Division of Organogenesis
Department of Brain Morphogenesis



  1. Rubenstein, J. L. R., Martinez, S., Shimamura, K., and Puelles, L. (1994). The embryonic vertebrate forebrain: the prosomeric model.

Science 226, 578-580.


  1. Bulfone, A., Smiga, S. M., Shimamura, K., Peterson, A., Puelles, L., and Rubenstein, J. L. R. (1995). T-Brain-1: a homolog of Brachyury whose expression defines molecularly distinct domains within the cerebral cortex.

Neuron 15, 63-78.


  1. Shimamura, K., Hartigan, D. J., Martinez, S., Puelles, L., and Rubenstein, J. L. R. (1995). Longitudinal organization of the anterior neural plate and neural tube. Development 121, 3923-3933.


  1. Shimamura, K. and Rubenstein, J. L. R. (1997). Inductive interactions direct early regionalization of the mouse forebrain.

Development 124, 2709-2718.


  1. Rubenstein, J. L. R., Shimamura, K., Martinez, S. and Puelles, L. (1998). Regionalization of the prosencephalic neural plate.

Ann. Rev. Neurosci. 21, 445-477.


  1. Qiu, M., Shimamura, K., Sussel, L., Chen, S. and Rubenstein, J. L. R. (1998). Control of anteroposterior and dorsoventral domains of Nkx-6.1 gene expression relative to other Nkx genes during vertebrate CNS development.

Mech. Dev. 72, 77-88.


  1. Ye, W., Shimamura, K., Rubenstein, J. L. R., Hynes, M. A. and Rosenthal, A. (1998). FGF and Shh signals control dopaminergic and serotonergic cell fate in the anterior neural plate.

Cell 93, 755-766.


8.Puelles, L., Kuwana, E., Puelles, E., Bulfone, A., Shimamura, K., Keleher, G., Smiga, S. M. and Rubenstein, J. L. R. (2000) Pallial and subpallial derivatives in the embryonic chick and mouse telencephalon, traced by the expression of the genes Dlx-2, Emx-1, Nkx-2.1, Pax-6 and Tbr-1.

  1. Comp. Neurol. 424, 409-438.


9.Mizuguchi, R., Sugimori, M., Takebayashi, H., Kosako, H., Nagao, M., Yoshida, S., Nabeshima, Y., Shimamura, K., and Nakafuku, M. (2001) Combinatorial roles of Olig2 and Neurogenin2 in the coordinated induction of pan-neuronal and subtype-specific properties of motoneurons.

Neuron 31, 759-773.


10.Cobos, I., Shimamura, K., Rubenstein, J. L. R., Martinez, S., and Puelles, L. (2001)  Fate map of the avian anterior forebrain at the 4 somite stage, based on the analysis of quail-chick chimeras.

Dev. Biol. 239, 46-67.


  1. Hatakeyama, J., Tomita, K., Inoue, T., Kageyama, R. (2001) Roles of homeobox and bHLH genes in specification of a retinal cell type.

Development 128(8), 1313-22.


12.Kobayashi, D., Kobayashi, M., Matsumoto, K., Ogura, T., Nakafuku, M., and Shimamura, K.  (2002) Early subdivisions in the neural plate define distinct competence for inductive signals.

Development 129, 83-93.


  1. Hide, T., Hatakeyama, J., Kimura-Yoshida, C., Tian, E., Takeda, N., Ushio, Y., Shiroishi, T., Aizawa, S., Matsuo, I. (2002) Genetic modifiers of otocephalic phenotypes in Otx2 heterozygous mutant mice.

Development 129(18), 4347-57.


14.Hatakeyama, J., Kageyama, R. (2002) Retrovirus-mediated gene transfer to retinal explants. 

Methods  28(4), 387-95.


15.Lagutin, O. V., Zhu, C. C., Kobayashi, D., Topczewski, J., Shimamura, K., Puelles, L., Russell, H. R. C., McKinnon, P. J., Solnica-Krezel, L., and Oliver, G. (2003) Six3 repression of Wnt signaling in the anterior neuroectoderm is essential for vertebrate forebrain development.

Genes Dev. 17, 368-379.


16.Hashimoto-Torii, K., Motoyama, J., Hui, C.-C., Kuroiwa, A., Nakafuku, M., and Shimamura, K. (2003) Differential activities of Sonic hedgehog mediated by Gli transcription factors define distinct neuronal subtypes in the dorsal thalamus.

Mech. Dev. 120, 1097-1111.


17.Watabe-Uchida, M., Masuda, A., Shimada, N., Endo, M., Shimamura, K., Yasuda, K., Sehara-Fujisawa, A. (2004) Novel metalloprotease-disintegrin, Meltrin epsilon (ADAM35), expressed in epithelial tissues during chick embryogenesis.

Dev. Dyn. 230, 557-568.


18.Hatakeyama, J., Kageyama, R.  (2004) Retinal cell fate determination and bHLH factors.

Seminars in Cell & Developmental Biology 15(1), 83-9.


19.Hatakeyama, J., Bessho, Y., Katoh, K., Ookawara, S., Fujioka, M., Guillemot, F., Kageyama, R. (2004) Hes genes regulate size, shape and histogenesis of the nervous system by control of the timing of neural stem cell differentiation. 

Development 131(22), 5539-50.    


  1. Takatsuka, K., Hatakeyama, J., Bessho, Y., Kageyama, R. (2004) Roles of the bHLH gene Hes1 in retinal morphogenesis.

Brain Research  1004(1-2),148-55.


21.Azuma, N., Tadokoro, K., Asaka, A., Yamada, M., Yamaguchi, Y., Handa, H., Matsushima, S., Watanabe, T., Kohsaka, S., Kida, Y., Ogura, T., Shimamura, K., Nakafuku, M. (2005) The Pax6 isoform bearing an alternative spliced exon promotes the development of the neural retinal structure.

Human Mol. Genet. 14, 735-745.


22.Azuma, N., Tadokoro, K., Asaka, A., Yamada, M., Yamaguchi, Y., Handa, H., Matsushima, S., Watanabe, T., Kida, Y., Ogura, T., Torii, M., Shimamura, K., Nakafuku, M. (2005) Transdifferentiation of the retinal pigment epithelia to the neural retina by transfer of the Pax6 transcriptional factor.

Human Mol. Genet. 14, 1059-1068.


23.Vieira, C., Garda, A.-L., Shimamura, K., Martinez, S. (2005) Thalamic development induced by Shh in the chick embryo.

Dev. Biol. 284, 351-363.


24.Kageyama, R., Ohtsuka, T., Hatakeyama, J., Ohsawa, R. (2005) Roles of bHLH genes in neural stem cell differentiation. 

Experimental Cell Research  306. 343-348.


25.Hatakeyama, J., Sakamoto, S., Kageyama, R. (2006) Hes1 and Hes5 regulate development of the cranial and spinal nerve systems. 

Developmental Neuroscience 2006 28(1-2), 92-101.


26.Baek, JH., Hatakeyama, J., Sakamoto, S., Ohtsuka, T., Kageyama, R. (2006) Persistent and high levels of Hes1 expression regulate boundary formation in the developing central nervous system. 

Development 133, 2467-2476. 


27.Hatakeyama, J., Kageyama, R. (2006) Notch1 expression is spatiotemporally correlated with neurogenesis and negatively regulated by Notch1-independent Hes genes in the developing nervous system. 

Cerebral Cortex 1, i132-137.


28.Lebel. M., Mo, R., Shimamura, K., Hui, C.-C. (2007) Gli2 and Gli3 play distinct roles in the dorsoventral patterning of the mouse hindbrain.

Dev. Biol. 302, 345-355.


29.Hirata, H., Watanabe, T., Hatakeyama, J., Sprague, SM., Saint-Amant, L., Nagashima, A., Cui, WW., Zhou, W., and Kuwada, JY. (2007) Zebrafish relatively-relaxed mutants have a ryanodine receptor defect, show slow swimming and provide a model of multi-minicore disease. 

Development 134(15), 2771-81.


30.Hatakeyama, J., Shimamura, K. (2008) Method for electroporation for the early chick embryo.

Develop. Growth Differ. 50, 449-452.


31.Katsumoto, K., Fukuda, K., Kimura, W., Shimamura, K., Yasugi, S., Kume, S. (2009) Origin of pancreatic precursors and the mechanism of endoderm regionalization in chick embryos.

Mech. Dev. 126, 539-551.


32.Hatakeyama, J., Shimamura, K. (2009) Method of electroporation for the early chick embryo.

In “Electroporation and Sonoporation in Developmental Biology”, 43-54, Springer. (Book chapter)


33.Kageyama, R., Ohtsuka, T., Ohsawa, R., Hatakeyama, J. (2009) Helix-loop-helix (bHLH) protein: Hes family. 

Encyclopedia of Neuroscience. (L.R. Squire, Editor). Oxford: Academic Press. Vol. 4, 1057-1065 (Book chapter)


34.Ozono, K., Komiya, S., Shimamura, K., Ito, T., Nagafuchi, A. (2011). Defining the roles of alpha-catenin in cell adhesion and cytoskeleton organization: Isolation of F9 cells completely lacking cadherin-catenin complex.

Cell Struct. Funct. 36, 131-143.


35.Sato H., Fukutani Y., Yamamoto Y., Tatara E., Takemoto M., Shimamura K., Yamamoto N. (2012) Thalamus-derived molecules promote survival and dendritic growth of developing cortical neurons.

J Neurosci. 32(44):15388-402.


36.Nagahara, N., Nagano, M., Ito, T., Akimoto, T., Shimamura, K., Suzuki, H. (2013). Antioxidant enzyme, 3-mercaptopyruvate sulfurtransferase-knockout mice exhibit increased anxiety-like behaviors: a model for human mercaptolactate-cysteine disulfiduria.

Sci. Rep. 3, 1986.


37.Guiu, J., Shimizu, R., D’Altri, T., Fraser, S.T., Hatakeyama, J., Bresnick, E.H., Kageyama, R., Dzierzak, E., Yamamoto, M., Espinosa, L., Bigas, A. (2013) Hes repressors are essential regulators of hematopoietic stem cell development downstream of Notch signaling.

Journal of Experimental Medicine 210(1):71-84.


  1. Hatakeyama, J., Wakamatsu, Y., Nagafuchi, A., Kageyama, R., Shigemoto, R., Shimamura, K. (2014) Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates.

Development 141(8):1671-82.


  1. Zhang, J., Hatakeyama, J., Eto, K., Abe, SI. (2014) Reconstruction of a seminiferous tubule-like structure in a 3 dimensional culture system of re-aggregated mouse neonatal testicular cells within a collagen matrix.

Gen Comp Endocrinol. 205: 121-32


  1. Ono K., Clavairoly A., Nomura T., Gotoh H., Uno A., Armant O., Takebayashi H., Zhang Q., Shimamura K., Itohara S., Parras CM., Ikenaka K. (2014) Development of the prethalamus is crucial for thalamocortical projection formation and is regulated by Olig2.

Development 141, 2075-2084.


  1. Hatakeyama, J., Shimamura, K. (2015). Electroporation for the chick embryonic CNS.

In “Electroporation methods in Neuroscience”, Saito T, ed., Neuromethods 102, 115-125.

42. Ha, T., Moon, K.H., Dai, L., Hatakeyama, J., Yoon, K., Park, H-S., Kong, Y-Y., Shimamura, K., Kim, J.W. (2017). The retinal pigment epithelium is a Notch signaling niche in the mouse retina.

Cell Rep. 19, 351-363.

43.Hatakeyama, J.*, Sato, H.*, and Shimamura, K. (2017) Developing guinea pig brain as a model for cortical folding.

Development, Growth & Differentiation 59(4), 286-301.

*Equal contribution



44.Kameyama, H., Kudoh, S., Hatakeyama, J., Matuo, A., Ito, T. (2017) Significance of Stat3 Signaling in Epithelial Cell Differentiation of Fetal Mouse Lungs.

Acta Histochemca et Cytochemica 50(1):1-9.


  1. Alchini, R.,Sato, H., Matsumoto, N., Shimogori, T., Sugo N., and Yamamoto, N. (2017) Nucleocytoplasmic Shuttling of Histone Deacetylase 9 Controls Activity-Dependent Thalamocortical Axon Branching.

Sci Rep. 7(1):6024.


46.Abe, S., Abe, K., Harada, T., Mizumoto, G., Oshikawa, H., Akiyama, H., Shimamura, K. (2017). Roles of CD34+ cells and ALK5 signaling in the reconstruction of seminiferous tuble-like structures in 3-D re-aggregate culture of dissociated cells from mouse testes.

PLoS One 12(11): e0188705.


  1. Hatakeyama, J., Shimamura, K. (2019) The pace of neurogenesiss is regulated by the transient retention of the apical endfeet of differentiating cells.

Cerebral Cortex 29(9) 3725-3737 


  1. Acebedo, AR., Suzuki, K., Hino, S., Alcantara, MC., Sato Y., Haga, H., Matsymoto, KI., Nakao, M., Shimamura, K., Takeo, T., Nakagata, N., Miyagawa, S., Nishinakamura, R., Adelstein, RS., Yamada, G. (2019) Mesenchymal actomyosin contractility is required for androgen-driven urethral masculinization in mice.

Communications Biology  2(1): 95


  1. Nasu, M., Shimamura, K., Esumi, S., Tamamaki, N. (2020) Formation of dorsal-ventral axis of the pallium derived from mouse embryonic stem cells.

Biochemical and Biophysical Research Communications

524(1) 117-122


  1. Nasu, M., Shimamura, K., Esumi, S., Tamamaki, N. (2020) Sequential pattern of sublayer formation in the paleocortex and neocortex.

Medical Molecular Morphology  53(3) 168-176


  1. Ito N., Riyadh, M. A., Ahmad S. A. I., Hattori, S., Kanemura Y., Kiyonari, H., Abe, T., Furuta, Y., Shinmyo, Y., Kaneko, N., Hirota, Y., Lupo, G., Hatakeyama, J., Abdulhaleem M, F. A., Anam, M. A., Yamaguchi, M., Takeo, T., Takebayashi, H., Takebayashi, M., Oike, Y., Nakagata, N., Shimamura, K., Holtzman, M. J., Takahashi, Y., Guillemot, F., Miyakawa, F., Sawamoto, K., Ohta, K. (2021) Dysfunction of the proteoglycan Tsukushi causes hydrocephalus through altered neurogenesis in the subventricular zone in mice.

Science Translational Medicine  13(587)  7896 


  1. Nasu, M., Esumi, S., Hatakeyama, J., Tamamaki, N., Shimamura, K. (2021) Two-phase lineage specification of telencephalin progenitors generated from mouse embryonic stem cells.

Frontiers in Cell and Developmental Biology  9:632381