title: Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells.
abstract: BACKGROUND
  High-throughput mutagenesis of the mammalian genome is a powerful means to facilitate analysis of gene function. Gene trapping in embryonic stem cells (ESCs) is the most widely used form of insertional mutagenesis in mammals. However, the rules governing its efficiency are not fully understood, and the effects of vector design on the likelihood of gene-trapping events have not been tested on a genome-wide scale.
  
  
  RESULTS
  In this study, we used public gene-trap data to model gene-trap likelihood. Using the association of gene length and gene expression with gene-trap likelihood, we constructed spline-based regression models that characterize which genes are susceptible and which genes are resistant to gene-trapping techniques. We report results for three classes of gene-trap vectors, showing that both length and expression are significant determinants of trap likelihood for all vectors. Using our models, we also quantitatively identified hotspots of gene-trap activity, which represent loci where the high likelihood of vector insertion is controlled by factors other than length and expression. These formalized statistical models describe a high proportion of the variance in the likelihood of a gene being trapped by expression-dependent vectors and a lower, but still significant, proportion of the variance for vectors that are predicted to be independent of endogenous gene expression.
  
  
  CONCLUSIONS
  The findings of significant expression and length effects reported here further the understanding of the determinants of vector insertion. Results from this analysis can be applied to help identify other important determinants of this important biological phenomenon and could assist planning of large-scale mutagenesis efforts.
authors.affiliation: Department of Medicine, MacDonald Medical Research Laboratories, University of California at Los Angeles, California, USA. nordalex@u.washington.edu
authors.forename: Alex S
authors.initials: AS
authors.lastname: Nord
authors.forename: Karen
authors.initials: K
authors.lastname: Vranizan
authors.forename: Whittemore
authors.initials: W
authors.lastname: Tingley
authors.forename: Alexander C
authors.initials: AC
authors.lastname: Zambon
authors.forename: Kristina
authors.initials: K
authors.lastname: Hanspers
authors.forename: Loren G
authors.initials: LG
authors.lastname: Fong
authors.forename: Yan
authors.initials: Y
authors.lastname: Hu
authors.forename: Peter
authors.initials: P
authors.lastname: Bacchetti
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ferrin
authors.forename: Patricia C
authors.initials: PC
authors.lastname: Babbitt
authors.forename: Scott W
authors.initials: SW
authors.lastname: Doniger
authors.forename: William C
authors.initials: WC
authors.lastname: Skarnes
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Young
authors.forename: Bruce R
authors.initials: BR
authors.lastname: Conklin
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods; D053595:Embryonic Stem Cells / Q000502:physiology*; D005091:Exons / Q000235:genetics; D015870:Gene Expression; D005822:Genetic Vectors; D016678:Genome; D016013:Likelihood Functions; D051379:Mice; D008957:Models, Genetic; D016254:Mutagenesis, Insertional; D020411:Oligonucleotide Array Sequence Analysis; D010957:Plasmids / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction