Regulatory changes underlying expression differences within and between Drosophila species

Nature Genetics

Volumn 40, Issue 3, 2008, Pages 346-350

  Wittkopp, Patricia J ^a,b   Haerum, Belinda K ^a,b   Clark, Andrew G ^a  

^a Cornell University ^*  (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; DIPLOIDY; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; GENE EXPRESSION REGULATION; GENETIC POLYMORPHISM; NATURAL SELECTION; NONHUMAN; PHENOTYPIC VARIATION; PRIORITY JOURNAL; SPECIES DIFFERENCE;

ANIMALS; CROSSES, GENETIC; DROSOPHILA; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, INSECT; MALE; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION FACTORS;

DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS;

EID: 39749116219     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.77     Document Type: Article

References (24)

1. Yvert, G. et al. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet. 35, 57-64 (2003).
2. Wittkopp, P.J., Haerum, B.K. & Clark, A.G. Evolutionary changes in cis and trans gene regulation. Nature 430, 85-88 (2004).
3. West, M. et al. Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics 175, 1441-1450 (2007).
4. Schadt, E.E. et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297-302 (2003).
5. Morley, M. et al. Genetic analysis of genome-wide variation in human gene expression. Nature 430, 743-747 (2004).
6. Li, Y. et al. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet. 2, e222 (2006).
7. Brem, R.B., Yvert, G., Clinton, R. & Kruglyak, L. Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752-755 (2002).
8. Gibson, G. et al. Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster. Genetics 167, 1791-1799 (2004).
9. Meiklejohn, C.D., Parsch, J., Ranz, J.M. & Hartl, D.L. Rapid evolution of male-biased gene expression in Drosophila. Proc. Natl. Acad. Sci. USA 100, 9894-9899 (2003).
10. Michalak, P. & Noor, M.A. Genome-wide patterns of expression in Drosophila pure species and hybrid males. Mol. Biol. Evol. 20, 1070-1076 (2003).
11. Ranz, J.M., Castillo-Davis, C.I., Meiklejohn, C.D. & Hartl, D.L. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300, 1742-1745 (2003).
12. Rifkin, S.A., Kim, J. & White, K.P. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet. 33, 138-144 (2003).
13. Powell, J.R. Progress and Prospects in Evolutionary Biology: the Drosophila Model (Oxford Univ. Press, New York, 1997).
14. Ranz, J.M., Namgyal, K., Gibson, G. & Hartl, D.L. Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Res. 14, 373-379 (2004).
15. Wittkopp, P.J., Haerum, B.K. & Clark, A.G. Parent-of-origin effects on mRNA expression in Drosophila melanogaster not caused by genomic imprinting. Genetics 173, 1817-1821 (2006).
16. Landry, C.R. et al. Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171, 1813-1822 (2005).
17. Storey, J.D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100, 9440-9445 (2003).
18. Osada, N., Kohn, M.H. & Wu, C.I. Genomic inferences of the cis-regulatory nucleotide polymorphisms underlying gene expression differences between Drosophila melanogaster mating races. Mol. Biol. Evol. 23, 1585-1591 (2006).
19. McDonald, J.H. & Kreitman, M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351, 652-654 (1991).
20. Wittkopp, P.J. Genomic sources of regulatory variation in cis and in trans. Cell. Mol. Life Sci. 62, 1779-1783 (2005).
21. Landry, C.R., Lemos, B., Rifkin, S.A., Dickinson, W.J. & Hartl, D.L. Genetic properties influencing the evolvability of gene expression. Science 317, 118-121 (2007).
22. Denver, D.R. et al. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nat. Genet. 37, 544-548 (2005).
23. Wray, G. The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 8, 206-216 (2007).
24. Akritas, M. & Bershady, M. Linear regression for astronomical data with measurement errors and intrinsic scatter. Astrophys. J. 470, 706-714 (1996).