Comparative environmental genomics in non-model species: Using heterologous hybridization to DNA-based microarrays

Journal of Experimental Biology

Volumn 210, Issue 9, 2007, Pages 1602-1606

  Buckley, Bradley A ^a  

^a PORTLAND STATE UNIVERSITY   (United States)

Author keywords

Comparative environmental genomics; DNA microarray; Gene expression; Heterologous hybridization

Indexed keywords

ACCLIMATIZATION; DNA MICROARRAY; ENVIRONMENT; GENE EXPRESSION; GENETIC VARIABILITY; GENETICS; GENOMICS; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; REVIEW; SPECIES DIFFERENCE;

ACCLIMATIZATION; ENVIRONMENT; GENE EXPRESSION; GENOMICS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RESEARCH DESIGN; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 34249714676     PISSN: 00220949     EISSN: None     Source Type: Journal    
DOI: 10.1242/jeb.002402     Document Type: Review

References (27)

1. Buckley, B. A., Gracey, A. Y. and Somero, G. N. (2006). The cellular response to heat stress in the goby Gillichthys mirabilis: a cDNA microarray and protein-level analysis. J. Exp. Biol. 209, 2660-2677.
2. Chen, D., Toone, W. M., Mata, J., Lyne, R., Burns, G., Kivinen, K., Brazma, A., Jones, N. and Bähler, J. (2003). Global transcriptional responses of fission yeast to environmental stress. Mol. Cell. Biol. 14, 214-229.
3. Enard, W., Khaltovich, P., Klose, J., Zollner, S., Heisseg, F., Giavalisco, P., Nieselt-Struwe, K., Muchmore, E., Varkl, A., Ravid, R. et al. (2002). Intra- and interspecific variation in primate gene expression patterns. Science 296, 340-343.
4. Feder, M. E. and Mitchell-Olds, T. (2003). Evolutionary and ecological functional genomics. Nat. Rev. Genet. 4, 649-655.
5. Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D. and Brown, P. O. (2000). Genomic expression programs in the response of yeast cells to environmental change. Mol. Biol. Cell 11, 4241-4257.
6. Gasch, A. P., Huang, M., Metzner, S., Botstein, D., Elledge, S. J. and Brown, P. O. (2001). Genomic expression responses to DNA-damaging agent and the regulatory role of the yeast ATR homolog Mec1p. Mol. Biol. Cell 12, 2987-3003.
7. Gilad, Y., Rifkin, S. A., Bertone, P., Gcrstein, M. and White, K. P. (2006). Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res. 15, 674-680.
8. Girardot, F., Monnier, F. and Tricoire, H. (2004). Genome wide analysis of common and specific stress responses in adult Drosophila melanogaster. BMC Genomics doi: 10.1186/1471-2164-5-74.
9. Gracey, A. Y. and Cossins, A. R. (2003). Application of microarray technology in environmental and comparative physiology. Annu. Rev. Physiol. 65, 231-259.
10. Gracey, A. Y., Troll, J. V. and Somero, G. N. (2001). Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proc. Natl. Acad. Sci. USA 98, 1993-1998.
11. Gracey, A. Y., Fraser, E. J., Li, W., Fang, Y., Taylor, R. R., Rogers, J., Brass, A. and Cossins, A. R. (2004). Coping with cold: an integrative, multitissue analysis of the transcriptome of a Poikilothermie vertebrate. Proc. Natl. Acad. Sci. USA 101, 16970-16975.
12. Hoheisel, J. D. (2006). Microarray technology: beyond transcript profiling and genotype profiling. Nat. Rev. Genet. 7, 200-210.
13. Ji, W., Zhou, W., Gregg, K., Yu, N., Davis, S. and Davis, S. (2004). A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucl. Acids Res. doi: 10.1093/nar/guh084.
14. Krasnov, A., Koskinen, H., Pehkonen, P., Rexroad, C. E., III, Afanasyev, S. and Molsa, H. (2005). Gene expression in the brain and kidney of rainbow trout in response to handling stress. BMC Genomics doi: 10.1186/1471-2164-6-3.
15. Lettieri, T. (2006). Recent applications of DNA microarray technology to toxicology and ecotoxicology. Env. Health Perspec. 114, 4-9.
16. Meiklejohn, C. D., Parsh, J., Ranz, J. M. and Haiti, D. L. (2003). Rapid evolution of male-biased gene expression in Drosophila. Proc. Natl. Acad. Sci. USA 100, 9894-9899.
17. Murray, J. I., Whitfield, M. L., Trinklein, N. D., Myers, R. M., Brown, P. O. and Botstein, D. (2004). Diverse and specific gene expression responses to stresses in cultured human cells. Mol. Biol Cell. 15, 2361-2374.
18. Oleksiak, M. F., Churchill, G. and Crawford, D. L. (2002). Variation in gene expression within and among natural populations. Nature Genet. 32, 261-266.
19. Podrabsky, J. E. and Somero, G. N. (2004). Changes in gene expression associated with acclimation to constant temperature and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J. Exp. Biol. 207, 2237-2254.
20. Ranz, J. M., Castillo-Davis, C. I., Meiklejohn, C. D. and Haiti, D. L. (2003). Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300, 1742-1745.
21. Renn, S. C. P., Aubin-Horth, N. and Hofmann, H. A. (2004). Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics doi: 10.1186/1471-2164-5-42.
22. Riehle, M. M., Bennett, A. F. and Long, A. D. (2005). Changes in gene expression following high-temperature adaptation in experimentally evolved populations of E. coli. Physiol. Biochem. Zool. 78, 299-315.
23. Rise, M. L., von Schalburg, K. R., Brown, G. D., Mawer, M. A., Devlin, R. H., Kuipers, N., Busby, M., Beetz-Sargent, M., Alberto, R., Gibbs, A. R. et al. (2004). Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res. 14, 478-490.
24. Sartor, M. A., Zorn, A. M., Schwanekamp, J. A., Halbleib, D., Karyala, S., Howell, M. L., Dean, G. E., Medvedovic, M. and Tomlinson, C. R. (2006). A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucl. Acids Res. 34, 185-200.
25. Sneddon, L. U., Margaretto, J. and Cossins, A. R. (2005). The use of transcriptomics to address questions in behaviour: production of a suppression subtractive hybridisation library from dominance hierarchies of rainbow trout. Physiol. Biochem. Zool. 78, 695-705.
26. von Schalburg, K. R., Rise, M. L., Cooper, G. A., Brown, G. D., Gibbs, A. R., Nelson, C. C., Davidson, W. S. and Koop, B. F. (2005). Fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics doi: 10.1186/1471-2164-6-126.
27. Vornanen, M., Hassinen, M., Koskinen, H. and Krasnov, A. (2005). Steady-state effects of temperature acclimation on the transcriptome of the rainbow trout heart. Am. J. Physiol. Regul. Integr. Comp. Physiol. 289, R1177-R1184.