Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans

被引:15
|
作者
Lawniczak, Mara K. N. [1 ]
Holloway, Alisha K. [2 ,3 ]
Begun, David J. [2 ,3 ]
Jones, Corbin D. [4 ,5 ]
机构
[1] Univ London Imperial Coll Sci Technol & Med, Div Cell & Mol Biol, London SW7 2AZ, England
[2] Univ Calif Davis, Dept Ecol & Evolut, Davis, CA 95616 USA
[3] Univ Calif Davis, Ctr Populat Biol, Davis, CA 95616 USA
[4] Univ N Carolina, Dept Biol, Chapel Hill, NC 27599 USA
[5] Univ N Carolina, Carolina Ctr Genome Sci, Chapel Hill, NC 27599 USA
关键词
D O I
10.1186/gb-2008-9-8-r125
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Understanding how DNA sequence polymorphism relates to variation in gene expression is essential to connecting genotypic differences with phenotypic differences among individuals. Addressing this question requires linking population genomic data with gene expression variation. Results: Using whole genome expression data and recent light shotgun genome sequencing of six Drosophila simulans genotypes, we assessed the relationship between expression variation in males and females and nucleotide polymorphism across thousands of loci. By examining sequence polymorphism in gene features, such as untranslated regions and introns, we find that genes showing greater variation in gene expression between genotypes also have higher levels of sequence polymorphism in many gene features. Accordingly, X-linked genes, which have lower sequence polymorphism levels than autosomal genes, also show less expression variation than autosomal genes. We also find that sex-specifically expressed genes show higher local levels of polymorphism and divergence than both sex-biased and unbiased genes, and that they appear to have simpler regulatory regions. Conclusion: The gene-feature-based analyses and the X-to-autosome comparisons suggest that sequence polymorphism in cis-acting elements is an important determinant of expression variation. However, this relationship varies among the different categories of sex-biased expression, and trans factors might contribute more to male-specific gene expression than cis effects. Our analysis of sexspecific gene expression also shows that female-specific genes have been overlooked in analyses that only point to male-biased genes as having unusual patterns of evolution and that studies of sexually dimorphic traits need to recognize that the relationship between genetic and expression variation at these traits is different from the genome as a whole.
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页数:14
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