In vivo protein trapping produces a functional expression codex of the vertebrate proteome. Academic Article uri icon

abstract

  • 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.

published proceedings

  • Nat Methods

author list (cited authors)

  • Clark, K. J., Balciunas, D., Pogoda, H., Ding, Y., Westcot, S. E., Bedell, V. M., ... Ekker, S. C.

complete list of authors

  • Clark, Karl J||Balciunas, Darius||Pogoda, Hans-Martin||Ding, Yonghe||Westcot, Stephanie E||Bedell, Victoria M||Greenwood, Tammy M||Urban, Mark D||Skuster, Kimberly J||Petzold, Andrew M||Ni, Jun||Nielsen, Aubrey L||Patowary, Ashok||Scaria, Vinod||Sivasubbu, Sridhar||Xu, Xiaolei||Hammerschmidt, Matthias||Ekker, Stephen C

publication date

  • June 2011