The evolution of gene regulatory interactions

BioScience

Volumn 60, Issue 1, 2010, Pages 15-23

  Garfield, David A ^a   Wray, Gregory A ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

Evolution; Gene expression; Gene networks; Gene regulation; Genomics

Indexed keywords

EID: 74549114711     PISSN: 00063568     EISSN: None     Source Type: Journal    
DOI: 10.1525/bio.2010.60.1.6     Document Type: Article

References (30)

1. Averof M, Patel NH. 1997. Crustacean appendage evolution associated with changes in Hox gene expression. Nature 388: 682-686.
2. Brem RB, Yvert G, Clinton R, Kruglyak L. 2002. Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
3. Brem RB, Storey JD, Whittle J, Kruglyak L. 2005. Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436: 701-703. (Pubitemid 41117272)
4. Clark AG, et al. 2003. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302: 1960-1963.
5. Cohn MJ, Tickle C. 1999. Developmental basis of limblessness and axial patterning in snakes. Nature 399: 474-479.
6. Fay JC, McCullough HL, Sniegowski PD, Eisen MB. 2004. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biology 5: R26.
7. Gilad Y, Rifkin SA, Pritchard JK. 2008. Revealing the architecture of gene regulation: The promise of eQTL studies. Trends in Genetics 24: 408-415.
8. Gilbert SC. 2006. Developmental Biology. Sinauer.
9. Gompel N, Prud'homme B, Wittkopp PJ, Kassner VA, Carroll SB. 2005. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433: 481-487.
10. Haygood R, Fedrigo O, Hanson B,Yokoyama KD, Wray GA. 2007. Promoter regions of many neural-and nutrition-related genes have experienced positive selection during human evolution. Nature Genetics 39: 1140-1144.
11. He Y,Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW. 2008. The antisense transcriptomes of human cells. Science 322: 1855-1857.
12. Hochachka PW, Somero GN. 2002. Biochemical Adaptation. Oxford University Press.
13. Holland PW, Hogan BL. 1988. Spatially restricted patterns of expression of the homeobox-containing gene Hox 2.1. during mouse embryogenesis. Development 102: 159-174.
14. Imai KS, Levine M, Satoh N, Satou Y. 2006. Regulatory blueprint for a chordate embryo. Science 312: 1183-1187.
15. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G. 2001. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nature Genetics 29: 389-395.
16. King MC, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
17. Lemons D, McGinnis W. 2006. Genomic evolution of Hox gene clusters. Science 313: 1918-1922.
18. Lettre G, et al. 2008. Identification of ten loci associated with height highlights new biological pathways in human growth. Nature Genetics 40: 584-591.
19. Lynch M, Walsh B. 1998. Genetics and Analysis of Quantitative Traits. Sinauer.
20. Nielsen R. 2005. Molecular signatures of natural selection. Annual Review of Genetics 39: 197-218.
21. Nielsen R, et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology 3: 976-985.
22. Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E. 2007. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nature Genetics 39: 730-732.
23. Oleksiak MF, Churchill GA, Crawford DL. 2002. Variation in gene expression within and among natural populations. Nature Genetics 32: 261-266.
24. Poustka AJ, Kuhn A, Groth D, Weise V, Yaguchi S, Burke RD, Herwig R, Lehrach H, Panopoulou G. 2007.A global view of gene expression in lithium and zinc treated sea urchin embryos: New components of gene regulatory networks. Genome Biology 8: R85.
25. Raff RA, Kaufman TC. 1983. Embryos, Genes, and Evolution: The Developmental-genetic Basis of Evolutionary Change. Macmillan.
26. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nature Biotechnology 26: 1135-1145.
27. Su YH, Li E, Geiss GK, Longabaugh WJ, Kramer A, Davidson EH. 2009. A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. Developmental Biology 329: 410-421.
28. Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: A revolutionary tool for transcriptomics. Nature Reviews Genetics 10: 57-63.
29. Weedon MN, et al. 2008. Genome-wide association analysis identifies 20 loci that influence adult height. Nature Genetics 40: 575-583.
30. Wray GA. 2007. The evolutionary significance of cis-regulatory mutations. Nature Reviews Genetics 8: 206-216.