Faculty Members

LANGUAGE ≫ Japanese


Areas of specialization
Laboratory/research office Molecular Developmental Biology Laboratory
In animal development, cells divide and subsequently differentiate into diverse cell types in a spatio-temporally controlled manner, which results in formation of tissues and organs. Our group is investigating how these processes are molecularly regulated, with a specific emphasis on gene expression mechanisms. To address these problems, our research utilizes a combination of genome editing technology and Danio rerio, a small tropical fish known as zebrafish.
Current research topics
Educational background
Professional background
Academic societies

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* Courses provided in English are shown with (E) mark

Undergraduate school
  • Graduation Thesis
  • Developmental biology
  • Molecular and cellular biology
  • Biology Experiment
  • Genetic Engineering 1
  • Cell Biology 1
Graduate school
  • Advanced Seminar 1
  • Advanced Seminar 2
  • Seminar 1
  • Seminar 2
  • Seminar 3
  • Seminar 4
  • Individual Work for Graduate

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Research activities

Research papers
  1. Authors: Kanae Aoki, Mai Yamasaki, Riku Umezono, Takanori Hamamoto, Yusuke KAMACHI
    Title: Systematic Comparison of Computational Tools for Sanger Sequencing-Based Genome Editing Analysis
    Journal: Cells, Vol. 13, No. 3, p. 261, MDPI
    Year: 2024
  2. Authors: Keita Okada, Kanae Aoki, Teruyuki Tabei, Kota Sugio, Katsunori Imai, Yuki Bonkohara, KAMACHI YUSUKE
    Title: Key sequence features of CRISPR RNA for dual-guide CRISPR-Cas9 ribonucleoprotein complexes assembled with wild-type or HiFi Cas9
    Journal: Nucleic Acids Research, Oxford University Press
    Year: 2022
  3. Authors: Chamila Deshani Ranawakage, Keita Okada, Kota Sugio, Yuya Kawaguchi, Yuki Bonkohara, Takuya Takada, KAMACHI YUSUKE
    Title: Efficient CRISPR-Cas9-mediated knock-in of composite tags in zebrafish using long ssDNA as a donor
    Journal: Front. Cell Dev. Biol., Vol. 8, p. 598634, Frontiers Media SA
    Year: 2020
  4. Authors: Ranawakage Chamila Deshani, Takuya Takada, Yusuke Kamachi
    Title: HiBiT-qIP, HiBiT-based quantitative immunoprecipitation, facilitates the determination of antibody affinity under immunoprecipitation conditions
    Journal: Scientific Reports, Springer Nature
    Year: 2019
  5. Authors: Okamoto Yu, Nishimura Naoko, Matsuda Kazunari, Ranawakage Chamila Deshani, Yusuke Kamachi, Kondoh Hisato, Uchikawa Masanori
    Title: Cooperation of Sall4 and Sox8 transcription factors in the regulation of the chicken Sox3 gene during otic placode development
    Journal: Development Growth and Differentiation, Vol. 60, No. 3
    Year: 2018
  6. Authors: Yasumi T., Inoue M., Maruhashi M., KAMACHI YUSUKE, Higashi Y., Kondoh H, Uchikawa M.
    Title: Regulation of trunk neural crest delamination by δEF1 and Sip1 in the chicken embryo.
    Journal: Dev. Growth. Differ., Vol. 58, pp. 205-214, Wiley
    Year: 2016
  7. Authors: Morimura H., Tanaka S.I., Ishitobi H., Mikami T., KAMACHI YUSUKE, Kondoh H., Inouye Y.
    Title: Nano-Analysis of DNA Conformation Changes Induced by Transcription Factor Complex Binding Using Plasmonic Nanodimers.
    Journal: ACS Nano., Vol. 23, pp. 10733-10740
    Year: 2013
  8. Authors: Iwafuchi-Doi M., Yoshida Y., Onichtchouk D., Leichsenring M., Driever W., Takemoto T., Uchikawa M., KAMACHI YUSUKE, Kondoh H.
    Title: The Pou5f1/Pou3f-dependent but SoxB-independent regulation of conserved enhancer N2 initiates Sox2 expression during epiblast to neural plate stages in vertebrates.
    Journal: Dev. Biol., Vol. 352, pp. 354-366
    Year: 2011
  9. Authors: Kobayashi I., Kojima K., Uchino K., Sezutsu H., Iizuka T., Tatematsu K., Yonemura N., Tanaka H., Yamakawa M., Ogura E., KAMACHI YUSUKE, Tamura T.
    Title: An efficient binary system for gene expression in the silkworm, Bombyx mori, using GAL4 variants.
    Journal: Arch. Insect. Biochem. Physiol., Vol. 76, pp. 195-210
    Year: 2011
  10. Authors: Okuda Y., Ogura E., Kondoh H., KAMACHI YUSUKE
    Title: B1 SOX coordinate cell specification with patterning and morphogenesis in the early zebrafish embryo.
    Journal: PLoS Genet., Vol. 6, No. 5, p. e1000936
    Year: 2010
  11. Authors: Ogura E., Okuda Y., Kondoh H., KAMACHI YUSUKE
    Title: Adaptation of GAL4 activators for GAL4 enhancer trapping in zebrafish.
    Journal: Dev. Dyn., Vol. 238, pp. 641-655
    Year: 2009
  12. Authors: Mon H., Sugahara R., Hong S.M., Lee J.M., KAMACHI YUSUKE, Kawaguchi Y., Kusakabe T.
    Title: Analysis of protein interactions with two-hybrid system in cultured insect cells.
    Journal: Anal. Biochem., Vol. 392, pp. 180-182
    Year: 2009
  13. Authors: KAMACHI YUSUKE, Okuda Y., Kondoh H.
    Title: Quantitative assessment of the knockdown efficiency of morpholino antisense oligonucleotides in zebrafish embryos using a luciferase assay.
    Journal: Genesis, Vol. 46, pp. 1-7
    Year: 2008
  14. Authors: Kanamori A., Toyama K., Kitagawa. S., Kamehara. A., Higuchi. T., KAMACHI YUSUKE, Kinoshita. M., Hori. H.
    Title: Comparative genomics approach to the expression of figα, one of the earliest marker genes of oocyte differentiation in medaka (Oryzias latipes).
    Journal: Gene, Vol. 423, pp. 180-187
    Year: 2008
  15. Authors: Sato N., KAMACHI YUSUKE, Kondoh H., Shima Y., Morohashi K., Horikawa R, Ogata T.
    Title: Hypogonadotropic hypogonadism in an adult female with a heterozygous hypomorphic mutation of SOX2.
    Journal: Eur. J. Endocrinol., Vol. 156, pp. 167-171
    Year: 2007
  16. Authors: Yasuhara N., Shibazaki N., Tanaka S., Nagai M., Kamikawa Y., Oe S., Asally M., KAMACHI YUSUKE, Kondoh H., Yoneda Y.
    Title: Triggering neural differentiation of ES cells by subtype switching of importin-α.
    Journal: Nat. Cell. Biol., Vol. 9, pp. 72-79
    Year: 2007
  17. Authors: Inoue M., KAMACHI YUSUKE, Matsunami H., Imada K., Uchikawa M., Kondoh H.
    Title: PAX6 and SOX2-dependent regulation of the Sox2 enhancer N-3 involved in embryonic visual system development.
    Journal: Genes Cells, Vol. 12, pp. 1049-1061
    Year: 2007
  18. Authors: Okuda Y., Yoda H., Uchikawa M., Furutani-Seiki M., Takeda H., Kondoh H., KAMACHI YUSUKE
    Title: Comparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolution.
    Journal: Dev. Dyn., Vol. 235, pp. 811-825
    Year: 2006
  19. Authors: Takemoto T., Uchikawa M., KAMACHI YUSUKE, Kondoh H.
    Title: Convergence of Wnt and FGF signals in the genesis of posterior neural plate through activation of the Sox2 enhancer N-1.
    Journal: Development, Vol. 133, pp. 297-306
    Year: 2006
  20. Authors: Blanco J., Girard F., KAMACHI YUSUKE, Kondoh H., Gehring WJ.
    Title: Functional analysis of the chicken delta1-crystallin enhancer activity in Drosophila reveals remarkable evolutionary conservation between chicken and fly.
    Journal: Development, Vol. 132, pp. 1895-1905
    Year: 2005
  21. Authors: Matsumata M., Uchikawa M., KAMACHI YUSUKE, Kondoh H.
    Title: Multiple N-cadherin enhancers identified by systematic functional screening indicate its Group B1 SOX-dependent regulation in neural and placodal development.
    Journal: Dev. Biol., Vol. 286, pp. 601-617
    Year: 2005
  22. Authors: Tanaka S., KAMACHI YUSUKE, Tanouchi A., Hamada H, Jing N., Kondoh H.
    Title: Interplay of SOX and POU factors in regulation of the Nestin gene in neural primordial cells.
    Journal: Mol. Cell. Biol., Vol. 24, pp. 8834-8846
    Year: 2004
  23. Authors: Uchikawa M., Ishida Y., Takemoto T., KAMACHI YUSUKE, Kondoh H.
    Title: Functional analysis of chicken Sox2 enhancers highlights an array of diverse regulatory elements that are conserved in mammals.
    Journal: Dev. Cell, Vol. 4, pp. 509-519
    Year: 2003
  24. Authors: Kuroiwa A., Uchikawa M., KAMACHI YUSUKE, Kondoh H., Nishida-Umehara C., Masabanda J., Griffin K.D., Matsuda Y.
    Title: Chromosome assignment of eight SOX family genes in the chicken.
    Journal: Cytogenet. Genome Res., Vol. 98, pp. 189-193
    Year: 2002
  25. Authors: Muta M., KAMACHI YUSUKE, Yoshimoto A., Higashi Y., Kondoh H.
    Title: Distinct roles of SOX2, Pax6 and Maf transcription factors in the regulation of lens-specific δ1-crystallin enhancer.
    Journal: Genes Cells, Vol. 7, pp. 791-805
    Year: 2002
  26. Authors: Olsson J.E., KAMACHI YUSUKE, Penning S., Muscat G.E.O., Kondoh H., Koopman P.
    Title: Sox18 expression in blood vessel and feather buds during chicken embryogenesis.
    Journal: Gene, Vol. 271, p. 151-158
    Year: 2001
  27. Authors: KAMACHI YUSUKE, Uchikawa M., Tanouchi A., Sekido R., Kondoh H
    Title: Pax6 and SOX2 form a co-DNA-binding partner complex that regulates initiation of lens development.
    Journal: Genes Dev., Vol. 15, pp. 1272-1286
    Year: 2001
  28. Authors: Uchikawa M., KAMACHI YUSUKE, Kondoh H.
    Title: Two distinct subgroups of Group B Sox genes for transcriptional activators and repressors: their expression during embryonic organogenesis of the chicken.
    Journal: Mech. Dev., Vol. 84, p. 103-120
    Year: 1999
  29. Authors: KAMACHI YUSUKE, Cheah K.S.E., Kondoh H
    Title: Mechanism of regulatory target selection by the SOX high-mobility-group domain proteins as revealed by comparison of SOX1/2/3 and SOX9.
    Journal: Mol. Cell. Biol., Vol. 19, pp. 107-120
    Year: 1999
  30. Authors: KAMACHI YUSUKE, Uchikawa M., Collignon J., Lovell-Badge R., Kondoh H.
    Title: Involvement of Sox1, 2 and 3 in the early and subsequent molecular events of lens induction.
    Journal: Development, Vol. 125, pp. 2521-2532
    Year: 1998
  31. Authors: Masaki S., KAMACHI YUSUKE, Quinlan R.O., Yonezawa S., Kondoh H.
    Title: Identification and functional analysis of the mouse filensin gene promoter.
    Journal: Gene, Vol. 214, pp. 77-86
    Year: 1998
  32. Authors: Sekido R., Murai K., KAMACHI YUSUKE, Kondoh H.
    Title: Two mechanisms in the action of repressor δEF1: binding site competition with an activator and active repression.
    Journal: Genes Cells, Vol. 2, pp. 771-783
    Year: 1997
  33. Authors: Kadokawa Y., Kusakabe T., KAMACHI YUSUKE, Isobe K., Kondoh H., Ohyama T.
    Title: A murine Thy-1.2 reporter vector containing a SV40 origin for rapid cloning and analysis of eukaryotic promoters.
    Journal: Gene, Vol. 153, pp. 277-278
    Year: 1995
  34. Authors: KAMACHI YUSUKE, Sockanathan S., Liu Q., Breitman M., Lovell-Badge R., Kondoh H.
    Title: Involvement of SOX proteins in lens-specific activation of crystallin genes.
    Journal: EMBO J., Vol. 14, pp. 3510-3519
    Year: 1995
  35. Authors: Sekido R., Murai K., Funahashi J., KAMACHI YUSUKE, Fujisawa A., Nabeshima Y., Kondoh H.
    Title: The δ-crystallin enhancer-binding protein δEF1 is a repressor of E2-box-mediated gene activation.
    Journal: Mol. Cell. Biol., Vol. 14, pp. 5692-5700
    Year: 1994
  36. Authors: KAMACHI YUSUKE, Kondoh H.
    Title: Overlapping positive and negative regulatory elements determine lens-specific activity of the δ1-crystallin enhancer.
    Journal: Mol. Cell. Biol., Vol. 13, pp. 5206-5215
    Year: 1993
  37. Authors: Funahashi J., Sekido R., Murai K., KAMACHI YUSUKE, Kondoh H.
    Title: δ-crystallin enhancer binding protein δEF1 is a zinc finger- homeodomain protein implicated in postgastrulation embryogenesis.
    Journal: Development, Vol. 119, pp. 433-446
    Year: 1993
  38. Authors: Funahashi J., KAMACHI YUSUKE, Goto K., Kondoh H.
    Title: Identification of nuclear factor δEF1 and its binding site essential for lens-specific activity of the δ1-crystallin enhancer.
    Journal: Nucleic Acids Res., Vol. 19, pp. 3543-3547
    Year: 1991
  39. Authors: KAMACHI YUSUKE, Ogawa E., Asano M., Ishida S., Murakami Y., Satake M., Ito Y., Shigesada K.
    Title: Purification of a mouse nuclear factor that binds to both the A and B cores of the polyomvirus enhancer.
    Journal: J. Virology, Vol. 64, pp. 4808-4819
    Year: 1990
Grants-in-Aid for Scientific Research from the Japanese government
  1. Project title: Regulation of microRNA genes by Sox transcription factors
    Category: Grant-in-Aid for Scientific Research (B)
    Project number: 25290066
    Project period: 2013-2016
    Total budget amount: 18,330,000 yen
  2. Project title: Development and application of methods for identifying protein-DNA interactions in a tissue-specific manner
    Category: Grant-in-Aid for Challenging Exploratory Research
    Project number: 15K14527
    Project period: 2015-2017
    Total budget amount: 4,030,000 yen
  3. Project title: In vivo function analysis of Sox-partner factor complexes in cell fate switch
    Category: Grant-in-Aid for Scientific Research (C)
    Project number: 18K06267
    Project period: 2018-2020
    Total budget amount: 4,420,000 yen

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Social activities

Committee roles
  1. Scientific Reports Editorial Board Member, 2019-

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