Papers - KUSAKABE Takehiro
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Retinal Cone Mosaic in sws1-Mutant Medaka (Oryzias latipes), A Teleost Reviewed International journal
Megumi Matsuo, Makoto Matsuyama, Tomoe Kobayashi, Shinji Kanda, Satoshi Ansai, Taichi Kawakami, Erika Hosokawa, Yutaka Daido, Takehiro G. Kusakabe, Kiyoshi Naruse, and Shoji Fukamachi
Investigative Opthalmology & Visual Science 63 ( 11 ) 21 - 21 2022.10
Publisher：Association for Research in Vision and Ophthalmology (ARVO)
PURPOSE: Ablation of short single cones (SSCs) expressing short-wavelength-sensitive opsin (SWS1) is well analyzed in the field of regenerative retinal cells. In contrast with ablation studies, the phenomena caused by the complete deletion of SWS1 are less well-understood. To assess the effects of SWS1 deficiency on retinal structure, we established and analyzed sws1-mutant medaka. METHODS: To visualize SWS1, a monoclonal anti-SWS1 antibody and transgenic reporter fish (Tg(sws1:mem-egfp)) were generated. We also developed a CRISPR/Cas-driven sws1-mutant line. Retinal structure of sws1 mutant was visualized using anti-SWS1, 1D4, and ZPR1 antibodies and coumarin derivatives and compared with wild type, Tg(sws1:mem-egfp), and another opsin (lws) mutant. RESULTS: Our rat monoclonal antibody specifically recognized medaka SWS1. Sws1 mutant retained regularly arranged cone mosaic as lws mutant and its SSCs had neither SWS1 nor long wavelength sensitive opsin. Depletion of sws1 did not affect the expression of long wavelength sensitive opsin, and vice versa. ZPR1 antibody recognized arrestin spread throughout double cones and long single cones in wild-type, transgenic, and sws1-mutant lines. CONCLUSIONS: Comparative observation of sws1-mutant and wild-type retinas revealed that ZPR1 negativity is not a marker for SSCs with SWS1, but SSCs themselves. Loss of functional sws1 did not cause retinal degeneration, indicating that sws1 is not essential for cone mosaic development in medaka. Our two fish lines, one with visualized SWS1 and the other lacking functional SWS1, offer an opportunity to study neural network synapsing with SSCs and to clarify the role of SWS1 in vision.
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Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate Reviewed International coauthorship
Prakriti Paul Chacha, Ryoko Horie, Takehiro G. Kusakabe, Yasunori Sasakura, Mona Singh, Takeo Horie, Michael Levine
Proceedings of the National Academy of Sciences 119 ( 4 ) e2118817119 - e2118817119 2022.1
Publisher：Proceedings of the National Academy of Sciences
The protovertebrate <italic>Ciona intestinalis</italic> type A (sometimes called <italic>Ciona robusta</italic>) contains a series of sensory cell types distributed across the head–tail axis of swimming tadpoles. They arise from lateral regions of the neural plate that exhibit properties of vertebrate placodes and neural crest. The sensory determinant <italic>POU IV/Brn3</italic> is known to work in concert with regional determinants, such as <italic>Foxg</italic> and <italic>Neurogenin</italic>, to produce palp sensory cells (PSCs) and bipolar tail neurons (BTNs), in head and tail regions, respectively. A combination of single-cell RNA-sequencing (scRNA-seq) assays, computational analysis, and experimental manipulations suggests that misexpression of <italic>POU IV</italic> results in variable transformations of epidermal cells into hybrid sensory cell types, including those exhibiting properties of both PSCs and BTNs. Hybrid properties are due to coexpression of <italic>Foxg</italic> and <italic>Neurogenin</italic> that is triggered by an unexpected <italic>POU IV</italic> feedback loop. Hybrid cells were also found to express a synthetic gene battery that is not coexpressed in any known cell type. We discuss these results with respect to the opportunities and challenges of reprogramming cell types through the targeted misexpression of cellular determinants.
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A single motor neuron determines the rhythm of early motor behavior in Ciona Reviewed
Taichi Akahoshi, Madoka K. Utsumi, Kouhei Oonuma, Makoto Murakami, Takeo Horie, Takehiro G. Kusakabe, Kotaro Oka, Kohji Hotta
Science Advances 7 ( 50 ) 2021.12
Publisher：American Association for the Advancement of Science (AAAS)
Single motor neuron regulates rhythmic tail flick in prehatching
<italic>Ciona</italic>
embryo. -
Evolution of Developmental Programs for the Midline Structures in Chordates: Insights From Gene Regulation in the Floor Plate and Hypochord Homologues of Ciona Embryos Reviewed International journal
Kouhei Oonuma, Maho Yamamoto, Naho Moritsugu, Nanako Okawa, Megumi Mukai, Miku Sotani, Shuto Tsunemi, Haruka Sugimoto, Eri Nakagome, Yuichi Hasegawa, Kotaro Shimai, Takeo Horie, Takehiro G. Kusakabe
Frontiers in Cell and Developmental Biology 9 ( 704367 ) 704367 - 704367 2021.5
Joint Work
Authorship：Last author, Corresponding author Publisher：Frontiers Media SA
In vertebrate embryos, dorsal midline tissues, including the notochord, the prechordal plate, and the floor plate, play important roles in patterning of the central nervous system, somites, and endodermal tissues by producing extracellular signaling molecules, such as Sonic hedgehog (Shh). In <italic>Ciona</italic>, <italic>hedgehog.b</italic>, one of the two <italic>hedgehog</italic> genes, is expressed in the floor plate of the embryonic neural tube, while none of the <italic>hedgehog</italic> genes are expressed in the notochord. We have identified a <italic>cis</italic>-regulatory region of <italic>hedgehog.b</italic> that was sufficient to drive a reporter gene expression in the floor plate. The <italic>hedgehog.b cis</italic>-regulatory region also drove ectopic expression of the reporter gene in the endodermal strand, suggesting that the floor plate and the endodermal strand share a part of their gene regulatory programs. The endodermal strand occupies the same topographic position of the embryo as does the vertebrate hypochord, which consists of a row of single cells lined up immediately ventral to the notochord. The hypochord shares expression of several genes with the floor plate, including <italic>Shh</italic> and <italic>FoxA</italic>, and play a role in dorsal aorta development. Whole-embryo single-cell transcriptome analysis identified a number of genes specifically expressed in both the floor plate and the endodermal strand in <italic>Ciona</italic> tailbud embryos. A <italic>Ciona</italic> FoxA ortholog FoxA.a is shown to be a candidate transcriptional activator for the midline gene battery. The present findings suggest an ancient evolutionary origin of a common developmental program for the midline structures in Olfactores.
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Kouhei Oonuma, Takehiro G. Kusakabe
Development dev.198754 ( 12 ) dev198754 2021.5
Joint Work
Authorship：Last author Publisher：The Company of Biologists
<title>ABSTRACT</title>
The Ciona larva has served as a unique model for understanding the development of dopaminergic cells at single-cell resolution owing to the exceptionally small number of neurons in its brain and its fixed cell lineage during embryogenesis. A recent study suggested that the transcription factors Fer2 and Meis directly regulate the dopamine synthesis genes in Ciona, but the dopaminergic cell lineage and the gene regulatory networks that control the development of dopaminergic cells have not been fully elucidated. Here, we reveal that the dopaminergic cells in Ciona are derived from a bilateral pair of cells called a9.37 cells at the center of the neural plate. The a9.37 cells divide along the anterior-posterior axis, and all of the descendants of the posterior daughter cells differentiate into the dopaminergic cells. We show that the MAPK pathway and the transcription factor Otx are required for the expression of Fer2 in the dopaminergic cell lineage. Our findings establish the cellular and molecular framework for fully understanding the commitment to dopaminergic cells in the simple chordate brain.DOI： 10.1242/dev.198754
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Cellular identity and Ca2+ signaling activity of the non-reproductive GnRH system in the Ciona intestinalis type A (Ciona robusta) larva. Reviewed International journal
Nanako Okawa, Kotaro Shimai, Kohei Ohnishi, Masamichi Ohkura, Junichi Nakai, Takeo Horie, Atsushi Kuhara, Takehiro G Kusakabe
Scientific reports 10 ( 1 ) 18590 - 18590 2020.10
Joint Work
Authorship：Last author, Corresponding author
Tunicate larvae have a non-reproductive gonadotropin-releasing hormone (GnRH) system with multiple ligands and receptor heterodimerization enabling complex regulation. In Ciona intestinalis type A larvae, one of the gnrh genes, gnrh2, is conspicuously expressed in the motor ganglion and nerve cord, which are homologous structures to the hindbrain and spinal cord, respectively, of vertebrates. The gnrh2 gene is also expressed in the proto-placodal sensory neurons, which are the proposed homologue of vertebrate olfactory neurons. Tunicate larvae occupy a non-reproductive dispersal stage, yet the role of their GnRH system remains elusive. In this study, we investigated neuronal types of gnrh2-expressing cells in Ciona larvae and visualized the activity of these cells by fluorescence imaging using a calcium sensor protein. Some cholinergic neurons and dopaminergic cells express gnrh2, suggesting that GnRH plays a role in controlling swimming behavior. However, none of the gnrh2-expressing cells overlap with glycinergic or GABAergic neurons. A role in motor control is also suggested by a relationship between the activity of gnrh2-expressing cells and tail movements. Interestingly, gnrh2-positive ependymal cells in the nerve cord, known as a kind of glia cells, actively produced Ca2+ transients, suggesting that active intercellular signaling occurs in the glia cells of the nerve cord.
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Spatio-temporal regulation of Rx and mitotic patterns shape the eye-cup of the photoreceptor cells in Ciona Reviewed
Oonuma, K., Kusakabe, T. G.
Developmental Biology 445 ( 2 ) 245 - 255 2019.1
Joint Work
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Regulatory cocktail for dopaminergic neurons in a protovertebrate identified by whole-embryo single-cell transcriptomics Reviewed
Horie, T., Horie, R., Chen, K., Cao, C., Nakagawa, M., Kusakabe, T. G., Satoh, N., Sasakura, Y., Levine, M.
Genes & Development 32 ( 19-20 ) 1297 - 1302 2018.10
Joint Work
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The Use of cis-Regulatory DNAs as Molecular Tools
Kotaro Shimai and Takehiro Kusakabe
Advances in Experimental Medicine and Biology 1029 49 - 68 2018.3
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ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets Reviewed
Brozovic, M., Dantec, C., Dardaillon, J., Dauga, D., Faure, E., Gineste, M., Louis, A., Naville, M., Nitta, K.R., Piette, J., Reeves, W., Scornavacca, C., Simion, P., Vincentelli, R., Bellec, M., Aicha, S.B., Fagotto, M., Guéroult-Bellone, M., Haeussler, M., Jacox, E., Lowe, E.K., Mendez, M., Roberge, A., Stolfi, A., Yokomori, R., Brown, C.T., Cambillau, C., Christiaen, L., Delsuc, F., Douzery, E., Dumollard, R,, Kusakabe, T., Nakai, K., Nishida, H., Satou, Y., Swalla, B., Veeman, M., Volff, J.N., Lemaire, P.
Nucleic Acids Research 46 ( D1 ) D718 - D725 2018.1
Joint Work
DOI： 10.1093/nar/gkx1108
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Constrained vertebrate evolution by pleiotropic genes Reviewed
Hu, H., Uesaka, M., Guo, S., Shimai, K., Lu, T.-M. Li, F., Fujimoto, S., Ishikawa, M., Liu, S., Sasagawa, Y., Zhang, G., Kuratani, S., Yu, J.-K. Kusakabe, T. G., Khaitovich, P., Irie, N., the EXPANDE Consortium
Nature Ecology and Evolution 1 (11), 1722-1730 1 ( 11 ) 1722 - 1730 2017.11
Joint Work
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Evolutionary steps involving counterion displacement in a tunicate opsin Reviewed
Kojima, K., Yamashita, T., Imamoto, Y., Kusakabe, T. G., Tsuda, M., Shichida, Y.
Proceedings of the National Academy of Sciences of the United States of America 114 ( 23 ) 6028 - 6033 2017.6
Joint Work
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Identifying vertebrate brain prototypes in deuterostomes
Takehiro G. Kusakabe
Brain Evolution by Design: From Neural Origin to Cognitive Architecture 153 - 186 2017.2
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Revised lineage of larval photoreceptor cells in Ciona reveals archetypal collaboration between neural tube and neural crest in sensory organ formation Reviewed
Oonuma, K., Tanaka, M., Nishitsuji, K., Kato, Y., Shimai, K., Kusakabe, T. G.
Developmental Biology 420 ( 1 ) 178 - 185 2016.12
Joint Work
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Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis Reviewed
Yokomori, R., Shimai, K., Nishitsuji, K., Suzuki, Y., Kusakabe, T. G. and Nakai K.
Genome Research 26 ( 1 ) 140 - 150 2016.1
Joint Work
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The pre-vertebrate origins of neurogenic placodes Reviewed
Abitua, P. A., Gainous, T. B., Kaczmarczyk, A. N., Winchell, C. J., Hudson, C., Kamata, K., Nakagawa, M., Tsuda, M., Kusakabe, T. G. and Levine, M.
Nature 524 ( 7566 ) 462 - 465 2015.8
Joint Work
DOI： 10.1038/nature14657
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Generation of Arabidopsis transformants expressing sphingoid long-chain base kinase (LCBK1)
Daiki Yanagawa, Osamu Tanaka, Takehiro Kusakabe, Daiske Honda, Ayako Gotoh, and Hiroyuki Imai
Memoirs of Konan University, Science and Engineering Series 62 ( 1 ) 1 - 18 2015
Joint Work
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Nonreproductive role of gonadotropin-releasing hormone in the control of ascidian metamorphosis Reviewed
Kamiya, C., Ohta, N., Ogura, Y., Yoshida, K., Horie, T., Kusakabe, T. G., Satake, H., and Sasakura, Y.
Developmental Dynamics 243 ( 12 ) 1524 - 1535 2014.12
Joint Work
DOI： 10.1002/dvdy.24176
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Transcriptional co-regulation of evolutionarily conserved microRNA/cone opsin gene pairs: Implications for photoreceptor subtype specification Reviewed
Daido, Y., Hamanishi, S., and Kusakabe, T. G.
Developmental Biology 392 ( 1 ) 117 - 129 2014.8
Joint Work
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Characterization of the compact bicistronic microRNA precursor, miR-1/miR-133, expressed specifically in Ciona muscle tissues Reviewed
Kusakabe, R., Tani, S., Nishitsuji, K., Shindo, M., Okamura, K., Miyamoto, Y., Nakai, K., Suzuki, Y., Kusakabe, T. G., and Inoue, K.
Gene Expression Patterns 13 ( 1-2 ) 43 - 53 2013.2
Joint Work