Exploiting Gene Expression Variation to Capture Gene-environment Interactions for Disease

Overview

Journal Front Genet

Date 2013 Jun 12

PMID 23755064

Citations 15

Authors

Youssef Idaghdour

Philip Awadalla

Affiliations

Soon will be listed here.

Abstract

Gene-environment interactions have long been recognized as a fundamental concept in evolutionary, quantitative, and medical genetics. In the genomics era, study of how environment and genome interact to shape gene expression variation is relevant to understanding the genetic architecture of complex phenotypes. While genetic analysis of gene expression variation focused on main effects, little is known about the extent of interaction effects implicating regulatory variants and their consequences on transcriptional variation. Here we survey the current state of the concept of transcriptional gene-environment interactions and discuss its utility for mapping disease phenotypes in light of the insights gained from genome-wide association studies of gene expression.

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References

Heap G, Trynka G, Jansen R, Bruinenberg M, Swertz M, Dinesen L . Complex nature of SNP genotype effects on gene expression in primary human leucocytes. BMC Med Genomics. 2009; 2:1. PMC: 2628677. DOI: 10.1186/1755-8794-2-1. View

Wray G, Hahn M, Abouheif E, Balhoff J, Pizer M, Rockman M . The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol. 2003; 20(9):1377-419. DOI: 10.1093/molbev/msg140. View

Nica A, Parts L, Glass D, Nisbet J, Barrett A, Sekowska M . The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet. 2011; 7(2):e1002003. PMC: 3033383. DOI: 10.1371/journal.pgen.1002003. View

Smith E, Kruglyak L . Gene-environment interaction in yeast gene expression. PLoS Biol. 2008; 6(4):e83. PMC: 2292755. DOI: 10.1371/journal.pbio.0060083. View

Le Marchand L, Hankin J, Wilkens L, Pierce L, Franke A, Kolonel L . Combined effects of well-done red meat, smoking, and rapid N-acetyltransferase 2 and CYP1A2 phenotypes in increasing colorectal cancer risk. Cancer Epidemiol Biomarkers Prev. 2001; 10(12):1259-66. View

Barreiro L, Tailleux L, Pai A, Gicquel B, Marioni J, Gilad Y . Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. Proc Natl Acad Sci U S A. 2012; 109(4):1204-9. PMC: 3268270. DOI: 10.1073/pnas.1115761109. View

Hunter D . Gene-environment interactions in human diseases. Nat Rev Genet. 2005; 6(4):287-98. DOI: 10.1038/nrg1578. View

Kraft P, Hunter D . Integrating epidemiology and genetic association: the challenge of gene-environment interaction. Philos Trans R Soc Lond B Biol Sci. 2005; 360(1460):1609-16. PMC: 1569522. DOI: 10.1098/rstb.2005.1692. View

Idaghdour Y, Quinlan J, Goulet J, Berghout J, Gbeha E, Bruat V . Evidence for additive and interaction effects of host genotype and infection in malaria. Proc Natl Acad Sci U S A. 2012; 109(42):16786-93. PMC: 3479498. DOI: 10.1073/pnas.1204945109. View

10.

Emilsson V, Thorleifsson G, Zhang B, Leonardson A, Zink F, Zhu J . Genetics of gene expression and its effect on disease. Nature. 2008; 452(7186):423-8. DOI: 10.1038/nature06758. View

11.

Ege M, Strachan D, Cookson W, Moffatt M, Gut I, Lathrop M . Gene-environment interaction for childhood asthma and exposure to farming in Central Europe. J Allergy Clin Immunol. 2011; 127(1):138-44, 144.e1-4. DOI: 10.1016/j.jaci.2010.09.041. View

12.

Cortessis V, Thomas D, Levine A, Breton C, Mack T, Siegmund K . Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet. 2012; 131(10):1565-89. PMC: 3432200. DOI: 10.1007/s00439-012-1189-8. View

13.

Skelly D, Ronald J, Akey J . Inherited variation in gene expression. Annu Rev Genomics Hum Genet. 2009; 10:313-32. DOI: 10.1146/annurev-genom-082908-150121. View

14.

Stranger B, Montgomery S, Dimas A, Parts L, Stegle O, Ingle C . Patterns of cis regulatory variation in diverse human populations. PLoS Genet. 2012; 8(4):e1002639. PMC: 3330104. DOI: 10.1371/journal.pgen.1002639. View

15.

Heinzen E, Ge D, Cronin K, Maia J, Shianna K, Gabriel W . Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol. 2009; 6(12):e1. PMC: 2605930. DOI: 10.1371/journal.pbio.1000001. View

16.

Grundberg E, Small K, Hedman A, Nica A, Buil A, Keildson S . Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet. 2012; 44(10):1084-9. PMC: 3784328. DOI: 10.1038/ng.2394. View

17.

Landry C, Lemos B, Rifkin S, Dickinson W, Hartl D . Genetic properties influencing the evolvability of gene expression. Science. 2007; 317(5834):118-21. DOI: 10.1126/science.1140247. View

18.

Smirnov D, Morley M, Shin E, Spielman R, Cheung V . Genetic analysis of radiation-induced changes in human gene expression. Nature. 2009; 459(7246):587-91. PMC: 3005325. DOI: 10.1038/nature07940. View

19.

Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M . Mapping complex disease traits with global gene expression. Nat Rev Genet. 2009; 10(3):184-94. PMC: 4550035. DOI: 10.1038/nrg2537. View

20.

Kwan T, Grundberg E, Koka V, Ge B, C L Lam K, Dias C . Tissue effect on genetic control of transcript isoform variation. PLoS Genet. 2009; 5(8):e1000608. PMC: 2719916. DOI: 10.1371/journal.pgen.1000608. View