Cis-regulatory variation is typically polyallelic in Drosophila

Genetics

Volumn 181, Issue 2, 2009, Pages 661-670

  Gruber, Jonathan D ^a,b   Long, Anthony D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT;

ALLELE; ARTICLE; CIS ISOMER; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE LOCUS; GENE MUTATION; GENETIC VARIABILITY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; ANIMALS; ANIMALS, WILD; DROSOPHILA MELANOGASTER; FEMALE; GENE EXPRESSION REGULATION; GENES, INSECT; GENETIC COMPLEMENTATION TEST; GENETIC VARIATION; GENETICS, POPULATION; MALE; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE;

DROSOPHILA MELANOGASTER;

EID: 62449248382     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.108.098459     Document Type: Article

References (37)

1. ANDOLFATTO, P., 2005 Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
2. ANDOLFATTO, P., 2007 Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res. 17: 1755-1762.
3. BRAY, N. J., and M. C. O'DONOVAN, 2006 Investigating cis-acting regulatory variation using assays of relative allelic expression. Psychiatr. Genet. 16: 173-177.
4. BRAY, N., P. BUCKLAND, M. OWEN and M. O'DONOVAN, 2003 Cis-acting variation in the expression of a high proportion of genes in human brain. Hum. Genet. 113: 149-153.
5. BREM, R., G. YVERT, R. CLINTON and L. KRUGLYAK, 2002 Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
6. CAMPBELL, C., A. KIRBY, J. NEMESH, M. DALY and J. HIRSCHHORN, 2008 A survey of allelic imbalance in F1 mice. Genome Res. 18: 555-563.
7. COWLES, C., J. HIRSCHHORN, D. ALTSHULER and E. LANDER, 2002 Detection of regulatory variation in mouse genes. Nat. Genet. 32: 432-437.
8. DE MEAUX, J., U. GOEBEL, A. POP and T. MITCHELL-OLDS, 2005 Allele-specific assay reveals functional variation in the chalcone synthase promoter of Arabidopsis thaliana that is compatible with neutral evolution. Plant Cell 17: 676-690.
9. DE MEAUX, J., A. POP and T. MITCHELL-OLDS, 2006 Cis-regulatory evolution of chalcone-synthase expression in the genus Arabidopsis. Genetics 174: 2181-2202.
10. DENVER, D., K. MORRIS, T. STREELMAN, S. KIM, M. LYNCH et al., 2005 The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nat. Genet. 37: 544-548.
11. ENCODE Project Consortium, E. Birney, J. A. Stamatoyannopoulos, A. Dutta, R. Guigó et al., 2007 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
12. EWENS, W. J., 1972 The sampling theory of selectively neutral alleles. Theor. Popul. Biol. 3: 87-112.
13. GENISSEL, A., L. MCINTYRE, M. WAYNE and S. NUZHDIN, 2008 Cis and trans regulatory effects contribute to natural variation in transcriptome of Drosophila melanogaster. Mol. Biol. Evol. 25: 101-110.
14. GRUBER, J. D., A. GENISSEL, S. J. MACDONALD and A. D. LONG, 2007 How repeatable are associations between polymorphisms in achaete-scute and bristle number variation in Drosophila? Genetics 175: 1987-1997.
15. HADDRILL, P. R., K. R. THORNTON, B. CHARLESWORTH and P. ANDOLFATTO, 2005 Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15: 790-799.
16. HOEKSTRA, H., and J. COYNE, 2007 The locus of evolution: Evo-Devo and the genetics of adaptation. Evolution 61: 995-1016.
17. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
18. LO, S., Z. WANG, Y. HU, H. YANG, S. GERE et al., 2003 Allelic variation in gene expression is common in the human genome. Genome Res. 13: 1855-1862.
19. MACDONALD, S. J., and A. D. LONG, 2004 A potential regulatory polymorphism upstream of hairy is not associated with bristle number variation in wild-caught Drosophila. Genetics 167: 2127-2131.
20. MACDONALD, S., T. PASTINEN, A. GENISSEL, T. CORNFORTH and A. LONG, 2005 A low-cost open-source SNP genotyping platform for association mapping applications. Genome Biol. 6: R105.
21. PANT, K., H. TAO, E. BEILHARZ, D. BALLINGER, D. COX et al., 2006 Analysis of allelic differential expression in human white blood cells. Genome Res. 16: 331-339.
22. PASTINEN, T., R. SLADEK, S. GURD, A. A. SAMMAK, B. GE et al., 2004 A survey of genetic and epigenetic variation affecting human gene expression. Physiol. Genomics 16: 184-193.
23. PASTINEN, T., B. GE, S. GURD, T. GAUDIN, C. DORE et al., 2005 Mapping common regulatory variants to human haplotypes. Hum. Mol. Genet. 14: 3963-3971.
24. PLETCHER, S., S. MACDONALD, R. MARGUERIE, U. CERTA, S. STEARNS et al., 2002 Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster. Curr. Biol. 12: 712-723.
25. RIFKIN, S., D. HOULE, J. KIM and K. WHITE, 2005 A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature 438: 220-223.
26. ROBIN, C., R. F. LYMAN, A. D. LONG, C. H. LANGLEY and T. F. C. MACKAY, 2002 hairy: a quantitative trait locus for Drosophila sensory bristle number. Genetics 162: 155-164.
27. ROZEN, S., and H. SKALETSKY, 2000 Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132: 365-386.
28. SOKAL, R., and J. ROHLF, 1995 Biometry. W.H. Freeman, San Francisco.
29. STERN, D. L., and V. ORGOGOZO, 2008 The loci of evolution: How predictable is genetic evolution? Evolution 62: 2155-2177.
30. TAO, H., D. COX and K. FRAZER, 2006 Allele-specific KRT1 expression is a complex trait. PLoS Genet. 2: e93.
31. WITTKOPP, P. J., 2005 Genomic sources of regulatory variation in cis and in trans. Cell. Mol. Life Sci. 62: 1779-1783.
32. WITTKOPP, P., B. HAERUM and A. CLARK, 2004 Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.
33. WITTKOPP, P. J., B. K. HAERUM and A. G. CLARK, 2008a Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster. Genetics 178: 1831-1835.
34. WITTKOPP, P. J., B. K. HAERUM and A. G. CLARK, 2008b Regulatory changes underlying expression differences within and between Drosophila species. Nat. Genet. 40: 346-350.
35. WRAY, G. A., 2007 The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 8: 206-216.
36. YAN, H., W. YUAN, V. E. VELCULESCU, B. VOGELSTEIN and K. W. KINZLER, 2002 Allelic variation in human gene expression. Science 297: 1143.
37. 1 hybrids. Genetics 177: 1987-1996.