title: In vivo protein trapping produces a functional expression codex of the vertebrate proteome.
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.
authors.affiliation: Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Karl J
authors.initials: KJ
authors.lastname: Clark
authors.forename: Darius
authors.initials: D
authors.lastname: Balciunas
authors.forename: Hans-Martin
authors.initials: HM
authors.lastname: Pogoda
authors.forename: Yonghe
authors.initials: Y
authors.lastname: Ding
authors.forename: Stephanie E
authors.initials: SE
authors.lastname: Westcot
authors.forename: Victoria M
authors.initials: VM
authors.lastname: Bedell
authors.forename: Tammy M
authors.initials: TM
authors.lastname: Greenwood
authors.forename: Mark D
authors.initials: MD
authors.lastname: Urban
authors.forename: Kimberly J
authors.initials: KJ
authors.lastname: Skuster
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Petzold
authors.forename: Jun
authors.initials: J
authors.lastname: Ni
authors.forename: Aubrey L
authors.initials: AL
authors.lastname: Nielsen
authors.forename: Ashok
authors.initials: A
authors.lastname: Patowary
authors.forename: Vinod
authors.initials: V
authors.lastname: Scaria
authors.forename: Sridhar
authors.initials: S
authors.lastname: Sivasubbu
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Xu
authors.forename: Matthias
authors.initials: M
authors.lastname: Hammerschmidt
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Ekker
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D004251:DNA Transposable Elements / Q000235:genetics; D020869:Gene Expression Profiling; D055785:Gene Knockdown Techniques / Q000379:methods; D023421:Models, Animal; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional / Q000379:methods*; D020543:Proteome / Q000235:genetics*; D040901:Proteomics / Q000379:methods; D015027:Zebrafish / Q000235:genetics*; D029961:Zebrafish Proteins / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D020543:Proteome; D029961:Zebrafish Proteins