Is ectopic expression caused by deregulatory mutations or due to gene-regulation leaks with evolutionary potential?

BioEssays

Volumn 27, Issue 6, 2005, Pages 592-601

  Rodríguez Trelles, Francisco ^a,b   Tarrío, Rosa ^a,b   Ayala, Francisco J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDE OXIDASE; MESSENGER RNA;

DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; EVOLUTION; GENE ACTIVITY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; MUTATION; NATURAL SELECTION; NONHUMAN; PHYLOGENY; PROTEIN ELECTROPHORESIS; PSEUDOGENE; QUANTITATIVE TRAIT; REVIEW; RNA TRANSCRIPTION; TRANSCRIPTOMICS;

ANIMALS; CHORISTOMA; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; HUMANS; MODELS, GENETIC; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EUKARYOTA;

EID: 21244442329     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20241     Document Type: Review

References (103)

1. Emerson BM. 2003. Specificity of gene regulation. Cell 109:267-270.
2. Fisher RA. 1930. The Genetical Theory of Natural Selection. New York: Dover Press.
3. Haldane JBS. 1932. The Causes of Evolution. New York: Longman.
4. Schrödinger E. 1944. What is Life? Cambridge: Cambridge University Press.
5. Monod J. 1971. Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology. Translated from the French by Austryn Wainhouse. New York: Knopf.
6. Davidson EH. 2001. Genomic Regulatory Systems-Development and Evolution. San Diego: Academic Press.
7. Carroll SB, Grenier JK, Weatherbee SD. 2001. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design. Malden, MA: Blackwell Scientific.
8. Wilkins AS. 2002. The Evolution of Developmental Pathways. Sunderland MA: Sinauer Associates.
9. Akam M. 1998. Hox genes, homeosis and the evolution of segment identity: no need for hopeless monsters. Int J Dev Biol 42:445-451.
10. García-Bellido A. 1975. Genetic control of wing disc development in Drosophila. In Cell Patterning. Ciba Found Symp 29:161-178.
11. Morata G, Lawrence PA. 1977. Homeotic genes, compartments and cell determination in Drosophila. Nature 265:211-216.
12. Yanai I, Graur D, Ophir R. 2004. Incongruent expression profiles between human and mouse orthologous genes suggest widspread neutral evolution of transcription control. OMICS 8:15-24.
13. Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, et al. 2004. A neutral model of transcriptome evolution. PloS Biol 2:682-689.
14. Rodríguez-Trelles F. 2004. Transcriptome evolution: much ado about nothing? Heredity 93:405-406.
15. Dickinson WJ. 1988. On the architecture of regulatory systems: evolutionary insights and implications. Bioessays 8:204-208.
16. Spellman PT, Rubin GM. 2002. Evidence for large domains of similarly expressed genes in the Drosophila genome. BMC J Biol 1:5.1-5.8.
17. Dickinson WJ. 1980. Evolution of patterns of gene expression in Hawaiian Picture-winged Drosophila. J Mol Evol 16:73-94.
18. Powell JR, Rico M, Andjelkovic M. 1980. Population genetics of Drosophila amylase. Evolution 34:209-213.
19. Thorpe PA, Loye J, Rote CA, Dickinson WJ. 1993. Evolution of regulatory genes and patterns: relationships to evolutionary rates and to metabolic functions. J Mol Evol 37:590-599.
20. Morton RA, Singh RS. 1985. Biochemical properties, homology, and genetic variation of Drosophila 'nonspecific' esterases. Biochem Genet 23:959-973.
21. Ross J, Fong PP, Cavener DR. 1994. Coordinate evolution of the cis-acting regulatory elements and developmental expression of the Drosophila Gld gene in seven species from the melanogaster subgroup. Dev Genet 15:38-50.
22. Thorpe PA, Dickinson WJ. 1988. The use of regulatory patterns in constructing phylogenies. Syst Zool 37:97-105.
23. Bowers CW. 1994. Superfluous neurotransmitters? TINS 8:315-320.
24. Dickinson WJ, Sullivan DT. 1975. Gene-enzyme systems in Drosophila. New York: Springer.
25. Zuckerkandl E. 1978. Multilocus enzymes, gene regulation and genetic sufficiency. J Mol Evol 12:57-89.
26. Goebl MG, Petes TD. 1986. Most of the yeast genomic sequences are not essential for cell growth and division. Cell 46:983-992.
27. Kwiatowski J, Skarecky D, Tyler R, Pascual M, Ayala FJ. 1991. A truncated P element is inserted in the transcribed region of the Cu,Zn SOD gene of an SOD "null" strain of Drosophila melanogaster. Free Rad Res Comms 12-13:429-435.
28. Rossant J, Moens C, Skarnes W, Gasca S, Hill D, et al. 1991. Identification and mutation of developmentally regulated genes in the mouse. FASEB J 5:A783.
29. Erickson HP. 1993. Gene knockouts of c-src, Transforming Growth Factor β1, and Tenascin suggest superfluous, nonfunctional expression of proteins. J Cell Biol 120:1079-1081.
30. Cook DL, Gerber AN, Tapscott SJ. 1998. Modelling stochastic gene expression: implications for haploinsufficiency. Proc Natl Acad Sci USA 95:15641-15646.
31. Veitia RA. 2002. Exploring the etiology of haploinsufficiency. Bioessays 24:175-184.
32. Balakirev ES, Ayala FJ. 2003. Pseudogenes: are they "junk" or functional DNA? Ann Rev Genet 37:123-151.
33. Boger ET, Sellers JR, Friedman TB. 2001. Human myosin XVBP is a transcribed pseudogene. J Muscle Res Cell Motil 22:447-483.
34. Edgar AJ. 2002. The human L-threonine 3-dehydrogenase gene is an expressed pseudogene. BMC Genet 3:18.1-18.13.
35. Lande R. 1976. Natural selection and random genetic drift in phenotype evolution. Evolution 30:314-334.
36. Lynch M, Hill WG. 1986. Phenotypic evolution by neutral mutation. Evolution 40:915-935.
37. Lynch M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. Am Nat 136:246-256.
38. Cheetam AH, Jackson JBC, Hayec LC. 1993. Quantitative genetics of bryozoan phenotypic evolution. I. Rates for random change versus selection in differentiation of living species. Evolution 47:1526-1538.
39. Felsenstein J. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, MS.
40. Oleksiak MF, Churchill GA, Crawford DL. 2002. Variation in gene expression within and among natural populations. Nat Genet 32:261-266.
41. Rifkin SA, Kim J, White KP. 2003. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet 33:138-144.
42. Uddin M, Wildman DE, Liu G, Xu W, Johnson RM, et al. 2004. Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. Proc Natl Acad Sci USA 101:2957-2962.
43. Felsenstein J. 1985. Phylogenies and the comparative method. Am Nat 125:1-15.
44. Arnason U, Gullberg A, Burgeuete AS, Janke A. 2000. Molecular estimates of primate divergences and new hypotheses for primate dispersal and the origin of modern humans. Hereditas 133:217-228.
45. Rodríguez-Trelles F, Tarrío R, Ayala FJ. 2002. A methodological bias toward overestimation of molecular evolutionary timescales. Proc Natl Acad Sci USA 99:8112-8115.
46. Graur D, Martin W. 2003. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. TIG 20:80-86.
47. Podlaha O, Zhang JZ. 2004. Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice. Mol Biol Evol 21:2202-2209.
48. 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.
49. 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.
50. Enard W, Khaitovich P, Klose J, Zollner S, Heissing F, et al. 2002. Intra- and interspecific variation in primate gene expression patterns. Science 296:340-343.
51. Gu J, Gu X. 2003. Induced gene expression in human brain after the split from chimpanzee. TIG 19:63-65.
52. Karaman MW, Houck ML, Chemnick LG, Nagpal S, Chawannakul D, et al. 2003. Comparative analysis of gene-expression patterns in human and African great ape cultured fibroblasts. Genome Research 13:1619-1630.
53. Wray GA, Hahn MW, Abouheif A, Balhoff JP, Pizer M, et al. 2003. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20:1377-1419.
54. Keightley PD, Lercher MJ, Eyre-Walker A. 2005. Evidence for widespread degradation of gene control regions in hominid genomes. Plos Biol 3:2e42.
55. Gu Z, Nicolae D, Lu HH-S, Li W-H. 2002. Rapid divergence in expression between duplicate genes inferred from microarray data. TIG 18:609-613.
56. Gu Z, Rifkin SA, White KP, Li W-H. 2004. Duplicate genes increase diversity within and between species. Nat Genet 36:577-579.
57. 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.
58. Duboule D, Wilkins AS. 1998. The evolution of 'bricolage'. TIG 14:54-58.
59. Stone JR, Wray GA. 2001. Rapid evolution of cis-regulatory sequences via local point mutations. Mol Biol Evol 18:1764-1770.
60. MacArthur S, Brookfield JFY. 2004. Expected rates and modes of evolution of enhancer sequences. Mol Biol Evol 21:1064-1073.
61. Rockman MV, Wray GA. 2002. Abundant raw material for cis-regulatory evolution in humans. Mol Biol Evol 19:1981-1990.
62. Tournamille C, Colin Y, Cartron JP, Kim CLV. 1995. Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals. Nat Genet 10:224-228.
63. Labie D, Pagnier J, Lapoumeroulie C, Roubahi F, Dunda-Belkhodia O, et al. 1985. Common haplotype dependency of high G gamma-globin gene expression and high Hb F levels in beta-thalassemia and sickle cell anemia patients. Proc Natl Acad Sci USA 82:2111-2114.
64. Lomvardas S, Thanos D. 2002. Modifying gene expression programs by altering core promoter chromatin architecture. Cell 110:261-271.
65. Kadam S, Emerson BM. 2002. Mechanisms of chromatin assembly and transcription. Curr Opin Cell Biol 14:262-268.
66. Cunliffe VT. 2003. Memory by modification: the influence of chromatin structure on gene expression during vertebrate development. Gene 305:141-150.
67. Gasser SM. 2001. Positions of potential: nuclear organization and gene expression. Cell 104:639-642.
68. Gierer A. 1973. Molecular models and combinatorial principles in cell differentiation and morphogenesis. Cold Spring Harbor Symp Quant Biol 38:951-961.
69. Kauffman SA. 1981. Pattern formation in the Drosophila embryo. Phil Trans Roy Soc Lond B 295:567-595.
70. Echols H. 1986. Multiple DNA-rpotein interactions governing high-precision DNA transactions. Science 233:1050-1056.
71. Ghazi A, VijayRaghavan K. 2000. Control by combinatorial codes. Nature 408:419-420.
72. Buchler N, Gerland U, Hwa T. 2003. On schemes of combinatorial transcription logic. Proc Natl Acad Sci USA 100:5136-5141.
73. Tsong AE, Miller MG, Raisner RM, Johnson AD. 2003. Evolution of a combinatorial transcriptional circuit: a case study in yeasts. Cell 115:389-399.
74. Travers A. 1993. DNA-Protein Interactions. London: Chapman and Hall.
75. Latchman DS. 1998. Eukaryotic Transcription Factors. San Diego: Academic Press.
76. Arnone MI, Davidson EH. 1997. The hardwiring of development: organization and function of genomic regulatory systems. Development 124:1851-1864.
77. Levine M, Tjian R. 2003. Transcription regulation and animal diversity. Nature 424:147-151.
78. De Laat W, Grosveld F. 2003. Spatial organization of gene expression: the active chromatin hyb. Chromosome Res 11:447-459.
79. Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA. 2004. Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14:283-291.
80. Fourel G, Magdinier F, Gilson E. 2002. Insulator dynamics and the setting of chromatin domains. Bioessays 26:523-532.
81. Mattick JS. 2003. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25:930-939.
82. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, et al. 2002. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296:916-919.
83. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, et al. 2004. Unbiased Mapping of Transcription Factor Binding Sites Along Human Chromosomes 21 and 22 Points to Widespread Regulation of Non-Coding RNAs. Cell 116:499-511.
84. Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, et al. 2004. Novel RNAs Identified from an In-depth Analysis of the Transcriptome of Human Chromosomes 21 and 22. Genome Res 14:331-342.
85. Johnson JM, Edwards S, Shoemaker D, Schadt EE. 2005. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. TIG 21:93-102.
86. Tatcher JW, Shaw JM, Dickinson WJ. 1998. Marginal fitness contributions of nonessential genes in yeast. Proc Natl Acad Sci USA 95:253-257.
87. Rolfe DFS, Brown GC. 1997. Cellular energy utilization and molecular origin of standard metabolic rate in mammals. Physiological Reviews 77:731-758.
88. Glick BR. 1995. Metabolic load and heterologous expression. Biotechnology Advances 13:247-261.
89. Storey KB, Storey JM. 2004. Metabolic rate depression in animals: transcriptional and translational controls. Biol Rev 79:207-233.
90. Akashi H. 2001. Gene expression and molecular evolution. Curr Opin Genet Dev 11:660-666.
91. Rodríguez-Trelles F, Tarrío R, Ayala FJ. 2003. Evolution of cis-regulatory regions versus codifying regions. Int J Dev Biol 47:665-673.
92. Bird AP. 1995. Gene number, noise reduction and biological complexity. TIG 11:94-100.
93. Lynch M, Conery JS. 2003. The origins of genome complexity. Science 302:1401-1404.
94. Saccone S, Federico C, Bernardi G. 2002. Localization of the gene-richest and the gene-poorest isochors in the interphase nuclei of mammals and birds. Gene 300:169-178.
95. Vinogradov AE. 2004. Compactness of human housekeeping genes: selection for economy or genomic design? TIG 20:248-253.
96. True JR, Carroll SB. 2002. Gene co-option in physiological and morphological evolution. Ann Rev Cell Dev 18:53-80.
97. Ohno S. 1970. Evolution by gene duplication. Springer-Verlag, NY.
98. Aharoni A, Gaidukov L, Khersonsky O, Gould SM, Roodveldt C, et al. 2005. The 'evolvability' of promiscuous protein functions. Nat Genet 37:73-76.
99. Kondrasov FA. 2005. In search of the limits of evolution. Nat Genet 37:9-10.
100. Rodríguez-Trelles F, Tarrío R, Ayala FJ. 2003. Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene. Proc Natl Acad Sci USA 100:13413-13417.
101. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
102. Lynch M, O'Hely M, Walsh B, Force A. 2001. The probability of preservation of a newly arisen gene duplicate. Genetics 159:1789-1804.
103. Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB. 2004. Noise minimization in eukaryotic gene expression. PLoS Biol 2:1-2.