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 investigates the molecular basis underlying these processes by focusing on gene regulatory mechanisms. Our research utilizes 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
  • Seminar 2
  • Seminar 3
  • Graduation Thesis
  • Developmental biology
  • Molecular and cellular biology
  • Dynamics of cell function
  • Biology Experiment
Graduate school
  • Advanced molecular cell biology
  • 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: 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  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: 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  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: 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  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: 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
  32. 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
  33. 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
  34. 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
  35. 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
  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., 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
  38. 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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