The University of Tokyo
Department of Life Sciences
Graduate School of Arts and Sciences
Yuichiro Watanabe / Masayuki Tsuzuki Lab

Publication lists in topics

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Small RNAs-mediated gene regulation

1. Tsuzuki, M., Futagami, K., Shimamura, M., Inoue, C., Kunimoto, K., Oogami, T., Tomita, Y., Inoue, K., Kohchi, T., Yamaoka, S., Araki, T., Hamada,T. and Watanabe, Y. (2019) An early arising role of the microRNA156/529-SPL module in reproductive development revealed by the liverwort Marchantia polymorpha. Current Biology 29,3307–3314. doi: 10.1016/j.cub.2019.07.084
2. Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Sugamata-Aki S, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund M, Florent S, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue S, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin S, Lindquist E, Lipzen AM, Lu C, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J. (2017) Insights into land plant evolution garnered from the Marchantia polymorpha genome. Marchantia polymorpha. Cell 171,287-304. doi.org/10.1016/j.cell.2017.09.030
3. Tsuzuki, M. and Watanabe, Y. (2017) Profiling New Small RNA Sequences. Methods in molecular biology (Clifton, N.J.) 1456, 177–188. doi: 10.1007/978-1-4899-7708-3_14
4. Bowman, J. L., Araki, T., Arteaga-Vazquez, M. A., Berger, F., Dolan, L., Haseloff, J., Ishizaki, K., Lin, S.-S., Nagasaki, H., Nakagami, H., Nakajima, K., Nakamura, Y., Ohashi-Ito, K., Sawa, S., Shimamura, M., Solano, R., Tsukaya, H., Ueda, T., Watanabe, Y., Yamato, K. T., Zachgo, S. and Kohchi, T. (2016) The Naming of Names: Guidelines for Gene Nomenclature in Marchantia. Plant Cell Physiol. 57, 257-261. doi: 10.1093/pcp/pcv193
5. Tsuzuki, M., Nishihama, R., Ishizaki, K., Kurihara, Y., Matsui, M., Bowman, J. L., Kohchi, T., Hamada, T., Watanabe, Y. (2016) Profiling and characterization of small RNAs in the liverwort, Marchantia polymorpha, belonging to the first diverged land plants. Plant Cell Physiol. 57, 359-372. doi: 10.1093/pcp/pcv182
6. Tsuzuki, M., Takeda, A., Watanabe, Y. (2014) Recovery of dicer-like 1-late flowering phenotype by miR172 expressed by the non-canonical DCL4-dependent biogenesis pathway. RNA, 20, 1320-1327. doi: 10.1261/rna.044966.114
7. Iwasaki, M., Takahashi, H., Iwakawa, H., Nakagawa, A., Ishikawa, T., Tanaka, H., Matsumura, Y., Pekker, I., Eshed, Y., Vial-Pradel, S., Ito, T., Watanabe, Y., Ueno, Y., Fukazawa, H., Kojima, S., Machida, Y., Machida, C. (2013) Dual regulation of ETTIN(ARF3) gene expression by AS1-AS2, which maintains the status of DNA methylation, is involved in stabilization of leaf adaxial-abaxial partitioning in Arabidopsis. Development, 140, 1958-1969. doi: 10.1242/dev.085365
8. Sakaguchi, J. and Watanabe, Y. (2012) miR165/166 and the development of land plants. Develop. Growth Differ. 54, 93-99.
9. Watanabe, Y. (2011) Overview of Plant RNAi. pp.1-11. In RNAi and Plant Gene Function Analysis – Methods and Protocols (Kodama, H. and Komamine, A. eds.) Human Press.
10. Tagami, Y. and Watanabe, Y. (2010) Cloning new small RNA sequences. pp.123-138. In Plant Epigenetics book / Methods in Molecular Biology series (Kovalchuk, I. and Zemp, F.J. eds.) Human Press.
11. Kurihara, Y. and Watanabe, Y. (2009) Processing of miRNA precursors. pp. 231-242. In Plant microRNA protocol book / Methods in Molecular Biology series (Green, P. and Blake eds.) Human Press.
12. Tagami, Y., Motose, H., Watanabe, Y. (2009) A dominant mutation in DCL1 suppresses the hyl1 mutantphenotype by promoting the processing of miRNA. RNA, 15, 450-458.
13. Meyers, B.C., Axtell, M. J., Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., Griffiths-Jones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qi, Y., Vaucheret, H., Vazquez, F., Voinnet, O., Watanabe, Y., Weigel, D., Zhu, J.K. (2008) Criteria For Annotation of Plant microRNAs. Plant Cell, 20, 3186-3190.
14. Takeda, A., Iwasaki, S., Watanabe, T., Utsumi, M., Watanabe, Y. (2008) The mechanism selecting the guide strand from small RNA duplexes is different among Argonaute proteins. Plant and Cell Physiol. 49, 493-500.
15. Tagami, Y., Inaba, N., Kutsuna, N., Kurihara,Y., Watanabe, Y. (2007) Specific enrichment of miRNAs in Arabidopsis thaliana infected with Tobacco mosaic virus. DNA Research, 14, 227-233.
16. Fujioka, Y., Utsumi, M., Ohba, Y. Watanabe, Y. (2007) Location of possible miRNA processing site in SmD3/SmB nuclear bodies in Arabidopsis. Plant Cell Physiol. 48, 1243-1253.
17. Kurihara,Y., Inaba, N., Kutsuna, N., Takeda, A., Tagami, Y., Watanabe, Y. (2007) The binding of tobamovirus replication protein with small RNA duplexes. J. Gen. Virol. 88, 2347-2352.
18. Kurihara, Y., Yuasa, T., Watanabe, Y. (2006) The in vivo interaction between DCL1 and HYL1 leads to efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA, 12, 206-212.
19. Kurihara, Y. and Watanabe, Y. (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. USA, 101, 12753-12758.

RNA granules responding to environmental changes (stress)

1. Hamada, T., Yako, M., Minegishi, M., Sato, M., Kamei, Y., Yanagawa, Y., Toyooka, K., Watanabe, Y., Hara-Nishimura, I. (2018) Stress granule formation is induced by a threshold temperature rather than a temperature difference in Arabidopsis. J Cell Sci. 131 jcs216051. doi: 10.1242/jcs.216051
2. Motomura, K., Le, Q.T-N., Hamada, T., Kutsuna, N., Mano, S., Nishimura, M., Watanabe, Y. (2015) Diffuse decapping enzyme DCP2 accumulates in DCP1 foci under heat stress in Arabidopsis thaliana. Plant Cell Physiol. 56, 107-115. doi: 10.1093/pcp/pcu151
3. Motomura, K., Le, Q.TN., Kumakura, N., Fukaya, T., Takeda, A., Watanabe, Y. (2012) Decapping proteins are involved in the accumulation of miRNA in Arabidopsis thaliana. RNA Biology, 9, 644-652.
4. Hamada, T., Tominaga, M., Fukaya,T., Nakamura,M., Nakano, A., Watanabe, Y., Hashimoto, T., Baskin, T.I. (2012) RNA processing bodies, peroxisomes, Golgi bodies, mitochondria, and Endoplasmic Reticulum tubule junctions frequently pause at cortical microtubules. Plant Cell Physiol. 53, 699-708.
5. Kumakura, N., Takeda, A., Fujioka, Y., Motose, H., Takano, R., Watanabe, Y. (2009) SGS3 and RDR6 interact and colocalize in cytoplasmic SGS3/RDR6-bodies. FEBS Lett. 583, 1261-1266.
6. Iwasaki, S., Takeda, A., Motose H., Watanabe, Y. (2007) Characterization of Arabidopsis decapping proteins AtDCP1 and AtDCP2, which are essential for post-embryonic development. FEBS Lett. 581, 2455-2459.

Shoot-to-Root Communication

1. Sakaguchi, J., Matsushita, T. and Watanabe, Y. (2019) DWARF4 accumulation in root tips is enhanced via blue light perception by cryptochromes. Plant, Cell Environ. 42 1615-1629. doi: 10.1111/pce.13510
2. Sakaguchi, J. and Watanabe, Y. (2017) Light perception in aerial tissues enhances DWF4 accumulation in root tips and induces root growth. Sci. Rep. 7, 1808.　doi: 10.1038/s41598-017-01872-4

Biological analysis of RNA decay systems

1. Chiam, N.C., Fujimura, T., Sano, R., Akiyoshi, N., Hiroyama, R., Watanabe, Y., Motose, H., Demura, T., Ohtani, M. (2019) Nonsense-mediated mRNA decay deficiency affects the auxin response and shoot regeneration in Arabidopsis. Plant Cell Physiol. in press. https://doi.org/10.1093/pcp/pcz154
2. Kumakura, N., Otsuki, H., Ito, M., Nomoto, M., Tada, Y., Ohta, K., Watanabe, Y. (2016) Arabidopsis AtRRP44 has ribonuclease activity that is required to complement the growth defect of yeast rrp44 mutant. Plant Biotech. 33, 77-85. doi: 10.5511/plantbiotechnology.16.0316a
3. Kumakura, N., Otsuki, H., Takeda, A. Watanabe, Y. (2013) Arabidopsis AtRRP44A is the functional homolog of Rrp44/Dis3, an exosome component, is essential for viability and is required for RNA processing and degradation. PLoS One, 8, e79219. doi: 10.1371/journal.pone.0079219
4. Hayashi, M., Nanba, C., Saito, M., Kondo, M., Takeda, A., Watanabe, Y., Nishimura, M. (2012) Loss of XRN4 function can trigger cosuppression in a sequence-dependent manner. Plant Cell Physiol. 53, 1310-1321.
5. Hori, K. and Watanabe, Y. (2008) In vivo analysis of plant NMD. In RNA Turnover, part B/ Methods in Enzymology. (Maquat, L. E. and Kiledjian, M. eds.) 449, 166-177.
6. Hori, K. and Watanabe, Y. (2007) Context analysis of termination codons in mRNA that are recognized by plant NMD. Plant Cell Physiol. 48, 1072-1078.
7. Hori, K. and Watanabe, Y. (2005) UPF3 suppresses aberrant spliced mRNA in Arabidopsis. Plant J. 43, 530-540.

Proteins in body maintenance

1. Kishi-Kaboshi, M., Muto, H., Takeda, A., Murata, T., Hasebe, M., Watanabe, Y. (2014) Identification of tobacco germin-like protein 1 in leaf intercellular space. Plant Physiol Biochem. 85, 1-8. doi: 10.1016/j.plaphy.2014.10.005
2. Hamada, T., Tominaga, M., Fukaya,T., Nakamura,M., Nakano, A., Watanabe, Y., Hashimoto, T., Baskin, T.I. (2012) RNA processing bodies, peroxisomes, Golgi bodies, mitochondria, and Endoplasmic Reticulum tubule junctions frequently pause at cortical microtubules. Plant Cell Physiol. 53, 699-708.
3. Motose, H., Hamada, T., Yoshimoto, K., Murata, T., Hasebe, M., Watanabe, Y., Hashimoto, T., Sakai, T., Takahashi, T. (2011) NIMA-related kinases 6, 4, and 5 interact with each other to regulate microtubule organization during epidermal cell expansion in Arabidopsis thaliana. Plant J. 67, 993-1005.
4. Sasaki, N., Ogata, T., Deguchi, M., Nagai, S., Tamai, A., Meshi, T., Kawakami, S., Watanabe, Y., Matsushita, Y., Nyunoya, H. (2009) Overexpression of putative transcriptional coactivator KELP interferes with Tomato mosaic virus cell-to-cell movement. Mol. Plant Pathol. 10, 161-173.
5. Motose, H., Tominaga, R., Wada, T., Sugiyama, M., Watanabe, Y. (2008) A NIMA-related protein kinase IBO1 modulates epidermal cell shape through the organization of cortical cytoskeleton in Arabidopsis. Plant J. 54, 829-844.
6. Tagami, Y., Watanabe, Y. (2007) Effects of brefeldin A on the localization of Tobamovirus movement protein and cell-to-cell movement of the virus. Virology, 361, 133-140.
7. Motose, H., Watanabe, Y., Fukuda, H. (2006) Glycosylphosphatidylinositol- anchored proteins in plants. In Frontiers in Life Science, (eds. M. Fujiwara, N. Sato and S. Ishiura) Kerala, India: Research Signpost. 111-126.
8. Kishi, M., Murata, T., Hasebe, M., Watanabe, Y. (2005) An extraction method for tobacco mosaic virus movement protein localizing in plasmodesmata. Protoplasma, 225, 85-92.
9. Takahashi, T., Watanabe, Y., Natsuaki, T., Okuda, S., Okada,Y. (1999) The movement protein of tomato mosaic tobamovirus induces tubular structures in tomato protoplasts. Ann. Phytopathol. Soc. Japan, 65, 612-615.

Plant Immunity /Plant-Microbe Interaction

1. Sato, M., Tsuda, K., Wang, L., Coller, J., Watanabe, Y., Glazebrook, J., Katagiri, F. (2010) Network modeling reveals prevalent negative regulatory relationships between signaling sectors in Arabidopsis immune signaling. PLoS Pathogen, 6, e1001011.
2. Tagami, Y. and Watanabe, Y. (2007) Effects of brefeldin A on the localization of Tobamovirus movement protein and cell-to-cell movement of the virus. Virol. 361, 133-140.
3. Oka-Kira, E., Tateno, K., Miura, K., Haga, T., Hayashi, M., Harada, K., Sato, S., Tabata, S., Shikazono, N., Tanaka, A., Watanabe, Y., Fukuhara, I., Nagata, T., Kawaguchi, M. (2005) klavier (klv), A novel hypernodulation mutant of Lotus japonicus affected in vascular tissue organization and floral induction. Plant J. 44, 505-515.
4. Sawada, H., Takeuchi, S., Matsumoto, K., Hamada, H., Kiba, A., Matsumoto, M., Watanabe, Y., Suzuki, K., Hikichi, Y. (2005) A new Tobamovirus-resistance gene, Hk, in Capsicum annuum. J. Japan Soc. Hort. Sci. 74, 289-294.
5. Takizawa, M., Goto, A., Watanabe, Y. (2005) Tobacco ubiquitin-activating enzymes NtE1A and NtE1B are induced by tobacco mosaic virus, wounding and stress hormones. Mol. Cells, 19, 228-231.
6. Kawakami, S., Watanabe, Y., Beachy, R.N. (2004) Tobacco mosaic virus infection spreads cell to cell as intact replication complexes. Proc. Natl. Acad. Sci. USA, 101, 6291-6296.
7. Kurihara, Y. and Watanabe, Y. (2004) A TMV-Cg mutant with a truncated coat protein induces cell death resembling the hypersensitive responses in Arabidopsis. Mol. Cells, 17, 334-339.
8. Hirashima, K. and Watanabe, Y. (2003) RNA helicase domain of tobamovirus replicase executes cell-to-cell movement possibly through collaboration with its non-conserved region. J. Virol. 77, 12357-12362.
9. Kawakami, S., Hori, K., Hosokawa, D., Okada, Y., Watanabe, Y. (2003) Defective tobamovirus movement protein lacking wild type phosphorylation sites can be complemented by substitutions found in revertants. J. Virol. 77, 1452-1461.
10. Kurihara, Y. and Watanabe, Y. (2003) Cross-protection against crucifer tobamovirus Cg was realized by its attenuated strain in Arabidopsis. Mol. Plant Pathol. 4, 259-269.
11. Hirashima, K. and Watanabe, Y. (2001) Tobamovirus replicase coding region is involved in cell-to-cell movement. J. Virol, 75, 8831-6.
12. Matsushita, Y., Hanazawa, K., Yoshioka, K., Oguchi, T., Kawakami, S., Watanabe, Y., Nishiguchi, M., Nyunoya, H. (2000) In vitro phosphorylation of the movement protein of tomato mosaic tobamovirus by a cellular kinase. J. Gen. Virol. 81, 2095-102.
13. Kawakami, S., Padgett, H. S., Hosokawa, D., Okada, Y., Beachy, R. N., Watanabe, Y. (1999) Phosphorylation and/or presence of serine 37 in the movement protein of tomato mosaic tobamovirus is essential for intracellular localization and stability in vivo. J. Virol. 73, 6831-6840.

New technology in plant systems

1. Yoshida, T., Kimura, E., Koike, S., Nojima, J., Futai, E., Sasagawa, N., Watanabe, Y., Ishiura, S. (2011) Transgenic rice expressing amyloid b -peptide for oral immunization. International Journal of Biological Sciences, 7, 301–307.
2. Nojima, J., Ishii-Katsuno, R., Futai, E., Sasagawa, N., Watanabe, Y., Yoshida, T., Ishiura, S. (2011) Production of anti-amyloid b antibodies in mice fed rice expressing amyloid b. Biosci. Biotech. Biochem. 75, 396-400.
3. Nojima, J., Maeda, A., Aoki, S., Suo, S., Yanagihara, D., Watanabe, Y.,Yoshida, T., Ishiura, S. (2011) Effect of rice-expressed amyloid b in the Tg2576 Alzhimer’s disease transgenic mouse model. Vaccine, 29, 6252-6258.
4. Ishii-Katsuno, R., Nakajima, A., Katsuno, T., Nojima, J., Futai, E., Sasagawa, N., Yoshida, T., Watanabe, Y., Ishiura, S. (2010) Reduction of amyloid beta-peptide accumulation in Tg2576 transgenic mice by oral vaccination. Biochem. Biophys. Res. Comm. 399, 593-599.
5. Kobayashi, M., Onodera, K., Watanabe, Y., Yamashita, I. (2010) Fabrication of 3-nm platinum wires using a tobacco mosaic virus template. Chemistry Letters, 39, 616-618.
6. Kobayashi, M., Seki, M., Tabata, H., Watanabe, Y.,Yamashita, I. (2010) Fabrication of aligned magnetic nanoparticles using tobamoviruses. Nano Letters, 10, 773–776
7. Saejung, W., Fujiyama, K., Takasaki, T., Ito, M., Hori, K., Malasit, P., Watanabe, Y., Kurane, I., Seki, T. (2007) Production of dengue 2 envelope domain III in plant using TMV-based vector system. Vaccine, 25, 6646-6654.
8. Takizawa, M., Hori, K., Inai, K., Takase, H., Hashimoto, T., Watanabe, Y. (2007) A virus-induced gene silencing approach for the suppression of nicotine content in Nicotiana benthamiana. Plant Biotech. 24, 295-300.
9. Fujiyama, K., Saejung, W., Yanagihara, I., Nakado, J., Misaki, R., Honda, T., Watanabe, Y., and Seki, T. (2006) In planta production of the immunogenic poliovirus peptide using TMV-based vector system. J. Biosci. Bioeng. 101, 398-402.
10. Szabo, B., Hori, K., Nakajima, A., Sasagawa, N., Watanabe, Y., Ishiura, S. (2004) Expression of amyloid-beta1-40 and 1-42 peptides in Capsicum annum var. angulosum for oral immunization. ASSAY Drug Develop. Tech. 2, 383-388.
11. Hori, K., Takizawa, M., Watanabe, Y. (2004) Use of attenuated strain of tobamovirus for early detection of virus-induced gene silencing. Plant Biotech. 21, 135-142.
12. Hori, K. and Watanabe, Y. (2003) Construction of a tobamovirus vector that can systemically spread and express foreign gene products in Solanaceous plants. Plant Biotech. 20, 129-136.
13. Lim, A.A., Tachibana, S., Watanabe, Y., Wong, S.M. (2002) Expression and purification of a neuropeptide nocistatin using two related plant viral vectors. Gene, 289, 69-79.

New experimental tools in plant systems

1. Aoki, K., Yano, K., Suzuki, A., Kawamura, S., Sakurai, N., Suda, K., Kurabayashi, A., Suzuki, T., Tsugane, T., Watanabe, M., Ooga, K., Torii, M., Takahashi, H., Watanabe, Y., Kodama, M., Ichinose, Y., Kikuchi, M., Fukushima, S., Okabe, A., Arie, T., Sato, Y., Yazawa, K., Satoh, S., Ezura, H. and Shibata, D. (2010) Large-scale analysis of full-length cDNA of tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for Solanaceae genomics. BMC Genomics, 11, 210.
2. Nakagawa, T., Suzuki, T., Murata, S., Nakamura, S., Hino, T., Maeo, K., Tabata, R., Kawai, T., Tanaka, K., Niwa, Y., Watanabe, Y., Nakamura, K., Kimura, T., Ishiguro, S. (2007) Improved gateway binary vectors: high-performance vectors for creation of fusion constructs in transgenic analysis of plants. Biosci. Biotech. Biochem. 71, 2095-2100.
3. Okamura, Y. and Watanabe, Y. (2006) Detecting RNA/DNA hybridization using double-labeled donor probes with enhanced FRET signals. In FRET and Beyond: Energy transfer nucleic acid probes, (ed. V. Didenko) Totowa, NJ: Humana Press. 43-56.
4. Yuasa,T., Sugiki, M., Watanabe, Y. (2005) Activation of SIPK in response to UV-C irradiation : utility of a glutathione-S transferase-tagged plant MAP kinase by transient expression with agroinfiltration. Plant Biotech. 22, 7-12.
5. Takahashi, H., Shimizu, A., Arie, T., Rosmalawati, S., Fukushima, S., Kikuchi, M., Hikichi, Y., Kanda, A., Takahashi, A., Kiba, A., Ohnishi, K., Ichinose, Y., Taguchi, F., Yasuda, C., Kodama, M., Egusa, M., Masuta, C., Sawada, H., Shibata, D., Hori, K., Watanabe, Y. (2005) Catalog of Micro-Tom tomato responses to common fungal, bacterial and viral pathogens. J. Gen. Plant Pathol. 71, 8-22.
6. Okamura, Y., Kondo, S., Sase, I., Suga, T., Mise, K., Furusawa, I., Kawakami, S., Watanabe, Y. (2000) Double-labeled donor probe can enhance the signal of fluorescence resonance energy transfer (FRET) in detection of nucleic acid hybridization. Nucl. Acids Res., 28, e107.

Collaboration conducted in animal systems

1. Oya, M., Suzuki, H., Watanabe, Y., Sato, M., Tsuboi, T. (2011) Amino acids taste receptor regulates insulin secretion in pancreatic b-cell line MIN6 cells. Genes to Cells, 16, 608-616.
2. Sasagawa, N., Ohno, E., Kino, Y., Watanabe, Y., Ishiura, S. (2009) Identification of Caenorhabditis elegans K02H8.1 (CeMBL) as the functional ortholog of the mammalian MBNL proteins. J. Neuroscience Res. 87, 1090-1097.

Before the shift to Todai-Komaba in 1998

1. Tsuda, S., Yoshioka, K., Tanaka,T., Iwata, A., Yoshikawa, A., Watanabe, Y., Okada, Y. (1998) Application of the human hepatitis B virus core antigen from transgenic tobacco plants for serological diagnosis. Vox Sanguinis, 74, 148-155.
2. Tsuda, S., Kirita, M., Watanabe, Y. (1998) Characterization of a pepper mild mottle tobamovirus strain capable of overcoming the L3 gene-mediated resistance, distinct from the resistance-breaking Italian isolate. Mol. Plant-Microbe Interact. 11, 327-331
3. Kirita, M., Akutsu, K., Watanabe, Y. and Tsuda, S. (1997) Nucleotide sequence of the Japanese isolate of pepper mild mottle tobamovirus (TMV-P) RNA. Ann. Phytopathol. Soc. Japan, 63, 373-376
4. Kawakami, S. and Watanabe, Y. (1997) Use of green fluorescent protein as a molecular tag of protein movement in vivo. Plant Biotech. 14, 127-130.
5. Hamamoto, H., Watanabe, Y., Kamada, H., Okada, Y. (1997) A single amino acid substitution in the virus-encoded replicase of tomato mosaic tobamovirus alters host specificity. Mol. Plant-Microbe Interat. 10, 1015-1018.
6. Padgett, H. S., Watanabe, Y., Beachy, R. N. (1997) Identification of the TMV replicase sequence that activates the N gene-mediated hypersensitive response. Mol. Plant-Microbe Interact. 10, 709-715.
7. Hamamoto, H., Watanabe, Y., Kamada, H., Okada, Y. (1997) Amino acid changes in the putative replicase of tomato mosaic tobamovirus that overcome resistance in Tm-1 tomato. J. Gen. Virol.. 78, 461-464.
8. Beachy, R.N., Padgett, H.S., Kahn, T., Bendahmane,M., Fitchen, J.H., Heinlein, M., Watanabe, Y. and Epel, B.L. (1996) Cellular and molecular mechanisms of coat protein and movement protein mediated resistance against TMV. In :Biology of Plant-Microbe Interactions. (eds. Stacey,G., Mullin, B., Gresshoff, P.M.) 259-264. International Society of Molecular Plant-Microbe Interactions
9. Padgett, H.S., Epel, B.L., Kahn,W.T., Heinlein, M.H., Watanabe, Y. and Beachy, R.N. (1996) Distribution of tobamovirus movement protein in infected leaves and implications for cell-to-cell spread of infection. Plant J. 10, 1079-1088.
10. Watanabe, Y., Ohnishi, J., Saito, H., Hosokawa, D., Okada, Y. (1996) Addition of nucleotides similar to deleted CAA repeats in the 5' noncoding region of tomato mosaic virus RNA following propagation. J. Gen. Virol. 77, 2353-2357.
11. Chng, C.G., Wong, S.M., Mahtani,P.H., Loh, C.S., Goh, C.J., Kao, M.C.C., Chung, M.C.M., Watanabe, Y. (1996) The complete sequence of a Singapore isolate of odontoglossum ringspot virus and comparison with other tobamoviruses. Gene, 171, 155-161.
12. Chen, J., Watanabe, Y., Sako, N., Ohshima, K., Okada, Y. (1996) Mapping of host range restriction of the rakkyo strain of tobacco mosaic virus in Nicotiana tabacum cv. Bright Yellow. Virol. 226, 198-204.
13. Chen, J., Sako, N., Ohshima, K., Watanabe, Y. (1996) Generation of antiserum reactive with the 30K movement protein of the tobacco mosaic virus Rakkyo strain. Bulletin of the Faculty of Agriculture, Saga University 81, 19-26.
14. Chen, J., Sako, N., Ohshima, K. Watanabe, Y. (1996) Specific detection of the Rakkyo strain of tobacco mosaic virus by reverse transcription and polymerase chain reaction. Ann. Phytopath. Soc. Japan, 62, 513-516.
15. Chen, J., Watanabe, Y., Sako, N., Ohshima, K., Okada, Y. (1996) Complete nucleotide sequence and synthesis of infectious in vitro transcripts from a full-length cDNA clone of a rakkyo strain of tobacco mosaic virus. Arch. Virol. 141, 885-900.
16. Watanabe, Y., Ogawa,T., Takahashi, H., Ishida, I., Takeuchi,Y., Yamamoto, M., Okada, Y. (1995) Resistance against multiple plant viruses in plants mediated by a double-stranded RNA specific ribonuclease. FEBS Lett. 372, 165-168.
17. Sugiyama, Y., Hamamoto, H., Takemoto, S., Watanabe, Y., Okada, Y. (1995) Systemic production of foreign peptides on the particle surface of tobacco mosaic virus. FEBS Lett. 359, 247-250.
18. Ikeda, R., Watanabe, E., Watanabe, Y., Okada, Y. (1993) Nucleotide sequence of tobamovirus Ob which can spread systemically in N gene tobacco. J. Gen. Virol. 74, 1939-1944.
19. Hosokawa, D., Watanabe, Y., Okada, Y. (1993)Time course analysis of immunolocalization of coat protein and replicase proteins in protoplasts inoculated with tobacco mosaic virus. Ann. Phytopath. Soc. Japan, 59, 143-154.
20. Hamamoto, H., Sugiyama, Y., Nakagawa, N., Hashida, E., Matsunaga, Y., Takemoto, S., Watanabe, Y., Okada, Y. (1993) A new tobacco mosaic virus vector and its use for the systemic production of angiotensin-I-converting enzyme inhibitor in transgenic tobacco and tomato. Bio/Tech. 11, 930-932.
21. Meshi, T., Watanabe, Y., Okada, Y. (1992) Molecular pathology of tobacco mosaic virus revealed by biologically active cDNAs. In Genetic Engineering with Plant Viruses. (eds. Wilson, T.M.A. and Davies, J.W. ) 149-186, CRC Press
22. Watanabe, Y.,Ogawa, T., Okada, Y. (1992) In vivo phosphorylation of the 30-kDa protein of tobacco mosaic virus. FEBS Lett. 313, 181-184.
23. Ogawa T., Watanabe, Y., Okada, Y. (1992) Cis-acting elements for in trans complementation of replication-defective mutant of tobacco mosaic virus. Virol. 191, 454-458.
24. Meshi, T., D. Hosokawa, M. Kawagishi, Watanabe, Y., Okada, Y. (1992) Reinvestigation of intracellular localization of the 30K protein in tobacco protoplasts infected with tobacco mosaic virus RNA. Virol. 187, 809-813.
25. Yamafuji, R., Watanabe, Y., Meshi, T., Okada, Y. (1991) Replication of TMV-L and Lta1 and their recombinants in TMV-resistant Tm-1 tomato protoplasts. Virol. 183, 99-105.
26. Takamatsu N., Watanabe, Y., Iwasaki, T., Shiba, T., Meshi, T., Okada, Y. (1991) Deletion analysis of the 5' untranslated leader sequence of tobacco mosaic virus RNA. J. Virol. 65, 1619-1622.
27. Ogawa, T., Watanabe, Y., Meshi, T., Okada, Y. (1991)　Trans complementation of virus-encoded replicase components of tobacco mosaic virus. Virol. 185, 580-584.
28. Anai, T., Hasegawa, K., Watanabe, Y., Uchimiya, H., Ishzaki, R., Matsui, M. (1991) Isolation and analysis of cDNAs encoding small GTP-binding proteins of Arabidopsis thaliana. Gene, 108, 259-264.
29. Okada, Y., Meshi, T. and Watanabe, Y. (1990) Structure and functions of tobacco mosaic virus RNA. In Viral Genes and Plant Pathologenesis. (eds. Pirone, T.P. and Shaw, J.G. ) 23-38. (Springer-Verlag)
30. Takamatsu, N., Watanabe, Y., Yanagi. H., Meshi, T., Shiba, T., Okada, Y. (1990) Production of enkephalin in tobacco protoplasts using tobacco mosaic virus RNA vector. FEBS Lett. 269, 73-76.
31. Takamatsu, N., Watanabe, Y., Meshi, T., Okada, Y. (1990) Mutational analysis of the pseudoknot region in the 3' noncoding region of tobacco mosaic virus RNA. J. Virol.. 64, 3686-3693.
32. Toriyama, S. and Watanabe, Y. (1989) Characterization of single- and double-stranded RNAs in particles of rice stripe virus. J. Gen. Virol. 70, 505-511.
33. Saito,T., Yamanaka, K., Watanabe, Y., Takamatsu, N., Meshi, T., Okada, Y. (1989) Mutational analysis of the coat protein gene of tobacco mosaic virus in relation to hypersensitive response in tobacco plants with the N' gene. Virol. 173, 11-20.
34. Meshi, T., Motoyoshi, F.,Adachi, A., Watanabe, Y., Takamatsu, N., Okada, Y. (1988) Two concomitant base substitutions in the putative replicase genes of tobacco mosaic virus confers the ability to overcome the effects of a tomato resistance gene, Tm-1. EMBO J. 7, 1575-1581
35. Ishikawa, M., Meshi, T., Watanabe, Y., Okada, Y. (1988) Replication of chimeric tobacco mosaic viruses which carry heterologous combinations of replicase genes and 3' noncoding regions. Virol. 164, 290-293.
36. Watanabe, Y., Morita, N., Nishiguchi, M. , Okada, Y. (1987) Attenuated strains of tobacco mosaic virus reduced synthesis of a viral protein with a cell-to-cell movement function. J. Mol. Biol. 194, 699-704.
37. Watanabe, Y., Meshi, T., Okada, Y. (1987) Infection of tobacco protoplasts with in vitro transcribed tobacco mosaic virus RNA using an improved electroporation method. FEBS Lett. 219, 65-69.
38. Watanabe, Y., Kishibayashi, N., Motoyoshi, F., Okada, Y. (1987) Characterization of Tm-1 gene action on replication of common isolates and a resistance-breaking isolate of TMV. Virol. 161, 527-532.
39. Meshi, T., Watanabe, Y., Saito, T., Sugimoto, A., Maeda, T., Okada, Y. (1987) Function of the 30kd protein of tobacco mosaic virus: involvement in cell-to-cell movement and dispensability for replication. EMBO J. 6, 2557-2563.
40. Watanabe, Y., Ooshika, I., Meshi, T., Okada, Y. (1986) Subcellular localization of the 30K protein in TMV-inoculated tobacco protoplasts. Virol. 152, 414-420.
41. Watanabe, Y., Okada, Y. (1986) In vitro viral RNA synthesis by a subcellular fraction of TMV-inoculated tobacco protoplasts. Virol. 149, 64-73.
42. Saito, T., Watanabe, Y., Meshi, T., Okada, Y. (1986) Preparation of antibodies that react with the large non-structural proteins of tobacco mosaic virus by using Escherichia coli expressed fragments. Mol. Gen. Genet. 205, 82-89.
43. Watanabe, Y., Meshi, T., Okada, Y. (1984) The initiation site for transcription of the TMV 30-kDa protein messenger RNA. FEBS Lett. 173, 247-250.
44. Watanabe, Y., Emori, Y., Ooshika, I., Meshi, T., Ohno, T., Okada, Y. (1984) Synthesis of TMV-specific RNAs and proteins at the early stage of infection in tobacco protoplasts: Transient expression of the 30K protein and its mRNA. Virol. 133, 18-24.
45. Ooshika, I., Watanabe, Y., Meshi, T., Okada, Y., Igano, K., Inouye, K., Yoshida, N. (1984) Identification of the 30K protein of TMV by immunoprecipitation with antibodies directed against a synthetic peptide. Virol. 132, 71-78.
46. Watanabe, Y., Ohno, T., Okada, Y. (1982) Virus multiplication in tobacco protoplasts inoculated with tobacco mosaic virus RNA encapsulated in large unilamellar vesicle liposomes. Virol. 120, 478-480.

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Reviews in Japanese (By Nov. 2012）

1. 放射線を科学的に理解する　　　鳥居寛之・小豆川勝見・渡辺雄一郎
   基礎からわかる東大教養の講義 2012年、丸善出版　
2. 身近な植物からの生物学への発信　　　渡辺雄一郎
   生命科学の未解決問題　第3章、p.55-68.　2012年、西村書店
3. サイレンシングの機構　　　渡辺雄一郎
   植物の分子育種学 第12章、p.135-143.　2011年、講談社
4. 遺伝子組換え食品は安全なの？　　　大坪 憲弘・渡辺雄一郎
   なぜなぜ生物学　第11章、p.139-152.　2010年12月、日本分子生物学会編
5. 特集にあたって　　　渡辺雄一郎・曵地康史
   -植物をねらう生物の戦略と植物の防御戦略 （渡辺雄一郎、曵地康史　編）
   生物の科学　遺伝　64巻、p.17-19.　2010年、エヌティーエヌ
6. 植物におけるmiRNAの生合成経路　　　渡辺雄一郎
   生体の科学　61巻、p.349-354.　2010年
7. 植物における小分子RNAの動態制御　　　渡辺雄一郎
   生化学 82巻、p.397-402.　2010年
8. 身近な植物から学べる現代生物学　　　渡辺雄一郎
   高校生のための東大授業ライブ　純情編　第12章　p.181-197.　2010年、東京大学出版会
9. 食の安全から、安心な食へー食コミュニケーション学の提案　　　岡田晃枝・渡辺雄一郎
   「食の安全科学の展開—食のリスク予測と制御に向けて」 p.267-277.　2010年、CMC出版
10. 植物のナンセンス変異依存mRNA分解(NMD)　　　堀孝一・渡辺雄一郎
    蛋白質核酸酵素　「mRNAプログラム　多様性と非対称性の獲得戦略」、p.2189-2194.　2009年、共立出版
11. 植物バイオテクノロジーと遺伝子組換え食品　　　本瀬宏康・渡辺雄一郎
    改訂第3版分子生物学イラストレイテッド、p.335-341　2009年、羊土社
12. 生物らしさを生み出すRNAの機能　　　渡辺雄一郎
    遺伝 62巻、p.73-74.　2008年、エヌティーエヌ
13. 植物に見いだされた短いRNAたち　　　渡辺雄一郎
    化学と工業 61巻、p.712-715.　2008年、日本化学会
14. 植物のmicroRNA　　　渡邊雄一郎
    「RNA実験ノート～RNAiの原理とその実際」
    第1章　RNAiの原理　３節、p.14-15.　2008年、羊土社
15. RNAiの植物への応用　　　堀孝一・渡邊雄一郎
    「RNA実験ノート〜RNAiの原理とその実際」 第3章　RNAiを用いた応用解析　5節　p.118-125.　2008年、羊土社
16. 植物で発現するsmall RNA: ta-siRNAと nat-siRNAの生成過程と機能　　　田上優子・渡邊雄一郎
    実験医学 25巻、p.818-822.　2007年
17. アルツハイマー病ワクチン作物開発の可能性　 吉田泰二・石井理華・渡邊雄一郎・石浦章一
    農業技術 62巻、p.67-71.　2007年
18. TMVの移行の分子機構　　　渡邊雄一郎
    「微生物の病原性と植物の防御応答」p.191-196.
    第7章　3節　タバコモザイクウイルスの複製・移行と宿主因子　2007年,、北海道大学出版会
19. 植物ウイルスの感染と宿主因子　　　佐藤昌直・渡邊雄一郎
    ウイルス 56巻、p.155-164.　2006年
20. 植物のsmall RNAに関する話題　　　竹田篤史・渡邊雄一郎
    蛋白質核酸酵素　増刊「RNAと生命」 51巻、p.2463-2470.　2006年
    
21. 遺伝子組換え植物を利用した神経変性疾患の新しい治療法とそのリスク評価　　　石浦章一・石井理華・吉田泰二・渡邊雄一郎
    遺伝 別冊19、p.61-65.　2006年
22. 原形質連絡—植物細胞間のユニークなコミュニケーション　　　渡邊雄一郎
    「プラントミメティックスー植物に学ぶ」第一章５節、p.160-164.　2006年、NTS
    
23. 植物でのRNAサイレンシングにおける発見　　　栗原志夫・渡邊雄一郎
    科学 76巻、p.519-521.　2006年
24. 植物ウイルスを有用物質生産に役立てる　　　渡邊雄一郎
    NIAS アグリバイオサイエンス・シリーズ No.2
    居在家義昭・岡成美・町井博明編 2006年　　独立行政法人　農業生物資源研究所
    
25. RNAサイレンシングの生物学　　　渡邊雄一郎・塩見美喜子・塩見春彦
    現代化学、p.56-60.　2006年
26. 植物ウイルスの宿主域決定因子　　滝澤真理・渡邊雄一郎
    実験医学　「解明が進むウイルス・細菌感染と免疫応答」
    笹川千尋、柳雄介、審良静男編 p.2574-2581.　2005年
27. 非細胞生命体の進化　　渡邊雄一郎
    シリーズ進化学3　「化学進化・細胞進化」
    石川統・斎藤成也・佐藤矩行・長谷川真理子編、p.151-190.　2004年、岩波書店
28. 植物ウイルスの細胞間移行　　　渡邊雄一郎
    植物細胞工学シリーズ　「分子レベルからみた植物の耐病性」
    島本功・渡邊雄一郎・柘植尚志編、19巻、p.163-171.　2004年、秀潤社
29. 植物での転写後サイレンシング(PTGS)　　　堀孝一・栗原志夫・渡邊雄一郎
    蛋白質　核酸　酵素　特集「RNAの細胞生物学」48巻、p.459-468.　2003年
30. ウイルスベクターによる有用遺伝子の発現　　　渡邊雄一郎・上田一郎
    化学と生物 41巻、p.183-189.　2003年
31. 植物細胞間の連絡と原形質連絡という構造　　　岸光子・渡邊雄一郎
    蛋白質/核酸/酵素　特集「植物の形作り」
    岡田清孝、町田泰則、島本功、福田裕穂、中村研三編、47巻、p.1740-1744.　2002年
32. ウイルス　　　渡邊雄一郎
    AERA Mook 「植物学がわかる」 p.108-111.　2001年
33. 植物がうちに秘めていた身をまもる戦略　　　渡邊雄一郎
    科学 70巻、p.579-586.　2000年
34. プラズモデスマータを介した細胞相互作用　　　渡邊雄一郎
    植物細胞工学シリーズ12「新版　植物の形を決める分子機構」
    岡田清孝、町田泰則、松岡信編、p.235-238.　2000年
35. 植物ウイルスのmovement protein (MP)をめぐる話題　　　川上茂樹・渡邊雄一郎
    ウイルス 49巻、p.107-118.　1999年
    
36. 弱毒ウイルスの新規作出方法　　　渡邊雄一郎
    バイオコントロール研究会レポート(PSJ Biocont. Rept.) 6巻、p.66-72.　1999年