The genomic determinants of genotype × environment interactions in gene expression

Trends in Genetics

Volumn 29, Issue 8, 2013, Pages 479-487

  Grishkevich, Vladislav ^a   Yanai, Itai ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

Evolution of gene expression; G E interactions; Gene regulation; Genetic assimilation; Phenotypic plasticity

Indexed keywords

CASPASE 8; PROTEIN;

ALCOHOL CONSUMPTION; ALLELE; BODY SIZE; BREAST CANCER; CAENORHABDITIS ELEGANS; CANCER RISK; DEVELOPMENT; DROSOPHILA; ENVIRONMENT; ENVIRONMENTAL CHANGE; ENVIRONMENTAL FACTOR; GENE EXPRESSION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME; GENOTYPE; GENOTYPE ENVIRONMENT INTERACTION; LONGEVITY; LOW TEMPERATURE; NONHUMAN; PHENOTYPIC PLASTICITY; PHENOTYPIC VARIATION; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE TRAIT LOCUS; RECOMBINANT INBRED STRAIN; REVIEW; SACCHAROMYCES CEREVISIAE; SINGLE NUCLEOTIDE POLYMORPHISM; TATA BOX;

EVOLUTION OF GENE EXPRESSION; G×E INTERACTIONS; GENE REGULATION; GENETIC ASSIMILATION; PHENOTYPIC PLASTICITY;

ANIMALS; BIOLOGICAL EVOLUTION; GENE EXPRESSION; GENE-ENVIRONMENT INTERACTION; GENETIC ASSOCIATION STUDIES; GENOMICS; GENOTYPE; HUMANS; PHENOTYPE; PROMOTER REGIONS, GENETIC;

EID: 84880950921     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2013.05.006     Document Type: Review

References (86)

1. Han M., Sternberg P.W. let-60, a gene that specifies cell fates during C. elegans vulval induction, encodes a ras protein. Cell 1990, 63:921-931.
2. Kammenga J.E., et al. A Caenorhabditis elegans wild type defies the temperature-size rule owing to a single nucleotide polymorphism in tra-3. PLoS Genet. 2007, 3:e34.
3. Rogers C., et al. Inhibition of Caenorhabditis elegans social feeding by FMRFamide-related peptide activation of NPR-1. Nat. Neurosci. 2003, 6:1178-1185.
4. Gutteling E.W., et al. Environmental influence on the genetic correlations between life-history traits in Caenorhabditis elegans. Heredity 2007, 98:206-213.
5. Gutteling E.W., et al. Mapping phenotypic plasticity and genotype-environment interactions affecting life-history traits in Caenorhabditis elegans. Heredity 2007, 98:28-37.
6. Dilda C.L., Mackay T.F.C. The genetic architecture of Drosophila sensory bristle number. Genetics 2002, 162:1655-1674.
7. Debat V., et al. Plasticity, canalization, and developmental stability of the Drosophila wing: joint effects of mutations and developmental temperature. Evolution 2009, 63:2864-2876.
8. Dreyer A.P., Shingleton A.W. The effect of genetic and environmental variation on genital size in male Drosophila: canalized but developmentally unstable. PLoS ONE 2011, 6:e28278.
9. Tang H.Y., et al. FOXO regulates organ-specific phenotypic plasticity in Drosophila. PLoS Genet. 2011, 7:e1002373.
10. Reed R.D., et al. Optix drives the repeated convergent evolution of butterfly wing pattern mimicry. Science 2011, 333:1137-1141.
11. Carroll S.B., et al. Pattern formation and eyespot determination in butterfly wings. Science 1994, 265:109-114.
12. Manceau M., et al. The developmental role of Agouti in color pattern evolution. Science 2011, 331:1062-1065.
13. Hobbs H.H., et al. Molecular genetics of the LDL receptor gene in familial hypercholesterolemia. Hum. Mutat. 1992, 1:445-466.
14. Rockman M.V., Kruglyak L. Genetics of global gene expression. Nat. Rev. Genet. 2006, 7:862-872.
15. Hodgins-Davis A., et al. Abundant gene-by-environment interactions in gene expression reaction norms to copper within Saccharomyces cerevisiae. Genome Biol. Evol. 2012, 4:1061-1079.
16. Rocha F., et al. The reaction norm for abdominal pigmentation and its curve in Drosophila mediopunctata depend on the mean phenotypic value. Evolution 2009, 63:280-287.
17. Streit M., et al. Reaction norms and genotype-by-environment interaction in the German Holstein dairy cattle. J. Anim. Breed. Genet. 2012, 129:380-389.
18. Doroszuk A., et al. A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans. Nucleic Acids Res. 2009, 37:e110.
19. Rodriguez M., et al. Genetic variation for stress-response hormesis in C. elegans lifespan. Exp. Gerontol. 2012, 47:581-587.
20. Vieira C., et al. Genotype-environment interaction for quantitative trait loci affecting life span in Drosophila melanogaster. Genetics 2000, 154:213-227.
21. Shook D.R., Johnson T.E. Quantitative trait loci affecting survival and fertility-related traits in Caenorhabditis elegans show genotype-environment interactions, pleiotropy and epistasis. Genetics 1999, 153:1233-1243.
22. Ungerer M.C., et al. Genotype-environment interactions at quantitative trait loci affecting inflorescence development in Arabidopsis thaliana. Genetics 2003, 165:353-365.
23. Gurganus M.C., et al. Genotype-environment interaction at quantitative trait loci affecting sensory bristle number in Drosophila melanogaster. Genetics 1998, 149:1883-1898.
24. Weinig C., et al. Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana. Genetics 2003, 165:321-329.
25. Brem R.B., et al. Genetic dissection of transcriptional regulation in budding yeast. Science 2002, 296:752-755.
26. Lynch M., Walsh B. Genetics and Analysis of Quantitative Traits 1998, Sinauer Associates.
27. Nickels S., et al. Evidence of gene-environment interactions between common breast cancer susceptibility loci and established environmental risk factors. PLoS Genet. 2013, 9:e1003284.
28. Kruglyak L. The road to genome-wide association studies. Nat. Rev. Genet. 2008, 9:314-318.
29. Li Y., et al. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet. 2006, 2:e222.
30. Grishkevich V., et al. A genomic bias for genotype-environment interactions in C. elegans. Mol. Syst. Biol. 2012, 8:587.
31. Hodgins-Davis A., Townsend J.P. Evolving gene expression: from G to E to G×E. Trends Ecol. Evol. 2009, 24:649-658.
32. Rifkin S.A., et al. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet. 2003, 33:138-144.
33. Yanai I., Hunter C.P. Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved. Genome Res. 2009, 19:2214-2220.
34. Khaitovich P., et al. A neutral model of transcriptome evolution. PLoS Biol. 2004, 2:E132.
35. Tirosh I., et al. A genetic signature of interspecies variations in gene expression. Nat. Genet. 2006, 38:830-834.
36. Tirosh I., Barkai N. Two strategies for gene regulation by promoter nucleosomes. Genome Res. 2008, 18:1084-1091.
37. Kemphues K. Essential genes. WormBook 2005, 10.1895/wormbook.1.57.1.
38. Landry C.R., et al. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene 2006, 366:343-351.
39. Landry C.R., et al. Genetic properties influencing the evolvability of gene expression. Science 2007, 317:118-121.
40. Rifkin S.A., et al. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature 2005, 438:220-223.
41. Denver D.R., et al. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nat. Genet. 2005, 37:544-548.
42. Promislow D. A regulatory network analysis of phenotypic plasticity in yeast. Am. Nat. 2005, 165:515-523.
43. Harbison C.T., et al. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431:99-104.
44. Runcie D.E., et al. Genetics of gene expression responses to temperature stress in a sea urchin gene network. Mol. Ecol. 2012, 21:4547-4562.
45. Idaghdour Y., et al. Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nat. Genet. 2010, 42:62-67.
46. Yvert G., et al. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet. 2003, 35:57-64.
47. Schadt E.E., et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 2003, 422:297-302.
48. Hubner N., et al. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat. Genet. 2005, 37:243-253.
49. Bystrykh L., et al. Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nat. Genet. 2005, 37:225-232.
50. Chesler E.J., et al. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat. Genet. 2005, 37:233-242.
51. DeCook R., et al. Genetic regulation of gene expression during shoot development in Arabidopsis. Genetics 2006, 172:1155-1164.
52. Morley M., et al. Genetic analysis of genome-wide variation in human gene expression. Nature 2004, 430:743-747.
53. Cheung V.G., et al. Mapping determinants of human gene expression by regional and genome-wide association. Nature 2005, 437:1365-1369.
54. Wang S., et al. Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet. 2006, 2:e15.
55. Wittkopp P.J., et al. Evolutionary changes in cis and trans gene regulation. Nature 2004, 430:85-88.
56. Wittkopp P.J., et al. Regulatory changes underlying expression differences within and between Drosophila species. Nat. Genet. 2008, 40:346-350.
57. Smith E.N., Kruglyak L. Gene-environment interaction in yeast gene expression. PLoS Biol. 2008, 6:e83.
58. Tirosh I., et al. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 2009, 324:659-662.
59. Tirosh I., et al. Extensive divergence of yeast stress responses through transitions between induced and constitutive activation. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:16693-16698.
60. Ihmels J., et al. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 2005, 309:938-940.
61. Via S., et al. Adaptive phenotypic plasticity: consensus and controversy. Trends Ecol. Evol. 1995, 10:212-217.
62. Lande R. Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation. J. Evol. Biol. 2009, 22:1435-1446.
63. Waddington C.H. Genetic assimilation. Adv. Genet. 1961, 10:257-293.
64. Waddington C.H. Canalization of development and the inheritance of acquired characters. Nature 1942, 150:563-565.
65. Losos J.B., et al. Evolutionary implications of phenotypic plasticity in the hindlimb of the lizard Anolis sagrei. Evolution 2000, 54:301-305.
66. Sword G.A. A role for phenotypic plasticity in the evolution of aposematism. Proc. Biol. Sci. 2002, 269:1639-1644.
67. Gurevitch J. Sources of variation in leaf shape among two populations of Achillea lanulosa. Genetics 1992, 130:385-394.
68. Pigliucci M., et al. Phenotypic plasticity and evolution by genetic assimilation. J. Exp. Biol. 2006, 209:2362-2367.
69. Pfennig D.W., et al. Phenotypic plasticity's impacts on diversification and speciation. Trends Ecol. Evol. 2010, 25:459-467.
70. Minelli A., Fusco G. Developmental plasticity and the evolution of animal complex life cycles. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2010, 365:631-640.
71. Moczek A.P., et al. The role of developmental plasticity in evolutionary innovation. Proc. Biol. Sci. 2011, 278:2705-2713.
72. Levin M., et al. Developmental milestones punctuate gene expression in the Caenorhabditis embryo. Dev. Cell 2012, 22:1101-1108.
73. Yanai I., et al. Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility. Dev. Cell 2011, 20:483-496.
74. Sommer R.J. Evolution of development in nematodes related to C. elegans. WormBook 2005, 10.1895/wormbook.1.46.1.
75. Sommer R.J., Streit A. Comparative genetics and genomics of nematodes: genome structure, development, and lifestyle. Annu. Rev. Genet. 2011, 45:1-20.
76. Capra E.J., et al. Comparative developmental expression profiling of two C. elegans isolates. PLoS ONE 2008, 3:e4055.
77. Viñuela A., et al. Genome-wide gene expression regulation as a function of genotype and age in C. elegans. Genome Res. 2010, 20:929-937.
78. Viñuela A., et al. Aging uncouples heritability and expression-QTL in Caenorhabditis elegans. G3 2012, 2:597-605.
79. Davidson E.H. Emerging properties of animal gene regulatory networks. Nature 2010, 468:911-920.
80. Peter I.S., Davidson E.H. Evolution of gene regulatory networks controlling body plan development. Cell 2011, 144:970-985.
81. Kalinka A.T., et al. Gene expression divergence recapitulates the developmental hourglass model. Nature 2010, 468:811-814.
82. Domazet-Lošo T., Tautz D. A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 2010, 468:815-818.
83. Arbeitman M.N., et al. Gene expression during the life cycle of Drosophila melanogaster. Science 2002, 297:2270-2275.
84. Jones A.R., et al. The Allen Brain Atlas: 5 years and beyond. Nat. Rev. Neurosci. 2009, 10:821-828.
85. Hashimshony T., et al. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2012, 2:666-673.
86. Burga A., Lehner B. Beyond genotype to phenotype: why the phenotype of an individual cannot always be predicted from their genome sequence and the environment that they experience. FEBS J. 2012, 279:3765-3775.