Yaguchi Lab (Developmental Biology)
Shimoda Marine Research Center, University of Tsukuba
Through sea urchin research, we are revealing the molecular mechanism that supports life phenomena and the mystery of the developmental process.
＜Topics＞
2022 Feb Our new paper is now published in PLOS Genetics.
2022 Jan Our new paper is now published in DGD.
2021 Jul New lab technician joined us.
2021 Apr Our new paper is now available in Experimental Animals
2021 Apr Our new paper is now available in BMC Biology. Many media introduced our work.
筑波大学、 JST、日経新聞、Science Magazine 、オプトロニクス社 、ScienceDaily 、Bioengineer.org 、Alpha-Galileo、Phys.org
＜Research＞
One cell, the egg, begins to divide after fertilization, and in the process, the cell-fate are decided and finally cells are differentiated. Even the seemingly simple early sea urchin embryo has a very complicated developmental process, and many mysteries are still hidden in its differentiation process. In our laboratory, we are studying which factors work at what timing and the fate of cells is determined using the early embryos of sea urchin. Currently, Yaguchi Lab is conducting research focusing on the following three points.
Axis specification
Similar to human being, sea urchin embryos have anterior-posterior, dorsal-abdominal, and left-right body axes. We are analyzing at the genetic level how each axis is determined and what kind of information is transmitted between each body axis.
Neurogenesis & Neural function
In the embryo of Hemicentrotus pulcherrimus, several serotonergic neurons are formed in the anterior neuroectoderm on the second day after fertilization. We are analyzing the molecular mechanism of serotonergic neuron differentiation and neuroectoderm formation, focusing on gene and protein expression patterns and functions.
We also analyze the neural function in the early development of sea urchins.
Sea urchin genetics
Echinoderms, including sea urchins, are recognized as non-model organisms because genetics cannot be applied due to its long breeding cycle. However, we found T. reevesii has short breeding cycle and succeeded to make inbred and genetically modified mutant strains. Using this species, we investigate the detailed function of sea urchin developmental genes.
Publication
●：First author is from Yaguchi lab and/or corresponding author is Yaguchi
◯：collaborating works with other laboratories
＜2022年＞
● Yaguchi S, Wada H. Marine genomics, transcriptomics, and beyond in developmental, cell, and evolutionary biology. Dev Growth Differ 2022; 64(4):196-197. (Preface for the special issue [Marine Genomics] in DGD)
● Kinjo S, Kiyomoto M, Suzuki H, Yamamoto T, Ikeo K, Yaguchi S. TrBase: A genome and transcriptome database of Temnopleurus reevesii. Dev Growth Differ 2022; 64(4):210-218.
● Yaguchi S, Taniguchi Y, Suzuki H, Kamata M, Yaguchi J. Planktonic sea urchin larvae change their swimming direction in response to strong photoirradiation. PLoS Genet. 2022; 18(2): e1010033.
● Yaguchi S, Yaguchi J. Temnopleurus reevesii as a new sea urchin model in genetics. Dev Growth Differ 2022; 64(1):59-66.
● Suzuki H, Yaguchi S. Direct TGF-ß signaling via alk4/5/7 pathway is involved in gut bending in sea urchin embryos. Developmental Dynamics. 2022; 251:226-234.
＜2021年＞
● Yaguchi S. Echinoderms: Temnopleurus reevesii. In Boutet and Schierwater (Ed.). Handbook of Marine Model Organisms in Experimental Biology (CRC Press). 2021; 335-339.
● Yaguchi J, Yaguchi S. Sea urchin larvae utilize light for regulating the pyloric opening. BMC Biology. 2021; 19:64
● Kiyozumi D, Yaguchi S, Yaguchi J, Yamazaki A, Sekiguchi K. Human disease-associated extracellular matrix orthologs ECM3 and QBRICK regulate primary mesenchymal cell migration in sea urchin embryos. Experimental Animals. 2021; 70:378-386.
● Kinjo S, Kiyomoto M, Yamamoto T, Ikeo K, Yaguchi S. Usage of the sea urchin Hemicentrotus pulcherrimus database, HpBase. Methods in Molecular Biology. 2021; 2219: 267-275.
◯ Formery L, Orange F, Formery A, Yaguchi S, Lowe CJ, Schubert M, Croce JC. Neural anatomy of echinoid early juveniles and comparison of nervous system organization in echinoderms. J Comp Neurol. 2021 ;529:1135-1156.
＜2020＞
● Yaguchi S, Yaguchi J, Suzuki H, Kinjo S, Kiyomoto M, Ikeo K, Yamamoto T. Establishment of homozygous knock-out sea urchins. Current Biology. 2020; 30:R427-429.
● Yaguchi S, Morino Y, Sasakura Y. Development of marine invertebrates. In Inaba K and Hall-Spencer J (Ed.). Japanese Marine Life (Springer). 2020; 109-124.
＜2019＞
● Yamazaki A, Yamamoto A, Yaguchi J, Yaguchi S. cis-Regulatory analysis for later phase of anterior neuroectoderm-specific foxQ2 expression in sea urchin embryos. genesis 2019; e23302.
● Yaguchi J, Yaguchi S. Evolution of nitric oxide regulation of gut function. Proc Natl Acad Sci USA (PNAS). 2019; 116:5607-5612. DOI: 10.1073/pnas.1816973116
● Yaguchi J. Microinjection methods for sea urchin eggs and blastomeres. Methods Cell Biol. 2019; 150:173-188.
● Yaguchi S. Temnopleurus as an emerging echinoderm model. Methods Cell Biol. 2019; 150:71-79.
◯ Burke RD, Yaguchi S. Analysis of neural activity with fluorescent protein biosensors. Methods Cell Biol. 2019; 151: 519-526.
◯ Erkenbrack EM, Croce JC, Miranda E, Gautam S, Martinez-Bartolome M, Yaguchi S, Range RC. Whole mount in situ hybridization techniques for analysis of the spatial distribution of mRNAs in sea urchin embryos and early larvae. Methods Cell Biol. 2019; 151:177-196.
＜2018＞
● Yaguchi J, Yamazaki A, Yaguchi S. Meis transcription factor maintains the neurogenic ectoderm and regulates the anterior-posteriot patterning in embryos of a sea urchin, Hemicentrotus pulcherrimus. Dev . Biol. 2018;444:1-8.
● Suzuki H, Yaguchi S. Transforming growth factor-ß signal regulates gut bending in the sea urchin embryo. Dev Growth Differ. 2018;60:216-225.
● Kinjo S, Kiyomoto M, Yamamoto T, Ikeo K, Yaguchi S. HpBase: A genome database of a sea urchin, Hemicentrotus pulcherrimus. Dev Growth Differ. 2018;60:174-182.
＜2017＞
● Yaguchi S§, Yaguchi J§, Tanaka H. Troponin-I is present as an essential component of muscles in echinoderm larvae. Sci Rep. 2017 Mar 8;7:43563. (§equally contributed)
◯Mizuno K, Shiba K, Yaguchi J, Shibata D, Yaguchi S, Pruliere G, Chenevert J, Inaba K. Calaxin establishes basal body orientation and coordinates movement of monocilia in sea urchin embryos. Sci Rep. 2017 Sep 7;7:10751.
＜2016＞
● Yaguchi J, Takeda N, Inaba K, Yaguchi S. Cooperative Wnt-Nodal signals regulate the patterning of anterior neuroectoderm. PLoS Genet. 2016 Apr 21; 12(4): e1006001.
＜2015＞
● Yaguchi S§, Yamazaki A§, Wada W, Tsuchiya Y, Sato T, Shinagawa H, Yamada Y, Yaguchi J. Early development and neurogenesis of Temnopleurus reevesii. Dev Growth Differ. 2015 Apr; 57: 242-250. (§equally contributed)
＜2014＞
● Yaguchi S, Yaguchi J, Inaba K. Bicaudal-C is required for the formation of anterior neurogenic ectoderm of the sea urchin embryo. Sci Rep. 2014 Oct 31;4:6852.
◯ Krupke O, Yaguchi S, Yaguchi J, Burke RD. Imaging neural development in embryonic and larval sea urchins. Methods Mol Biol. 2014;1128:147-60
＜2013＞
◯ Jin Y, Yaguchi S, Shiba K, Yamada L, Yaguchi J, Shibata D, Sawada H, Inaba K. Glutathione transferase theta in apical ciliary tuft regulates mechanical reception and swimming behavior of Sea Urchin Embryos.Cytoskeleton (Hoboken). 2013 Aug;70(8):453-70
＜2012＞
● Yaguchi J, Angerer LM, Inaba K, Yaguchi S. Zinc finger homeobox is required for the differentiation of serotonergic neurons in the sea urchin embryo.Dev Biol. 2012 Mar 1;363(1):74-83.
＜2011＞
● Yaguchi S, Yaguchi J, Wei Z, Jin Y, Angerer LM, Inaba K. Fez function is required to maintain the size of animal plate in the sea urchin embryo. Development. 2011 Oct;138(19):4233-43.
◯ Angerer LM, Yaguchi S, Angerer RC, Burke RD. The evolution of nervous system patterning; insights from sea urchin development. Development. 2011 Sep;138(17):3613-23. Reveiw article.
◯ Yoshiyama-Yanagawa T, Enya S, Shimada-Niwa Y, Yaguchi S, Haramoto Y, Matsuya T, Shiomi K, Sasakura Y, Takahashi S, Asashima M, Kataoka H, Niwa R. The Conserved Rieske Oxygenase DAF-36/Neverland Is a Novel Cholesterol-metabolizing Enzyme. J Biol Chem. 2011 Jul 22;286(29):25756-62.
＜2010＞
● Yaguchi S§, Yaguchi J§, Wei Z, Shiba K, Angerer LM, Inaba K. ankAT-1 is a novel gene mediating the apical tuft formation in the sea urchin embryo. Dev Biol. 2010 Dec 1;348(1):67-75. (§equally contributed)
● Yaguchi S, Yaguchi J, Angerer RC, Angerer LM, Burke RD. TGFbeta signaling positions the ciliary band and patterns neurons in the sea urchin embryo. Dev Biol. 2010 Nov 1;347(1):71-81.
◯ Katow H, Suyemitsu T, Ooka S, Yaguchi J, Jin-Nai T, Kuwahara I, Katow T, Yaguchi S, Abe H. Development of a dopaminergic system in sea urchin embryos and larvae. J Exp Biol. 2010 Aug 15;213(Pt 16):2808-19.
● Sasakura Y§, Yaguchi J§, Yaguchi S, Yajima M. Excision and transposition activity of Tc1/mariner superfamily transposons in sea urchin embryos. Zoolog Sci. 2010 Mar;27(3):256-62 (§equally contributed)
◯ Ooka S, Katow T, Yaguchi S, Yaguchi J, Katow H. Spatiotemporal expression pattern of an encephalopsin orthologue of the sea urchin Hemicentrotus pulcherrimus during early development, and its potential role in larval vertical migration. Dev Growth Differ. 2010 Feb;52(2):195-207
＜2009＞
◯ Wei Z, Yaguchi J, Yaguchi S, Angerer RC, Angerer LM. The sea urchin animal pole domain is a Six3-dependent neurogenic patterning center. Development. 2009 Apr;136(7):1179-89
＜2008＞
● Yaguchi S, Yaguchi J, Angerer RC, Angerer LM. A Wnt-FoxQ2-nodal pathway links primary and secondary axis specification in sea urchin embryos. Dev Cell. 2008 Jan;14(1):97-107.
＜2007＞
● Yaguchi S, Yaguchi J, Burke RD. Sp-Smad2/3 mediates patterning of neurogenic ectoderm by nodal in the sea urchin embryo. Dev Biol. 2007 Feb 15;302(2):494-503.
◯ Poustka AJ, Kühn A, Groth D, Weise V, Yaguchi S, Burke RD, Herwig R, Lehrach H, Panopoulou G. A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks. Genome Biol. 2007;8(5):R85
◯ Katow H, Yaguchi S, Kyozuka K. Serotonin stimulates [Ca2+]i elevation in ciliary ectodermal cells of echinoplutei through a serotonin receptor cell network in the blastocoel. J Exp Biol. 2007 Feb;210(Pt 3):403-12
＜2006＞
◯ Sea Urchin Genome Sequencing Consortium. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006 Nov 10;314(5801):941-52
◯ Burke RD, Angerer LM, Elphick MR, Humphrey GW, Yaguchi S, Kiyama T, Liang S, Mu X, Agca C, Klein WH, Brandhorst BP, Rowe M, Wilson K, Churcher AM, Taylor JS, Chen N, Murray G, Wang D, Mellott D, Olinski R, Hallböök F, Thorndyke MC. A genomic view of the sea urchin nervous system. Dev Biol. 2006 Dec 1;300(1):434-60
● Yaguchi S, Yaguchi J, Burke RD. Specification of ectoderm restricts the size of the animal plate and patterns neurogenesis in sea urchin embryos. Development. 2006 Jun;133(12):2337-46.
◯ Burke RD, Osborne L, Wang D, Murabe N, Yaguchi S, Nakajima Y. Neuron-specific expression of a synaptotagmin gene in the sea urchin Strongylocentrotus purpuratus. J Comp Neurol. 2006 May 10;496(2):244-51
● Yaguchi S, Nakajima Y, Wang D, Burke RD. Embryonic expression of engrailed in sea urchins. Gene Expr Patterns. 2006 Jun;6(5):566-71
＜Contact information＞
Shunsuke Yaguchi
E-mail：yag@@@shimoda.tsukuba.ac.jp (please remove two ＠)
Phone：+81-558-22-6716
Adress：Shimoda Marine Research Center
5-10-1 Shimoda, Shizuoka, 415-0025 JAPAN