Updated on 2022/03/17

写真a

 
ONIMARU Koh
 
Organization
Graduate School of Medicine Center for Neurological Diseases and Cance Division Assistant Professor
Graduate School
Graduate School of Medicine
Undergraduate School
School of Medicine Department of Medicine
Title
Assistant Professor
Contact information
メールアドレス
External link

Degree 1

  1. 博士(理学) ( 2013.3   東京工業大学 ) 

Research Interests 5

  1. Evolutionary biology

  2. Biology

  3. Comparative genomics

  4. Machine learning

  5. Systems biology

Research Areas 1

  1. Life Science / Evolutionary biology

Research History 7

  1. Nagoya University   Graduate School of Medicine   Assistant Professor

    2020.12

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    Country:Japan

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  2. RIKEN   Center for Biosystems Dynamics Research   Special postdoctoral researcher

    2018.4 - 2020.11

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    Country:Japan

  3. RIKEN Center for Biosystems Dynamics Research   SPDR

    2018.4 - 2020.11

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  4. RIKEN   Center for Life Science ans Technologies   Researcher

    2016.5 - 2018.3

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    Country:Japan

  5. RIKEN Center for Life Science Technologies   Researcher

    2016.5 - 2018.3

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  6. Centre for Genomic Regulation (CRG), Spain   Systems Biology   Researcher

    2013.10 - 2016.4

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  7. Tokyo Institute of Technology   Researcher

    2013.4 - 2013.9

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Education 2

  1. Tokyo Institute of Technology   Graduate School, Division of Life Science and Engineering

    2010.4 - 2013.3

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    Country: Japan

  2. Tokyo Institute of Technology   Faculty of Life Science and Engineering

    - 2008.3

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    Country: Japan

Professional Memberships 2

  1. 日本分子生物学会

  2. 日本発生生物学会

Awards 2

  1. Paper Award

    2021.7   The evolutionary origin of developmental enhancers in vertebrates: Insights from non‐model species

    Koh onimaru

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  2. Poster award

    2019.9   Predicting gene regulatory regions with a convolutional neural network for processing double-strand genome sequence information

    Koh Onimaru

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Papers 19

  1. Biomolecular condensates in cancer biology

    Suzuki Hiroshi I, Onimaru Koh

    CANCER SCIENCE   Vol. 113 ( 2 ) page: 382 - 391   2022.2

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Cancer Science  

    Understanding the characteristics of cancer cells is essential for the development of improved diagnosis and therapeutics. From a gene regulation perspective, the super-enhancer concept has been introduced to systematically understand the molecular mechanisms underlying the identities of various cell types and has been extended to the analysis of cancer cells and cancer genome alterations. In addition, several characteristic features of super-enhancers have led to the recognition of the link between gene regulation and biomolecular condensates, which is often mediated by liquid-liquid phase separation. Several lines of evidence have suggested molecular and biophysical principles and their alterations in cancer cells, which are particularly associated with gene regulation and cell signaling (“ transcriptional” and “signaling” condensates). These findings collectively suggest that the modification of biomolecular condensates represents an important mechanism by which cancer cells acquire various cancer hallmark traits and establish functional innovation for cancer initiation and progression. The condensate model also provides the molecular basis of the vulnerability of cancer cells to transcriptional perturbation and further suggests the possibility of therapeutic targeting of condensates. This review summarizes recent findings regarding the relationships between super-enhancers and biomolecular condensate models, multiple scenarios of condensate alterations in cancers, and the potential of the condensate model for therapeutic development.

    DOI: 10.1111/cas.15232

    Web of Science

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  2. Spatial regulation by multiple Gremlin1 enhancers provides digit development with cis-regulatory robustness and evolutionary plasticity Reviewed

    Jonas Malkmus, Laurène Ramos Martins, Shalu Jhanwar, Bonnie Kircher, Victorio Palacio, Rushikesh Sheth, Francisca Leal, Amandine Duchesne, Javier Lopez-Rios, Kevin A. Peterson, Robert Reinhardt, Koh Onimaru, Martin J. Cohn, Aimée Zuniga, Rolf Zeller

    Nature Communications   Vol. 12 ( 1 ) page: 5557   2021.9

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    <title>Abstract</title>Precise <italic>cis</italic>-regulatory control of gene expression is essential for normal embryogenesis and tissue development. The BMP antagonist <italic>Gremlin1</italic> (<italic>Grem1</italic>) is a key node in the signalling system that coordinately controls limb bud development. Here, we use mouse reverse genetics to identify the enhancers in the <italic>Grem1</italic> genomic landscape and the underlying <italic>cis</italic>-regulatory logics that orchestrate the spatio-temporal <italic>Grem1</italic> expression dynamics during limb bud development. We establish that transcript levels are controlled in an additive manner while spatial regulation requires synergistic interactions among multiple enhancers. Disrupting these interactions shows that altered spatial regulation rather than reduced <italic>Grem1</italic> transcript levels prefigures digit fusions and loss. Two of the enhancers are evolutionary ancient and highly conserved from basal fishes to mammals. Analysing these enhancers from different species reveal the substantial spatial plasticity in <italic>Grem1</italic> regulation in tetrapods and basal fishes, which provides insights into the fin-to-limb transition and evolutionary diversification of pentadactyl limbs.

    DOI: 10.1038/s41467-021-25810-1

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    Other Link: https://www.nature.com/articles/s41467-021-25810-1

  3. Systems Biology Approach to the Origin of the Tetrapod Limb Invited Reviewed International coauthorship International journal

    Koh Onimaru, Luciano Marcon

    Evolutionary Systems Biology     page: 89 - 113   2021.8

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Part of collection (book)   Publisher:Springer International Publishing  

    DOI: 10.1007/978-3-030-71737-7_5

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  4. Developmental hourglass and heterochronic shifts in fin and limb development Reviewed International journal

    Koh Onimaru, Kaori Tatsumi, Chiharu Tanegashima, Mitsutaka Kadota, Osamu Nishimura, Shigehiro Kuraku

    eLife   Vol. 10   2021.2

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:eLife Sciences Publications, Ltd  

    How genetic changes are linked to morphological novelties and developmental constraints remains elusive. Here we investigate genetic apparatuses that distinguish fish fins from tetrapod limbs by analyzing transcriptomes and open chromatin regions (OCRs). Specifically, we compared mouse forelimb buds with the pectoral fin buds of an elasmobranch, the brown-banded bamboo shark (<italic>Chiloscyllium punctatum</italic>). A transcriptomic comparison with an accurate orthology map revealed both a mass heterochrony and hourglass-shaped conservation of gene expression between fins and limbs. Furthermore, open-chromatin analysis suggested that access to conserved regulatory sequences is transiently increased during mid-stage limb development. During this stage, stage-specific and tissue-specific OCRs were also enriched. Together, early and late stages of fin/limb development are more permissive to mutations than middle stages, which may have contributed to major morphological changes during the fin-to-limb evolution. We hypothesize that the middle stages are constrained by regulatory complexity that results from dynamic and tissue-specific transcriptional controls.

    DOI: 10.7554/eLife.62865

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    Other Link: https://cdn.elifesciences.org/articles/62865/elife-62865-v1.xml

  5. The evolutionary origin of developmental enhancers in vertebrates: Insights from non‐model species Invited Reviewed

    Koh Onimaru

    Development, Growth & Differentiation   Vol. 62 ( 5 ) page: 326 - 333   2020.6

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Wiley  

    DOI: 10.1111/dgd.12662

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    Other Link: https://onlinelibrary.wiley.com/doi/full-xml/10.1111/dgd.12662

  6. Predicting gene regulatory regions with a convolutional neural network for processing double-strand genome sequence information.

    Onimaru K, Nishimura O, Kuraku S

    PloS one   Vol. 15 ( 7 ) page: e0235748   2020

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1371/journal.pone.0235748

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  7. Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates.

    Hara Y, Yamaguchi K, Onimaru K, Kadota M, Koyanagi M, Keeley SD, Tatsumi K, Tanaka K, Motone F, Kageyama Y, Nozu R, Adachi N, Nishimura O, Nakagawa R, Tanegashima C, Kiyatake I, Matsumoto R, Murakumo K, Nishida K, Terakita A, Kuratani S, Sato K, Hyodo S, Kuraku S

    Nature ecology & evolution   Vol. 2 ( 11 ) page: 1761-1771   2018.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s41559-018-0673-5

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  8. A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra.

    Onimaru K, Tatsumi K, Shibagaki K, Kuraku S

    Scientific data   Vol. 5   page: 180197   2018.10

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/sdata.2018.197

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  9. Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.

    Onimaru K, Kuraku S

    Briefings in functional genomics   Vol. 17 ( 5 ) page: 352-361   2018.9

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/bfgp/ely008

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  10. A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum).

    Onimaru K, Motone F, Kiyatake I, Nishida K, Kuraku S

    Developmental dynamics : an official publication of the American Association of Anatomists   Vol. 247 ( 5 ) page: 712-723   2018.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/dvdy.24623

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  11. Migratory appendicular muscles precursor cells in the common ancestor to all vertebrates. Reviewed International journal

    Eri Okamoto, Rie Kusakabe, Shigehiro Kuraku, Susumu Hyodo, Alexandre Robert-Moreno, Koh Onimaru, James Sharpe, Shigeru Kuratani, Mikiko Tanaka

    Nature ecology & evolution   Vol. 1 ( 11 ) page: 1731 - 1736   2017.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    In amniote embryos, skeletal muscles in the trunk are derived from epithelial dermomyotomes, the ventral margin of which extends ventrally to form body wall muscles. At limb levels, ventral dermomyotomes also generate limb-muscle precursors, an Lbx1-positive cell population that originates from the dermomyotome and migrates distally into the limb bud. In elasmobranchs, however, muscles in the paired fins were believed to be formed by direct somitic extension, a developmental pattern used by the amniote body wall muscles. Here we re-examined the development of pectoral fin muscles in catsharks, Scyliorhinus, and found that chondrichthyan fin muscles are indeed formed from Lbx-positive muscle precursors. Furthermore, these precursors originate from the ventral edge of the dermomyotome, the rest of which extends towards the ventral midline to form body wall muscles. Therefore, the Lbx1-positive, de-epithelialized appendicular muscle precursors appear to have been established in the body plan before the divergence of Chondrichthyes and Osteichthyes.

    DOI: 10.1038/s41559-017-0330-4

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  12. Publisher Correction: Migratory appendicular muscles precursor cells in the common ancestor to all vertebrates.

    Okamoto E, Kusakabe R, Kuraku S, Hyodo S, Robert-Moreno A, Onimaru K, Sharpe J, Kuratani S, Tanaka M

    Nature ecology & evolution   Vol. 1 ( 11 ) page: 1784   2017.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s41559-017-0374-5

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  13. The fin-to-limb transition as the re-organization of a Turing pattern.

    Onimaru K, Marcon L, Musy M, Tanaka M, Sharpe J

    Nature communications   Vol. 7   page: 11582   2016.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/ncomms11582

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  14. A shift in anterior-posterior positional information underlies the fin-to-limb evolution.

    Onimaru K, Kuraku S, Takagi W, Hyodo S, Sharpe J, Tanaka M

    eLife   Vol. 4   2015.8

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.7554/eLife.07048

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  15. Acquisition of the paired fins: a view from the sequential evolution of the lateral plate mesoderm.

    Tanaka M, Onimaru K

    Evolution & development   Vol. 14 ( 5 ) page: 412-20   2012.9

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1111/j.1525-142X.2012.00561.x

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  16. Development and evolution of the lateral plate mesoderm: comparative analysis of amphioxus and lamprey with implications for the acquisition of paired fins.

    Onimaru K, Shoguchi E, Kuratani S, Tanaka M

    Developmental biology   Vol. 359 ( 1 ) page: 124-136   2011.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.ydbio.2011.08.003

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  17. Mechanisms of heart development in the Japanese lamprey, Lethenteron japonicum.

    Kokubo N, Matsuura M, Onimaru K, Tiecke E, Kuraku S, Kuratani S, Tanaka M

    Evolution & development   Vol. 12 ( 1 ) page: 34-44   2010.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1111/j.1525-142X.2009.00389.x

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  18. Heterochronic shift in Hox-mediated activation of sonic hedgehog leads to morphological changes during fin development.

    Sakamoto K, Onimaru K, Munakata K, Suda N, Tamura M, Ochi H, Tanaka M

    PloS one   Vol. 4 ( 4 ) page: e5121   2009

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1371/journal.pone.0005121

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  19. Identification of four Engrailed genes in the Japanese lamprey, Lethenteron japonicum. Reviewed International journal

    Manami Matsuura, Hidenori Nishihara, Koh Onimaru, Nobuhiro Kokubo, Shigehiro Kuraku, Rie Kusakabe, Norihiro Okada, Shigeru Kuratani, Mikiko Tanaka

    Developmental dynamics : an official publication of the American Association of Anatomists   Vol. 237 ( 6 ) page: 1581 - 9   2008.6

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    Language:English   Publishing type:Research paper (scientific journal)  

    We have isolated four homologs of Engrailed genes from the Japanese lamprey, Lethenteron japonicum, an agnathan that occupies a critical phylogenic position between cephalochordates and gnathostomes. We named these four genes LjEngrailedA, LjEngrailedB, LjEngrailedC, and LjEngrailedD. LjEngrailedA, LjEngrailedB, and LjEngrailedD share a major expression domain in the presumptive midbrain-hindbrain boundary region of the central nervous system, although their levels and timing of expression differed. On the other hand, LjEngrailedC transcripts were in the pharyngeal ectoderm and the ventral ectoderm of the body wall. In addition, LjEngrailedA was expressed in the ventral side of the epibranchial muscle precursors. LjEngrailedD transcripts were seen in the mesodermal cells of the mandibular arch and later in a group of cells responsible for the formation of the upper lip, lower lip, and velum. Our results provide clues to the evolution of these structures as well as a possible scenario for duplication events of Engrailed genes.

    DOI: 10.1002/dvdy.21552

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Books 1

  1. ヒレと四肢の遺伝子発現から発生において進化方向性にバイアスをかける実体を探る

    鬼丸洸、工樂樹洋( Role: Joint author)

    羊土社、実験医学 2021年7月号 Vol.39 No.11  2021.6  ( ISBN:978-4-7581-2545-1

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    Total pages:4   Responsible for pages:4   Language:Japanese Book type:Scholarly book

Other research activities 1

  1. https://github.com/koonimaru/DeepGMAP

    2018.6

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    https://github.com/koonimaru/DeepGMAP
    A software to train deep learning models to predict enhancer/gene regulatory sequences in genomes

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KAKENHI (Grants-in-Aid for Scientific Research) 1

  1. Development of transcriptional regulatory network prediction methods in morphogenesis

    Grant number:17K15132  2017.4 - 2020.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Young Scientists (B)

    Onimaru Koh

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    Authorship:Principal investigator 

    Grant amount:\4030000 ( Direct Cost: \3100000 、 Indirect Cost:\930000 )

    This project was aimed at development of transcriptional regulatory prediction methods in morphogenesis by applying deep learning. We set the following two tasks to achieve this goal: a) the genome-wide identification of morphogenic transcriptional enhancers using mouse limb buds; b) developing deep learning methods to analyze enhancer sequences and infer gene regulatory networks. We successfully determined limb-associated morphogenic enhancers and analyzed the characteristics of these sequences. Moreover, we developed a deep learning-based regulatory sequence classifier that outperformed previous studies. This software can extract information that is critical for transcriptional regulation from genomic sequences. As an output of this project, we have published one peer-reviewed original research paper and two original research papers as preprints and released the developed program as an open-source software.