In vivo protein trapping produces a functional expression codex of the vertebrate proteome

Nat Methods. 2011 Jun;8(6):506-15. doi: 10.1038/nmeth.1606. Epub 2011 May 8.


We describe a conditional in vivo protein-trap mutagenesis system that reveals spatiotemporal protein expression dynamics and can be used to assess gene function in the vertebrate Danio rerio. Integration of pGBT-RP2.1 (RP2), a gene-breaking transposon containing a protein trap, efficiently disrupts gene expression with >97% knockdown of normal transcript amounts and simultaneously reports protein expression for each locus. The mutant alleles are revertible in somatic tissues via Cre recombinase or splice-site-blocking morpholinos and are thus to our knowledge the first systematic conditional mutant alleles outside the mouse model. We report a collection of 350 zebrafish lines that include diverse molecular loci. RP2 integrations reveal the complexity of genomic architecture and gene function in a living organism and can provide information on protein subcellular localization. The RP2 mutagenesis system is a step toward a unified 'codex' of protein expression and direct functional annotation of the vertebrate genome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Animals, Genetically Modified
  • DNA Transposable Elements / genetics
  • Gene Expression Profiling
  • Gene Knockdown Techniques / methods
  • Models, Animal
  • Molecular Sequence Data
  • Mutagenesis, Insertional / methods*
  • Proteome / genetics*
  • Proteomics / methods
  • Zebrafish / genetics*
  • Zebrafish Proteins / genetics*


  • DNA Transposable Elements
  • Proteome
  • Zebrafish Proteins

Associated data

  • GENBANK/HQ335166
  • GENBANK/HQ335167
  • GENBANK/HQ335168
  • GENBANK/HQ335169
  • GENBANK/HQ335170
  • GENBANK/HQ335171
  • GENBANK/HQ335172