Abstract
Forward genetic approaches to identify genes involved in complex traits such as common human diseases have met with limited success. Fine mapping of linkage regions and validation of positional candidates are time-consuming and not always successful. Here we detail a hybrid procedure to map loci involved in complex traits that leverages the strengths of forward and reverse genetic approaches. By integrating genotypic and expression data in a segregating mouse population, we show how clusters of expression quantitative trait loci linking to regions of the genome accurately reflect the underlying perturbation to the transcriptional network induced by DNA variations in genes that control the complex traits. By matching patterns of gene expression in a segregating population with expression responses induced by single-gene perturbation experiments, we show how genes controlling clusters of expression and clinical quantitative trait loci can be mapped directly. We demonstrate the utility of this approach by identifying 5-lipoxygenase as underlying previously identified quantitative trait loci in an F2 cross between strains C57BL/6J and DBA/2J and showing that it has pleiotropic effects on body fat, lipid levels and bone density.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
McClung, J.P. et al. Development of insulin resistance and obesity in mice overexpressing cellular glutathione peroxidase. Proc. Natl. Acad. Sci. USA 101, 8852–8857 (2004).
Brem, R.B., Yvert, G., Clinton, R. & Kruglyak, L. Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752–755 (2002).
Grupe, A. et al. In silico mapping of complex disease-related traits in mice. Science 292, 1915–1918 (2001).
Karp, C.L. et al. Identification of complement factor 5 as a susceptibility locus for experimental allergic asthma. Nat. Immunol. 1, 221–226 (2000).
Klose, J. et al. Genetic analysis of the mouse brain proteome. Nat. Genet. 30, 385–393 (2002).
Liao, G. et al. In silico genetics: identification of a functional element regulating H2-Ealpha gene expression. Science 306, 690–695 (2004).
Monks, S.A. et al. Genetic inheritance of gene expression in human cell lines. Am. J. Hum. Genet. 75, 1094–1105 (2004).
Morley, M. et al. Genetic analysis of genome-wide variation in human gene expression. Nature 430, 743–747 (2004).
Schadt, E.E. et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297–302 (2003).
Bystrykh, L. et al. Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nat. Genet. 37, 225–232 (2005).
Chesler, E.J. et al. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat. Genet. 37, 233–242 (2005).
Hubner, N. et al. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat. Genet. 37, 243–253 (2005).
Chu, S. et al. The transcriptional program of sporulation in budding yeast. Science 282, 699–705 (1998).
Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863–14868 (1998).
Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109–126 (2000).
Mootha, V.K. et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267–273 (2003).
Toth, A. et al. Functional genomics identifies monopolin: a kinetochore protein required for segregation of homologs during meiosis i. Cell 103, 1155–1168 (2000).
Drake, T.A. et al. Genetic loci determining bone density in mice with diet-induced atherosclerosis. Physiol. Genomics 5, 205–215 (2001).
Villa-Colinayo, V., Shi, W., Araujo, J. & Lusis, A.J. Genetics of atherosclerosis: the search for genes acting at the level of the vessel wall. Curr. Atheroscler. Rep. 2, 380–389 (2000).
Darvasi, A. Experimental strategies for the genetic dissection of complex traits in animal models. Nat. Genet. 18, 19–24 (1998).
Hubbard, T. et al. The Ensembl genome database project. Nucleic Acids Res. 30, 38–41 (2002).
Mural, R.J. et al. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296, 1661–1671 (2002).
Waterston, R.H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002).
Doss, S., Schadt, E.E., Drake, T.A. & Lusis, A.J. Cis-acting expression quantitative trait loci in mice. Genome Res. 15, 681–691 (2005).
Klein, R.F. et al. Regulation of bone mass in mice by the lipoxygenase gene Alox15. Science 303, 229–232 (2004).
Schadt, E.E. et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nat. Genet. 37, 710–717 (2005).
Mehrabian, M. et al. Identification of 5-lipoxygenase as a major gene contributing to atherosclerosis susceptibility in mice. Circ. Res. 91, 120–126 (2002).
Kuhn, H., Anton, M., Gerth, C. & Habenicht, A. Amino acid differences in the deduced 5-lipoxygenase sequence of CAST atherosclerosis-resistance mice confer impaired activity when introduced into the human ortholog. Arterioscler. Thromb. Vasc. Biol. 23, 1072–1076 (2003).
Mehrabian, M. & Allayee, H. 5-lipoxygenase and atherosclerosis. Curr. Opin. Lipidol. 14, 447–457 (2003).
Yu, S. et al. Adipocyte-specific gene expression and adipogenic steatosis in the mouse liver due to peroxisome proliferator-activated receptor gamma1 (PPARgamma1) overexpression. J. Biol. Chem. 278, 498–505 (2003).
Zhu, J. et al. An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenet. Genome Res. 105, 363–374 (2004).
Yoshitake, H., Rittling, S.R., Denhardt, D.T. & Noda, M. Osteopontin-deficient mice are resistant to ovariectomy-induced bone resorption. Proc. Natl. Acad. Sci. USA 96, 8156–8160 (1999).
Beattie, J.H. et al. Obesity and hyperleptinemia in metallothionein (-I and -II) null mice. Proc. Natl. Acad. Sci. USA 95, 358–363 (1998).
Pei, L. & Tontonoz, P. Fat's loss is bone's gain. J. Clin. Invest. 113, 805–806 (2004).
Golub, T.R. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531–537 (1999).
Ramaswamy, S., Ross, K.N., Lander, E.S. & Golub, T.R. A molecular signature of metastasis in primary solid tumors. Nat. Genet. 33, 49–54 (2003).
Zhang, W. et al. The functional landscape of mouse gene expression. J. Biol. 3, 21 (2004).
Hughes, T.R. et al. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19, 342–347 (2001).
He, Y.D. et al. Microarray standard data set and figures of merit for comparing data processing methods and experiment designs. Bioinformatics 19, 956–965 (2003).
Mehrabian, M. et al. Genetic locus in mice that blocks development of atherosclerosis despite extreme hyperlipidemia. Circ. Res. 89, 125–130 (2001).
Parhami, F. et al. Atherogenic high-fat diet reduces bone mineralization in mice. J. Bone Miner. Res. 16, 182–188 (2001).
Acknowledgements
We thank the Rosetta Gene Expression Lab for microarray work; J. Berger, K. Wong, J. Thompson, E. Tan and E. Muise for sharing the Pparg expression data; J.G. Menke for sharing the LTB4 data; and J. Zhu for discussion on network analysis. This work was supported in part by grants from the US National Institutes of Health (A.J.L.).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Fig. 1
Chromosome 6 lod score curves for fat mass, cholesterol, and bone traits in the BXD cross. (PDF 10 kb)
Supplementary Fig. 2
Portion of the 5LO gene sequence highlighting 2 mutations (I645V and V646I) identified in the CAST/Ei strain of mouse that lead to a dramatic decrease in the 5LO activity. (PDF 13 kb)
Supplementary Fig. 3
Chromosome 6 genomic region running from 113MB to 128MB (x-axis) and flanking the Alox5 locus in Alox5−/− mice comprised of DNA from the 129 strain. (PDF 85 kb)
Supplementary Fig. 4
Expression of Pparg and Alox5. (PDF 128 kb)
Supplementary Table 1
Liver gene expression traits from the BXD cross that were significantly linked to the Alox5 locus. (PDF 108 kb)
Supplementary Table 2
Liver gene expression signature for Alox5−/− mice, relative to control C57BL/6J mice, as described in the main text. (PDF 25 kb)
Supplementary Table 3
Genes in the liver gene expression signature for Alox5−/− mice that also have expression QTL that are linked to the Alox5 locus. (PDF 13 kb)
Supplementary Table 4
Genes in the liver gene expression signature for Alox5−/− mice that also have expression QTL that are linked to the Alox5 locus and that are correlated with fat mass in the BXD Set. (PDF 9 kb)
Rights and permissions
About this article
Cite this article
Mehrabian, M., Allayee, H., Stockton, J. et al. Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat Genet 37, 1224–1233 (2005). https://doi.org/10.1038/ng1619
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ng1619
This article is cited by
-
Genetical genomics of growth in a chicken model
BMC Genomics (2018)
-
Panx3 links body mass index and tumorigenesis in a genetically heterogeneous mouse model of carcinogen-induced cancer
Genome Medicine (2016)
-
Expression quantitative trait loci infer the regulation of isoflavone accumulation in soybean (Glycine max L. Merr.) seed
BMC Genomics (2014)
-
Deletion of Alox5 gene decreases osteogenic differentiation but increases adipogenic differentiation of mouse induced pluripotent stem cells
Cell and Tissue Research (2014)
-
Body composition and gene expression QTL mapping in mice reveals imprinting and interaction effects
BMC Genetics (2013)