PUBLICATION

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

Authors
Clark, K.J., Balciunas, D., Pogoda, H.M., Ding, Y., Westcot, S.E., Bedell, V.M., Greenwood, T.M., Urban, M.D., Skuster, K.J., Petzold, A.M., Ni, J., Nielsen, A.L., Patowary, A., Scaria, V., Sivasubbu, S., Xu, X., Hammerschmidt, M., and Ekker, S.C.
ID
ZDB-PUB-110523-11
Date
2011
Source
Nature Methods   8(6): 506-512 (Journal)
Registered Authors
Balciunas, Darius, Bedell, Victoria, Clark, Karl, Ding, Yonghe, Ekker, Stephen C., Hammerschmidt, Matthias, Petzold, Andrew, Pogoda, Hans-Martin, Sivasubbu, Sridhar, Westcot, Stephanie, Xu, Xiaolei
Keywords
none
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*
PubMed
21552255 Full text @ Nat. Methods
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.
Genes / Markers
Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes