Publications

2013

Original Papers

Nishiyama, R., Watanabe, Y., Leyva-Gonzalez, M.,b, 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 (in press).

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 (in press).

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 (in press).

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.