Regulatory divergence in Drosophila revealed by mRNA-seq

Genome Research

Volumn 20, Issue 6, 2010, Pages 816-825

  McManus, C Joel ^a   Coolon, Joseph D ^b   Duff, Michael O ^a   Eipper Mains, Jodi ^a   Graveley, Brenton R ^a   Wittkopp, Patricia J ^b  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ANIMAL EXPERIMENT; ARTICLE; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA SECHELLIA; FEEDING BEHAVIOR; GENE EXPRESSION; GENETIC VARIABILITY; GENOME; INHERITANCE; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; SPECIES COMPARISON;

ANIMALS; DROSOPHILA; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; RNA, MESSENGER; SPECIES SPECIFICITY;

DROSOPHILA MELANOGASTER; DROSOPHILA SECHELLIA;

EID: 77953010033     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.102491.109     Document Type: Article

References (50)

1. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Ahmadian A, Gharizadeh B, Gustafsson AC, Sterky F, Nyren P, Uhlen M, Lundeberg J. 2000. Single-nucleotide polymorphism analysis by pyrosequencing. Anal Biochem 280: 103-110.
3. Carroll SB. 2005. Evolution at two levels: On genes and form. PLoS Biol 3: e245. doi: 10.1371/journal.pbio.0030245.
4. Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, et al. 2002. Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol 3: research0079. doi: 10.1186/gb-2002-3-12-research0079.
5. Cowles CR, Hirschhorn JN, Altshuler D, Lander ES. 2002. Detection of regulatory variation in mouse genes. Nat Genet 32: 432-437. (Pubitemid 35266121)
6. Cutter AD. 2008. Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Mol Biol Evol 25: 778-786.
7. Denver DR, Morris K, Streelman JT, Kim SK, Lynch M, Thomas WK. 2005. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nat Genet 37: 544-548. (Pubitemid 40617285)
8. Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
9. Dworkin I, Jones CD. 2009. Genetic changes accompanying the evolution of host specialization in Drosophila sechellia. Genetics 181: 721-736.
10. Genissel A, McIntyre LM, Wayne ML, Nuzhdin SV. 2008. Cis and trans regulatory effects contribute to natural variation in transcriptome of Drosophila melanogaster. Mol Biol Evol 25: 101-110.
11. Gibson G, Weir B. 2005. The quantitative genetics of transcription. Trends Genet 21: 616-623.
12. Gibson G, Riley-Berger R, Harshman L, Kopp A, Vacha S, Nuzhdin S, Wayne M. 2004. Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster. Genetics 167: 1791-1799. (Pubitemid 39265915)
13. Graze RM, McIntyre LM, Main BJ, Wayne ML, Nuzhdin SV. 2009. Regulatory divergence in Drosophila melanogaster and D. simulans, a genomewide analysis of allele-specific expression. Genetics 183: 547-561.
14. Hsieh W-P, Chu T-M, Wolfinger RD, Gibson G. 2003. Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics 165: 747-757. (Pubitemid 37337640)
15. Hoekstra HE, Coyne JA. 2007. The locus of evolution: Evo devo and the genetics of adaptation. Evolution 61: 995-1016.
16. Jones CD. 2004. Genetics of egg production in Drosophila sechellia. Heredity 92: 235-241.
17. Jones CD. 2005. The genetics of adaptation in Drosophila sechellia. Genetica 123: 137-145.
18. Kliman RM, Andolfatto P, Coyne JA, Depaulis F, Kreitman M, Berry AJ, McCarter J, Wakeley J, Hey J. 2000. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156: 1913-1931. (Pubitemid 32001252)
19. Landry CR, Wittkopp PJ, Taubes CH, Ranz JM, Clark AG, Hartl DL. 2005. Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171: 1813-1822.
20. Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL. 2007. Genetic properties influencing the evolvability of gene expression. Science 317: 18-21. (Pubitemid 47056469)
21. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25.
22. Legrand D, Tenaillon MI, Matyot P, Gerlach J, Lachaise D, Cariou ML. 2009. Species-wide genetic variation and demographic history of Drosophila sechellia, a species lacking population structure. Genetics 182: 1197-1206.
23. Lemos B, Araripe LO, Fontanillas P, Hartl DL. 2008. Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression. Proc Natl Acad Sci 105: 14471-14476.
24. Main BJ, Bickel RD, McIntyre LM, Graze RM, Calabrese PP, Nuzhdin SV. 2009. Allele-specific expression assays using Solexa. BMC Genomics 10: 422. doi: 10.1186/1471-2164-10-422.
25. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. 2008. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
26. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. (Pubitemid 351911867)
27. Nelson CE, Hersh BM, Carroll SB. 2004. The regulatory content of intergenic DNA shapes genome architecture. Genome Biol 5: R25. http://genomebiology.com/2004/5/4/R25.
28. Nuzhdin SV, Wayne ML, Harmon KL, McIntyre LM. 2004. Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol Biol Evol 21: 1308-1317.
29. Ranz JM, Machado CA. 2006. Uncovering evolutionary patterns of gene expression using microarrays. Trends Ecol Evol 21: 29-37. (Pubitemid 41827462)
30. Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL. 2003. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300: 1742-1745. (Pubitemid 36712569)
31. Ranz JM, Namgyal K, Gibson G, Hartl DL. 2004. Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Res 14: 373-379. (Pubitemid 38386604)
32. Rifkin SA, Kim J, White KP. 2003. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet 33: 138-144. (Pubitemid 36177064)
33. Rockman MV, Kruglyak L. 2006. Genetics of global gene expression. Nat Rev Genet 7: 862-872.
34. Ronald J, Akey JM. 2007. The evolution of gene expression QTL in Saccharomyces cerevisiae. PLoS One 2: e678. doi: 10.1371/journal.pone.0000678. (Pubitemid 351325420)
35. Santamaria P. 1977. On the causes of sterility in some interspecific hybrids from the melanogaster subgroup of Drosophila. Wilhelm Roux's Archives 82: 305-310. (Pubitemid 8162570)
36. Sawamura K, Watanabe TK, Yamamoto M-T. 1993. Hybrid lethal systems in the Drosophila melanogaster species complex. Genetica 88: 175-185.
37. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, et al. 2003. Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302. (Pubitemid 36378355)
38. Serre D, Gurd S, Ge B, Sladek R, Sinnett D, Harmsen E, Bibikova M, Chudin E, Barker DL, Dickinson T, et al. 2008. Differential allelic expression in the human genome: A robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet 4: e1000006. doi: 10.1371/journal.pgen.1000006.
39. Stern DL, Orgogozo V. 2008. The loci of evolution: How predictable is genetic evolution? Evolution 62: 2155-2177.
40. Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc Natl Acad Sci 100: 9440-9445.
41. Taylor J, Schenck I, Blankenberg D, Nekrutenko A. 2007. Using galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinformatics 19: 10.5. doi: 10.1002/0471250953.bi1005s19.
42. Tirosh I, Reikhav S, Levy AA, Barkai N. 2009. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324: 659-662.
43. Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG. 2008. Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One 3: e3839. doi: 10.1371/journal.pone.0003839.
44. Whitehead A, Crawford DL. 2006. Variation within and among species in gene expression: Raw material for evolution. Mol Ecol 15: 1197-1211.
45. Wittkopp PJ. 2005. Genomic sources of regulatory variation in cis and in trans. Cell Mol Life Sci 62: 1779-1783.
46. Wittkopp PJ, Haerum BK, Clark AG. 2004. Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.
47. Wittkopp PJ, Haerum BK, Clark AG. 2008. Regulatory changes underlying expression differences within and between Drosophila species. Nat Genet 40: 346-350.
48. Wray GA. 2007. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8: 206-216.
49. Zhang X, Borevitz JO. 2009. Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics 182: 943-954.
50. Zhang K, Li JB, Gao Y, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, Leproust EM, et al. 2009. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods 6: 613-618.