eLife (Aug 2020)
Building the vertebrate codex using the gene breaking protein trap library
- Noriko Ichino,
- MaKayla R Serres,
- Rhianna M Urban,
- Mark D Urban,
- Anthony J Treichel,
- Kyle J Schaefbauer,
- Lauren E Tallant,
- Gaurav K Varshney,
- Kimberly J Skuster,
- Melissa S McNulty,
- Camden L Daby,
- Ying Wang,
- Hsin-kai Liao,
- Suzan El-Rass,
- Yonghe Ding,
- Weibin Liu,
- Jennifer L Anderson,
- Mark D Wishman,
- Ankit Sabharwal,
- Lisa A Schimmenti,
- Sridhar Sivasubbu,
- Darius Balciunas,
- Matthias Hammerschmidt,
- Steven Arthur Farber,
- Xiao-Yan Wen,
- Xiaolei Xu,
- Maura McGrail,
- Jeffrey J Essner,
- Shawn M Burgess,
- Karl J Clark,
- Stephen C Ekker
Affiliations
- Noriko Ichino
- ORCiD
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- MaKayla R Serres
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Rhianna M Urban
- ORCiD
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Mark D Urban
- ORCiD
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Anthony J Treichel
- ORCiD
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Kyle J Schaefbauer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Lauren E Tallant
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Gaurav K Varshney
- ORCiD
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States; Functional & Chemical Genomics Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
- Kimberly J Skuster
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Melissa S McNulty
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Camden L Daby
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Ying Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
- Hsin-kai Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
- Suzan El-Rass
- ORCiD
- 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
- Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States; Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
- Weibin Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States; Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
- Jennifer L Anderson
- Department of Embryology, Carnegie Institution for Science, Baltimore, United States
- Mark D Wishman
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Ankit Sabharwal
- ORCiD
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Lisa A Schimmenti
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States; Department of Clinical Genomics, Mayo Clinic, Rochester, United States; Department of Otorhinolaryngology, Mayo Clinic, Rochester, United States
- Sridhar Sivasubbu
- Genomics and Molecular Medicine Unit, CSIR–Institute of Genomics and Integrative Biology, Delhi, India
- Darius Balciunas
- ORCiD
- Department of Biology, Temple University, Philadelphia, United States
- Matthias Hammerschmidt
- ORCiD
- Institute of Zoology, Developmental Biology Unit, University of Cologne, Cologne, Germany
- Steven Arthur Farber
- ORCiD
- Department of Embryology, Carnegie Institution for Science, Baltimore, United States
- 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
- Xiaolei Xu
- ORCiD
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States; Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
- Maura McGrail
- ORCiD
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
- Jeffrey J Essner
- ORCiD
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
- Shawn M Burgess
- ORCiD
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
- Karl J Clark
- ORCiD
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- Stephen C Ekker
- ORCiD
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
- DOI
- https://doi.org/10.7554/eLife.54572
- Journal volume & issue
-
Vol. 9
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 1200 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.
Keywords
- protein trap
- gene-break transposon
- disease model
- human genetic disorders
- light sheet microscopy
- gene reversion
