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
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 polymorphaPlant 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 ArabidopsisCurr. 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

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 (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
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)