Biologically Meaningful Expression Profiling Across Species Using Heterologous Hybridization to a CDNA Microarray

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2004 Jul 9

PMID 15238158

Citations 68

Authors

Susan C P Renn

Nadia Aubin-Horth

Hans A Hofmann

Affiliations

Soon will be listed here.

Abstract

Background: Unravelling the path from genotype to phenotype, as it is influenced by an organism's environment, is one of the central goals in biology. Gene expression profiling by means of microarrays has become very prominent in this endeavour, although resources exist only for relatively few model systems. As genomics has matured into a comparative research program, expression profiling now also provides a powerful tool for non-traditional model systems to elucidate the molecular basis of complex traits.

Results: Here we present a microarray constructed with approximately 4500 features, derived from a brain-specific cDNA library for the African cichlid fish Astatotilapia burtoni (Perciformes). Heterologous hybridization, targeting RNA to an array constructed for a different species, is used for eight different fish species. We quantified the concordance in gene expression profiles across these species (number of genes and fold-changes). Although most robust when target RNA is derived from closely related species (<10 MA divergence time), our results showed consistent profiles for other closely related taxa (approximately 65 MA divergence time) and, to a lesser extent, even very distantly related species (>200 MA divergence time).

Conclusion: This strategy overcomes some of the restrictions imposed on model systems that are of importance for evolutionary and ecological studies, but for which only limited sequence information is available. Our work validates the use of expression profiling for functional genomics within a comparative framework and provides a foundation for the molecular and cellular analysis of complex traits in a wide range of organisms.

Citing Articles

Dissecting the Transcriptional Patterns of Social Dominance across Teleosts.

Renn S, ORourke C, Aubin-Horth N, Fraser E, Hofmann H Integr Comp Biol. 2016; 56(6):1250-1265.

PMID: 27940616 PMC: 5146711. DOI: 10.1093/icb/icw118.

Using an integrative approach to investigate the evolution of behaviour.

Aubin-Horth N Evol Appl. 2016; 9(1):166-80.

PMID: 27087846 PMC: 4780388. DOI: 10.1111/eva.12300.

Comprehensive and quantitative proteomic analyses of zebrafish plasma reveals conserved protein profiles between genders and between zebrafish and human.

Li C, Tan X, Lim T, Lin Q, Gong Z Sci Rep. 2016; 6:24329.

PMID: 27071722 PMC: 4829857. DOI: 10.1038/srep24329.

Transcriptome Analysis in Domesticated Species: Challenges and Strategies.

Hekman J, Johnson J, Kukekova A Bioinform Biol Insights. 2016; 9(Suppl 4):21-31.

PMID: 26917953 PMC: 4756862. DOI: 10.4137/BBI.S29334.

Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes.

Ockendon N, OConnell L, Bush S, Monzon-Sandoval J, Barnes H, Szekely T Mol Ecol Resour. 2015; 16(2):446-58.

PMID: 26358618 PMC: 4982090. DOI: 10.1111/1755-0998.12465.

References

Oleksiak M, Churchill G, Crawford D . Variation in gene expression within and among natural populations. Nat Genet. 2002; 32(2):261-6. DOI: 10.1038/ng983. View

Townsend J, Cavalieri D, Hartl D . Population genetic variation in genome-wide gene expression. Mol Biol Evol. 2003; 20(6):955-63. DOI: 10.1093/molbev/msg106. View

Miya M, Takeshima H, Endo H, Ishiguro N, Inoue J, Mukai T . Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol. 2002; 26(1):121-38. DOI: 10.1016/s1055-7903(02)00332-9. View

Verheyen E, Salzburger W, Snoeks J, Meyer A . Origin of the superflock of cichlid fishes from Lake Victoria, East Africa. Science. 2003; 300(5617):325-9. DOI: 10.1126/science.1080699. View

Lee M, Kuo F, Whitmore G, Sklar J . Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci U S A. 2000; 97(18):9834-9. PMC: 27599. DOI: 10.1073/pnas.97.18.9834. View

Jin W, Riley R, Wolfinger R, White K, GIBSON G . The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet. 2001; 29(4):389-95. DOI: 10.1038/ng766. View

Gu J, Gu X . Induced gene expression in human brain after the split from chimpanzee. Trends Genet. 2003; 19(2):63-5. DOI: 10.1016/s0168-9525(02)00040-9. View

Kirkness E, Bafna V, Halpern A, Levy S, Remington K, Rusch D . The dog genome: survey sequencing and comparative analysis. Science. 2003; 301(5641):1898-903. DOI: 10.1126/science.1086432. View

Feder M, Mitchell-Olds T . Evolutionary and ecological functional genomics. Nat Rev Genet. 2003; 4(8):651-7. DOI: 10.1038/nrg1128. View

10.

Nakazawa M, Cebria F, Mineta K, Ikeo K, Agata K, Gojobori T . Search for the evolutionary origin of a brain: planarian brain characterized by microarray. Mol Biol Evol. 2003; 20(5):784-91. DOI: 10.1093/molbev/msg086. View

11.

Salzburger W, Meyer A, Baric S, Verheyen E, Sturmbauer C . Phylogeny of the Lake Tanganyika cichlid species flock and its relationship to the Central and East African haplochromine cichlid fish faunas. Syst Biol. 2002; 51(1):113-35. DOI: 10.1080/106351502753475907. View

12.

Evans S, Datson N, Kabbaj M, Thompson R, Vreugdenhil E, de Kloet E . Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE analysis. Serial Analysis of Gene Expression. Eur J Neurosci. 2002; 16(3):409-13. DOI: 10.1046/j.1460-9568.2002.02097.x. View

13.

Churchill G . Fundamentals of experimental design for cDNA microarrays. Nat Genet. 2002; 32 Suppl:490-5. DOI: 10.1038/ng1031. View

14.

Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, Giavalisco P . Intra- and interspecific variation in primate gene expression patterns. Science. 2002; 296(5566):340-3. DOI: 10.1126/science.1068996. View

15.

Streelman J, Zardoya R, Meyer A, Karl S . Multilocus phylogeny of cichlid fishes (Pisces: Perciformes): evolutionary comparison of microsatellite and single-copy nuclear loci. Mol Biol Evol. 2000; 15(7):798-808. DOI: 10.1093/oxfordjournals.molbev.a025985. View

16.

Oleksiak M, Kolell K, Crawford D . Utility of natural populations for microarray analyses: isolation of genes necessary for functional genomic studies. Mar Biotechnol (NY). 2004; 3(Supplement 1):S203-11. DOI: 10.1007/s10126-001-0043-0. View

17.

Holt R, Subramanian G, Halpern A, Sutton G, Charlab R, Nusskern D . The genome sequence of the malaria mosquito Anopheles gambiae. Science. 2002; 298(5591):129-49. DOI: 10.1126/science.1076181. View

18.

Ju Z, Dunham R, Liu Z . Differential gene expression in the brain of channel catfish ( Ictalurus punctatus) in response to cold acclimation. Mol Genet Genomics. 2002; 268(1):87-95. DOI: 10.1007/s00438-002-0727-9. View

19.

Whitfield C, Cziko A, Robinson G . Gene expression profiles in the brain predict behavior in individual honey bees. Science. 2003; 302(5643):296-9. DOI: 10.1126/science.1086807. View

20.

Meyer A . Phylogenetic relationships and evolutionary processes in East African cichlid fishes. Trends Ecol Evol. 2011; 8(8):279-84. DOI: 10.1016/0169-5347(93)90255-N. View