Skip to main content
SpringerLink
Log in

Functional annotation of mouse mutations in embryonic stem cells by use of expression profiling

  • Published:
Mammalian Genome Aims and scope Submit manuscript

Abstract

Expression profiling offers a potential high-throughput phenotype screen for mutant mouse embryonic stem (ES) cells. We have assessed the ability of expression arrays to distinguish among heterozygous mutant ES cell lines and to accurately reflect the normal function of the mutated genes. Two ES cell lines hemizygous for overlapping regions of mouse Chromosome (Chr) 5 differed substantially from the wildtype parental line and from each other. Expression differences included frequent downregulation of hemizygous genes and downstream effects on genes mapping to other chromosomes. Some genes were affected similarly in each deletion line, consistent with the overlap of the deletions. To determine whether such downstream effects reveal pathways impacted by a mutation, we examined ES cell lines heterozygous for mutations in either of two well-characterized genes. A heterozygous mutation in the gene encoding the cell cycle regulator, cyclin D kinase 4 (Cdk4), affected expression of many genes involved in cell growth and proliferation. A heterozygous mutation in the ATP binding cassette transporter family A, member 1 (Abca1) gene, altered genes associated with lipid homeostasis, the cytoskeleton, and vesicle trafficking. Heterozygous Abca1 mutation had similar effects in liver, indicating that ES cell expression profile reflects changes in fundamental processes relevant to mutant gene function in multiple cell types.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3

Similar content being viewed by others

References

  1. M Ashburner CA Ball JA Blake D Botstein H Butler et al. (2000) ArticleTitleGene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25 25–29 Occurrence Handle1:CAS:528:DC%2BD3cXjtFSlsbc%3D Occurrence Handle10802651

    CAS  PubMed  Google Scholar 

  2. VC Bode (1984) ArticleTitleEthylnitrosourea mutagenesis and the isolation of mutant alleles for specific genes located in the T region of mouse chromosome 17. Genetics 108 457–470 Occurrence Handle1:STN:280:BiqD2M3ks1E%3D Occurrence Handle6500258

    CAS  PubMed  Google Scholar 

  3. C Buechler SM Bared C Aslanidis M Ritter W Drobnik et al. (2002a) ArticleTitleMolecular and functional interaction of the ATP-binding cassette transporter A1 with Fas-associated death domain protein. J Biol Chem 277 41307–41310 Occurrence Handle1:CAS:528:DC%2BD38XotF2htL0%3D

    CAS  Google Scholar 

  4. C Buechler A Boettcher SM Bared MC Probst G Schmitz (2002b) ArticleTitleThe carboxyterminus of the ATP-binding cassette transporter A1 interacts with a beta2-syntrophin/utrophin complex. Biochem Biophys Res Commun 293 759–765 Occurrence Handle1:CAS:528:DC%2BD38XksVGhtLk%3D

    CAS  Google Scholar 

  5. T Burdon A Smith P Savatier (2002) ArticleTitleSignalling, cell cycle and pluripotency in embryonic stem cells. Trends Cell Biol 12 432–438 Occurrence Handle10.1016/S0962-8924(02)02352-8 Occurrence Handle1:CAS:528:DC%2BD38XmvVWlt7s%3D Occurrence Handle12220864

    Article  CAS  PubMed  Google Scholar 

  6. Celera (2002) This data was generated through use of the Celera Discovery System and Celera’s associated databases made possible in part by the AMDeC Foundation, Inc.

  7. BK Chauhan NA Reed W Zhang MK Duncan MW Kilimann et al. ((2002)) ArticleTitleIdentification of genes downstream of Pax6 in the mouse lens using cDNA microarrays. J Biol Chem 277 11539–11548

    Google Scholar 

  8. Y Chen J Schimenti T Magnuson (2000a) ArticleTitleToward the yeastification of mouse genetics: chemical mutagenesis of embryonic stem cells. Mamm Genome 11 598–602 Occurrence Handle1:CAS:528:DC%2BD3cXlvFCksbg%3D

    CAS  Google Scholar 

  9. Y Chen D Yee K Dains A Chatterjee J Cavalcoli et al. (2000b) ArticleTitleGenotype-based screen for ENU-induced mutations in mouse embryonic stem cells. Nat Genet 24 314–317 Occurrence Handle1:CAS:528:DC%2BD3cXhvFaqtL0%3D

    CAS  Google Scholar 

  10. RJ Cho M Huang MJ Campbell H Dong L Steinmetz et al. (2001) ArticleTitleTranscriptional regulation and function during the human cell cycle. Nat Genet 27 48–54 Occurrence Handle1:CAS:528:DC%2BD3MXis1yksQ%3D%3D Occurrence Handle11137997

    CAS  PubMed  Google Scholar 

  11. SM Clee JJ Kastelein M van Dam M Marcil K Roomp et al. (2000) ArticleTitleAge and residual cholesterol efflux affect HDL cholesterol levels and coronary artery disease in ABCA1 heterozygotes. J Clin Invest 106 1263–1270 Occurrence Handle1:CAS:528:DC%2BD3cXotlChu7o%3D Occurrence Handle11086027

    CAS  PubMed  Google Scholar 

  12. MB Eisen PT Spellman PO Brown D Botstein (1998) ArticleTitleCluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95 14863–14868 Occurrence Handle1:CAS:528:DyaK1cXotVGmurk%3D Occurrence Handle9843981

    CAS  PubMed  Google Scholar 

  13. CJ Friddle T Koga EM Rubin J Bristow (2000) ArticleTitleExpression profiling reveals distinct sets of genes altered during induction and regression of cardiac hypertrophy. Proc Natl Acad Sci USA 97 6745–6750 Occurrence Handle10.1073/pnas.100127897 Occurrence Handle1:CAS:528:DC%2BD3cXktFaitb4%3D Occurrence Handle10829065

    Article  CAS  PubMed  Google Scholar 

  14. RS Gitan H Shi CM Chen PS Yan TH Huang (2002) ArticleTitleMethylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res 158–164 Occurrence Handle1:CAS:528:DC%2BD38XksV2qtQ%3D%3D Occurrence Handle11779841

    CAS  PubMed  Google Scholar 

  15. TR Golub DK Slonim P Tamayo C Huard M Gaasenbeek et al. (1999) ArticleTitleMolecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286 531–537 Occurrence Handle10.1126/science.286.5439.531 Occurrence Handle10521349

    Article  PubMed  Google Scholar 

  16. Y Hamon C Broccardo O Chambenoit MF Luciani F Toti et al. (2000) ArticleTitleABC1 promotes engulfment of apoptotic cells and transbilayer redistribution of phosphatidylserine. Nat Cell Biol 2 399–406 Occurrence Handle10.1038/35017029 Occurrence Handle1:CAS:528:DC%2BD3cXkvFCqtro%3D Occurrence Handle10878804

    Article  CAS  PubMed  Google Scholar 

  17. K Hirano F Matsuura K Tsukamoto Z Zhang A Matsuyama et al. (2000) ArticleTitleDecreased expression of a member of the Rho GTPase family, Cdc42Hs, in cells from Tangier disease—the small G protein may play a role in cholesterol efflux. FEBS Lett 484 275–279 Occurrence Handle10.1016/S0014-5793(00)02171-2 Occurrence Handle1:CAS:528:DC%2BD3cXotVCku70%3D Occurrence Handle11078892

    Article  CAS  PubMed  Google Scholar 

  18. S Hitotsumachi DA Carpenter WL Russell (1985) ArticleTitleDose-repetition increases the mutagenic effectiveness of N-ethyl-N-nitrosourea in mouse spermatogonia. Proc Natl Acad Sci USA 82 6619–6621 Occurrence Handle1:CAS:528:DyaL2MXlsleku7g%3D Occurrence Handle3863118

    CAS  PubMed  Google Scholar 

  19. MH Hrabe Angelis de H Flaswinkel H Fuchs B Rathkolb D Soewarto et al. (2000) ArticleTitleGenome-wide, large-scale production of mutant mice by ENU mutagenesis. Nat Genet 25 444–447 Occurrence Handle10932192

    PubMed  Google Scholar 

  20. M Kanzaki JE Pessin (2002) ArticleTitleCaveolin-associated filamentous actin (Cav-actin) defines a novel F-actin structure in adipocytes. J Biol Chem 277 25867–25869 Occurrence Handle10.1074/jbc.C200292200 Occurrence Handle1:CAS:528:DC%2BD38XlsFKrs7s%3D Occurrence Handle12039946

    Article  CAS  PubMed  Google Scholar 

  21. J McNeish RJ Aiello D Guyot T Turi C Gabel et al. (2000) ArticleTitleHigh density lipoprotein deficiency and foam cell accumulation in mice with targeted disruption of ATP-binding cassette transporter-1. Proc Natl Acad Sci USA 97 4245–4250 Occurrence Handle10.1073/pnas.97.8.4245 Occurrence Handle1:CAS:528:DC%2BD3cXislSgu7k%3D Occurrence Handle10760292

    Article  CAS  PubMed  Google Scholar 

  22. KJ Mitchell KI Pinson OG Kelly J Brennan J Zupicich et al. (2001) ArticleTitleFunctional analysis of secreted and transmembrane proteins critical to mouse development. Nat Genet 28 241–249 Occurrence Handle10.1038/90074 Occurrence Handle1:CAS:528:DC%2BD3MXltFSnu78%3D Occurrence Handle11431694

    Article  CAS  PubMed  Google Scholar 

  23. RJ Munroe RA Bergstrom QY Zheng B Libby R Smith et al. (2000) ArticleTitleMouse mutants from chemically mutagenized embryonic stem cells. Nat Genet 24 318–321 Occurrence Handle10.1038/73563 Occurrence Handle1:CAS:528:DC%2BD3cXhvFaqtLo%3D Occurrence Handle10700192

    Article  CAS  PubMed  Google Scholar 

  24. JH Nadeau (2000) ArticleTitleMuta-genetics or muta-genomics: the feasibility of large-scale mutagenesis and phenotyping programs. Mamm Genome 11 603–607 Occurrence Handle10.1007/s003350010115 Occurrence Handle1:CAS:528:DC%2BD3cXlvFCksbk%3D Occurrence Handle10886031

    Article  CAS  PubMed  Google Scholar 

  25. EB Neufeld AT Remaley SJ Demosky JA Stonik AM Cooney et al. (2001) ArticleTitleCellular localization and trafficking of the human ABCA1 transporter. J Biol Chem 276 27584–27590 Occurrence Handle10.1074/jbc.M103264200 Occurrence Handle1:CAS:528:DC%2BD3MXlsV2isbw%3D Occurrence Handle11349133

    Article  CAS  PubMed  Google Scholar 

  26. PM Nolan J Peters M Strivens D Rogers J Hagan et al. (2000) ArticleTitleA systematic, genome-wide, phenotype-driven mutagenesis programme for gene function studies in the mouse. Nat Genet 25 440–443 Occurrence Handle1:CAS:528:DC%2BD3cXlvVeqsr4%3D Occurrence Handle10932191

    CAS  PubMed  Google Scholar 

  27. JF Oram RM Lawn (2001) ArticleTitleABCA1. The gatekeeper for eliminating excess tissue cholesterol. J Lipid Res 42 1173–1179 Occurrence Handle1:CAS:528:DC%2BD3MXlvFeks78%3D Occurrence Handle11483617

    CAS  PubMed  Google Scholar 

  28. M Ramalho-Santos S Yoon Y Matsuzaki RC Mulligan DA Melton (2002) ArticleTitle“Stemness”: transcriptional profiling of embryonic and adult stem cells. Science 298 597–600 Occurrence Handle10.1126/science.1072530 Occurrence Handle1:CAS:528:DC%2BD38XnvFSqur4%3D Occurrence Handle12228720

    Article  CAS  PubMed  Google Scholar 

  29. SG Rane P Dubus RV Mettus EJ Galbreath G Boden et al. (1999) ArticleTitleLoss of Cdk4 expression causes insulin-deficient diabetes and Cdk4 activation results in beta-islet cell hyperplasia. Nat Genet 22 44–52 Occurrence Handle10.1038/8751 Occurrence Handle1:CAS:528:DyaK1MXjtVags7o%3D Occurrence Handle10319860

    Article  CAS  PubMed  Google Scholar 

  30. J Rathjen PD Rathjen (2001) ArticleTitleMouse ES cells: experimental exploitation of pluripotent differentiation potential. Curr Opin Genet Dev 11 587–594 Occurrence Handle10.1016/S0959-437X(00)00237-9 Occurrence Handle1:CAS:528:DC%2BD3MXmt1KrtL8%3D Occurrence Handle11532403

    Article  CAS  PubMed  Google Scholar 

  31. EM Rinchik DA Carpenter (1999) ArticleTitleN-ethyl-N-nitrosourea mutagenesis of a 6- to 11-cM subregion of the Fah-Hbb interval of mouse chromosome 7: completed testing of 4557 gametes and deletion mapping and complementation analysis of 31 mutations. Genetics 152 373–383 Occurrence Handle1:CAS:528:DyaK1MXjs1aktL4%3D Occurrence Handle10224267

    CAS  PubMed  Google Scholar 

  32. WL Russell EM Kelly PR Hunsicker JW Bangham SC Maddux et al. (1979) ArticleTitleSpecific-locus test shows ethylnitrosourea to be the most potent mutagen in the mouse. Proc Natl Acad Sci USA 76 5818–5819 Occurrence Handle1:CAS:528:DyaL3cXlt12ltQ%3D%3D Occurrence Handle293686

    CAS  PubMed  Google Scholar 

  33. JC Schimenti BJ Libby RA Bergstrom LA Wilson D Naf et al. (2000) ArticleTitleInterdigitated deletion complexes on mouse chromosome 5 induced by irradiation of embryonic stem cells. Genome Res 10 1043–1050 Occurrence Handle10.1101/gr.10.7.1043 Occurrence Handle1:CAS:528:DC%2BD3cXltFGjtr4%3D Occurrence Handle10899153

    Article  CAS  PubMed  Google Scholar 

  34. M Serrano GJ Hannon D Beach (1993) ArticleTitleA new regulatory motif in cell-cycle control causing specific inhibition of cyclin D/CDK4. Nature 366 704–707 Occurrence Handle1:CAS:528:DyaK2cXhsFOgu7Y%3D Occurrence Handle8259215

    CAS  PubMed  Google Scholar 

  35. WC Skarnes (2000) ArticleTitleGene trapping methods for the identification and functional analysis of cell surface proteins in mice. Methods Enzymol 328 592–615 Occurrence Handle1:CAS:528:DC%2BD3cXosFSjt74%3D Occurrence Handle11075368

    CAS  PubMed  Google Scholar 

  36. WL Stanford JB Cohn SP Cordes (2001) ArticleTitleGene-trap mutagenesis: past, present and beyond. Nat Rev Genet 2 756–768 Occurrence Handle10.1038/35093548 Occurrence Handle1:CAS:528:DC%2BD38Xmt1Wgtbc%3D Occurrence Handle11584292

    Article  CAS  PubMed  Google Scholar 

  37. D Stryke M Kawamoto CC Huang SJ Johns LA King et al. (2003) ArticleTitleBayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res 31 278–281 Occurrence Handle10.1093/nar/gkg064 Occurrence Handle1:CAS:528:DC%2BD3sXhvFSms7k%3D Occurrence Handle12520002

    Article  CAS  PubMed  Google Scholar 

  38. TS Tanaka T Kunath WL Kimber SA Jaradat CA Stagg et al. (2002) ArticleTitleGene expression profiling of embryo-derived stem cells reveals candidate genes associated with pluripotency and lineage specificity. Genome Res 12 1921–1928

    Google Scholar 

  39. K Tsukamoto K Hirano K Tsujii C Ikegami Z Zhongyan et al. (2001) ArticleTitleATP-binding cassette transporter-1 induces rearrangement of actin cytoskeletons possibly through Cdc42/N-WASP. Biochem Biophys Res Commun 287 757–765 Occurrence Handle10.1006/bbrc.2001.5575 Occurrence Handle1:CAS:528:DC%2BD3MXmvV2jsr4%3D Occurrence Handle11563861

    Article  CAS  PubMed  Google Scholar 

  40. T Tsutsui B Hesabi DS Moons PP Pandolfi KS Hansel et al. (2001) ArticleTitleTargeted disruption of CDK4 delays cell cycle entry with enhanced p27(Kip1) activity. Mol Cell Biol 19 7011–7019

    Google Scholar 

  41. MJ Van de Vijver YD He LJ Van’t Veer H Dai AA Hart et al. (2002) ArticleTitleA gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347 1999–2009 Occurrence Handle10.1056/NEJMoa021967 Occurrence Handle12490681

    Article  PubMed  Google Scholar 

  42. MV Wiles F Vauti J Otte EM Fuchtbauer P Ruiz et al. (2000) ArticleTitleEstablishment of a gene-trap sequence tag library to generate mutant mice from embryonic stem cells. Nat Genet 24 13–14 Occurrence Handle10.1038/71622 Occurrence Handle1:CAS:528:DC%2BD3cXks1entw%3D%3D Occurrence Handle10615117

    Article  CAS  PubMed  Google Scholar 

  43. BP Zambrowicz GA Friedrich EC Buxton SL Lilleberg C Person et al. (1998) ArticleTitleDisruption and sequence identification of 2,000 genes in mouse embryonic stem cells. Nature 392 608–611 Occurrence Handle1:CAS:528:DyaK1cXis1SqsL8%3D Occurrence Handle9560157

    CAS  PubMed  Google Scholar 

  44. X Zha J Jr Genest R McPherson (2001) ArticleTitleEndocytosis is enhanced in Tangier fibroblasts: possible role of ATP-binding cassette protein A1 in endosomal vesicular transport. J Biol Chem 276 39476–39483 Occurrence Handle10.1074/jbc.M105067200 Occurrence Handle1:CAS:528:DC%2BD3MXnvVemt7c%3D Occurrence Handle11504722

    Article  CAS  PubMed  Google Scholar 

  45. HS Zhang M Gavin A Dahiya AA Postigo D Ma et al. (2000) ArticleTitleExit from G1 and S phase of the cell cycle is regulated by represser complexes containing HDAC-Rb-hSWI/SNF and Rb-hSWI/SNF. Cell 101 79–89 Occurrence Handle1:CAS:528:DC%2BD3cXisVaitbc%3D Occurrence Handle10778858

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by grant HL6668101 from the National Heart Lung and Blood Institute, National Institutes of Health grants HL07279 and HD35984. The authors thank Elaine Gong for arrays, Willow Dean for database management and clone quality control, Melissa Brykailo and Brian Curley for expert technical assistance, and the Wadsworth Center Microarray and Molecular Genetics Core Facilities. Gene expression data are available at the NCBI Gene Expression Omnibus (http://www.ncbi.nim.nih.gov/geo ) under accession GSE614.

Author information

Authors and Affiliations

  1. Genome Sciences Department, Lawrence Berkeley National Lab, Berkeley, California, 94720, USA

    Derek J. Symula, Yiwen Zhu & Edward M. Rubin

  2. The Jackson Laboratory, Bar Harbor, Maine 04609, USA

    John C. Schimenti

  3. Genomics Institute, Wadsworth Center, Troy, NY 12180, USA

    Derek J. Symula

Authors
  1. Derek J. Symula
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yiwen Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. John C. Schimenti
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Edward M. Rubin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Edward M. Rubin.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Symula, D.J., Zhu, Y., Schimenti, J.C. et al. Functional annotation of mouse mutations in embryonic stem cells by use of expression profiling . Mamm Genome 15, 1–13 (2004). https://doi.org/10.1007/s00335-002-2228-x

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00335-002-2228-x

Keywords

Search

Navigation