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MBE Advance Access published online on June 5, 2006
Molecular Biology and Evolution, 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
Accepted May 16, 2006

Research Article

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

Naoki Osada 1 {sect}, Michael H. Kohn 2 {sect}, and Chung-I Wu 3 *

1 Division of Biomedical Research Resources, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
2 Department of Ecology & Evolutionary Biology, Rice University, MS 170, 6100 Main Street, Houston, Texas 77005, U.S.A.
3 Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL, 60637-1573, U.S.A.

* To whom correspondence should be addressed.
Chung-I Wu, E-mail: ciwu{at}uchicago.edu


  Abstract

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 weight 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 two D. 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 two 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, i.e. 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.

Keywords: cis- and trans-regulation; gene expression; gene regulation; microarray; polymorphism; promoter evolution.

{sect}Authors contributed equally


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