Naoaki Sakamoto

Last Updated :2025/01/08

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Associate Professor
Web Site
https://www.mls.sci.hiroshima-u.ac.jp/smg/index.html
E-mail
naosakahiroshima-u.ac.jp
Self-introduction
During the early development of sea urchin, nuclear environment undergo dramatic changes. Under such changes, genetic informations express precisely on the long nuclear genome. To understand the regulatory mechanism of the gene expression, I investigate the nuclear environment in the early embryos, intranuclear positioning of genes and function of chromatin insulator using sea urchin, Hemicentrotus pulcherrimus. Furthermore, I investigate the molecular mechanism of the sea urchin development, such as formation of body axis.

Basic Information

Major Professional Backgrounds

  • 1997/06/01, 2000/05/25, Institute of Biosciences & Technology, Texas A&M University, Postdoctoral researcher
  • 2000/06/01, 2002/04/30, RIKEN Brain Science Institute, Postdoctoral researcher
  • 2002/05/01, 2004/03/31, Graduate School of Science, Hiroshima University, Postdoctoral researcher

Educational Backgrounds

  • Hiroshima University, Graduate School, Division of Natural Science, Japan, 1994/04, 1997/03
  • Yamaguchi University, Faculty of Science, Japan, 1988/04, 1992/03

Academic Degrees

  • Doctor of Science, Hiroshima University
  • Master of Science, Hiroshima University

Educational Activity

  • [Bachelor Degree Program] School of Science : Biological Sciences : Biology
  • [Master's Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Mathematical and Life Sciences
  • [Master's Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Biomedical Science
  • [Doctoral Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Mathematical and Life Sciences
  • [Doctoral Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Biomedical Science

In Charge of Primary Major Programs

  • Biology

Research Fields

  • Biological Sciences;Genome science;Genome biology
  • Biology;Biological Science;Molecular biology
  • Biology;Biological Science;Developmental biology

Research Keywords

  • sea urchin
  • DNA structure
  • chromatin
  • insulator
  • genome editing

Affiliated Academic Societies

  • The Zoological Society of Japan
  • The Molecular Biology Society of Japan
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  • Japanese Society of Developmental Biologists
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  • The Japanese Society for Genome Editing
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Educational Activity

Course in Charge

  1. 2024, Liberal Arts Education Program1, 3Term, Introduction to Biology
  2. 2024, Liberal Arts Education Program1, 2Term, Introductory Seminar for First-Year Students
  3. 2024, Undergraduate Education, 1Term, Seminar on Biological Science
  4. 2024, Undergraduate Education, 2Term, Advanced Biology
  5. 2024, Undergraduate Education, 1Term, Molecular Genetics A
  6. 2024, Undergraduate Education, Second Semester, Seminar for Molecular Genetics
  7. 2024, Undergraduate Education, First Semester, Special Study for Graduation
  8. 2024, Undergraduate Education, Second Semester, Special Study for Graduation
  9. 2024, Undergraduate Education, First Semester, Practice for Fundamental Biology I
  10. 2024, Undergraduate Education, Second Semester, Practice for Fundamental Biology II
  11. 2024, Undergraduate Education, Second Semester, Practice for Fundamental Biology IV
  12. 2024, Undergraduate Education, 3Term, Laboratory Work in Biology A
  13. 2024, Graduate Education (Master's Program) , 3Term, Research Methods in Life Science
  14. 2024, Graduate Education (Master's Program) , 1Term, Introduction to Life Science
  15. 2024, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Mathematical and Life Sciences
  16. 2024, Graduate Education (Master's Program) , 2Term, Molecular Genetics
  17. 2024, Graduate Education (Master's Program) , 2Term, Topical Seminar in Life Science C
  18. 2024, Graduate Education (Master's Program) , 4Term, Topical Seminar in Life Science D
  19. 2024, Graduate Education (Master's Program) , First Semester, Exercises in Life Science A
  20. 2024, Graduate Education (Master's Program) , Second Semester, Exercises in Life Science B
  21. 2024, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar A
  22. 2024, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar B
  23. 2024, Graduate Education (Master's Program) , 1Term, Advanced Technologies for Life Science
  24. 2024, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar C
  25. 2024, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar D
  26. 2024, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar E
  27. 2024, Graduate Education (Master's Program) , 4Term, Introduction to Genetics and Genomics

Research Activities

Academic Papers

  1. ★, CRISPR-Cas9-Mediated Gene Knockout in a Non-Model Sea Urchin, Heliocidaris crassispina, Zoological Science, 41(2), 159-166, 202404
    Link to Paper Search Results by DOI
  2. ★, Assembly of continuous high-resolution draft genome sequence of Hemicentrotus pulcherrimus using long-read sequencing, Development Growth & Differentiation, 66(4), 297-304, 202405
    Link to Paper Search Results by DOI
  3. Identification of the genes encoding candidate septate junction components expressed during early development of the sea urchin, Strongylocentrotus purpuratus, and evidence of a role for Mesh in the formation of the gut barrier, Developmental Biology, 495, 21-34, 202303
    Link to Paper Search Results by DOI
  4. ★, The crucial role of CTCF in mitotic progression during early development of sea urchin., Development, Growth & Differentiation, 65(7), 395-407, 20230920
    Link to Paper Search Results by DOI
  5. Possibilities of skin coat color-dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA-seq data., Genes to Cells, in press, 20231021
    Link to Paper Search Results by DOI
  6. ★, Partial exogastrulation due to apical-basal polarity of F-actin distribution disruption in sea urchin embryo by omeprazole, Genes to Cells, 27(6), 392-408, 202206
    Link to Paper Search Results by DOI
  7. CRISPR-Cas9 editing of non-coding genomic loci as a means of controlling gene expression in the sea urchin, Developmental Biology, 472, 85-97, 202104
    Link to Paper Search Results by DOI
  8. Recycling endosomes associate with Golgi stacks in sea urchin embryos., Communicative and Integrative Biology, 13(1), 59-62, 20200430
    Link to Paper Search Results by DOI
  9. Insulator Activities of Nucleosome-Excluding DNA Sequences without Bound Chromatin Looping Proteins, JOURNAL OF PHYSICAL CHEMISTRY B, 123(5), 1035-1043, 20190207
    Link to Paper Search Results by DOI
  10. ★, Establishment of knockout adult sea urchins by using a CRISPR-Cas9 system., Development, Growth & Differentiation, 61(6), 378-388, 2019
    Link to Paper Search Results by DOI
  11. Biased genome editing using the local accumulation of DSB repair molecules system., Nature Communications, 9(1), 3270, 2018
  12. The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry, FRONTIERS IN PHYSIOLOGY, 8, 20170314
    Link to Paper Search Results by DOI
  13. Establishment of expanded and streamlined pipeline of PITCh knock-in - a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO, BIOENGINEERED, 8(3), 302-308, 2017
    Link to Paper Search Results by DOI
  14. ★, Dynamic changes in the interchromosomal interaction of early histone gene loci during development of sea urchin, JOURNAL OF CELL SCIENCE, 130(24), 4097-4107, 201712
    Link to Paper Search Results by DOI
  15. In vivo tracking of histone H3 lysine 9 acetylation in Xenopus laevis during tail regeneration., Genes to Cells, 2016
  16. ★, Cilia play a role in breaking left–right symmetry of the sea urchin embryo., Genes to Cells, 2016
  17. Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence., PLoS One, 211(4), 775-784, 2015
    Link to Paper Search Results by DOI
  18. Viable neuronopathic Gaucher disease model in Medaka (Oryzias latipes) displays axonal accumulation of alpha-synuclein., PLoS Genetics, 11, e1005065, 2015
    Link to Paper Search Results by DOI
  19. LOC-Based High-Throughput Cell Morphology Analysis System., IEEE transactions on automation science and engineering, 12(4), 1346-1356, 2015
    Link to Paper Search Results by DOI
  20. Targeted mutagenesis in sea urchin embryos using TALENs., Development Growth and Differentiation, 56(1), 92-97, 2014
    Link to Paper Search Results by DOI
  21. Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9., Nature Communications, 5, 5560, 2014
    Link to Paper Search Results by DOI
  22. Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity., Scientific Reports, 3, 3379, 2013
    Link to Paper Search Results by DOI
  23. The 3 ' UTR of nanos2 directs enrichment in the germ cell lineage of the sea urchin, Developmental Biology, 377(1), 275-283, 2013
    Link to Paper Search Results by DOI
  24. ★, Nucleosome exclusion from the interspecies conserved central AT-rich region of the Ars insulator., Journal of Biochemistry, 151(1), 75-87, 2012
    Link to Paper Search Results by DOI
  25. Zinc-finger nuclease-mediated targeted insertion of reporter genes for quantitative imaging of gene expression in sea urchin embryos., Proc Natl Acad Sci U S A, 109(27), 10915-10920, 2012
    Link to Paper Search Results by DOI
  26. HpSumf1 is involved in the activation of sulafatases responsible for regulation of skeletogenesis during sea urchin development., Development Genes and Evolution, 221(3), 157-166, 2011
    Link to Paper Search Results by DOI
  27. Targeted mutagenesis in the sea urchin embryo using zinc-finger nucleases., Genes to Cells, 15(8), 875-885, 2010
    Link to Paper Search Results by DOI
  28. HpSulf, a heparan sulfate 6-O-endosulfatase, is involved in the regulation of VEGF signaling during sea urchin development., Mechanisms of Development, 127(3-4), 235-245, 2010
    Link to Paper Search Results by DOI
  29. Mammalian arlysulfatase A functions as a novel component of the extracellular matrix., Connective Tissue Research, 51(5), 388-396, 2010
    Link to Paper Search Results by DOI
  30. Implication of HpEts in gene regulatory networks responsible for specification of sea urchin skeletogenic primary mesenchyme cells., Zoological Science, 27(8), 638-646, 2010
    Link to Paper Search Results by DOI
  31. ★, Dicer is required for the normal development of sea urchin, Hemicentrotus pulcherrimus., Zoological Science, 27(6), 477-486, 2010
    Link to Paper Search Results by DOI
  32. Suppressor of Hairless (Su(H)) is required for foregut development in the sea urchin embryo., Zoological Science, 26(10), 686-690, 200910
    Link to Paper Search Results by DOI
  33. Role of nanos homolog during sea urchin development., Developmental Dynamics, 238(10), 2511-2521, 2009
    Link to Paper Search Results by DOI
  34. Analysis of cis-regulatory elements controlling spatio-temporal expression of T-brain gene in sea urchin, Hemicentrotus pulcherrimus., Mechanisms of Development, 125(1-2), 2-17, 2008
    Link to Paper Search Results by DOI
  35. The Ars insulator facilitates I-SceI meganuclease-mediated transgenesis in the sea urchin embryo., Developmental Dynamics, 237(9), 2475-2482, 2008
    Link to Paper Search Results by DOI
  36. DNA variations within the sea urchin Otx gene enhancer., FEBS Letter, 581(27), 5234-5240, 200711
    Link to Paper Search Results by DOI
  37. ★, Unichrom, a novel nuclear matrix protein, binds to the ars insulator and canonical Mars., Zoological Science, 23(1), 9-21, 2006
    Link to Paper Search Results by DOI
  38. Developmental expression of HpNanos, the Hemicentrotus pulcherrimus homologue of nanos., Gene Expression Patterns, 6(5), 572-577, 2006
    Link to Paper Search Results by DOI
  39. Sodium channel beta4 subunit: down-regulation and possible involvement in neuritic degeneration in Huntington's disease transgenic mice., Journal of Neurochemistry, 98(2), 518-529, 2006
  40. Functional analysis of the sea urchin-derived arylsulfatase (Ars)-element in mammalian cells., Genes to Cells, 11(9), 1009-1021, 2006
    Link to Paper Search Results by DOI
  41. Decreased expression of hypothalamic neuropeptides in Huntington disease transgenic mice with expanded polyglutamine-EGFP fluorescent aggregates., Journal of Neurochemistry, 93(3), 641-653, 2005
  42. The Otx binding site is required for the activation of HpOtxL mRNA expression in the sea urchin, Hemicentrotus pulcherrimus., Development Growth and Differentiation, 46(1), 61-67, 2004
    Link to Paper Search Results by DOI
  43. A new G-stretch-DNA-binding protein, Unichrom, displays cell-cycle-dependent expression in sea urchin embryos., Development Growth and Differentiation, 46(4), 335-341, 2004
    Link to Paper Search Results by DOI
  44. Utilization of a particle gun DNA introduction system for the analysis of cis-regulatory elements controlling the spatial expression pattern of the arylsulfatase gene (HpArs) in sea urchin embryos., Development Genes and Evolution, 213(1), 44-49, 2003
    Link to Paper Search Results by DOI
  45. Pro-apoptotic protein kinase C delta is associated with intranuclear inclusions in a transgenic model of Huntington's disease., Journal of Neurochemistry, 87(2), 395-406, 2003
  46. T-brain homologue (HpTb) is involved in the archenteron induction signals of micromere descendant cells in the sea urchin embryo., Development, 129(22), 5205-5216, 2002
    Link to Paper Search Results by DOI
  47. Functional annotation of a full-length mouse cDNA collection., Nature, 409(6821), 685-690, 2001
  48. ★, Sticky DNA, a self-associated complex formed at long GAA•TTC repeats in intron 1 of the frataxin gene, inhibits transcription., Journal of Biological Chemistry, 276(29), 27171-27177, 2001
  49. ★, GGA•TCC-interrupted triplets in long GAA•TTC repeats inhibit the formation of triplex and sticky DNA structures, alleviate transcription inhibition, and reduce genetic instabilities., Journal of Biological Chemistry, 276(29), 27178-27187, 2001
  50. ★, Self-Association Properties of Long GAA•TTC Repeats in R•R•Y Triplex Structures from Friedreich's Ataxia., Molecular Cell, 3(3), 465-475, 1999
  51. A nonpathogenic GAAGGA repeat in the Friedreich gene: implications for pathogenesis., Neurology, 53(8), 1854-1857, 1999
  52. Structure and Function of Sea Urchin Orthodenticle-Related Gene (HpOtx)., Developmental Biology, 193(2), 139-145, 1998
  53. Differential expression of sea urchin Otx isoform (HpOtxE and HpOtxL) mRNAs during early development., International Journal of Developmental Biology, 42(5), 645-651, 1998
  54. ★, Two Isoforms of Orthodenticle-Related Proteins (HpOtx) Bind to the Enhancer Element of Sea Urchin Arylsulfatase Gene., Developmental Biology, 181(2), 284-295, 1997
  55. ★, A Triplex DNA Structure of the Polypyrimidine: Polypurine Stretch in the 5' Flanking Region of the Sea Urchin Arylsulfatase Gene., Zoological Science, 13(1), 105-109, 1996
  56. Corrected Structure of the 5' Flanking Region of Arylsulfatase Gene of the Sea Urchin, Hemicentrotus pulcherrimus., Development Growth and Differentiation, 36(4), 633-636, 1994
  57. The Egg Nucleus Regulates the Behavior of Sperm Nuclei as well as Cycling of MPF in Physiologically Polyspermic Newt Eggs., Developmental Biology, 160(1), 15-27, 1993

Publications such as books

  1. 2006/04, DNA Structure, Chromatin and Gene Expression, Chapter 14, "Involvement of nuclear matrix and chromatin loop formation in the function of insulators.", 2006, 04, Scholarly Book, Cocompilation, 8178952289

Invited Lecture, Oral Presentation, Poster Presentation

  1. The Crucial Role of CTCF in Mitotic Progression during Early Development of Sea Urchin., Kaichi Watanabe, Megumi Fujita, Kazuko Okamoto, Hajime Yoshioka, Miki Moriwaki, Hideki Tagashira, Akinori Awazu, Takashi Yamamoto, Naoaki Sakamoto, The 46th Annual Meeting of the Molecular Biology Society of Japan, 2023/12/07, Without Invitation, English, Kobe