Predominant gain of promoter TATA box after gene duplication associated with stress responses

Molecular Biology and Evolution

Volumn 28, Issue 10, 2011, Pages 2893-2904

  Zou, Yangyun ^a   Huang, Wei ^a   Gu, Zhenglong ^c   Gu, Xun ^a,b,d  

^a FUDAN UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

^c Department of Molecular Biology and Genetics   (United States)

^d IOWA STATE UNIVERSITY   (United States)

Author keywords

environmental stress; expression divergence; gene duplication; gene family; maximum parsimony; TATA box

Indexed keywords

TATA BINDING PROTEIN;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; ENVIRONMENTAL STRESS; GENE DUPLICATION; GENE EXPRESSION; GENETIC ASSOCIATION; HUMAN; NONHUMAN; STRESS; YEAST;

ANIMALS; ARABIDOPSIS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENOME; HUMANS; INVERTEBRATES; PHYLOGENY; STRESS, PHYSIOLOGICAL; TATA BOX; YEASTS;

ARABIDOPSIS; EUKARYOTA;

EID: 80053215814     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr116     Document Type: Article

References (80)

1. Basehoar AD, Zanton SJ, Pugh BF. 2004. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116:699-709. (Pubitemid 38326728)
2. Blanc G, Hokamp K, Wolfe KH. 2003. A recent polyploidy superimposed on older large-scale duplications in the Arabi-dopsis genome. Genome Res. 13:137-144. (Pubitemid 36575763)
3. Blanc G, Wolfe KH. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell. 16:1667-1678. (Pubitemid 38908767)
4. Byrne KP, Wolfe KH. 2005. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15:1456-1461. (Pubitemid 41400914)
5. Chain FJ, Ilieva D, Evans BJ. 2008. Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization. BMC Evol Biol. 8:43.
6. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. 1998. The transcriptional program of sporulation in budding yeast. Science 282:699-705. (Pubitemid 28489376)
7. Cunningham CW, Omland KE, Oakley TH. 1998. Reconstructing ancestral character states: a critical reappraisal. Trends Ecol Evol. 13:361-366. (Pubitemid 28385525)
8. Dennis G Jr., Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4:P3.
9. Dujon B. 2006. Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet. 22:375-387. (Pubitemid 44015974)
10. Dujon B, Sherman D, Fischer G, et al. 2004. (67 co-authors). Genome evolution in yeasts. Nature 430:35-44. (Pubitemid 38915217)
11. Ekman S, Andersen HL, Wedin M. 2008. The limitations of ancestral state reconstruction and the evolution of the ascus in the Lecanorales (lichenized Ascomycota). Syst Biol. 57:141-156.
12. Farris JS. 1970. Methods for computing wagner trees. Syst Zool. 19:83-92.
13. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
14. Felsentein J. 1973. Maximum-likelihood and minimum-steps methods for estimating evolutionary trees from discrete characters. Syst Zool. 22:240-249.
15. Fitch MW. 1971. Toward defining the course of evolution: minimum change for a specified tree topology. Syst Zool. 20:406-416.
16. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545. (Pubitemid 29177561)
17. Frumhoff PC, Reeve HK. 1994. Using phylogenies to test hypotheses of adaptation: a critique of some current proposals. Evolution 48:172-180. (Pubitemid 2113203)
18. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 11:4241-4257.
19. Gu X, Zhang Z, Huang W. 2005. Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc Natl Acad Sci USA. 102:707-712. (Pubitemid 40282730)
20. Gu Z, Nicolae D, Lu HHS, Li W-H. 2002. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18:609-613. (Pubitemid 35346678)
21. Gu Z, Rifkin SA, White KP, Li W-H. 2004. Duplicate genes increase gene expression diversity within and between species. Nat Genet. 36:577-579. (Pubitemid 38715982)
22. Guan Y, Dunham MJ, Troyanskaya OG. 2006. Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics 175: 933-943.
23. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704. (Pubitemid 37365050)
24. Ha M, Kim E-D, Chen ZJ. 2009. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci USA. 106:2295-2300.
25. Ha M, Li W-H, Chen ZJ. 2007. External factors accelerate expression divergence between duplicate genes. Trends Genet. 23:162-166. (Pubitemid 46509543)
26. Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH. 2008. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 148:993-1003. (Pubitemid 352847556)
27. Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinfor-matics resources. Nat Protoc. 4:44-57.
28. Huelsenbeck JP, Rannala B, Masly JP. 2000. Accommodating phylogenetic uncertainty in evolutionary studies. Science 288: 2349-2350. (Pubitemid 30448155)
29. Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755. (Pubitemid 32851390)
30. Huisinga KL, Pugh BF. 2004. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol Cell. 13:573-585. (Pubitemid 38299384)
31. Huminiecki L, Wolfe KH. 2004. Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res. 14:1870-1879. (Pubitemid 39386500)
32. Innan H, Kondrashov F. 2010. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 11:97-108.
33. Jermann TM, Opitz JG, Stackhouse J, Benner SA. 1995. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 374:57-59.
34. Kim Y, Lee JH, Babbitt GA. 2010. The enrichment of TATA box and the scarcity of depleted proximal nucleosome in the promoters of duplicated yeast genes. J Mol Evol. 70:69-73.
35. Kondrashov FA, Kondrashov AS. 2006. Role of selection in fixation of gene duplications. J Theor Biol. 239:141-151.
36. Kondrashov FA, Koonin EV. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet. 20:287-290.
37. Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL. 2007. Genetic properties influencing the evolvability of gene expression. Science 317:118-121. (Pubitemid 47056469)
38. Leach LJ, Zhang Z, Lu C, Kearsey MJ, Luo Z. 2007. The role of cis-regulatory motifs and genetical control of expression in the divergence of yeast duplicate genes. Mol Biol Evol. 24:2556-2565. (Pubitemid 350060456)
39. Leschen RA, Buckley TR. 2007. Multistate characters and diet shifts: evolution of Erotylidae (Coleoptera). Syst Biol. 56:97-112.
40. Li J, Musso G, Zhang Z. 2008. Preferential regulation of duplicated genes by microRNAs in mammals. Genome Biol. 9:R132
41. Li W-H, Yang J, Gu X. 2005. Expression divergence between duplicate genes. Trends Genet. 21:602-607. (Pubitemid 41429288)
42. Li Z, Zhang H, Ge S, Gu X, Gao G, Luo J. 2009. Expression pattern divergence of duplicated genes in rice. BMC Bioinformatics. 10(Suppl 6):S8.
43. Lynch M, Force A. 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459-473. (Pubitemid 30045935)
44. Maddison WP, Maddison DR. 1992. MaClade: analysis of phylogeny and character evolution. Sunderland (MA): Sinauer Associates.
45. Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y. 2005. Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci USA. 102:5454-5459. (Pubitemid 40530279)
46. Makino T, McLysaght A. 2010. Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proc Natl Acad Sci USA. 107:9270-9274.
47. Makova KD, Li WH. 2003. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 13:1638-1645. (Pubitemid 36874481)
48. Moore RC, Purugganan MD. 2005. The evolutionary dynamics of plant duplicate genes. Curr Opin Plant Biol. 8:122-128. (Pubitemid 40323539)
49. Moran AL. 2004. Egg size evolution in tropical American arcid bivalves: the comparative method and the fossil record. Evolution 58:2718-2733. (Pubitemid 40084149)
50. Nikolski M, Sherman DJ. 2007. Family relationships: should consensus reign?-consensus clustering for protein families. Bioinformatics 23:e71-e76. (Pubitemid 46189638)
51. Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol. 302:205-217.
52. Ohno S. 1970. Evolution by gene duplication. New York: Springer-Verlag.
53. Orphanides G, Lagrange T, Reinberg D. 1996. The general transcription factors of RNA polymerase II. Genes Dev. 10:2657-2683. (Pubitemid 26384488)
54. Page RDM, Charleston MA. 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol Phylogenet Evol. 7:231-240. (Pubitemid 127345887)
55. Pagel M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst Biol. 48:612-622. (Pubitemid 129479567)
56. Pagel M, Meade A, Barker D. 2004. Bayesian estimation of ancestral character states on phylogenies. Syst Biol. 53:673-684. (Pubitemid 39579641)
57. Papp B, Pal C, Hurst LD. 2003. Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet. 19:417-422. (Pubitemid 36930023)
58. Qian W, Liao B-Y, Chang AY-F, Zhang J. 2010. Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends Genet. 26:425-430.
59. Rizzon C, Ponger L, Gaut BS. 2006. Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol. 2:e115.
60. Rodin SN, Parkhomchuk DV, Riggs AD. 2005. Epigenetic changes and repositioning determine the evolutionary fate of duplicated genes. Biochemistry(Mosc). 70:559-567. (Pubitemid 40920800)
61. Ronquist F. 2004. Bayesian inference of character evolution. Trends Ecol Evol. 19:475-481. (Pubitemid 39151667)
62. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
63. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
64. Schluter D. 1995. Uncertainty in ancient phylogenies. Nature 377:108-110.
65. Schultz TR, Cocroft RB, Churchill GA. 1996. The reconstruction of ancestral character states. Evolution 50:504-511. (Pubitemid 26483517)
66. Schulz TA, Creutz CE. 2004. The tricalbin C2 domains: lipid-binding properties of a novel, synaptotagmin-like yeast protein family. Biochemistry 43:3987-3995. (Pubitemid 38437065)
67. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 9:3273-3297. (Pubitemid 28551928)
68. Swofford DL, Maddison WP. 1987. Reconstructing ancestral character states under Wagner parsimony. Math Biosci. 87:199-229.
69. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 24:1596-1599. (Pubitemid 47236692)
70. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882. (Pubitemid 28022245)
71. Tirosh I, Berman J, Barkai N. 2007. The pattern and evolution of yeast promoter bendability. Trends Genet. 23:318-321. (Pubitemid 46962796)
72. Tirosh I, Weinberger A, Carmi M, Barkai N. 2006. A genetic signature of interspecies variations in gene expression. Nat Genet. 38:830-834. (Pubitemid 43980606)
73. Vanderpoorten A, Goffinet B. 2006. Mapping uncertainty and phylogenetic uncertainty in ancestral character state reconstruction: an example in the moss genus Brachytheciastrum. Syst Biol. 55:957-971.
74. Wagner A. 2000. Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate. Proc Natl Acad Sci USA. 97:6579-6584. (Pubitemid 30412756)
75. Wolfe KH, Shields DC. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713. (Pubitemid 27270611)
76. Yang Z, Nielsen R. 2000. Estimating synonymous and nonsynon-ymous substitution rates under realistic evolutionary models. Mol Biol Evol. 17:32-43. (Pubitemid 30056990)
77. Zhang Z, Gu J, Gu X. 2004. How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution? Trends Genet. 20:403-407. (Pubitemid 39094567)
78. Zheng D. 2008. Asymmetric histone modifications between the original and derived loci of human segmental duplications. Genome Biol. 9:R105.
79. Zou C, Lehti-Shiu MD, Thomashow M, Shiu SH. 2009a. Evolution of stress-regulated gene expression in duplicate genes of Arabi-dopsis thaliana. PLoS Genet. 5:e1000581.
80. Zou Y, Su Z, Yang J, Zeng Y, Gu X. 2009b. Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscape. J Exp Zool B Mol Dev Evol. 312B:722-733.