Gene network polymorphism is the raw material of natural selection: The selfish gene network hypothesis

Journal of Molecular Evolution

Volumn 59, Issue 3, 2004, Pages 340-357

  Boldogköi, Zsolt ^a  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

Development; Gene network; Neuroscience; Polymorphism; Population genetics; Selfish gene

Indexed keywords

ALLELE; ARTICLE; BEHAVIOR; GENE; GENE NETWORK POLYMORPHISM; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC TRAIT; MOLECULAR EVOLUTION; PROMOTER REGION; SELFISH GENE;

ALLELES; EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; GENETICS, POPULATION; MODELS, GENETIC; POLYMORPHISM, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID; SELECTION (GENETICS);

EID: 4344679779     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-2629-4     Document Type: Article

References (97)

1. Averof M, Patel NH (1997) Crustacean appendage evolution associated with changes in Hox gene expression. Nature 388:682-686
2. Bailey A, Ledent C, Kelly M et al. (2002) Changes in spinal delta and kappa opioid systems in mice deficient in the A2A receptor gene. J Neurosci 22:9210-9220
3. Bejar R, Yasuda R, Krugers H et al. (2002) Transgenic calmodulin-dependent protein kinase II activation: Dose-dependent effects on synaptic plasticity, learning, and memory. J Neurosci 22:5719-5726
4. Belting HG, Shashikant CS, Ruddle FH (1998) Modification of expression and cis-regulation of Hoxc8 in the evolution of diverged axial morphology. Proc Natl Acad Sci USA 95:2355-2360
5. Bhan A, Galas DJ, Dewey TG (2002) A duplication growth model of gene expression networks. Bioinformatics 18:1486-1493
6. Blalock JE (1990) Complementarity of peptides specified by sense and antisense strand of DNA. Trends Biotechn 8:40-144
7. Boldogköi Z (2000) Coding in the noncoding DNA strand: A novel mechanism of gene evolution?. J Mol Evol 51:600-606
8. Boldogköi Z, Barta E (1999) Specific amino acid content and codon usage account for the existence of overlapping ORFS. Biosystems 51:95-100
9. Boldogköi Z, Murvai J (1994) A novel explanation for the existence of open reading frames on latency-associated transcripts of alphaherpesviruses. Virus Genes 9:47-51
10. Boldogköi Z, Nógrádi A (2003) Gene and cancer therapy - Pseudorabies virus: A novel research and therapeutic tool?. Curr Gene Ther 3:155-182
11. Boldogköi Z, Murvai J, Fodor I (1995) G and C accumulation at silent positions of codons produces additional ORFs. Trends Genet 1 1:125-126
12. Boldogköi Z, Schütz B, Sallach J et al. (2002) P2X(3) receptor expression at early stage of mouse embryogenesis. Mech Dev 118:255-260
13. Bonner JT (1988) The evolution of complexity. Princeton University Press, Princeton, NJ
14. Brown SJ, Patel NH, Denell RE (1994) Embryonic expression of the single Tribolium engrailed homolog. Dev Genet 15:7-18
15. Brown S, Holtzman S, Kaufman T et al. (1999) Characterization of the Tribolium Deformed ortholog and its ability to directly regulate Deformed target genes in the rescue of a Drosophila Deformed null mutant. Dev Genes Evol 209:389-398
16. Burrow CR (2000) Regulatory molecules in kidney development. Pediatr Nephrol 14:240-253
17. Bymaster FP, Zhang W, Carter PA et al. (2002) Fluoxetine, but not other selective serotonin uptake inhibitors, increases norepinephrine and dopamine extracellular levels in prefrontal cortex. Psychopharmacology 160:353-361
18. Calon F, Morissette M, Ghribi O et al. (2002) Alteration of glutamate receptors in the striatum of dyskinetic 1-methyl-4-phenyl-1,2,3,6- tetrahydropyridine-treated monkeys following dopamine agonist treatment. Prog Neuropsychopharmacol Biol Psychiatry 26:127-138
19. Cantile M, Procino A, D'armentino M et al. (2003) HOX gene network is involved in the transcriptional regulation of in vivo human adipogenesis. J Cell Physiol 194:225-236
20. Cebrat S, Dudek MR (1996) Generation of overlapping open reading frames. Trends Genet 12:12
21. Claverie J, Ogata H (2003) The insertion of palindromic repeats in the evolution of proteins. Trends Biochem Sci 28:75-80
22. Cowles CR, Hirschhorn JN, Altshuler D, Lander ES (2002) Detection of regulatory variation in mouse genes. Nat Genet 32:432-437
23. Cripps RM, Olson EN (2002) Control of cardiac development by an evolutionarily conserved transcriptional network. Dev Biol 246:14-28
24. Davidson EH, Rast JP, Olivery P et al. (2002) A genomic regulatory network for development. Science 295:1669-1678
25. Dawkins R (1976) The selfish gene Oxford University Press, Oxford
26. de la Pompa JL, Wakeham A, Correia KM et al. (1997) Conservation of the Notch signaling pathway in mammalian neurogenesis. Development 124:1139-1148
27. Delattre M, Felix MA (2001) Polymorphism and evolution of vulval precursor cell lineages within two nematode genera, Caenorhabditis and Oscheius. Curr Biol 11:631-643
28. Dickinson WJ (1980) Evolution of patterns of gene expression in hawaiian picture-winged Drosophila. J Mol Evol 16:73-94
29. Eldredge N, Gould SJ (1972) Punctuated equilibria: An alternative to phyletic gradualism In: Models in paleobiology, Freeman, Copper and Co., San Francisco
30. Erb C, Troost J, Kopf S et al. (2001) Compensatory mechanisms enhance hippocampal acetylcholine release in transgenic mice expressing human acetylcholinesterase. J Neurochem 77:638-646
31. Falciani F, Hausdorf B, Schroder R, Akam M, Tautz D, Denell R, Brown S (1996) Class 3 Hox genes in insects and the origin of zen. Proc Natl Acad Sci USA 93:8479-8484
32. Featherstone DE, Broadie K (2002) Wrestling with pleiotropy: Genomic and topological analysis of the yeast gene expression network. BioEssays 24:267-274
33. Félix MA, Sternberg PW (1997) Two nested gonadal inductions of the vulva in nematodes. Development 124:253-259
34. Félix MA, De Ley P, Sommer RJ, Frisse L, Nadler SA, Thomas WK, Vanfleteren J, Steraberg PW (2002) Evolution of vulva development in the Cephalobina (Nematoda). Dev Biol 221:68-86
35. Fisher RA (1930) The genetical theory of natural selection Oxford University Press, Oxford,
36. Galant R, Carroll SB (2002) Evolution of a transcriptional repression domain in an insect Hox protein. Nature 415:910-913
37. Galis F, van Dooren TJ, Metz JA (2002) Conservation of the segmented germband stage: robustness or pleiotropy?. Trends Genet 18:504-509
38. Gallet A, Angelats C, Kerridge S, Therond PP (2000) Cubitus interruptus-independent transduction of the Hedgehog signal in Drosophila. Development 127:5509-5522
39. Grbic M, Nagy LM, Carroll S B, Strand M (1996) Polyembryonic development: Insect pattern formation in a cellularized environment. Development 122:795-804
40. Gerlai R (1996) Gene-targeting studies of mammalian behavior: Is it the mutation or the background genotype?. Trends Neurosci 19:177-181
41. Grenier JK, Carroll SB (2000) Functional evolution of the Ultrabithorax protein. Proc Natl Acad Sci USA 97:704-709
42. Horton WA (2003) Skeletal development: insights from targeting the mouse genome. Lancet 362:560-569
43. Ihmels J, Friedlander G, Bergmann S et al. (2002) Revealing modular organization in the yeast transcriptional network. Nat Genet 31:370-377
44. Jareborg N, Birney E, Durbin R (1999) Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res 9:815-824
45. Jeong H, Tombor B, Albert R et al. (2000) The large-scale organization of metabolic networks. Nature 407:651-654
46. Keranen SV, Kettunen P, Aberg T et al. (1999) Gene expression patterns associated with suppression of odontogenesis in mouse and vole diastema regions. Dev Genes Evol 209:495-506
47. Kest B, Hopkins E, Palmese CA et al. (2001) Morphine tolerance and dependence in nociceptin/orphanin FQ transgenic knockout mice. Neuroscience 104:217-222
48. Keys DN, Lewis DL, Selegue JE et al. (1999) Recruitment of a hedgehog regulatory circuit in butterfly eyespot evolution. Science 283:532-534
49. Keyvani K, Witte OW, Reinecke S et al. (2002) Use-related gene expression patterns of rat motor cortex. Neuroreport 13:953-956
50. Kimura M (1968) Evolutionary rate at the molecular level. Nature 217:624-626
51. Lawrence JG, Roth JR (1996) Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843-1860
52. Liu A, Joyner AL, Turnbull DH (1998) Alteration of limb and brain patterning in early mouse embryos by ultrasound-guided injection of Shh-expressing cells. Mech Dev 75:107-115
53. Ludwig MZ, Bergman C, Patel NH et al. (2000) Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403:564-567
54. MacGowan GA, Du C, Wieczorek DF et al. (2001) Compensatory changes in Ca(2+) and myocardial O(2) consumption m beta-tropomyosin transgenic hearts. Am J Physiol Heart Circ Physiol 281:H2539-H2548
55. Middlemiss DN, Price GW, Watson JM (2002) Serotonergic targets in depression. Curr Opin Pharmacol 2:18-22
56. Mitchison NA, Muller B, Segal RM (2000) Natural variation in immune responsiveness, with special reference to immunodeficiency and promoter polymorphism in class II MHC genes. Hum Immunol 61:177-181
57. Mitsialis SA, Kafatos FC (1985) Regulatory elements controlling chorion gene expression are conserved between flies and moths. Nature 317:453-456
58. Müller H, Samanta R, Wieschaus E (1999) Wingless signaling in the Drosophila embryo: Zygotic requirements and the role of the frizzled genes. Development 126:577-586
59. Nieoullon A (2002) Dopamine and the regulation of cognition and attention. Prog Neurobiol 67:53-83
60. Okazaki Y et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420:563-573
61. Oleksiak MF, Churchill GA, Crawford DL (2002) Variation in gene expression within and among natural populations. Nat Genet 32:261-266
62. Patel NH, Kornberg TB, Goodman CS (1989) Expression of engrailed during segmentation in grasshopper and crayfish. Development 107:201-212
63. Patthy L (1999) Genome evolution of exon-shuffling - A review. Gene 238:103-114
64. Podani J, Oltvai ZN, Jeong H et al. (2001) Comparable system-level organization of Archaea and Eukaryotes. Nat Genet 29:54-56
65. Popper KR, Eccles JC (1986) The self and its brain Routledge, New York,
66. Raff R (1996) The shape of life development and the evolution of animal form University of Chicago Press, Chicago
67. Romano LA, Wray GA (2003) Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis- and trans-acting components of transcriptional regulation. Development 130:4187-4199
68. Ronshaugen M, McGinnis N, McGinnis W (2002) Hox protein mutation and macroevolution of the insect body plan. Nature 415:914-917
69. Rutherford SL, Lindquist S (1998) Hsp90 as a capacitor for morphological evolution. Nature 396:336-342
70. Schmid G, Wang ZQ, Wesierska-Gadek J (1999) Compensatory expression of p73 in PARP-deficient mouse fibroblasts as response to a reduced level of regularly spliced wild-type p53 protein. Biochem Biophys Res Commun 255:399-405
71. Schütz B, Weihe E, Eiden LE (2001) Independent patterns of transcription for the products of the rat cholinergic gene locus. Neuroscience 104:633-642
72. Shashikant CS, Kim CB, Borbely MA et al. (1998) Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element. Proc Natl Acad Sci USA 95:15446-15451
73. Simmonds AJ, Brook WJ, Cohen SM, Bell JB (1995) Distinguishable functions for engrailed and invected in anterior-posterior patterning in the Drosophila wing. Nature 376:424-427
74. Simpson GG (1944) Tempo and mode in evolution Columbia University Press, New York
75. Spitz F, Gonzalez F, Peichel C et al. (2001) Large scale transgenic and cluster deletion analysis of the HoxD complex separate an ancestral regulatory module from evolutionary innovations. Genes Dev 15:2209-2214
76. Steiner H, Bonner TI, Zimmer AM et al. (1999) Altered gene expression in striatal projection, neurons in CB1 cannabinoid receptor knockout mice. Proc Natl Acad Sci USA 96:5786-5790
77. Stephens JC, Schneider JA, Tanguay DA et al. (2001) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293:489-493
78. Stern MJ, Marengere LE, Daly RJ et al. (1993) The human GRB2 and Drosophila Drk genes can functionally replace the Caenorhabditis elegans cell signaling gene sem-5. Mol Biol Cell 4:1175-1188
79. Sucena E, Stern DL (2000) Divergence of larval morphology between Drosophila sechellia and its sibling species caused by cis-regulatory evolution of ovo/shaven-baby. Proc Natl Acad Sci USA 97:4530-4534
80. Takahashi H, Mitani Y, Satoh G et al. (1999) Evolutionary alterations of the minimal promoter for notochord-specific Brachyury expression in ascidian embryos. Development 126:3725-3734
81. Ting CT, Tsaur SC, Wu ML et al. (1998) A rapidly evolving homeobox at the site of a hybrid sterility gene. Science 282:1501-1504
82. True JR, Carroll SB (2002) Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol 18:53-80
83. Van Valen L (1973) A new evolutionary law. Evol Theory 1:1-30
84. von Dassow G, Munro E (1999) Modularity in animal development and evolution: elements of a conceptual framework for EvoDevo. J Exp Zool 285:307-325
85. von Dassow G, Meir E, Munro EM et al. (2000) The segment polarity network is a robust developmental module. Nature 406:188-192
86. Wagner GP (1996) Homologues, natural kinds and the evolution of modularity. American Zoologist 36:36-43
87. Wasserman WW, Palumbo M, Thompson W et al. (2000) Human-mouse genome comparisons to locate regulatory sites. Nat Genet 26:225-228
88. Waterston RH, Lindblad-Toh K, Birney E et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562
89. Weatherbee SD, Halder G, Kim J et al. (1998) Ultrabithorax regulates genes at several levels of the wing-patterning hierarchy to shape the development of the Drosophila haltere. Genes Dev 12:1474-1482
90. Wilson ME, Scheel D, German MS (2003) Gene expression cascades in pancreatic development. Mech Dev 120:65-80
91. Wyrick JJ, Young RA (2002) Deciphering gene expression regulatory networks. Curr Opin Genet Dev 12:130-136
92. Xu PX, Zhang X, Heaney S et al. (1999) Regulation of Pax6 expression is conserved between mice and flies. Development 126:383-395
93. Xue ZG, Xue XJ, Quox-l, LeDourin NM (1993) Quox-1, an Antp-like homeobox gene of the avian embryo: A developmental study using a Quox-1-specific antiserum. Mech Dev 43:149-158
94. Yelin R, Dahary D, Sorek R et al. (2003) Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 21:379-386
95. Young SN, Leyton M (2002) The role of serotonin in human mood and social interaction. Insight from altered tryptophan levels. Pharmacol Biochem Behav 71:857-865
96. Yomo T, Urabe I, Okada H (1992) No stop codons in the antisense strands of the genes for nylon oligomer degradation. Proc Natl Acad Sci USA 89:3780-3784
97. Zull JE, Smith SK (1990) Is genetic redundancy related to retention of structural information in both DNA strands?. Trends Biochem Sci 15:257-261