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. Greif, 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. SchimmentiSridhar Sivasubbu, Darius Balciunas, Matthias Hammerschmidt, Steven A. Farber, Xiao Yan Wen, Xiaolei Xu, Maura McGrail, Jeffrey J. Essner, Shawn M. Burgess, Karl J. Clark, Stephen C. Ekker

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article numbere54572
Pages (from-to)1-60
Number of pages60
JournaleLife
Volume9
DOIs
StatePublished - Aug 2020

Keywords

  • Disease model
  • Gene reversion
  • Gene-break transposon
  • Human genetic disorders
  • Light sheet microscopy
  • Protein trap
  • Zebrafish

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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