title: A lacZ reporter gene expression atlas for 313 adult KOMP mutant mouse lines.
abstract: Expression of the bacterial beta-galactosidase reporter gene (lacZ) in the vector used for the Knockout Mouse Project (KOMP) is driven by the endogenous promoter of the target gene. In tissues from KOMP mice, histochemical staining for LacZ enzyme activity can be used to determine gene expression patterns. With this technique, we have produced a comprehensive resource of gene expression using both whole mount (WM) and frozen section (FS) LacZ staining in 313 unique KOMP mutant mouse lines. Of these, ∼ 80% of mutants showed specific staining in one or more tissues, while ∼ 20% showed no specific staining, ∼ 13% had staining in only one tissue, and ∼ 25% had staining in >6 tissues. The highest frequency of specific staining occurred in the brain (∼ 50%), male gonads (42%), and kidney (39%). The WM method was useful for rapidly identifying whole organ and some substructure staining, while the FS method often revealed substructure and cellular staining specificity. Both staining methods had >90% repeatability in biological replicates. Nonspecific LacZ staining occurs in some tissues due to the presence of bacteria or endogenous enzyme activity. However, this can be effectively distinguished from reporter gene activity by the combination of the WM and FS methods. After careful annotation, LacZ staining patterns in a high percentage of mutants revealed a unique structure-function not previously reported for many of these genes. The validation of methods for LacZ staining, annotation, and expression analysis reported here provides unique insights into the function of genes for which little is currently known.
authors.affiliation: Children's Hospital of Oakland Research Institute (CHORI), Oakland, California 94609, USA; dwest@chori.org.
authors.forename: David B
authors.initials: DB
authors.lastname: West
authors.affiliation: Mouse Biology Program, University of California, Davis, California 95618, USA.
authors.forename: Ravi K
authors.initials: RK
authors.lastname: Pasumarthi
authors.affiliation: Mouse Biology Program, University of California, Davis, California 95618, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Baridon
authors.affiliation: Mouse Biology Program, University of California, Davis, California 95618, USA.
authors.forename: Esi
authors.initials: E
authors.lastname: Djan
authors.affiliation: Mouse Biology Program, University of California, Davis, California 95618, USA.
authors.forename: Amanda
authors.initials: A
authors.lastname: Trainor
authors.affiliation: Mouse Biology Program, University of California, Davis, California 95618, USA.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Griffey
authors.affiliation: Mouse Biology Program, University of California, Davis, California 95618, USA.
authors.forename: Eric K
authors.initials: EK
authors.lastname: Engelhard
authors.affiliation: Mouse Biology Program, University of California, Davis, California 95618, USA.
authors.forename: Jared
authors.initials: J
authors.lastname: Rapp
authors.affiliation: Mouse Biology Program, University of California, Davis, California 95618, USA.
authors.forename: Bowen
authors.initials: B
authors.lastname: Li
authors.affiliation: Children's Hospital of Oakland Research Institute (CHORI), Oakland, California 94609, USA;
authors.forename: Pieter J
authors.initials: PJ
authors.lastname: de Jong
authors.affiliation: Mouse Biology Program, University of California, Davis, California 95618, USA.
authors.forename: K C Kent
authors.initials: KC
authors.lastname: Lloyd
mesh_terms: D000818:Animals; D001271:Atlases as Topic; D005260:Female; D015870:Gene Expression; D005786:Gene Expression Regulation / Q000235:genetics*; D017930:Genes, Reporter / Q000235:genetics*; D007763:Lac Operon / Q000235:genetics*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D011401:Promoter Regions, Genetic / Q000235:genetics*; D013194:Staining and Labeling; D013329:Structure-Activity Relationship