Naoaki Sakamoto

Last Updated :2021/07/02

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Associate Professor
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
  • 【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
  • Japanese Society of Developmental Biologists
  • The Japanese Society for Genome Editing

Educational Activity

Course in Charge

  1. 2021, Liberal Arts Education Program1, 3Term, Introduction to Biology
  2. 2021, Liberal Arts Education Program1, 2Term, Introductory Seminar for First-Year Students
  3. 2021, Undergraduate Education, 1Term, Seminar on Biological Science
  4. 2021, Undergraduate Education, 2Term, Advanced Biology
  5. 2021, Undergraduate Education, 1Term, Molecular Genetics A
  6. 2021, Undergraduate Education, Second Semester, Seminar for Molecular Genetics
  7. 2021, Undergraduate Education, First Semester, Special Study for Graduation
  8. 2021, Undergraduate Education, Second Semester, Special Study for Graduation
  9. 2021, Undergraduate Education, First Semester, Practice for Fundamental Biology I
  10. 2021, Undergraduate Education, Second Semester, Practice for Fundamental Biology II
  11. 2021, Undergraduate Education, Second Semester, Practice for Fundamental Biology IV
  12. 2021, Undergraduate Education, 3Term, Laboratory Work in Biology A
  13. 2021, Graduate Education (Master's Program) , 3Term, Research Methods in Life Science
  14. 2021, Graduate Education (Master's Program) , 1Term, Introduction to Life Science
  15. 2021, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Mathematical and Life Sciences
  16. 2021, Graduate Education (Master's Program) , 1Term, Exercises in Life Science A
  17. 2021, Graduate Education (Master's Program) , 2Term, Exercises in Life Science A
  18. 2021, Graduate Education (Master's Program) , 3Term, Exercises in Life Science B
  19. 2021, Graduate Education (Master's Program) , 4Term, Exercises in Life Science B
  20. 2021, Graduate Education (Master's Program) , 2Term, Topical Seminar in Life Science A
  21. 2021, Graduate Education (Master's Program) , 4Term, Topical Seminar in Life Science B
  22. 2021, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar A
  23. 2021, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar B
  24. 2021, Graduate Education (Master's Program) , 1Term, Advanced Technologies for Life Science
  25. 2021, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar C
  26. 2021, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar D
  27. 2021, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar E
  28. 2021, Graduate Education (Master's Program) , 4Term, Introduction to Genetics and Genomics

Research Activities

Academic Papers

  1. Recycling endosomes associate with Golgi stacks in sea urchin embryos., Communicative and Integrative Biology, 13(1), 59-62, 20200430
  2. ★, Establishment of knockout adult sea urchins by using a CRISPR-Cas9 system., Development, Growth & Differentiation, 61(6), 378-388, 2019
  3. Insulator Activities of Nucleosome-Excluding DNA Sequences without Bound Chromatin Looping Proteins, JOURNAL OF PHYSICAL CHEMISTRY B, 123(5), 1035-1043, 20190207
  4. Biased genome editing using the local accumulation of DSB repair molecules system., Nature Communications, 9(1), 3270, 2018
  5. ★, 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
  6. The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry, FRONTIERS IN PHYSIOLOGY, 8, 20170314
  7. 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
  8. ★, Cilia play a role in breaking left–right symmetry of the sea urchin embryo., Genes to Cells, 2016
  9. In vivo tracking of histone H3 lysine 9 acetylation in Xenopus laevis during tail regeneration., Genes to Cells, 2016
  10. Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence., PLoS One, 211(4), 775-784, 2015
  11. Viable neuronopathic Gaucher disease model in Medaka (Oryzias latipes) displays axonal accumulation of alpha-synuclein., PLoS Genetics, 11, e1005065, 2015
  12. LOC-Based High-Throughput Cell Morphology Analysis System., IEEE transactions on automation science and engineering, 12(4), 1346-1356, 2015
  13. Targeted mutagenesis in sea urchin embryos using TALENs., Development Growth and Differentiation, 56(1), 92-97, 2014
  14. Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9., Nature Communications, 5, 5560, 2014
  15. Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity., Scientific Reports, 3, 3379, 2013
  16. The 3 ' UTR of nanos2 directs enrichment in the germ cell lineage of the sea urchin, Developmental Biology, 377(1), 275-283, 2013
  17. ★, Nucleosome exclusion from the interspecies conserved central AT-rich region of the Ars insulator., Journal of Biochemistry, 151(1), 75-87, 2012
  18. 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
  19. 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
  20. Targeted mutagenesis in the sea urchin embryo using zinc-finger nucleases., Genes to Cells, 15(8), 875-885, 2010
  21. 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
  22. Mammalian arlysulfatase A functions as a novel component of the extracellular matrix., Connective Tissue Research, 51(5), 388-396, 2010
  23. Implication of HpEts in gene regulatory networks responsible for specification of sea urchin skeletogenic primary mesenchyme cells., Zoological Science, 27(8), 638-646, 2010
  24. ★, Dicer is required for the normal development of sea urchin, Hemicentrotus pulcherrimus., Zoological Science, 27(6), 477-486, 2010
  25. Suppressor of Hairless (Su(H)) is required for foregut development in the sea urchin embryo., Zoological Science, 26(10), 686-690, 200910
  26. Role of nanos homolog during sea urchin development., Developmental Dynamics, 238(10), 2511-2521, 2009
  27. 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
  28. The Ars insulator facilitates I-SceI meganuclease-mediated transgenesis in the sea urchin embryo., Developmental Dynamics, 237(9), 2475-2482, 2008
  29. DNA variations within the sea urchin Otx gene enhancer., FEBS Letter, 581(27), 5234-5240, 200711
  30. ★, Unichrom, a novel nuclear matrix protein, binds to the ars insulator and canonical Mars., Zoological Science, 23(1), 9-21, 2006
  31. Developmental expression of HpNanos, the Hemicentrotus pulcherrimus homologue of nanos., Gene Expression Patterns, 6(5), 572-577, 2006
  32. 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
  33. Functional analysis of the sea urchin-derived arylsulfatase (Ars)-element in mammalian cells., Genes to Cells, 11(9), 1009-1021, 2006
  34. Decreased expression of hypothalamic neuropeptides in Huntington disease transgenic mice with expanded polyglutamine-EGFP fluorescent aggregates., Journal of Neurochemistry, 93(3), 641-653, 2005
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. Functional annotation of a full-length mouse cDNA collection., Nature, 409(6821), 685-690, 2001
  41. ★, 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
  42. ★, 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
  43. ★, 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
  44. A nonpathogenic GAAGGA repeat in the Friedreich gene: implications for pathogenesis., Neurology, 53(8), 1854-1857, 1999
  45. Structure and Function of Sea Urchin Orthodenticle-Related Gene (HpOtx)., Developmental Biology, 193(2), 139-145, 1998
  46. Differential expression of sea urchin Otx isoform (HpOtxE and HpOtxL) mRNAs during early development., International Journal of Developmental Biology, 42(5), 645-651, 1998
  47. ★, Two Isoforms of Orthodenticle-Related Proteins (HpOtx) Bind to the Enhancer Element of Sea Urchin Arylsulfatase Gene., Developmental Biology, 181(2), 284-295, 1997
  48. ★, 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
  49. 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
  50. 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