Building the vertebrate codex using the gene breaking protein trap library

  1. Noriko Ichino
  2. MaKayla R Serres
  3. Rhianna M Urban
  4. Mark D Urban
  5. Anthony J Treichel
  6. Kyle J Schaefbauer
  7. Lauren E Greif
  8. Gaurav K Varshney
  9. Kimberly J Skuster
  10. Melissa S McNulty
  11. Camden L Daby
  12. Ying Wang
  13. Hsin-kai Liao
  14. Suzan El-Rass
  15. Yonghe Ding
  16. Weibin Liu
  17. Jennifer L Anderson
  18. Mark D Wishman
  19. Ankit Sabharwal
  20. Lisa A Schimmenti
  21. Sridhar Sivasubbu
  22. Darius Balciunas
  23. Matthias Hammerschmidt
  24. Steven Arthur Farber
  25. Xiao-Yan Wen
  26. Xiaolei Xu
  27. Maura McGrail
  28. Jeffrey J Essner
  29. Shawn M Burgess
  30. Karl J Clark  Is a corresponding author
  31. Stephen C Ekker  Is a corresponding author
  1. Mayo Clinic, United States
  2. Oklahoma Medical Research Foundation, United States
  3. Iowa State University, United States
  4. Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto & University of Toronto, Canada
  5. Carnegie Institution for Science, United States
  6. CSIR-Institute of Genomics and Integrative Biology, India
  7. Temple University, United States
  8. University of Cologne, Germany
  9. National Human Genome Research Institute, National Institutes of Health, United States

Abstract

One key bottleneck in understanding the human genome is the relative under-characterization of 90% of protein coding regions. We report a collection of 1,200 transgenic zebrafish strains made with the gene-break transposon (GBT) protein trap to simultaneously report and reversibly knockdown the tagged genes. Protein trap-associated mRFP expression shows previously undocumented expression of 35% and 90% of cloned genes at 2 and 4 days post-fertilization, respectively. Further, investigated alleles regularly show 99% gene-specific mRNA knockdown. Homozygous GBT animals in ryr1b, fras1, tnnt2a, edar and hmcn1 phenocopied established mutants. 204 cloned lines trapped diverse proteins, including 64 orthologs of human disease-associated genes with 40 as potential new disease models. Severely reduced skeletal muscle Ca2+ transients in GBT ryr1b homozygous animals validated the ability to explore molecular mechanisms of genetic diseases. This GBT system facilitates novel functional genome annotation towards understanding cellular and molecular underpinnings of vertebrate biology and human disease.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figure 3, Figure 4, Figure 4-Figure Supplement 1, Figure 5 and Figure 6.

Article and author information

Author details

  1. Noriko Ichino

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7009-8299
  2. MaKayla R Serres

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Rhianna M Urban

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Mark D Urban

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Anthony J Treichel

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4393-7034
  6. Kyle J Schaefbauer

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Lauren E Greif

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Gaurav K Varshney

    Functional and Chemical Genomics Research Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0429-1904
  9. Kimberly J Skuster

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Melissa S McNulty

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Camden L Daby

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Ying Wang

    Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Hsin-kai Liao

    Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Suzan El-Rass

    Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto & University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2075-4275
  15. Yonghe Ding

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Weibin Liu

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  17. Jennifer L Anderson

    Department of Embryology, Carnegie Institution for Science, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Mark D Wishman

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  19. Ankit Sabharwal

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  20. Lisa A Schimmenti

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  21. Sridhar Sivasubbu

    Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
    Competing interests
    The authors declare that no competing interests exist.
  22. Darius Balciunas

    Department of Biology, Temple University, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1938-3243
  23. Matthias Hammerschmidt

    Institute for Zoology, Developmental Biology Unit, University of Cologne, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3709-8166
  24. Steven Arthur Farber

    Embryology, Carnegie Institution for Science, Baltimore, Maryland, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8037-7312
  25. Xiao-Yan Wen

    Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto & University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  26. Xiaolei Xu

    Biochemistry and Molecular biology, Mayo Clinic, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4928-3422
  27. Maura McGrail

    Genetics, Development and Cell Biology, Iowa State University, Ames, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9308-6189
  28. Jeffrey J Essner

    Genetics, Development and Cell Biology, Iowa State University, Ames, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8816-3848
  29. Shawn M Burgess

    Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1147-0596
  30. Karl J Clark

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    For correspondence
    Clark.Karl@mayo.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9637-0967
  31. Stephen C Ekker

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
    For correspondence
    ekker.stephen@mayo.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0726-4212

Funding

National Institutes of Health (GM63904)

  • Stephen C Ekker

Council of Scientific and Industrial Research (MLP1801)

  • Sridhar Sivasubbu

National Institutes of Health (DA14546)

  • Stephen C Ekker

National Institutes of Health (DK093399)

  • Stephen C Ekker

National Institutes of Health (HG006431)

  • Stephen C Ekker

The Mayo Foundation (Internal)

  • Stephen C Ekker

Natural Sciences and Engineering Research Council of Canada (RGPIN 05389-14)

  • Xiao-Yan Wen

The intramural Reserch Program of the National Human Genome Research Institute, National Institutes of Health (1ZIAHG000183)

  • Shawn M Burgess

The Roy J. Carver Charitable Trust (07-2991)

  • Maura McGrail

The Roy J. Carver Charitable Trust (07-2991)

  • Jeffrey J Essner

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All zebrafish were maintained according to the guidelines and the standard procedures approved by the Mayo Clinic Institutional Animal Care and Use Committee (Mayo IACUC). The Mayo IACUC approved all protocols involving live vertebrate animals (A23107, A21710 and A34513).

Reviewing Editor

  1. Wenbiao Chen, Vanderbilt University, United States

Publication history

  1. Received: December 19, 2019
  2. Accepted: August 7, 2020
  3. Accepted Manuscript published: August 11, 2020 (version 1)
  4. Version of Record published: September 11, 2020 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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  1. Noriko Ichino
  2. MaKayla R Serres
  3. Rhianna M Urban
  4. Mark D Urban
  5. Anthony J Treichel
  6. Kyle J Schaefbauer
  7. Lauren E Greif
  8. Gaurav K Varshney
  9. Kimberly J Skuster
  10. Melissa S McNulty
  11. Camden L Daby
  12. Ying Wang
  13. Hsin-kai Liao
  14. Suzan El-Rass
  15. Yonghe Ding
  16. Weibin Liu
  17. Jennifer L Anderson
  18. Mark D Wishman
  19. Ankit Sabharwal
  20. Lisa A Schimmenti
  21. Sridhar Sivasubbu
  22. Darius Balciunas
  23. Matthias Hammerschmidt
  24. Steven Arthur Farber
  25. Xiao-Yan Wen
  26. Xiaolei Xu
  27. Maura McGrail
  28. Jeffrey J Essner
  29. Shawn M Burgess
  30. Karl J Clark
  31. Stephen C Ekker
(2020)
Building the vertebrate codex using the gene breaking protein trap library
eLife 9:e54572.
https://doi.org/10.7554/eLife.54572

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