The genome strikes back: The evolutionary importance of defence against mobile elements

Evolutionary Biology

Volumn 34, Issue 3-4, 2007, Pages 121-129

  Johnson, Louise J ^a  

^a UNIVERSITY OF READING   (United Kingdom)

Author keywords

Epigenetics; Evolution of genetic systems; Intragenomic conflict; Transposable elements

Indexed keywords

EID: 61349094203     PISSN: 00713260     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11692-007-9012-5     Document Type: Article

References (84)

1. Agrawal, N., & Dasaradhi, P., et al. (2003). RNA interference: Biology, mechanism, and applications. Microbiology and Molecular Biology Reviews, 67(4), 657-688.
2. Antonovics, J., & Abrams, J. (2004). Intratetrad mating and the evolution of linkage relationships. Evolution, 58(4), 72-709.
3. Arkhipova, I., & Meselson, M. (2000). Transposable elements in sexual and ancient asexual taxa. Proceedings of the National Academy Sciences United States of America, 97(26), 14473-14477.
4. Arkhipova, I., & Meselson, M. (2004). Deleterious transposable elements and the extinction of asexuals. Bioessays, 27, 76-85.
5. Barlow, D. P. (1993) Methylation and imprinting: From host defense to gene regulation? Science, 260(5106), 309-310.
6. Bergman, C. M., et al. (2006) Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila Melanogaster genome. Genome Biology, 7:R112. doi: 10.1186/Gb-2006-7-11-R112.
7. Bernstein, E., & Allis, C. (2005). RNA meets chromatin. Genes and Development, 19, 1635-1655.
8. Braun, F. N., & Liberles, D. A. (2004). Repeat-modulated population genetic effects in fungal proteins. Journal of Molecular Evolution, 59, 97-102.
9. Brookfield, J. F. Y. (1986). The population biology of transposable elements. Philosophical Transactions of the Royal Society of London Series B, 312(1154), 217-226.
10. Brookfield, J. F. Y. (1991). Models of repression of transposition in P-M hybrid dysgenesis by P cytotype and by zygotically encoded repressor proteins. Genetics, 128, 471-486.
11. Brookfield, J. F. Y. (2005). The ecology of the genome: Mobile DNA elements and their hosts. Nature Reviews Genetics, 6(2), 128-136.
12. Brookfield, J. F. Y., & Badge, R. M. (1997). Population genetics models of transposable elements. Genetica, 100, 281-294.
13. Burt, A. (2003). Site-specific selfish genes as tools for the control and genetic engineering of natural populations. Proceedings of the Royal Society of London Series B-Biological Sciences, 270, 921-928.
14. Cambareri, E. B., Singer, M. J. et al. (1991). Recurrence of repeat-induced point mutation (RIP) in Neurospora crassa. Genetics, 127(4), 699-710.
15. Cameron, J., & Loh, E., et al. (1979). Evidence for transposition of dispersed repetitive DNA families in yeast. Cell, 16, 739-751.
16. Chakalova, L., Debrand, E. et al. (2005). Replication and transcription: Shaping the landscape of the genome. Nature Reviews Genetics, 6, 669-677.
17. Chan, S. W.-L. et al. (2005). Gardening the genome: DNA methylation in Arabidopsis Thaliana. Nature Reviews Genetics, 6, 351-360.
18. Charlesworth, B., Charlesworth, D. et al. (2003). The effects of genetic and geographic structure on neutral variation. Annual Review Of Ecology and Systematics, 34, 99-125.
19. Charlesworth, B., & Langley, C. H. (1989). The population genetics of drosophila transposable elements. Annual Review of Genetics, 23, 251-287.
20. Cheng, X. (1995). Structure and function of DNA methyltransferases. Annual Review of Biophysics and Biomolecular Structure, 24, 293-318.
21. Clark, J. B., & Kidwell, M. G. (1997). A phylogenetic perspective on P transposable element evolution in Drosophila. Proceedings of the National Academy of Sciences USA, 11428-11433.
22. Clutterbuck, A. (2004). MATE transposable elements in Aspergillus nidulans: Evidence of repeat-induced point mutation. Fungal Genetics and Biology, 41, 308-316.
23. Colot, V., & Rossignol, J.-L. (1999). Eukaryotic DNA methylation as an evolutionary device. Bioessays, 21, 402-411.
24. Daboussi, M.-J., & Capy, P. (2003). Transposablde elements in filamentous fungi. Annual Review Of Microbiology, 57, 275-299.
25. Daboussi, M.-J., Daviere, J.-M. et al. (2002). Evolution of the Fot1 transposons in the genus Fusarium: Discontinuous distribution and epigenetic inactivation. Molecular Biology and Evolution, 19, 510-520.
26. Daniels, S. B. et al. (1990). Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics, 124, 339-255.
27. Deininger, P. L., Batzer, M. A. et al. (1992). Master genes in mammalian repetitive DNA amplification. Trends in Genetics, 8(9), 307-311.
28. Dimitri, P., Corradini, N., et al. (2005). The paradox of functional heterochromatin. Bioessays, 27, 29-41.
29. Edwards, R. J., & Brookfield, J. F. Y. (2003). Transiently beneficial insertions could maintain mobile DNA sequences in variable environments. Molecular Biology and Evolution, 20, 30-37.
30. Engels, W. (1997). Invasions of P elements. Genetics, 145, 11-15.
31. Fincham, J. R. S., et al. (1989). Premeiotic disruption of duplicated and triplicated copies of the Neurospora crassa Am (Glutamate Dehydrogenase) gene. Current Genetics, 15, 327-334.
32. Finnegan, D. J. (1992) Transposable elements. Current Opinion in Genetics and Development, 2(6), 861-867.
33. Freitag, M., & Selker, E. U. (2005). Controlling DNA methylation: Many roads to one modification. Current Opinion in Genetics and Development, 15, 191-199.
34. Galagan, J. A., Calvo, S. E., et al. (2003). The genome sequence of the filamentous fungus Neurospora crassa. Nature, 422, 859-868.
35. Galagan, J. A., & Selker E. U. (2004). RIP: The evolutionary cost of genome defense. Trends in Genetics, 20(9), 417-423.
36. Goddard, M. R., & Burt, A. (1999). Recurrent invasion and extinction of a selfish gene. Proceedings of the National Academy of Sciences of the United States of America, 96(24), 13880-13885.
37. Gutierrez, A., & Sommer, R. (2004). Evolution of Dnmt-2 and Mbd-2-like genes in the free-living Nematodes pristionchus pacificus, Caenorhabditis Elegans and Caenorhabditis Briggsae. Nucleic Acids Research, 32, 6388-6396.
38. Hamann, A., Feller, F., et al. (2000). The degenerate DNA transposon Pat and repeat-induced point mutation (RIP) in Podospora anserina. Molecular and General Genetics, 263, 1061-1069.
39. Hastings, I. M. (1994). Selfish DNA as a method of pest control. Philosophical Transactions of the Royal Society of London Series B, 344, 313-324.
40. Hastings, I. M. (1999). The costs of sex due to deleterious intracellular parasites. Journal Of Evolutionary Biology, 12(1), 177-183.
41. Hirochika, H., Okamoto, H. et al. (2000). Silencing of retrotransposons in arabidopsis and reactivation by the Ddm1 mutation. Plant Cell, 12, 357-368.
42. Hood, M. E. (2005). Repetitive DNA in the automictic fungus Microbotryum violaceum. Genetica, 124(1), 1-10.
43. Hurst, G. D. D., Hurst, L. D. et al. (1992). Intranuclear conflict and its role in evolution. Trends in Ecology and Evolution, 7(11), 373-378.
44. Huttenhofer, A. et al. (2005). Non-coding RNAs: Hope or hype? Trends of Genetics, 21, 289-297.
45. Ikeda, K., Nakayashiki, H. et al. (2002). Repeat-induced point mutation (RIP) in Magnaporthe grisea: Implications for its sexual cycle in the natural field environment. Molecular Microbiology, 45(5), 1355-1364.
46. Janowski, B. A. et al. (2007). Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nature Chemical Biology, 3, 166-173.
47. Jia, D., Jurkowska R. Z., Zhang, X., Jeltsch, A., & Cheng, X. (2007) Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature, 449, 248-251.
48. Johnson, J. M., Edwards, S. et al. (2005). Dark matter in the genome: Evidence of widespread transcrition detected by microarray tiling experiments. Trends in Genetics, 21(2), 93-104.
49. Johnson, L. J. et al. (2005). The evolution of intratetrad mating rates. Evolution, 59(12), 2525-2532.
50. Jones, P. A., & Takai, D. (2001). The role of DNA methylation in mammalian epigenetics. Science, 293, 1068-1070.
51. Jordan, I. K., & Mcdonald, J. F. (1999). Tempo and mode of Ty element evolution in Saccharomyces cerevisiae. Genetics, 151, 1341-1351.
52. Josse, T., Teysset, L., et al. (2007). Telomeric trans-silencing: An epigenetic repression combining RNA silencing and heterochromatin formation. PLOS Genetics. doi: 10.1371/Journal.Pgen.0030158.Eor.
53. Kato, M., Takashima, K. et al. (2004). Epigenetic control of CACTA transposon mobility in Arabidopsis Thaliana. Genetics, 168, 961-969.
54. Kazazian, H. H. (1998) Mobile elements and disease. Current Opinion in Genetics Development, 8(3), 343-350.
55. Kidwell, M. G., & Lisch, D. R. (2001). Transposable elements, parasitic DNA and genome evolution. Evolution, 55(1), 1-24.
56. Kinsey, J. A., & Helber, J. (1989). Isolation of a transposable element from Neurospora crassa. Proceedings of the National Academy of Sciences United States of America, 86, 1929-1933.
57. Klose, R. J., & Bird, A. P. (2006) Genomic DNA methylation: The mark and its mediators. Trends of Biochemical Science, 31, 89-97.
58. Koufopanou, V., Goddard, M. R. et al. (2002). Adaptation for horizontal transfer in a homing endonuclease. Molecular Biology and Evolution, 19(3), 239-246.
59. Langley, C. H., Montgomery, E. et al. (1988). On the role of unequal exchange in the containment of transposable element copy number. Genetical Research, 52(3), 223-235.
60. Levine E, Zhang Z, Kuhlman T, Hwa, T (2007) Quantitative characteristics of gene regulation by small RNA. PLoS Biology, 5(9), e229.
61. Li, E. et al. (1992). Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell, 69, 915-926.
62. Martello, G. et al. (2007) MicroRNA control of nodal signalling. Nature, 449, 183-189.
63. Mette, M., Van Der Winden, J. et al. (2002). Short RNAs can identify new candidate transposable element families in Arabidopsis. Plant Physiology, 130, 6-9.
64. Nagy, J., Victor, E. et al. (2007). Why don't all whales have cancer? A novel hypothesis resolving Peto's Paradox. Integrative and Comparative Biology, 47, 317-328.
65. Naumov, G. I., Naumova, E. S., & Sniegowski, P. D. (1998). Saccharomyces paradoxus and Saccharomyces cerevisiae are associated with exudates of North American oaks. Canadian Journal of Microbiology, 44(11), 1045-1050.
66. Nee, S., & Smith, J. M. (1990). The evolutionary biology of molecular parasites. Parasitology, 100, S5-S18.
67. Ng, H.-H., & Bird A. (1999). DNA methylation and chromatin modification. Current Opinion in Genetics and Development, 9, 158-163.
68. Noubissi, F. K., Aparna, K. et al. (2001). Evidence for dominant suppression of repeat-induced point mutation (RIP) in crosses with the wild-isolated Neurospora crassa strains sugartown and adiopodoume-7. Journal of Genetics, 80, 55-61.
69. Nuzhdin, S. V., & Petrov D. A. (2003). Transposable elements in clonal lineages: Lethal hangover from sex. Biological Journal of the Linnaean Society, 79, 33-41.
70. Petrov, D. A., & Hartl D. L. (1997). Trash DNA is what gets thrown away:high rate of DNA loss in Drosophila. Gene, 205, 279-289.
71. Promislow, D. et al. (1999) Genomic demography: A life-history analysis of transposable element evolution. Proceedings of the Royal Society of London Series B, 266, 1555-1560.
72. Robertson, H. M. (1995). The Tc1-mariner superfamily of transposons in animals. Journal of Insect Physiology, 41, 99-105.
73. Rowold, D. J., & Herrera, R. J. (2000). Alu elements and the human genome. Genetica, 108(1), 57-72.
74. Selker, E. U. (1990). Premeiotic instability of repeated sequences in Neurospora crassa. Annual Review of Genetics, 24, 579-613.
75. Selker E. U. (2002). Repeat-induced gene silencing in fungi. Advances in Genetics, 46, 439-450.
76. Selker, E. U., & Garrett P. (1988). DNA sequence duplications trigger gene inactivation in Neurospora crassa. Proceedings of National Academy Sciences United States of America, 85, 6870-6874.
77. Suzuki S., Ono R., Narita T., Pask A. J., Shaw G., et al. (2007) Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genetics, 3(4), e55.
78. Vastenhouw, N., Fischer, S. et al. (2003). A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans. Current Biology, 13, 1311-1316.
79. Vinogradov, A. E. (2003). Selfish DNA is Maladaptive; evidence from the plant red list. Trends in Genetics, 19(11), 609-614.
80. Yao, M.-C., & Chao, L.-J. (2005). RNA-guided DNA deletion in tetrahymena: An RNAi-based mechanism for programmed genome rearrangements. Annual Review of Genetics, 39, 537-559.
81. Yi, S., & Streelman, T. (2005). Genome size is negatively correlated with effective population size in ray-finned fish. Trends In Genetics, 21, 643-646.
82. Yoder, J. A. (1997). Cytosine methylation and the ecology of intragenomic parasites. Trends of Genetics, 13(8), 335-340.
83. Zilberman, D. et al. (2003). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology, 14, 1214-1220.
84. Zhang, X., et al. (2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell, 126(6), 1189-1201.