Abstract
Gene expression profiling is a powerful new end point for ecotoxicology and a means for bringing the genomics revolution to this field. We review the usefulness of gene expression profiling as an end point in ecotoxicology and describe methods for applying this approach to non-model organisms. Since genomes contain thousands of genes representing hundreds of pathways, it is possible to identify toxicant-specific responses from this wide array of possibilities. Stressor-specific signatures in gene expression profiles can be used to diagnose which stressors are impacting populations in the field. Screening for stress-induced genes requires special techniques in organisms without sequenced genomes. These techniques include differential display polymerase chain reaction (DD PCR), suppressive subtractive hybridization PCR (SSH PCR), and representational difference analysis. Gene expression profiling in model organisms like yeast has identified hundreds of genes that are up-regulated in response to various stressors, including several that are well characterized (e.g., hsp78, metallothionein, superoxide dismutase). Using consensus PCR primers from several animal sequences, it is possible to amplify some of these well characterized stress-induced genes from organisms of interest in ecotoxicology. We describe how several stress-induced genes can be grouped into cDNA arrays for rapidly screening samples.
Similar content being viewed by others
References
Berger, A., Mutch, D.M., German, J.B. and Roberts, M.A. (2002). Unraveling lipid metabolism with microarrays: effects of archidonate and docosahexaenoate acid on murine hepatic and hippocampal gene expression. Genome Biology 3: preprint 0004.1–0004.53.
Causton, H.C., Ren, B., Koh, S.S., Harbison, C.T., Kanin, E., Jennings, E.G., Lee, T.I., True, H.L., Lander, E.S. and Young, R.A., (2001). Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell. 12, 323-37.
Daibo, S., Kimura, M.T. and Goto, S.G. (2001). Up-regulation of genes belonging to the drosomycin family in diapausing adults of Drosophila triauraria. Gene 278, 177-84.
Denslow, N.D., Bowman, C.J., Robinson, G., Lee, H.S., Ferguson, R.J., Hemmer, M.J. and Folmer, L.C. (1999). Biomarkers of endocrine disruption at the mRNA level. In D.S. Henshel, M.C. Black and M.C. Harrass (eds) Environmental Toxicology and Risk Assessment: Standardization of Biomarkers of Endocrine Disruption and Environmental Assessment, Vol. 8, pp. 24-35. West Conshohocken, PA, USA: American Society for Testing and Materials.
Denslow, N.D., Bowman, C.J., Ferguson, R.J., Lee, H.S., Hemmer, M.J. and Folmar, L.C. (2001a). Induction of gene expression in sheepshead minnows (Cyprinodon variegatus) treated with 17B-estradiol, diethylstilbestrol, or ethinylestradiol: the use of mRNA fingerprints as an indicator of gene regulation. Gen. Comp. Endocrinol. 121, 250-260.
Denslow, N.D., Lee, H.S., Bowman, C.J., Hemmer, M.J. and Folmar, L.C. (2001b). Multiple responses in gene expression in fish treated with estrogen. Comp. Biochem. Physiol. B 129, 277-282.
Diatchenko, L., Lau, Y., Campbell, F.C., Chenchil, A.P., Moqadam, A., Huang, F., Lukyanov, B., Lukyanov, S., Gurskaya, K., Sverdlov, N. and Siebert, E.D. (1996). Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93, 6025-30.
Edman, C.F., Prigent, S.A., Schipper, A. and Feramisco, J.R. (1997). Identification or ErbB3-stimulated genes using modified representational difference analysis. Biochem. J. 323, 113-18.
Gasch, A.P., Kao, C.M., Huang, M., Carmel-Harel, O., Storz, G., Elledge, S.J., Botstein, D. and Brown, P.O. (2000). A common genomic expression program in the response of S. cerevisiae to diverse environmental stresses. Mol. Biol. Cell. 11, 4241-42.
Gibson, G. (2002). Microarrays in ecology and evolution: a preview. Mol. Ecol. 11, 17-24.
Gurskaya, N.G., Diatchenko, L., Chenchik, L., Siebert, P.D., Khaspekov, G.L., Lukyanov, G.L., Vagner, K.A., Ermolaeva, L.L., Lukyanov, O.D. and Sverdlov, E.D. (1996). Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate. Anal. Biochem. 240, 90-97.
Heidenreich, B., Mayer, K., Sandermann, H. Jr and Ernst, D. (2001). Mercury-induced genes in Arabidopsis thaliana: identification of induced genes upon long-term mercuric ion exposure. Plant, Cell Environ. 24, 1227-34.
Hoffmann, A.A. and Parsons, P.A. (1991). Evolutionary Genetics and Environmental Stress, 284 p. New York: Oxford University Press.
Holter, N., Mitra, M., Maritan, A., Cieplak, M., Banavar, J. and Federoff, N. (2000). Fundamental patterns underlying gene expression profiles: simplicity from complexity. PNAS USA 97, 8409-14.
Hubank, M. and Schatz, D.G. (1999). cDNA representational difference analysis: a sensitive and flexible method for identification of differentially expressed genes. Meth. Enzymol. 303, 325-49.
Kerr, M.K. and Churchill, G. (2001). Statistical design and the analysis of gene expression microarray data. Genetical Res. 77, 123-28.
Larkin, P., Folmar, L.C., Hemmer, M.J., Poston, A.J., Lee, H.S. and Denslow, N.D. (2002). Array technology as a tool to monitor exposure of fish to xenoestrogens. Mar. Environ. Res. 54, 395-9.
Liang, P. and Pardee, A.B. (1992). Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257, 967-71.
Liang, P., Zhu, W., Zhang, X., Guo, Z., O'Connell, R.P., Averboukh, L., Wang, F. and Pardee, A.B. (1994). Differential display using one-base anchored oligo-dT primers. Nuc. Acids Res. 22, 5763-64.
Lisitsyn, N. and Wigler, M. (1993). Cloning the differences between two complex genomes. Science 259, 946-51.
Mak, C.H., Sun, K.W. and Ko, R.C. (2001). Identification of some heat-induced genes of Trichinella spiralis. Parisitology 123, 293-300.
Momose, Y. and Iwahashi, H. (2001). Bioassay of cadmium using DNA microarray: genome-wide expression patterns of Saccharomyces cerevisiae response to cadmium. Environ. Toxicol. Chem. 20, 2353-60.
Morgan, M., Vogelien, D.L. and Snell, T.W. (2001). Assessing coral stress responses using molecular biomarkers of gene transcription. Environ. Toxicol. Chem. 20, 537-43.
Morgan, M.B. and Snell, T.W. (2002). Characterizing stress gene expression in reef-building corals exposed to the mosquitoside dibrom.. Mar Pollut. Bull. 44, 1206-18.
Pastorian, K., Hawel, L. and Byus, C.V. (2000). Optimization of cDNA representational difference analysis for the identification of differentially expressed mRNAs. Anal. Biochem. 283, 89-98.
Pearson, G., Serrao, E.A. and Cancela, M.L. (2001). Suppression subtractive hybridization for studying gene expression during aerial exposure and desiccation in fucoid algae. Europ. J. Phycol. 36, 359-66.
Ramdas, L., Coombes, K.R., Baggerly, K., Abruzzo, L., Highsmith, W.E., Krogmann, T., Hamilton, S.R. and Zhang, W. (2001). Sources of nonlinearity in cDNA microarray expression measurements. Genome Biol. 2(11), 1-7.
Rhodes, L.E. and Van Beneden, R.J. (1996). Gene expression analysis in aquatic animals using differential display polymerase chain reaction. In G.K. Ostrander (ed.) Techniques in Aquatic Toxicology, pp. 161-83. Boca Raton, FL: CRC Lewis Publishers.
Sanders, B.M. (1993). Stress proteins in aquatic organisms: an environmental perspective. Crit. Rev. Toxicol. 23, 49-75.
Schena, M., Salon, D., Davis, R.W. and Brown, P.O. (1995). Quantitative monitoring of gene expression patterns with a cDNA microarray. Science 270, 467-70.
Sultan, A., Abelson, A., Bresler, V., Fishelson, L. and Mokady, O. (2000). Biomonitoring marine environmental quality at the level of gene expression—testing the feasibility of a new approach. Water Sci. Tech. 42, 269-74.
Tohyama, H., Tomoyasu, T., Inoue, M., Joho, M. and Murayama, T. (1992). The gene for cadmium metallothionein from cadmium-resistant yeast appears to be identical to CUP1 in copper-resistant strain. Curr. Gen. 21, 275-80.
Travers, K.J., Patil, C.K., Wodicka, L., Lockhart, D.J., Weissman, J.S. and Walter, P. (2000). Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101, 249-58.
US EPA. (2000). Stressor Identification Guidance Document, Washington, DC: Office fo Water. EPA-B-025.
Wodicka, L., Dong, H., Mittmann, M., Ho, M. and Lockhart, D.J. (1997). Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotech. 15, 1359-67.
Zoldos, V., Siljak-Yakovlev, S., Papes, D., Sarr, A. and Panaud, O. (2001). Representational difference analysis reveals genomic differences between Quercus robur and Q. suber: implications for the study of genome evolution in the genus Quercus. Mol. Gen. Genomics 265, 234-41.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Snell, T.W., Brogdon, S.E. & Morgan, M.B. Gene Expression Profiling in Ecotoxicology. Ecotoxicology 12, 475–483 (2003). https://doi.org/10.1023/B:ECTX.0000003033.09923.a8
Issue Date:
DOI: https://doi.org/10.1023/B:ECTX.0000003033.09923.a8