Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays.
BACKGROUND
Cross-species gene-expression comparison is a powerful tool for the discovery of evolutionarily conserved mechanisms and pathways of expression control. The usefulness of cDNA microarrays in this context is that broad areas of homology are compared and hybridization probes are sufficiently large that small inter-species differences in nucleotide sequence would not affect the analytical results. This comparative genomics approach would allow a common set of genes within a specific developmental, metabolic, or disease-related gene pathway to be evaluated in experimental models of human diseases. The objective of this study was to investigate the feasibility and reproducibility of cross-species analysis employing a human cDNA microarray as probe.


RESULTS
As a proof of principle, total RNA derived from human and bovine fetal brains was used as a source of labelled targets for hybridisation onto a human cDNA microarray composed of 349 characterised genes. Each gene was spotted 20 times representing 6,980 data points thus enabling highly reproducible spot quantification. Employing high stringency hybridisation and washing conditions, followed by data analysis, revealed slight differences in the expression levels and reproducibility of the signals between the two species. We also assigned each of the genes into three expression level categories- i.e. high, medium and low. The correlation co-efficient of cross hybridisation between the orthologous genes was 0.94. Verification of the array data by semi-quantitative RT-PCR using common primer sequences enabled co-amplification of both human and bovine transcripts. Finally, we were able to assign gene names to previously uncharacterised bovine ESTs.


CONCLUSIONS
Results of our study demonstrate the harnessing and utilisation power of comparative genomics and prove the feasibility of using human microarrays to facilitate the identification of co-expressed orthologous genes in common tissues derived from different species.
Adjaye
James
J
Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestrasse 73, D-14195, Berlin, Germany. adjaye@molgen.mpg.de
Herwig
Ralf
R
Herrmann
Doris
D
Wruck
Wasco
W
Benkahla
Alia
A
Brink
Thore C
TC
Nowak
Monika
M
Carnwath
Joseph W
JW
Hultschig
Claus
C
Niemann
Heiner
H
Lehrach
Hans
H
D000818:Animals; D001921:Brain / Q000196:embryology / Q000378:metabolism; D001923:Brain Chemistry / Q000235:genetics; D002417:Cattle; D018076:DNA, Complementary / Q000235:genetics*; D019143:Evolution, Molecular; D005240:Feasibility Studies; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation / Q000235:genetics; D018507:Gene Expression Regulation, Developmental / Q000235:genetics; D005796:Genes / Q000502:physiology; D014644:Genetic Variation / Q000235:genetics; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D016415:Sequence Alignment / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
D018076:DNA, Complementary