Plant Biotechnol. J. 9: 736-746.

Iida, K., Kawaguchi, S., Kobayashi, N.,Yoshida, Y.,Ishii, M., Harada, E., Hanada, K., Matsui, A., Okamoto, M., Seki, M. and Toyoda, T. (2011) ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic-Structure-Based Dynamic Expression (DSDE) Analyses. Plant Cell Physiol. 52:254-264.

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.

Review Papers

Kurihara, Y. and Seki, M. (2011) Genome-wide analysis of RNA degradation in Arabidopsis. In “RNA Technologies (Edited by Volker A. Erdmann and Jan Barciszewski)”. Springer Publisher, Berlin Heidelberg, pp. 79-89.

Umemura, Y., Jagadish, R., Seki, M., Utsumi, Y., Narangajavana, J. and Ishitani, M. (2011) Cassava genetic improvement: Omics approaches for facing global challenges. In "Improving Crop Resistance to Abiotic Stress (Edited by Edited by Narendra Tuteja, Sarvajeet Singh Gill, Antonio F. Tiburcio, and Renu Tuteja)". Wiley-VCH Verlag GmbH & Co., Germany, pp. 1049-1065.