PUBLICATION
Research articles with our corresponding authorship
| Goh T, Song Y, Yonekura T, Obushi N, Den Z, Imizu K, Tomizawa Y, Kondo Y, Miyashima S, Iwamoto Y, Inami M, Chen Y-W, Nakajima K. In-depth quantification of cell division and elongation dynamics at the tip of growing Arabidopsis roots using 4D-microscopy, AI-assisted image processing, and data sonification. Plant Cell Physiol. 64, 1262-1278 (2023) PubMed Publisher (free) Press Research highlight |
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| Cui, Y., Hisanaga, T., Kajiwara, T., Yamaoka, S., Kohchi, T., Goh, T. and Nakajima, K. Three-dimensional morphological analysis revealed the cell patterning bases for the sexual dimorphism development in the liverwort Marchantia polymorpha. Plant Cell Physiol. 64, 866-879 (2023)PubMed Publisher (free) |
| Fujiwara, M., Imamura, M., Matsushita, K., Roszak, P., Yamashino, T., Hosokawa, Y., Nakajima, K., Fujimoto K. and Miyashima, S. Patterned proliferation orients tissue-wide stress to control root vascular symmetry in Arabidopsis. Curr. Biol. 33, 886-898.e8 (2023)PubMed Publisher (free) Press |
| Goh, T., Sakamoto, K., Wang, P., Kozono, S., Ueno, K., Miyashima, S., Toyokura, K., Fukaki, H., Kang, B. and Nakajima, K. Autophagy promotes organelle clearance and organized cell separation of living root cap cells in Arabidopsis thaliana. Development 149, dev.200593 (2022)PubMed Publisher (free) Interview Press |
| Hisanaga, T., Fujimoto, S., Cui, Y., Sato, K., Sano, R., Yamaoka, S., Kohchi, T., Berger, F. and Nakajima, K. Deep evolutionary origin of gamete-directed zygote activation by KNOX/BELL transcription factors in green plants. eLife 10: e57090 (2021) PubMed Publisher (free) Press |
| Fujiwara, M., Goh, T., Tsugawa, S., Nakajima, K., Fukaki, H. and Fujimoto, K. Tissue growth constrains root organ outlines into an isometrically scalable shape. Development 148, dev196253 (2021).PubMed Publisher (free) Press |
| Hisanaga, T, Okahashi, K., Yamaoka, S., Kajiwara, T., Nishihama, R., Shimamura, M., Yamato, K. T., Bowman, J. L., Kohchi, T. and Nakajima, K. A cis-acting bidirectional transcription switch controls sexual dimorphism in the liverwort. EMBO J. 38, e100240 (2019). PubMed Publisher (free) Press |
| Hashimoto, K., Miyashima, S., Sato-Nara, K., Yamada, T. and Nakajima, K. Functionally diversified members of the MIR165/6 gene family regulate ovule morphogenesis in Arabidopsis thaliana. Plant Cell Physiol. 59, 1017-1026 (2018). PubMed Publisher (free) |
| Kamiya, M., Higashio, S., Isomoto, A., Kim, J-M., Seki, M., Miyashima, S. and Nakajima, K., Control of root cap maturation and cell detachment by BEARSKIN transcription factors in Arabidopsis. Development 143, 4063-4072. (2016). PubMed Publisher (free) Press |
| Koi, S., Hisanaga, T., Sato, K., Shimamura, M., Yamato, K. T., Ishizaki, K., Kohchi, T., and Nakajima, K. An evolutionarily conserved plant RKD factor controls germ cell differentiation. Curr. Biol . 26, 1775-1781. (2016).PubMed Publisher (free) Press |
| Miyashima, S., Honda, M., Hashimoto, K., Tatematsu, K., Hashimoto, T., Sato-Nara, K., Okada, K., and Nakajima, K. A Comprehensive Expression Analysis of the Arabidopsis MICRORNA165/6 Gene Family during Embryogenesis Reveals a Conserved Role in Meristem Specification and a Non-cell-autonomous Function. Plant Cell Physiol., 54, 375-384. (2013)PubMed Publisher (free) |
| Waki T., Miyashima, S., Nakanishi, M., Ikeda, Y., Hashimoto, T. and Nakajima, K. A GAL4-based targeted activation tagging system in Arabidopsis thaliana. Plant J. 73, 357-367. (2013).PubMed Publisher (free) |
| Waki, T., Hiki, T., Watanabe, R., Hashimoto, T., and Nakajima, K., The Arabidopsis RWP-RK protein RKD4 triggers gene expression and pattern formation in early embryogenesis. Curr. Biol . 21, 1277-1281 (2011). PubMed Publisher (free) Press |
| Miyashima, S., Koi, S., Hashimoto, T., and Nakajima, K., Non-cell-autonomous microRNA165 acts in a dose-dependent manner to regulate multiple differentiation status in the Arabidopsis root. Development. 138, 2303-2313 (2011). PubMed Publisher (free) Press |
| Miyashima, S., Hashimoto, T., and Nakajima, K., ARGONAUTE1 acts in Arabidopsis root radial pattern formation independently of the SHR/SCR pathway. Plant Cell Physiol. 50, 626-634 (2009). PubMed Publisher (free) |
Research articles from collaborating labs with our co-authorship
| Liu, Z., Wang, P., Goh, T., Nakajima, K., Kang, B.H. Mucilage secretion from the root cap requires the NAC family transcription factor BEARSKIN2, Plant Physiol. kiae402 (2024).PubMedPublisher |
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| Soyano, T., Akamatsu, A., Takeda, N., Watahiki, M. K., Goh, T., Okuma, N., Suganuma, N, Kojima, M., Takebayashi, Y., Sakakibara, H., Nakajima, K., and Kawaguchi, M. Periodic cytokinin responses in Lotus japonicus rhizobium infection and nodule development. Science 6706, 288-294 (2024). PubMed Publisher Press |
| Fan, L., Zhang, C., Gao, B., Zhang, Y., Stewart, E., Jez, J., Nakajima, K., and Chen. X.. Microtubules promote the non-cell autonomous action of microRNAs by inhibiting their cytoplasmic loading onto ARGONAUTE1 in Arabidopsis. Dev. Cell 8, 995-1008 (2022). PubMed Publisher |
| Goh, T., Toyokura, K., Yamaguchi, N., Okamoto, Y., Uehara, T., Kaneko, S., Takebayashi, Y., Kasahara, H., Ikeyama, Y., Okushima, Y., Nakajima, K., Mimura, T., Tasaka, M. and Fukaki, H. Lateral root initiation requires the sequential induction of transcription factors LBD16 and PUCHI in Arabidopsis thaliana. New Phytologist 224, 749-760 (2019). PubMed Publisher |
| Miyashima, S., Roszak, P., Sevilem. I., Toyokura, K., Blob, B., Heo, J., Mellor, N., Help-Rinta-Rahko, H., Otero, S., Smet, W., Boekschoten, M., Hooiveld, G., Hashimoto, K., Smetana, O., Siligato, R., Wallner, E.-S., Mähönen, A. P., Kondo, Y., Melnyk, C. W., Greb, T., Nakajima, K., Sozzani, R., Bishopp, A., De Rybel, B., and Helariutta, Y., Mobile PEAR transcription factors integrate positional cues to prime cambial growth. Nature 565, 490–494 (2019). Publisher Press |
| Toyokura, K., Goh, T., Shinohara, H., Shinoda, A., Kondo, Y., Okamoto, Y., Uehara, T., Fujimoto, K., Okushima, Y.,Ikeyama, Y., Nakajima, K., Mimura, T., Tasaka, M., Matsubayashi, Y. and Fukaki, H., Lateral Inhibition by a Peptide Hormone-Receptor Cascade during Arabidopsis Lateral Root Founder Cell Formation. Dev. Cell 48, 64-75 (2019). PubMed PublisherPress |
| Nakamura, K., Hisanaga, T., Fujimoto, K., Nakajima, K., and Wada, H. Plant-inspired pipettes. J. R. Soc. Interface 15, 20170868 (2018). Publisher (free) |
| Durr, J., Papareddy, R., Nakajima, K., and Gutierrez-Marcos, J. Highly efficient heritable targeted deletions of gene clusters and non-coding regulatory regions in Arabidopsis using CRISPR/Cas9. Sci. Rep. 8, 4443 (2018) PubMed Publisher (free) |
| Bowman, J.L., Araki, T., Arteaga-Vazquez, M.A., Berger, F., Dolan, L., Haseloff, J., Ishizaki, K., Kyozuka, J., 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. The Naming of Names: Guidelines for Gene Nomenclature in Marchantia. Plant Cell Physiol. (2015) PubMed Publisher (free) |
| Yamada, T., Sasaki, Y., Hashimoto, K., Nakajima, K., and Gasser, CS. CORONA, PHABULOSA and PHAVOLUTA collaborate with BELL 1 to confine WUSCHEL expression to the nucellus in Arabidopsis ovules. Development (2015) PubMed Publisher (free) |
| Tatematsu, K., Toyokura, K., Miyashima, S., Nakajima, K., and Okada, K. A molecular mechanism that confines the activity pattern of miR165 in Arabidopsis leaf primordia.. Plant J., 82, 596-608. (2015) PubMed Publisher (free) |
| Zhou, Y., Honda, M., Zhu, H., Zhang, Z., Guo, X., Li, T., Li Z., Peng, X., Nakajima, K., Duan, L., Zhang X. Spatiotemporal Sequestration of miR165/166 by Arabidopsis Argonaute10 Promotes Shoot Apical Meristem Maintenance. Cell Rep. 24, 1819–1827. (2015). PubMed Publisher (free) |
| Ursache, R., Miyashima, S., Chen, Q., Vaten, A., Nakajima, K., Carlsbecker, A., Zhao, Y., Helariutta, Y., Dettmer, J., Tryptophan-dependent auxin biosynthesis is required for HD-ZIP III-mediated xylem patterning. Development 141, 1250-1259. (2014). PubMed Publisher (free) |
| Fukao, Y, Yoshida, M, Kurata, R, Kobayashi, M, Nakanishi, M, Fujiwara, M, Nakajima, K., and Ferjani, A. Peptide Separation Methodologies for In-depth Proteomics in Arabidopsis. Plant Cell Physiol. 54, 808-815. (2013). PubMed Publisher (free) |
| Vaten, A., Dettmer, J., Wu, S., Stierhof, Y.D., Miyashima, S., Yadav, S.R., Roberts, C.J., Campilho, A., Bulone, V., Lichtenberger, R., Lehesranta, S., Mahonen, A.P., Kim, J.Y., Jokitalo, E., Sauer, N., Scheres, B., Nakajima, K., Carlsbecker, A., Gallagher, K.L., and Helariutta, Y., Callose Biosynthesis Regulates Symplastic Trafficking during Root Development. Dev Cell. 21, 1144-1155 (2011). PubMed Publisher (free) |
| Sarkar, A.K., Luijten, M., Miyashima, S., Lenhard, M., Hashimoto, T., Nakajima, K., Scheres, B., Heidstra, R., and Laux, T., Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers. Nature. 446, 811-814 (2007). PubMed Publisher Press |
| Levesque, M.P., Vernoux, T., Busch, W., Cui, H., Wang, J.Y., Blilou, I., Hassan, H., Nakajima, K., Matsumoto, N., Lohmann, J.U., Scheres, B., and Benfey, P.N., Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol. 4, e143 (2006). PubMed Publisher (free) |
| Gallagher, K.L., Paquette, A.J., Nakajima, K., and Benfey, P.N., Mechanisms Regulating SHORT-ROOT Intercellular Movement. Curr Biol. 14, 1847-1851 (2004). PubMed Publisher (free) |
| Nakajima, K., Sena, G., Nawy, T., and Benfey, P.N., Intercellular movement of the putative transcription factor SHR in root patterning. Nature. 413, 307-311 (2001). PubMed Publisher |
| Helariutta, Y., Fukaki, H., Wysocka-Diller, J., Nakajima, K., Jung, J., Sena, G., Hauser, M.T., and Benfey, P.N., The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell. 101, 555-567. (2000). PubMed Publisher (free) |
Review/Editorial papers
| Nakajima, K. An old mission revealed for BZRs. Nature Plants 10 (2024) Publisher |
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| Nakajima, K., Higaki, T., Ueda, T. and Inami, M. Gaining new insights in plant biology through human-machine collaboration. Plant Cell Physiol. 64, 1257-1261 (2023) PubMed Publisher |
| Nakajima, K., GELP, not just any boundary. Nature Plants 7, 248-249 (2021). Publisher |
| Hisanaga,T., Yamaoka, S., Kawashima, T., Higo, A., Nakajima, K., Araki, T., Kohchi, T. and Berger, F. Building new insights in plant gametogenesis from an evolutionary perspective. Nature Plants 5, 663–669 (2019). PubMedPublisher |
| Nakajima, K., Be my baby: patterning toward plant germ cells. Curr. Opin. Plant Biol. 41, 110-115 (2018). PubMed Publisher |
| Hisanaga, T, Miyashima, S. and Nakajima, K., Small RNAs as positional signal for pattern formation. Curr. Opin. Plant Biol. 21, 37-42 (2014). PubMed Publisher |
| Miyashima, S. and Nakajima, K., The root endodermis: A hub of developmental signals and nutrient flow. Plant Signal Behav. 6, 1954-1958 (2011). PubMed Publisher (free) |
| Nakajima, K. and Benfey, P.N., Signaling in and out: control of cell division and differentiation in the shoot and root. Plant Cell. 14 Suppl, S265-276 (2002). PubMed Publisher (free) |