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Environmental Genomics pp 81–110Cite as

Comparative Molecular Physiological Genomics

Heterologous Probing of cDNA Arrays

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 410))

Summary

The use of DNA microarrays has gained wider acceptance as a standard tool for molecular biology studies over the past decade. In particular, biomedical studies embraced this technology as soon as arrays were produced for the common laboratory species. Slower to develop, however, has been the use of microarray screening with non-standard animal models, even though these species present fascinating physiological phenomena for study. The very high cost and huge amount of work involved in developing and producing a DNA array or microarray for a new species is prohibitive for most researchers working in comparative biology. The alternative is to explore the use of heterologous array hybridization, screening for stress-induced gene expression in one species using an array developed for another species. This chapter provides a comprehensive review of the current literature on heterologous DNA array hybridization and explores the factors that must be taken into account when performing heterologous microarray analysis on nonstandard species. Changes in methodology (e.g. hybridization conditions, stringency of washing) to optimize the percent cross reaction, the potential for false positives and false negatives to occur, and techniques for downstream analysis and confirmation of array data are all discussed. Examples of cross-hybridization using human microarrays are discussed using phylogenetically diverse species ranging from ground squirrels to frogs to snails. As with any new technology, the willingness to grasp cross-species analysis has been slow but the future looks bright for heterologous DNA hybridization and microarray analysis now that the initial hurdles have been overcome.

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References

  1. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 467–470.

    Article  CAS  PubMed  Google Scholar 

  2. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P. O., and Davis, R. W. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA 93, 10614–10619.

    Google Scholar 

  3. Pease, A. C., Solas, D., Sullivan, E. J., Cronin, M. T., Holmes, C. P., and Fodor, S. P. (1994) Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA 91, 5022–5026.

    Google Scholar 

  4. DeRisi, J., Penland, L., Brown, P. O., Bittner, M. L., Meltzer, P. S., Ray, M., Chen, Y., Su, Y. A., and Trent, J. M. (1996) Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14, 457–460.

    Article  CAS  PubMed  Google Scholar 

  5. Shalon, D., Smith, S. J., and Brown, P. O. (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639–645.

    Article  CAS  PubMed  Google Scholar 

  6. Urisman, A., Fischer, K. F., Chiu, C. Y., Kistler, A. L., Beck, S., Wang, D., and DeRisi, J. L. (2005) E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Genome Biol. 6, R78.

    Article  PubMed  Google Scholar 

  7. Wang, D., Coscoy, L., Zylberberg, M., Avila, P. C., Boushey, H. A., Ganem, D., and DeRisi, J. L. (2002) Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. USA 99, 15687–15692.

    Google Scholar 

  8. Wang, D., Urisman, A., Liu, Y. T., Springer, M., Ksiazek, T. G., Erdman, D. D., Mardis, E. R., Hickenbotham, M., Magrini, V., Eldred, J., Latreille, J. P., Wilson, R. K., Ganem, D., and DeRisi, J. L. (2003) Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 1, E2.

    Google Scholar 

  9. Makalowski, W., and Boguski, M. S. (1998) Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc. Natl. Acad. Sci. USA 95, 9407–9412.

    Google Scholar 

  10. Makalowski, W., Zhang, J., and Boguski, M. S. (1996) Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res. 6, 846–857.

    Article  CAS  PubMed  Google Scholar 

  11. Wheelan, S. J., Boguski, M. S., Duret, L., and Makalowski, W. (1999) Human and nematode orthologs—lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans. Gene 238, 163–170.

    Article  CAS  PubMed  Google Scholar 

  12. Eddy, S. F., and Storey, K. B. (2004) Up-regulation of fatty acid-binding proteins during hibernation in the little brown bat, Myotis lucifugus. Biochim. Biophys. Acta 1676, 63–70.

    CAS  PubMed  Google Scholar 

  13. Hittel, D., and Storey, K. B. (2002) The translation state of differentially expressed mRNAs in the hibernating 13-lined ground squirrel (Spermophilus tridecemlineatus). Arch. Biochem. Biophys. 401, 244–254.

    Article  CAS  PubMed  Google Scholar 

  14. Hittel, D., and Storey, K. B. (2001) Differential expression of adipose- and heart-type fatty acid binding proteins in hibernating ground squirrels. Biochim. Biophys. Acta 1522, 238–243.

    CAS  PubMed  Google Scholar 

  15. Morin, P., Jr., and Storey, K. B. (2005) Cloning and expression of hypoxia-inducible factor 1alpha from the hibernating ground squirrel, Spermophilus tridecemlineatus. Biochim. Biophys. Acta 1729, 32–40.

    CAS  PubMed  Google Scholar 

  16. Eddy, S. F., Morin, P., Jr., and Storey, K. B. (2005) Cloning and expression of PPAR-gamma and PGC-1alpha from the hibernating ground squirrel, Spermophilus tridecemlineatus. Mol. Cell. Biochem. 269, 175–182.

    Article  CAS  PubMed  Google Scholar 

  17. Eddy, S. F., McNally, J. D., and Storey, K. B. (2005) Up-regulation of a thioredoxin peroxidase-like protein, proliferation-associated gene, in hibernating bats. Arch. Biochem. Biophys. 435, 103–111.

    Article  CAS  PubMed  Google Scholar 

  18. Hittel, D. S., and Storey, K. B. (2002) Differential expression of mitochondria-encoded genes in a hibernating mammal. J. Exp. Biol. 205, 1625–1631.

    CAS  PubMed  Google Scholar 

  19. Fahlman, A., Storey, J. M., and Storey, K. B. (2000) Gene up-regulation in heart during mammalian hibernation. Cryobiology 40, 332–342.

    Article  CAS  PubMed  Google Scholar 

  20. Cai, D., McCarron, R. M., and Hallenbeck, J. (2004) Cloning and characterization of a forkhead transcription factor gene, FoxO1a, from thirteen-lined ground squirrel. Gene 343, 203–209.

    Article  CAS  PubMed  Google Scholar 

  21. Yu, E. Z., Hallenbeck, J. M., Cai, D., and McCarron, R. M. (2002) Elevated arylalkylamine-N-acetyltransferase (AA-NAT) gene expression in medial habenular and suprachiasmatic nuclei of hibernating ground squirrels. Brain Res. Mol. Brain Res. 102, 9–17.

    Article  CAS  PubMed  Google Scholar 

  22. Cai, Q., and Storey, K. B. (1997) Freezing-induced genes in wood frog (Rana sylvatica): fibrinogen upregulation by freezing and dehydration. Am. J. Physiol. 272, R1480–1492.

    Google Scholar 

  23. Cai, Q., Greenway, S. C., and Storey, K. B. (1997) Differential regulation of the mitochondrial ADP/ATP translocase gene in wood frogs under freezing stress. Biochim. Biophys. Acta 1353, 69–78.

    CAS  PubMed  Google Scholar 

  24. Wu, S., and Storey, K. B. (2005) Up-regulation of acidic ribosomal phosphoprotein P0 in response to freezing or anoxia in the freeze tolerant wood frog, Rana sylvatica. Cryobiology 50, 71–82.

    Article  CAS  PubMed  Google Scholar 

  25. De Croos, J. N., McNally, J. D., Palmieri, F., and Storey, K. B. (2004) Upregulation of the mitochondrial phosphate carrier during freezing in the wood frog Rana sylvatica: potential roles of transporters in freeze tolerance. J. Bioenerg. Biomembr. 36, 229–239.

    Article  PubMed  Google Scholar 

  26. Cai, Q., and Storey, K. B. (1996) Anoxia-induced gene expression in turtle heart. Upregulation of mitochondrial genes for NADH-ubiquinone oxidoreductase subunit 5 and cytochrome c oxidase subunit 1. Eur. J. Biochem. 241, 83–92.

    Article  CAS  PubMed  Google Scholar 

  27. Larade, K., and Storey, K. B. (2004) Anoxia-induced transcriptional upregulation of sarp-19: cloning and characterization of a novel EF-hand containing gene expressed in hepatopancreas of Littorina littorea. Biochem. Cell. Biol. 82, 285–293.

    Article  CAS  PubMed  Google Scholar 

  28. Larade, K., and Storey, K. B. (2004) Accumulation and translation of ferritin heavy chain transcripts following anoxia exposure in a marine invertebrate. J. Exp. Biol. 207, 1353–1360.

    Article  CAS  PubMed  Google Scholar 

  29. Larade, K., Nimigan, A., and Storey, K. B. (2001) Transcription pattern of ribosomal protein L26 during anoxia exposure in Littorina littorea. J. Exp. Zool. 290, 759–768.

    Article  CAS  PubMed  Google Scholar 

  30. Bilgen, T., English, T. E., McMullen, D. C., and Storey, K. B. (2001) EsMlp, a muscle-LIM protein gene, is up-regulated during cold exposure in the freeze-avoiding larvae of Epiblema scudderiana. Cryobiology 43, 11–20.

    Article  CAS  PubMed  Google Scholar 

  31. Eddy, S. F., and Storey, K. B. (2002) Dynamic use of cDNA arrays: Heterologous probing for gene discovery and exploration of organismal adaptations to environmental stress, in Cell and Molecular Responses to Stress (Storey, K.B., and Storey, J.M., eds.), Elsevier, Amsterdam, pp. 315–325.

    Google Scholar 

  32. Storey, K. B. (2004) Strategies for exploration of freeze responsive gene expression: advances in vertebrate freeze tolerance. Cryobiology 48, 134–145.

    Article  CAS  PubMed  Google Scholar 

  33. Larade, K., and Storey, K. B. (2002) A profile of the metabolic responses to anoxia in marine invertebrates, in Cell and Molecular Responses to Stress (Storey, K.B., and Storey, J.M., eds.), Elsevier, Amsterdam, pp. 27–46.

    Google Scholar 

  34. King, P. A., Rosholt, M. N., and Storey, K. B. (1995) Seasonal changes in plasma glucose transport. Can. J. Zool. 73, 1–9.

    Article  CAS  Google Scholar 

  35. Storey, K. B., and Storey, J. M. (1984) Biochemical adaptation for freezing tolerance in the wood frog, Rana sylvatica. J. Comp. Physiol. B 155, 29–36.

    Article  CAS  Google Scholar 

  36. Moody, D. E., Zou, Z., and McIntyre, L. (2002) Cross-species hybridisation of pig RNA to human nylon microarrays. BMC Genom. 3, 27.

    Google Scholar 

  37. Hogstrand, C., Balesaria, S., and Glover, C. N. (2002) Application of genomics and proteomics for study of the integrated response to zinc exposure in a non-model fish species, the rainbow trout. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 133, 523–535.

    Article  PubMed  Google Scholar 

  38. Becher, M., Talke, I. N., Krall, L., and Kramer, U. (2004) Cross-species microarray transcript profiling reveals high constitutive expression of metal homeostasis genes in shoots of the zinc hyperaccumulator Arabidopsis halleri. Plant J. 37, 251–268.

    Article  CAS  PubMed  Google Scholar 

  39. Adjaye, J., Herwig, R., Herrmann, D., Wruck, W., Benkahla, A., Brink, T. C., Nowak, M., Carnwath, J. W., Hultschig, C., Niemann, H., and Lehrach, H. (2004) Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays. BMC Genomics 5, 83.

    Google Scholar 

  40. Rinaudo, J. A., and Gerin, J. L. (2004) Cross-species hybridization: characterization of gene expression in woodchuck liver using human membrane arrays. J. Med. Virol. 74, 300–313.

    Article  CAS  PubMed  Google Scholar 

  41. Shah, G., Azizian, M., Bruch, D., Mehta, R., and Kittur, D. (2004) Cross-species comparison of gene expression between human and porcine tissue, using single microarray platform—preliminary results. Clin. Transplant. 18 Suppl 12, 76–80.

    Article  PubMed  Google Scholar 

  42. Renn, S. C., Aubin-Horth, N., and Hofmann, H. A. (2004) Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genom. 5, 42.

    Google Scholar 

  43. Wang, Z., Dooley, T. P., Curto, E. V., Davis, R. L., and VandeBerg, J. L. (2004) Cross-species application of cDNA microarrays to profile gene expression using UV-induced melanoma in Monodelphis domestica as the model system. Genomics 83, 588–599.

    Article  CAS  PubMed  Google Scholar 

  44. Chitko-McKown, C. G., Fox, J. M., Miller, L. C., Heaton, M. P., Bono, J. L., Keen, J. E., Grosse, W. M., and Laegreid, W. W. (2004) Gene expression profiling of bovine macrophages in response to Escherichia coli O157:H7 lipopolysaccharide. Dev. Comp. Immunol. 28, 635–645.

    Article  CAS  PubMed  Google Scholar 

  45. Medhora, M., Bousamra, M., 2nd, Zhu, D., Somberg, L., and Jacobs, E. R. (2002) Upregulation of collagens detected by gene array in a model of flow-induced pulmonary vascular remodeling. Am. J. Physiol. Heart Circ. Physiol. 282, H414–422.

    Google Scholar 

  46. Gladney, C. D., Bertani, G. R., Johnson, R. K., and Pomp, D. (2004) Evaluation of gene expression in pigs selected for enhanced reproduction using differential display PCR and human microarrays: I. Ovarian follicles. J. Anim. Sci. 82, 17–31.

    CAS  PubMed  Google Scholar 

  47. Ji, W., Zhou, W., Gregg, K., Yu, N., and Davis, S. (2004) A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucleic Acids Res 32, e93.

    Google Scholar 

  48. Geschwind, D. H. (2001) Sharing gene expression data: an array of options. Nat. Rev. Neurosci. 2, 435–438.

    Article  CAS  PubMed  Google Scholar 

  49. Becker, K. G. (2001) The sharing of cDNA microarray data. Nat. Rev. Neurosci. 2, 438–440.

    Article  CAS  PubMed  Google Scholar 

  50. Miles, M. F. (2001) Microarrays: lost in a storm of data? Nat. Rev. Neurosci. 2, 441–443.

    Article  CAS  PubMed  Google Scholar 

  51. Edgar, R., Domrachev, M., and Lash, A. E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30, 207–210.

    Article  CAS  PubMed  Google Scholar 

  52. Barrett, T., Suzek, T. O., Troup, D. B., Wilhite, S. E., Ngau, W. C., Ledoux, P., Rudnev, D., Lash, A. E., Fujibuchi, W., and Edgar, R. (2005) NCBI GEO: mining millions of expression profiles—database and tools. Nucleic Acids Res. 33, D562–566.

    Article  CAS  PubMed  Google Scholar 

  53. Parkinson, H., Sarkans, U., Shojatalab, M., Abeygunawardena, N., Contrino, S., Coulson, R., Farne, A., Lara, G. G., Holloway, E., Kapushesky, M., Lilja, P., Mukherjee, G., Oezcimen, A., Rayner, T., Rocca-Serra, P., Sharma, A., Sansone, S., and Brazma, A. (2005) ArrayExpress—a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 33, D553–555.

    Article  CAS  PubMed  Google Scholar 

  54. Sarkans, U., Parkinson, H., Lara, G. G., Oezcimen, A., Sharma, A., Abeygunawardena, N., Contrino, S., Holloway, E., Rocca-Serra, P., Mukherjee, G., Shojatalab, M., Kapushesky, M., Sansone, S. A., Farne, A., Rayner, T., and Brazma, A. (2005) The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinformatics 21, 1495–1501.

    Article  CAS  PubMed  Google Scholar 

  55. Rocca-Serra, P., Brazma, A., Parkinson, H., Sarkans, U., Shojatalab, M., Contrino, S., Vilo, J., Abeygunawardena, N., Mukherjee, G., Holloway, E., Kapushesky, M., Kemmeren, P., Lara, G. G., Oezcimen, A., and Sansone, S. A. (2003) ArrayExpress: a public database of gene expression data at EBI. C. R. Biol. 326, 1075–1078.

    Article  CAS  PubMed  Google Scholar 

  56. Brazma, A., Parkinson, H., Sarkans, U., Shojatalab, M., Vilo, J., Abeygunawardena, N., Holloway, E., Kapushesky, M., Kemmeren, P., Lara, G. G., Oezcimen, A., Rocca-Serra, P., and Sansone, S. A. (2003) ArrayExpress—a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31, 68–71.

    Article  CAS  PubMed  Google Scholar 

  57. Brauch, K. M., Dhruv, N. D., Hanse, E. A., and Andrews, M. T. (2005) Digital transcriptome analysis indicates adaptive mechanisms in the heart of a hibernating mammal. Physiol. Genom. 23,227–234.

    Article  CAS  Google Scholar 

  58. Lindell, S. L., Klahn, S. L., Piazza, T. M., Mangino, M. J., Torrealba, J. R., Southard, J. H., and Carey, H. V. (2005) Natural resistance to liver cold ischemia-reperfusion injury associated with the hibernation phenotype. Am. J. Physiol. Gastrointest. Liver Physiol. 288, G473–480.

    Article  CAS  PubMed  Google Scholar 

  59. MacDonald, J. A., and Storey, K. B. (2005) Mitogen-activated protein kinases and selected downstream targets display organ-specific responses in the hibernating ground squirrel. Int. J. Biochem. Cell. Biol. 37, 679–691.

    Article  CAS  PubMed  Google Scholar 

  60. Cai, D., McCarron, R. M., Yu, E. Z., Li, Y., and Hallenbeck, J. (2004) Akt phosphorylation and kinase activity are down-regulated during hibernation in the 13-lined ground squirrel. Brain Res. 1014, 14–21.

    Article  CAS  PubMed  Google Scholar 

  61. Zapala, M. A., Lockhart, D. J., Pankratz, D. G., Garcia, A. J., and Barlow, C. (2002) Software and methods for oligonucleotide and cDNA array data analysis. Genome Biol. 3, SOFTWARE0001.

    Google Scholar 

  62. Lee, J. K., Laudeman, T., Kanter, J., James, T., Siadaty, M. S., Knaus, W. A., Prorok, A., Bao, Y., Freeman, B., Puiu, D., Wen, L. M., Buck, G. A., Schlauch, K., Weller, J., and Fox, J. W. (2004) Gene X Va: VBC open source microarray database and analysis software. Biotechniques 36, 634–638, 640, 642.

    CAS  PubMed  Google Scholar 

  63. Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstrale, M., Laurila, E., Houstis, N., Daly, M. J., Patterson, N., Mesirov, J. P., Golub, T. R., Tamayo, P., Spiegelman, B., Lander, E. S., Hirschhorn, J. N., Altshuler, D., and Groop, L. C. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267–273.

    Article  CAS  PubMed  Google Scholar 

  64. Carlisle, A. J., Prabhu, V. V., Elkahloun, A., Hudson, J., Trent, J. M., Linehan, W. M., Williams, E. D., Emmert-Buck, M. R., Liotta, L. A., Munson, P. J., and Krizman, D. B. (2000) Development of a prostate cDNA microarray and statistical gene expression analysis package. Mol. Carcinog. 28, 12–22.

    Article  CAS  PubMed  Google Scholar 

  65. Wang, X., Ghosh, S., and Guo, S. W. (2001) Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res. 29, E75–75.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

Appreciation and thanks are extended to J. Storey for critical reading and suggestions for the manuscript. This work was supported in part to funding to S.F.E. (Ontario Graduate Scholarship) and K.B.S. (NSERC). K.B.S. holds a Canada Research Chair in Molecular Physiology.

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Authors and Affiliations

  1. Department of Biochemistry Boston University School of Medicine, Women’s Health Interdisciplinary Research Center, Boston, MA

    Sean F. Eddy

  2. Institute of Biochemistry, Departments of Biology and Chemistry, Carleton University, Ottawa, Ontario, Canada

    Kenneth B. Storey

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  1. Sean F. Eddy
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Editors and Affiliations

  1. Center for Advanced Research in Environmental Genomics (CAREG),Department of Biology, University of Ottawa, Ottawa, Canada

    C. Cristofre Martin

  2. Department of Biochemistry, St. George’s University Medical School, St. George’s, Grenada, West Indies

    C. Cristofre Martin

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Eddy, S.F., Storey, K.B. (2008). Comparative Molecular Physiological Genomics. In: Martin, C.C., Martin, C.C. (eds) Environmental Genomics. Methods in Molecular Biology, vol 410. Humana Press. https://doi.org/10.1007/978-1-59745-548-0_6

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  • DOI: https://doi.org/10.1007/978-1-59745-548-0_6

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