A lacZ reporter gene expression atlas for 313 adult KOMP mutant mouse lines

David B. West, Ravi K. Pasumarthi, Brian Baridon, Esi Djan, Amanda Trainor, Stephen M Griffey, Eric K. Engelhard, Jared Rapp, Bowen Li, Pieter J. De Jong, Kevin C K Lloyd

Research output: Contribution to journalArticle

13 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)598-607
Number of pages10
JournalGenome Research
Volume25
Issue number4
DOIs
StatePublished - Apr 1 2015

Fingerprint

Lac Operon
Atlases
Reporter Genes
Knockout Mice
Staining and Labeling
Gene Expression
Frozen Sections
Genes
Gonads
Enzymes
beta-Galactosidase

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

A lacZ reporter gene expression atlas for 313 adult KOMP mutant mouse lines. / West, David B.; Pasumarthi, Ravi K.; Baridon, Brian; Djan, Esi; Trainor, Amanda; Griffey, Stephen M; Engelhard, Eric K.; Rapp, Jared; Li, Bowen; De Jong, Pieter J.; Lloyd, Kevin C K.

In: Genome Research, Vol. 25, No. 4, 01.04.2015, p. 598-607.

Research output: Contribution to journalArticle

West, DB, Pasumarthi, RK, Baridon, B, Djan, E, Trainor, A, Griffey, SM, Engelhard, EK, Rapp, J, Li, B, De Jong, PJ & Lloyd, KCK 2015, 'A lacZ reporter gene expression atlas for 313 adult KOMP mutant mouse lines', Genome Research, vol. 25, no. 4, pp. 598-607. https://doi.org/10.1101/gr.184184.114
West, David B. ; Pasumarthi, Ravi K. ; Baridon, Brian ; Djan, Esi ; Trainor, Amanda ; Griffey, Stephen M ; Engelhard, Eric K. ; Rapp, Jared ; Li, Bowen ; De Jong, Pieter J. ; Lloyd, Kevin C K. / A lacZ reporter gene expression atlas for 313 adult KOMP mutant mouse lines. In: Genome Research. 2015 ; Vol. 25, No. 4. pp. 598-607.
@article{ab50938714d949a7bad9e152f1a71ac9,
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.",
author = "West, {David B.} and Pasumarthi, {Ravi K.} and Brian Baridon and Esi Djan and Amanda Trainor and Griffey, {Stephen M} and Engelhard, {Eric K.} and Jared Rapp and Bowen Li and {De Jong}, {Pieter J.} and Lloyd, {Kevin C K}",
year = "2015",
month = "4",
day = "1",
doi = "10.1101/gr.184184.114",
language = "English (US)",
volume = "25",
pages = "598--607",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "4",

}

TY - JOUR

T1 - A lacZ reporter gene expression atlas for 313 adult KOMP mutant mouse lines

AU - West, David B.

AU - Pasumarthi, Ravi K.

AU - Baridon, Brian

AU - Djan, Esi

AU - Trainor, Amanda

AU - Griffey, Stephen M

AU - Engelhard, Eric K.

AU - Rapp, Jared

AU - Li, Bowen

AU - De Jong, Pieter J.

AU - Lloyd, Kevin C K

PY - 2015/4/1

Y1 - 2015/4/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84927740488&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84927740488&partnerID=8YFLogxK

U2 - 10.1101/gr.184184.114

DO - 10.1101/gr.184184.114

M3 - Article

C2 - 25591789

AN - SCOPUS:84927740488

VL - 25

SP - 598

EP - 607

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 4

ER -