HIROSHI OCHIAI

Last Updated :2022/06/01

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Associate Professor
Web Site
E-mail
ochiaihiroshima-u.ac.jp
Other Contact Details
Kagamiyama 3-10-23,Higashi-Hiroshima 739-0046 JAPAN, Japan
TEL : (+81)82-424-4008 FAX : (+81)82-424-4008
Self-introduction
Gene expression is mainly regulated by transcription, but its regulatory mechanisms are complex and vary widely among genes. Currently, we are conducting research to elucidate the regulatory mechanism of transcription, especially the phenomenon called the transcriptional bursting, using mouse embryonic stem cells.

Basic Information

Major Professional Backgrounds

  • 2021/04/01, Hiroshima University, Graduate School of Integrated Sciences for Life, Associate Professor
  • 2019/04/01, 2021/03/31, Hiroshima University, Graduate School of Integrated Sciences for Life, Associate Professor or Lecturer
  • 2015/10/01, 2019/03/31, Japan Science and Technology Agency, Graduate School of Science, Department of Mathematical and Life Sciences, Hiroshima University, PRESTO researcher
  • 2013/04/01, 2015/09/30, Hiroshima University, Graduate School of Science, Lecturer (Special Appointment)
  • 2012/06/01, 2013/03/31, Hiroshima University, Research Institute for Radiation Biology and Medicine, Assistant professor
  • 2011/04/01, 2012/05/31, Japan Society for the Promotion of Science, Hiroshima University, Research Fellow PD
  • 2009/04/01, 2011/03/31, Japan Society for the Promotion of Science, Hiroshima University, Research Fellow DC2

Educational Backgrounds

  • Hiroshima University, Graduate School, Division of Natural Science, Department of Mathematical and Life Sciences, Japan, 2008/04, 2011/03
  • Hiroshima University, Graduate School, Division of Natural Science, Department of Mathematical and Life Sciences, Japan, 2007/04, 2008/03
  • Hiroshima University, Faculty of Science, Departmet of Biological Science, Japan, 2003/04, 2007/03

Academic Degrees

  • Ph.D. (Science), Hiroshima University
  • Master (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

Research Fields

  • Biology;Biological Science;Molecular biology
  • Biological Sciences;Genome science;System genome science
  • Environmental science;Environmental analyses and evaluation;Risk sciences of radiation and chemicals
  • Biological Sciences;Genome science;Medical genome science

Research Keywords

  • single cell analysis
  • pluripotent stem cells
  • ES cell
  • CRISPR
  • Live imaging
  • Gene expression noise
  • zinc-finger nuclease
  • TALEN
  • SNP

Affiliated Academic Societies

  • THE MOLECULAR BIOLOGY SOCIETY OF JAPAN
  • The Japanese Society for Epigenetics
  • The Japanese society for Genome Editing
  • THE BIOPHYSICAL SOCIETY OF JAPAN

Educational Activity

Course in Charge

  1. 2022, Undergraduate Education, 2Term, Advanced Biology
  2. 2022, Undergraduate Education, 1Term, Systems Biology
  3. 2022, Undergraduate Education, Second Semester, Seminar for Molecular Genetics
  4. 2022, Undergraduate Education, First Semester, Special Study for Graduation
  5. 2022, Undergraduate Education, Second Semester, Special Study for Graduation
  6. 2022, Undergraduate Education, First Semester, Practice for Fundamental Biology I
  7. 2022, Undergraduate Education, Second Semester, Practice for Fundamental Biology II
  8. 2022, Undergraduate Education, First Semester, Practice for Fundamental Biology III
  9. 2022, Undergraduate Education, Second Semester, Practice for Fundamental Biology IV
  10. 2022, Undergraduate Education, 3Term, Laboratory Work in Biology A
  11. 2022, Graduate Education (Master's Program) , 1Term, Introduction to Life Science
  12. 2022, Graduate Education (Master's Program) , 2Term, Molecular Genetics
  13. 2022, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar A
  14. 2022, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar B
  15. 2022, Graduate Education (Master's Program) , 1Term, Advanced Technologies for Life Science
  16. 2022, Graduate Education (Master's Program) , 1Term, Exercises in Biomedical Science A
  17. 2022, Graduate Education (Master's Program) , 2Term, Exercises in Biomedical Science A
  18. 2022, Graduate Education (Master's Program) , 3Term, Exercises in Biomedical Science B
  19. 2022, Graduate Education (Master's Program) , 4Term, Exercises in Biomedical Science B
  20. 2022, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Biomedial Science
  21. 2022, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar C
  22. 2022, Graduate Education (Doctoral Program) , Academic Year, Research for Academic Degree Dissertation in Integrated Life Sciences
  23. 2022, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar D
  24. 2022, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar E
  25. 2022, Graduate Education (Doctoral Program) , 3Term, Trends of Genome Editing in Life Science

Research Activities

Academic Papers

  1. Ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly, Life Science Alliance, 5(7), e202101045, 20220323
  2. iPSC reprogramming-mediated aneuploidy correction in autosomal trisomy syndromes, PLoS One, 17(3), e0264965, 20220310
  3. ★, Single-gene imaging links genome topology, promoter–enhancer communication and transcription control, Nature Structural & Molecular Biology, 27, 1032-1040, 20200921
  4. ★, Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells, Science Advances, 6(25), eaaz6699, 20200617
  5. Insufficiency of ciliary cholesterol in hereditary Zellweger syndrome, The EMBO Journal, 39, e103499, 20200505
  6. PHi-C: deciphering Hi-C data into polymer dynamics, NAR Genomics and Bioinformatics, 2(2), lqaa020, 20200331
  7. ★, Role of dynamic nuclear deformation on genomic architecture reorganization, PLoS Computational Biology, 15(9), e1007289, 20190911
  8. ★, Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells, Cell, 178(2), 491-506, 20190530
  9. ★, Simultaneous live imaging of the transcription and nuclear position of specific genes, Nucleic Acids Research, 43(19), e127, 20150619
  10. The Microtubule-Depolymerizing Activity of a Mitotic Kinesin Protein KIF2A Drives Primary Cilia Disassembly Coupled with Cell Proliferation, CELL REPORTS, 10(5), 664-673, 20150210
  11. ★, Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells, SCIENTIFIC REPORTS, 4, 7125, 20141120
  12. ★, TALEN-mediated single-base-pair editing identification of an intergenic mutation upstream of BUB1B as causative of PCS ( MVA) syndrome, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(4), 1461-1466, 20140128
  13. Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity., Scientific Reports, 3, 3379, 20131101
  14. High efficiency TALENs enable F0 functional analysis by targeted gene disruption in Xenopus laevis embryos, BIOLOGY OPEN, 2(5), 448-452, 20130515
  15. Equarin is involved as an FGF signaling modulator in chick lens differentiation, DEVELOPMENTAL BIOLOGY, 368(1), 109-117, 20120801
  16. ★, Zinc-finger nuclease-mediated targeted insertion of reporter genes for quantitative imaging of gene expression in sea urchin embryos, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109(27), 10915-10920, 20120703
  17. Efficient targeted mutagenesis of the chordate Ciona intestinalis genome with zinc-finger nucleases, DEVELOPMENT GROWTH & DIFFERENTIATION, 54(5), 535-545, 20120528
  18. Functional analysis using CRISPR library, 676, 201902
  19. Dynamic changes in the interchromosomal interaction of early histone gene loci during early development of sea urchin, Journal of Cell Science, 130(24), 4097-4107, 201711
  20. Ligation-mediated PCR with a back-to-back adapter reduces amplification bias resulting from variations in GC content, Analytical Biochemistry, 531(15), 37-44, 201705
  21. Analysis of individual differences in radiosensitivity using genome editing, ANNALS OF THE ICRP, 201603
  22. Single-Base Pair Genome Editing in Human Cells by Using Site-Specific Endonucleases, International Journal of Molecular Sciences, 16(9), 21128-21137, 201509
  23. Identification of mutation causing cancer-prone hereditary disease using a novel method for the introduction of single-nucleotide substitution, 252(2), 153-158, 201501
  24. ★, Efficient TALEN construction and evaluation methods for human cell and animal applications, GENES TO CELLS, 18(4), 315-326, 201304
  25. Genome editing in cultured cells using TALEN, 31(1), 95-100, 201301
  26. Non-transgenic genome modifications in a hemimetabolous insect using zinc-finger and TAL effector nucleases, NATURE COMMUNICATIONS, 3, 1017, 201208
  27. Targeted disruption of exogenous EGFP gene in medaka using zinc-finger nucleases, DEVELOPMENT GROWTH & DIFFERENTIATION, 54(5), 546-556, 201206
  28. HpSumf1 is involved in the activation of sulfatases responsible for regulation of skeletogenesis during sea urchin development, DEVELOPMENT GENES AND EVOLUTION, 221(3), 157-166, 201108
  29. Targeted mutagenesis in the sea urchin embryo using zinc-finger nucleases, GENES TO CELLS, 15(8), 875-885, 201008
  30. Dicer is required for the normal development of sea urchin, Hemicentrotus pulcherrimus, ZOOLOGICAL SCIENCE, 27(6), 477-486, 201006
  31. Role of the nanos homolog during sea urchin development, Developmental Dynamics, 238(10), 2511-2521, 200910
  32. Suppressor of Hairless (Su(H)) is required for foregut development in the sea urchin embryo., ZOOLOGICAL SCIENCE, 26(10), 686-690, 200910
  33. The Ars insulator facilitates I-SceI meganuclease-mediated transgenesis in the sea urchin embryo, DEVELOPMENTAL DYNAMICS, 237(9), 2475-2482, 200809
  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, 200802

Publications such as books

  1. 2019/08/13, Imaging Gene Expression, Shav-Tal Y. (eds), Real-Time Observation of Localization and Expression (ROLEX) System for Live Imaging of the Transcriptional Activity and Nuclear Position of a Specific Endogenous Gene, Humana, 2019/08/13, 20190813, Scholarly Book, Joint work, Hiroshi Ochiai, 978-1-4939-9674-2, 35-45
  2. 2018/06, 医療応用をめざすゲノム編集 最新動向から技術・倫理的課題まで 真下 知士/金田 安史 編, KAGAKUDOJIN, Single work, Japanese, Hiroshi Ochiai, 274, 65-75
  3. 2017/06, Genome Editing in Animals, Springer New York, Scholarly Book, English, Hiroshi Ochiai, Takashi Yamamoto, 978-1-4939-7128-2, 1-24, Construction and Evaluation of Zinc Finger Nucleases
  4. 2014/12, Targeted Genome Editing Using Site-specific Nucleases: ZFNs, TALENs, and the CRISPR/Cas9 System, Genome Editing Using Zinc-Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs), Springer, 2014, 12, Scholarly Book, English, Hiroshi Ochiai, Takashi Yamamoto, 978-4-431-55227-7, 205, 3-24, Genome editing using zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs)

Invited Lecture, Oral Presentation, Poster Presentation

  1. Relationship between Transcriptional Dynamics and Clusters of Transcriptional Regulators Revealed by Super-Resolution Imaging, Hiroshi Ochiai, The 78th Annual Meeting of The Japanese Society of Microscopy, 2022/05/11, With Invitation, Japanese, The Japanese Society of Microscopy, Koriyama, Fukushima
  2. STREAMING-tag system: A novel technology to analyze the spatiotemporal relationship between transcriptional regulators and transcriptional dynamics at the single gene level, Hiroshi Ochiai, The 30th Hot Spring Harbor International Symposium -Chromatin Potential in Development and Differentiation -, 2022/01/18, With Invitation, English, Yasuyuki Ohkawa, Hiroshi Kimura, Noriko Saitoh, Online
  3. Genome-wide kinetic properties of transcriptional bursting revealed by single cell analysis, Hiroshi Ochiai, The 2nd ASHBi SignAC Workshop, Integrating Single-cell Analysis and Mathematics, 2021/12/10, With Invitation, English, Yasuaki Hiraoka, Toshiaki Yachimura,Takuya Yamamoto, Taro Tsujimura, Mitinori Saitou (ASHBi, Kyoto University), Online
  4. Elucidation of the regulatory mechanism of transcriptional bursting that induces intercellular heterogeneity in gene expression, Hiroshi Ochiai, Kuroda lab seminar, 2021/11/18, With Invitation, Japanese, Online
  5. Relationship between higher-order genome structural dynamics and transcriptional dynamics, Hiroshi Ochiai, Fugaku Project Seminar, 2021/09/14, With Invitation, English, Online
  6. Single-gene imaging reveals the relationship between the transcriptional activity of single genes and the formation of transcriptional regulatory factor clusters, Hiroaki Ohishi, Seiru Shimada, Satoshi Uchino, Li Jieru, Yuko Sato, Alexandros Pertsinidis, Takashi Yamamoto, Hiroshi Kimura, Hiroshi Ochiai., Cold Spring Harbor Laboratory Meeting, Mechanisms of Eukaryotic Transcription, 2021/08/31, Without Invitation, English, Michael Levine, Jane Mellor, Eva Nogales, Online
  7. Establishment of primitive endoderm differentiation reporter mouse ES cell line using CRISPR-Cas9, Hitoshi Owada, Hiroshi Ochiai, Takashi Yamamoto, The 5th Annunal Meeting of JSGE, 2021/06/17, Without Invitation, Japanese, Online
  8. Elucidation of the mechanism of transcriptional burst regulation in mammalian cells, Hiroshi Ochiai, Center for Novel Model Organism Development Open Seminar: Genome Editing Technical Seminar III, 2021/02/03, With Invitation, Japanese, Online
  9. Regulation of transcriptional bursting by chromatin potential, Hiroshi Ochiai, The 43rd Annual Meeting of the Molecular Biology Society of Japan, 2020/12/02, With Invitation, English, Online
  10. Transcriptional bursting induces gene expression heterogeneity in mES cells, Hiroshi Ochiai, Chromosome Dynamics 2019, 2019/12/08, With Invitation, English, Basel
  11. Transcriptional bursting induces gene expression heterogeneity in mouse embryonic stem cells, Hiroshi Ochiai, Single Molecule & Chromatin Symposium, 2019/11/28, With Invitation, English, Melbourne
  12. CRISPR library screening enables identification of transcriptional bursting related genes, Hiroshi Ochiai, Takashi Yamamoto, Takashi Yamamoto, 4th Annual Meeting of The Japanease Society for Genome Editing, 2019/06/05, Without Invitation, English, The Japanease Society for Genome Editing, Tokyo
  13. Role of dynamic nuclear deformation on genomic architecture reorganization, Hiroshi Ochiai, S. Seirin-Lee, Fumitaka Osakada, Junichi Takeda, The 41th Annual Meeting of the Molecular Biology Society of Japan, 2018/11/30, Without Invitation, Japanese
  14. Development of comprehensive analysis technology for intercellular phenotypic heterogeneity, Hiroshi Ochiai, The 41th Annual Meeting of the Molecular Biology Society of Japan, 2018/11/28, Without Invitation, Japanese
  15. Comprehensive analysis of regulatory mechanisms of gene expression noise in mouse embryonic stem cells, Hiroshi Ochiai, The 91st Annual Meeting of the Japanese Biochemical Society, 2018/09/26, Without Invitation, Japanese
  16. Understanding Higher-order genomic structure using genome editing technology, Hiroshi Ochiai, JAAM2018, 2018/05/25, Without Invitation, Japanese
  17. Comprehensive analysis of regulatory mechanisms of intrinsic gene expression noise in mouse embryonic stem cells, Hiroshi Ochiai, Mana Umeda, Tetsutaro Hayashi, Mika Yoshimura, Akihito Harada, Yasuyuki Ohkawa, Takashi Yamamoto, Itoshi Nikaido, The 12th Annual Meeting of the Japanese Society for Epigenetics, 2018/05/24, Without Invitation, Japanese
  18. Relationship between kinetics of higher genome structure and transcription activity, Hiroshi Ochiai, ConBio2017, 2017/12/07, Without Invitation, Japanese, Kobe, Japan
  19. Relationship between kinetics of higher-order genomic structure and transcriptional activity, Hiroshi Ochiai, The 55th Annual Meeting of the Biophysical Society of Japan, 2017/09/21, Without Invitation, English, Kumamoto
  20. Dynamic nuclear deformation induces nuclear architecture remodeling, Hiroshi Ochiai, Seirin S. Lee, The 39th Annual Meeting of the Molecular Biology Society of Japan, 2016/11/30, Without Invitation, English, Yokohama, Japan
  21. Single Base Pair Genome-Editing Technology and Its Future Applications, Hiroshi Ochiai, 13th Japanese-German Frontiers of Science Symposium, 2016/10/07, Without Invitation, English
  22. A challenging interdisciplinary approach to elucidate a mystery of remodeling process in nuclear architecture (Part II: Experiment), Hiroshi Ochiai, JSMB2016, 2016/09/09, Without Invitation, English
  23. Relationship between nuclear dynamics and gene expression noise in pluripotent stem cell, Hiroshi Ochiai, The 68th Annual Meeting of the Japan Society for Cell Biology, 2016/06/16, Without Invitation, English
  24. Active nuclear dynamics promotes heterochromatin clustering, Hiroshi Ochiai, The 4th International Symposium of the Mathematics on Chromatin Live Dynamics, 2015/12/09, With Invitation, English
  25. Simultaneous live imaging of a specific gene's transcription and dynamics., Ochiai H., Sugawara T. & Yamamoto T., BMB2015, 2015/12/03, Without Invitation, English
  26. Simultaneous live imaging of the transcription and nuclear position of specific genes, Hiroshi Ochiai, 2015 TIC (Transcription Imaging Consortium) meeting, Janelia Research Campus (VA), USA, 2015/09/10, Without Invitation, English, TIC, Janelia Research Campus (VA), USA
  27. Simultaneous Live Imaging of the Transcription and Nuclear Position of Specific Genes, Hiroshi Ochiai, International Symposium on Chromatin Structure, Dynamics, and Function, Awaji, Japan, 2015/08/23, With Invitation, English, Awaji Yumebutai International Conference Center Awaji, Japan
  28. Simultaneous live-imaging of gene position and its transcriptional activity in mouse embryonic stem cells, Hiroshi Ochiai, Takeshi Sugawara, Takashi Yamamoto, 4D nucleome, Hiroshima, 2014/12/18, With Invitation, English
  29. Stochastic promoter activation affects gene expression variability in murine embryonic stem cells, Hiroshi Ochiai, Takeshi Sugawara, Tetsushi Sakuma, Takashi Yamamoto, CSHL meeting, NUCLEAR ORGANIZATION & FUNCTION, CSHL, NY, 2014/08/19, With Invitation, English, Cold Spring Harbor Laboratory Meeting & Courses, CSHL, NY
  30. TALEN-mediated single-base-pair editing in PCS syndrome, Hiroshi Ochiai, 3rd International Genome Engineering & Genome Editing-2014 Meeting on 'Synthetic Biology to Zinc Finger Nucleases & CRISPRs Regulation', Waltham, MA(USA), 2014/05/05, Without Invitation, English, Waltham, MA(USA)
  31. TALEN-mediated single-base-pair editing reveals the functional significance of an intergenic single nucleotide variant, Hiroshi Ochiai, International Symposium on RNAi and Genome Editing Research, Tokushima University, 2014/03/14, Without Invitation, English, Tokushima, Japan

Awards

  1. 2021/10, Distinguished Researcher, Hiroshima University
  2. 2016/11, Hiroshima University President Award
  3. 2008/06, Hiroshima University Excellent Student Scholarship
  4. 2007/03, Faculty of Science Commendation

Patented

  1. Patent
  2. Patent

External Funds

Acceptance Results of Competitive Funds

  1. Grant-in-Aid for Scientific Research (B), Elucidation of the linkage between higher-order genome structural dynamics and gene expression, 2022/04/01, 2025/03/31
  2. Grant-in-Aid for Scientific Research on Innovative Areas (Publicly Offered Research), Elucidation of the linkage between non-genomic information replication and transcriptional dynamics between sister chromatids, 2022/04/01, 2024/03/31
  3. Transformative Research Areas(A) (Publicly Offered Research), Elucidation of factors regulating genomic modality in the determination of inactivating X chromosomes, 2021/09/10, 2023/03/31
  4. Strategic Basic Research Programs(CREST), 2020/04/01, 2022/03/31
  5. KAKENHI, 2019/06/28, 2021/03/31
  6. KAKENHI, 2019/04/01, 2022/03/31
  7. Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), 2018/06/29, 2023/03/31
  8. Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), 2016/04/01, 2018/03/31
  9. KAKENHI, 2015/04/01, 2018/03/31
  10. KAKENHI, 2013/04/01, 2015/03/31
  11. PRESTO, 2015/10, 2019/03
  12. 2015/04, 2016/03
  13. 2014/10, 2017/03
  14. Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells, 2015, 2015
  15. 2013, 2013
  16. 2013, 2013
  17. KAKENHI, 2011, 2013
  18. KAKENHI, 2009, 2010

Social Activities

History as Committee Members

  1. Associate Editor of Journal of Biochemistry, 2022/01, 2024/12
  2. Senior Scientific Research Specialist, Grants-in-Aid for Scientific Research (KAKENHI), 2021/08, 2023/07, Ministry of Education, Culture, Sports, Science and Technology - Japan
  3. Editorial Board Member, 2015/07, 2021/05