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MBE Advance Access originally published online on June 5, 2006
Molecular Biology and Evolution 2006 23(8):1585-1591; doi:10.1093/molbev/msl023
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Genomic Inferences of the cis-Regulatory Nucleotide Polymorphisms Underlying Gene Expression Differences between Drosophila melanogaster Mating Races

Naoki Osada*,1, Michael H. Kohn{dagger},1 and Chung-I Wu{ddagger}

* Division of Biomedical Research Resources, National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan; {dagger} Department of Ecology and Evolutionary Biology, Rice University; and {ddagger} Department of Ecology and Evolution, University of Chicago

E-mail: ciwu{at}uchicago.edu.

Nucleotide sequence polymorphisms affecting gene expression occur in the regulatory region of genes (in cis) and elsewhere in the genome (in trans). Further study is required to weigh the relative importance of cis- and trans-acting mutations in mediating gene expression differences within and between species. Here, microarray hybridization experiments were used to isolate 363 gene expression differences between the female fly head transcriptomes of 2 Drosophila melanogaster strains. One strain (French) represented the cosmopolitan M mating race and the other strain (ZS30) represented the Z mating race derived from Zimbabwe, Africa. From chromosomal substitution strains engineered from the 2 strains, we inferred that the expression differences between M and Z alleles largely could be attributed to the genotype of the chromosomes where the differentially expressed genes were located, that is, cis-regulatory polymorphisms prominently influence gene expression differences between M and Z. The effects of trans-regulatory polymorphisms were apparent yet difficult to quantify. Results have implications for models of gene regulatory evolution as well as experimental studies trying to identify the nucleotide sequence polymorphisms underlying gene expression differences between Drosophila strains.

Key Words: cis- and trans-regulation • gene expression • gene regulation • microarray • polymorphism • promoter evolution


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