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Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements

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Transposons and the Dynamic Genome

Part of the book series: Genome Dynamics and Stability ((GENOME,volume 4))

Abstract

All genomes contain, to a greater or lesser extent, sequences that do not seem to be beneficial. The most preeminent group consists of transposable elements (TEs). These repeated DNA sequences have a significant influence on genome dynamics and evolution. One of the main challenges facing modern molecular evolution is to understand and measure their impact on evolution. The aim of this paper is to establish the relevance and contribution of population studies, as well as the species comparative approaches, to understanding the dynamics of TEs. Most of the examples cited concern the species Drosophila melanogaster, since this is one of the genetic key-model organisms, for which an enormous amount of data has been collected over a period of 100 years of genetic research, and which represents a genus for which the genomes of 12 species have been sequenced.

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References

  1. Aminetzach YT, Macpherson JM, Petrov DA (2005) Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila. Science 309:764–767

    PubMed  CAS  Google Scholar 

  2. Aravin AA, Hannon GJ, Brennecke J (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318:761–764

    PubMed  CAS  Google Scholar 

  3. Bassett DE Jr, Basrai MA, Connelly C, Hyland KM, Kitagawa K, Mayer ML, Morrow DM, Page AM, Resto VA, Skibbens RV, Hieter P (1996) Exploiting the complete yeast genome sequence. Curr Opin Genet Dev 6:763–766

    PubMed  CAS  Google Scholar 

  4. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D (2004) Ultraconserved elements in the human genome. Science 304:1321–1325

    PubMed  CAS  Google Scholar 

  5. Berdasco M, Fraga MF, Esteller M (2009) In: Tost J (ed) Quantification of global DNA methylation by capillary electrophoresis and mass spectrometry DNA methylation methods and protocols, 2nd edn. Springer Protocols, The Netherlands, pp 23–34

    Google Scholar 

  6. Biémont C, Monti-Dedieu L, Lemeunier F (2004) Detection of transposable elements in Drosophila salivary gland polytene chromosomes by in situ hybridization. Methods Mol Biol 260:21–28

    PubMed  Google Scholar 

  7. Biémont C, Nardon C, Decelière G, Lepetit D, Loevenbruck C, Vieira C (2003) Worldwide distribution of transposable element copy number in natural populations of Drosophila simulans. Evolution 57:159–167

    PubMed  Google Scholar 

  8. Biémont C, Tsitrone A, Vieira C, Hoogland C (1997) Transposable element distribution in Drosophila. Genetics 147:1997–1999

    PubMed  Google Scholar 

  9. Biémont C (1994) Dynamic equilibrium between insertion and excision of P elements in highly inbred lines from an M′ strain of Drosophila melanogaster. J Mol Evol 39:466–472

    PubMed  Google Scholar 

  10. Biémont C, Lemeunier F, Garcia Guerreiro MP, Brookfield JF, Gautier C, Aulard S, Pasyukova EG (1994) Population dynamics of the copia, mdg1, mdg3, gypsy, and P transposable elements in natural populations of Drosophila melanogaster. Genet Res 63:197–212

    PubMed  Google Scholar 

  11. Boissinot S, Furano AV (2005) The recent evolution of human L1 retrotransposons. Cytogenet Genome Res 110:402–406

    PubMed  CAS  Google Scholar 

  12. Bowen NJ, McDonald JF (2001) Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res 11:1527–1540

    PubMed  CAS  Google Scholar 

  13. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128:1089–1103

    PubMed  CAS  Google Scholar 

  14. Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ (2008) An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322:1387–1392

    PubMed  CAS  Google Scholar 

  15. Bridges CB (1935) Salivary chromosome maps: with a key to the banding of the chromosomes of Drosophila melanogaster. J Hered 26:60–64

    Google Scholar 

  16. Buchon N, Vaury C (2006) RNAi: a defensive RNA-silencing against viruses and transposable elements. Heredity 96:195–202

    PubMed  CAS  Google Scholar 

  17. Buratowski S, Moazed D (2005) Gene regulation: expression and silencing coupled. Nature 435:1174–1175

    PubMed  CAS  Google Scholar 

  18. Cavalli G, Paro R (1999) Epigenetic inheritance of active chromatin after removal of the main transactivator. Science 286:955–958

    PubMed  CAS  Google Scholar 

  19. Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6:590

    CAS  Google Scholar 

  20. Clark JB, Maddison WP, Kidwell MG (1994) Phylogenetic analysis supports horizontal transfer of P transposable elements. Mol Biol Evol 11:40–50

    PubMed  CAS  Google Scholar 

  21. Conley AB, Miller WJ, Jordan IK (2008) Human cis natural antisense transcripts initiated by transposable elements. Trends Genet 24:53–56

    PubMed  CAS  Google Scholar 

  22. Cordaux R, Hedges DJ, Herke SW, Batzer MA (2006a) Estimating the retrotransposition rate of human Alu elements. Gene 373:134–137

    PubMed  CAS  Google Scholar 

  23. Cordaux R, Lee J, Dinoso L, Batzer MA (2006b) Recently integrated Alu retrotransposons are essentially neutral residents of the human genome. Gene 373:138–144

    PubMed  CAS  Google Scholar 

  24. Costas J, Valade E, Naveira H (2001) Amplification and phylogenetic relationships of a subfamily of blood, a retrotransposable element of Drosophila. J Mol Evol 52:342–350

    PubMed  CAS  Google Scholar 

  25. Crow JF, Simmons MJ (1983) The mutation load in Drosophila. In: Carson HL, Ashburner M, Thomson JN (eds) The genetics and biology of Drosophila. Academic Press, London, pp 1–35

    Google Scholar 

  26. Cuzin F, Grandjean V, Rassoulzadegan M (2008) Inherited variation at the epigenetic level: paramutation from the plant to the mouse. Curr Opin Genet Dev 18:193–196

    PubMed  CAS  Google Scholar 

  27. Desset S, Buchon N, Meignin C, Coiffet M, Vaury C (2008) In Drosophila melanogaster the COM locus directs the somatic silencing of two retrotransposons through both Piwi-dependent and independent pathways. PLoS ONE 2:e1526

    Google Scholar 

  28. Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203–218

    Google Scholar 

  29. Eickbush TH, Furano AV (2002) Fruit flies and humans respond differently to retrotransposons. Curr Opin Genet Dev 12:669–674

    PubMed  CAS  Google Scholar 

  30. Engels WR (1997) Invasions of P elements. Genetics 145:11–15

    PubMed  CAS  Google Scholar 

  31. Engels WR, Preston SR (1980) Components of hybrid dysgenesis in a wild population of Drosophila melanogaster. Genetics 95:111–128

    PubMed  CAS  Google Scholar 

  32. Fablet M, McDonald JF, Biémont C, Vieira C (2006) Ongoing loss of the tirant transposable element in natural populations of Drosophila simulans. Gene 375:54–62

    PubMed  CAS  Google Scholar 

  33. Fablet M, Rebollo R, Biémont C, Vieira C (2007a) The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes. Gene 390:84–91

    PubMed  CAS  Google Scholar 

  34. Fablet M, Souames S, Biémont C, Vieira C (2007b) Evolutionary pathways of the tirant LTR retrotransposon in the Drosophila melanogaster subgroup of species. J Mol Evol 64:438–447

    PubMed  CAS  Google Scholar 

  35. Fedoroff N, Botstein D (1992) The dynamic genomeBarbara McClintock's ideas in the century of genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  36. Feschotte C, Pritham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331–368

    PubMed  CAS  Google Scholar 

  37. Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5:103–107

    PubMed  CAS  Google Scholar 

  38. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811

    PubMed  CAS  Google Scholar 

  39. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suner D, Cigudosa JC, Urioste M, Benitez J, Boix-Chornet M, Sanchez-Aguilera A, Ling C, Carlsson E, Poulsen P, Vaag A, Stephan Z, Spector TD, Wu YZ, Plass C, Esteller M (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 102:10604–10609

    PubMed  CAS  Google Scholar 

  40. Gall JG, Pardue ML (1969) Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci USA 63:378–383

    PubMed  CAS  Google Scholar 

  41. Gao X, Hou Y, Ebina H, Levin HL, Voytas DF (2008) Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res 18:359–369

    PubMed  CAS  Google Scholar 

  42. Gendrel AV, Lippman Z, Yordan C, Colot V, Martienssen RA (2002) Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297:1871–1873

    PubMed  CAS  Google Scholar 

  43. Goldberg AD, Allis CD, Bernstein E (2007) Epigenetics: a landscape takes shape. Cell 128:635–638

    PubMed  CAS  Google Scholar 

  44. Goodstadt L, Ponting CP (2006) Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput Biol 29:e133

    Google Scholar 

  45. Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A, Grewal SI (2002) Establishment and maintenance of a heterochromatin domain. Science 297:2232–7

    PubMed  CAS  Google Scholar 

  46. Hellman A, Chess A (2007) Gene body-specific methylation on the active X chromosome. Science 315:1141–3

    PubMed  CAS  Google Scholar 

  47. Herrera RJ, Lowery RK, Alfonso A, McDonald JF, Luis JR (2006) Ancient retroviral insertions among human populations. J Hum Genet 51:353–362

    PubMed  CAS  Google Scholar 

  48. Hiraizumi Y, Slatko B, Langley C, Nill A (1973) Recombination in Drosophila melanogaster male. Genetics 73:439–444

    PubMed  CAS  Google Scholar 

  49. Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG et al (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science 298:129–149

    PubMed  CAS  Google Scholar 

  50. Honeybee Genome Sequencing Consortium (2006) Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443:931–49

    Google Scholar 

  51. Hoogland C, Biémont C (1996) Chromosomal distribution of transposable elements in Drosophila melanogaster: test of the ectopic recombination model for maintenance of insertion site number. Genetics 144:197–204

    PubMed  CAS  Google Scholar 

  52. Hoskins RA, Carlson JW, Kennedy C, Acevedo D, Evans-Holm M, Frise E, Wan KH, Park S, Mendez-Lago M, Rossi F, Villasante A, Dimitri P, Karpen GH, Celniker SE (2007) Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science 316:1625–1628

    PubMed  CAS  Google Scholar 

  53. Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945

    Google Scholar 

  54. Huijser P, Kirchhoff C, Lankenau DH, Hennig W (1988) Retrotransposon-like sequences are expressed in Y chromosomal lampbrush loops of Drosophila hydei. J Mol Biol 203:689–697

    PubMed  CAS  Google Scholar 

  55. Jablonka E, Lamb MJ (2002) The changing concept of epigenetics. Ann NY Acad Sci 981:82–96

    Article  PubMed  Google Scholar 

  56. Jeltsch A, Nellen W, Lyko F (2006) Two substrates are better than one: dual specificities for Dnmt2 methyltransferases. Trends Biochem Sci 31:306–308

    PubMed  CAS  Google Scholar 

  57. Jordan IK, McDonald JF (1999) Tempo and mode of Ty element evolution in Saccharomyces cerevisiae. Genetics 151:1341–1351

    PubMed  CAS  Google Scholar 

  58. Jordan IK, McDonald JF (1998) Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements. J Mol Evol 47:14–20

    PubMed  CAS  Google Scholar 

  59. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97:6603–6607

    PubMed  CAS  Google Scholar 

  60. Kapitonov VV, Jurka J (2008) A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 9:411–412; author reply 414

    PubMed  Google Scholar 

  61. Kapitonov VV, Jurka J (2005) RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3:e181

    PubMed  Google Scholar 

  62. Kavi HH, Fernandez HR, Xie W, Birchler JA (2005) RNA silencing in Drosophila. FEBS Lett 579:5940–9

    PubMed  CAS  Google Scholar 

  63. Kawamura Y, Saito K, Kin T, Ono Y, Asai K, Sunohara T, Okada TN, Siomi MC, Siomi H (2008) Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453:793–797

    PubMed  CAS  Google Scholar 

  64. Kazazian HH Jr (1998) Mobile elements and disease. Curr Opin Genet Dev 8:343–350

    PubMed  CAS  Google Scholar 

  65. Kidwell MG, Kidwell JF, Sved JA (1977) Hybrid dysgenesis in Drosophila melanogaster: a syndrome of aberrant traits, including mutation, sterility and male recombination. Genetics 86:813–833

    PubMed  CAS  Google Scholar 

  66. Kidwell MG (1977) Reciprocal differences in female recombination associated with hybrid dysgenesis in Drosophila melanogaster. Genet Res 30:77–88

    Article  PubMed  CAS  Google Scholar 

  67. Kucharski R, Maleszka J, Foret S, Maleszka R (2008) Nutritional control of reproductive status in honeybees via DNA methylation. Science 319:1827–1830

    PubMed  CAS  Google Scholar 

  68. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    PubMed  CAS  Google Scholar 

  69. Langley CH, Montgomery E, Hudson R, Kaplan N, Charlesworth B (1988) On the role of unequal exchange in the containment of transposable element copy number. Genet Res 52:223–235

    PubMed  CAS  Google Scholar 

  70. Lankenau S, Corces VG, Lankenau DH (1994) The Drosophila micropia retrotransposon encodes a testis-specific antisense RNA complementary to reverse transcriptase. Mol Cell Biol 14:1764–1775

    PubMed  CAS  Google Scholar 

  71. Lankenau DH, Huijser P, Jansen E, Miedema K, Hennig W (1990) DNA sequence comparison of micropia transposable elements from Drosophila hydei and Drosophila melanogaster. Chromosoma 99:111–117

    PubMed  CAS  Google Scholar 

  72. Lankenau DH, Huijser P, Jansen E, Miedema K, Hennig W (1988) Micropia : a retrotransposon of Drosophila combining structural features of DNA viruses, retroviruses and non-viral transposable elements. J Mol Biol 204:233–246

    PubMed  CAS  Google Scholar 

  73. Le Rouzic A, Decelière G (2005) Models of the population genetics of transposable elements. Genet Res 85:171–181

    PubMed  Google Scholar 

  74. Lerat E, Capy P, Biémont C (2002a) The relative abundance of dinucleotides in transposable elements in five species. Mol Biol Evol 19:964–967

    PubMed  CAS  Google Scholar 

  75. Lerat E, Capy P, Biémont C (2002b) Codon usage by transposable elements and their host genes in five species. J Mol Evol 54:625–637

    PubMed  CAS  Google Scholar 

  76. Lerat E, Rizzon C, Biémont C (2003) Sequence divergence within transposable element families in the Drosophila melanogaster genome. Genome Res 13:1889–1896

    PubMed  CAS  Google Scholar 

  77. Lim AK, Kai T (2007) Unique germ-line organelle, nuage, functions to repress selfish genetic elements in Drosophila melanogaster. Proc Natl Acad Sci USA 104:6714–6719

    PubMed  CAS  Google Scholar 

  78. Lipatov M, Lenkov K, Petrov DA, Bergman CM (2005) Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol 3:24

    PubMed  Google Scholar 

  79. Lyko F (2001) DNA methylation learns to fly. Trends Genet 17:169–72

    PubMed  CAS  Google Scholar 

  80. Lyko F, Ramsahoye BH, Jaenisch R (2000) DNA methylation in Drosophila melanogaster. Nature 408:538–40

    PubMed  CAS  Google Scholar 

  81. Macas J, Neumann P, Navratilova A (2007) Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics 8:427

    PubMed  Google Scholar 

  82. Macpherson JM, González J, Witten DM, Davis JC, Rosenberg NA, Hirsh AE, Petrov DA (2008) Nonadaptive explanations for signatures of partial selective sweeps in Drosophila. Mol Biol Evol 25:1025–1042

    PubMed  CAS  Google Scholar 

  83. Malik HS, Eickbush TH (2001) Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res 11:1187–1197

    PubMed  CAS  Google Scholar 

  84. Malik HS, Burke WD, Eickbush TH (1999) The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol 16:793–805

    PubMed  CAS  Google Scholar 

  85. Malik HS, Eickbush TH (1999) Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J Virol 73:5186–5190

    PubMed  CAS  Google Scholar 

  86. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman, et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    PubMed  CAS  Google Scholar 

  87. Marhold J, Rothe N, Pauli A, Mund C, Kuehle K, Brueckner B, Lyko F (2004) Conservation of DNA methylation in dipteran insects. Insect Mol Biol 13:117–123

    PubMed  CAS  Google Scholar 

  88. Martens JH, O'Sullivan RJ, Braunschweig U, Opravil S, Radolf M, Steinlein P, Jenuwein T (2005) The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J 24:800–812

    PubMed  CAS  Google Scholar 

  89. Mathews LM, Chi SY, Greenberg N, Ovchinnikov I, Swergold GD (2003) Large differences between LINE-1 amplification rates in the human and chimpanzee lineages. Am J Hum Genet 72:739–748

    PubMed  CAS  Google Scholar 

  90. Matranga C, Zamore PD (2007) Small silencing RNAs. Curr Biol 17:R789–93

    PubMed  CAS  Google Scholar 

  91. Matyunina LV, Jordan IK, McDonald JF (1996) Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation. Proc Natl Acad Sci USA 93:7097–102

    PubMed  CAS  Google Scholar 

  92. McClintock B (1984) The significance of responses of the genome to challenge. Science 226:792–801

    PubMed  CAS  Google Scholar 

  93. McClintock B (1950) The origin and behavior of mutable loci in maize. Proc Natl Acad Sci USA 36:344–355

    PubMed  CAS  Google Scholar 

  94. McCollum AM, Ganko EW, Barass PA, Rodriguez JM, McDonald JF (2002) Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene. BMC Evol Biol 2:5

    PubMed  Google Scholar 

  95. McDonald JF, Matyunina LV, Wilson S, Jordan IK, Bowen NJ and Miller WJ (1997) LTR retrotransposons and the evolution of eukaryotic enhancers. Genetica 100:3–13

    PubMed  CAS  Google Scholar 

  96. Mhanni AA, McGowan RA (2004) Global changes in genomic methylation levels during early development of the zebrafish embryo. Dev Genes Evol 214:412–417

    PubMed  CAS  Google Scholar 

  97. Miller WJ, McDonald JF, Pinsker W (1997) Molecular domestication of mobile elements. Genetica 100:261–270

    PubMed  CAS  Google Scholar 

  98. Morgan TH, Sturtevant AH, Muller HJ, Bridges CB (1915) The mechanisms of Mendelian heredity. H Holt and Co, New York

    Google Scholar 

  99. Mugnier N, Biémont C, Vieira C (2005) New regulatory regions of Drosophila 412 retrotransposable element generated by recombination. Mol Biol Evol 22:747–757

    PubMed  CAS  Google Scholar 

  100. Mugnier N, Gueguen L, Vieira C, Biémont C (2008) The heterochromatic copies of the LTR retrotransposons as a record of the genomic events that have shaped the Drosophila melanogaster genome. Gene 411:87–93

    PubMed  CAS  Google Scholar 

  101. Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z et al (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science 316:1718–1723

    PubMed  CAS  Google Scholar 

  102. Nuzhdin SV, Mackay TFC (1995) The genomic rate of transposable elements movement in Drosophila melanogaster. Mol Biol Evol 12:180–181

    PubMed  CAS  Google Scholar 

  103. Pane A, Wehr K, Schüpbach T (2007) Zucchini and squash encode two putative nucleases required for rasiRNA production in the Drosophila germline. Dev Cell 12:851–862

    PubMed  CAS  Google Scholar 

  104. Pardue ML, Gall JG (1969) Molecular hybridization of radioactive DNA to the DNA of cytological preparations. Proc Natl Acad Sci USA 64:600–604

    PubMed  CAS  Google Scholar 

  105. Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D, Knowles BB (2004) Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell 7:597–606

    PubMed  CAS  Google Scholar 

  106. Pélisson A, Sarot E, Payen-Groschene G, Bucheton A (2007) A novel repeat-associated small interfering RNA-mediated silencing pathway downregulates complementary sense gypsy transcripts in somatic cells of the Drosophila ovary. J Virol 81:1951–60

    PubMed  Google Scholar 

  107. Picard G (1976) Non-mendelian female sterility in Drosophila melanogaster: hereditary transmission of the I factor. Genetics 1983:107–123

    Google Scholar 

  108. Ponger L, Li WH (2005) Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. Mol Biol Evol 22:1119–1128

    PubMed  CAS  Google Scholar 

  109. Pradhan S, Esteve PO (2003) Mammalian DNA (cytosine-5) methyltransferases and their expression. Clin Immunol 109:6–16

    PubMed  CAS  Google Scholar 

  110. Rebollo R, Lerat E, Kleine Lopez L, Biémont C, Vieira C (2008) Losing helena: the extinction of a Drosophila LINE-like element. BMC Genomics 9:149

    PubMed  Google Scholar 

  111. Reik W (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447:425–32

    PubMed  CAS  Google Scholar 

  112. Richards EJ (2008) Population epigenetics. Curr Opin Genet Dev 18:221–226

    PubMed  CAS  Google Scholar 

  113. Saedler H, Starlinger P (1992) Twenty-five years of transposable element research in Köln. In: Fedoroff N, Botstein D (eds) The dynamic genome. Cold Spring Harbor, Cold Spring Harbor, pp 243–263

    Google Scholar 

  114. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45

    PubMed  CAS  Google Scholar 

  115. Schaefer M, Lyko F (2007) DNA methylation with a sting: an active DNA methylation system in the honeybee. Bioessays 29:208–211

    PubMed  CAS  Google Scholar 

  116. Shapiro JA (1969) Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli. J Mol Biol 40:93–105

    PubMed  CAS  Google Scholar 

  117. Silva JC, Kidwell MG (2004) Evolution of P elements in natural populations of Drosophila willistoni and D. sturtevanti. Genetics 168:1323–1335

    PubMed  CAS  Google Scholar 

  118. Simmons MJ, Raymond JD, Grimes CD, Belinco C, Haake BC, Jordan M, Lund C, Ojala TA, Papermaster D (1996) Repression of hybrid dysgenesis in Drosophila melanogaster by heat-shock-inducible sense and antisense P-element constructs. Genetics 144:1529–1544

    PubMed  CAS  Google Scholar 

  119. Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8:272–285

    PubMed  CAS  Google Scholar 

  120. Soper SFC, van der Heijden GW, Hardiman TC, Goodheart M, Martin SL, de Boer P, Bortvin A (2008) Mouse Maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. Dev Cell 15:285–297

    PubMed  CAS  Google Scholar 

  121. Suh DS, Choi EH, Yamazaki T, Harada K (1995) Studies on the transposition rates of mobile genetic elements in a natural population of Drosophila melanogaster. Mol Biol Evol 12:748–758

    PubMed  CAS  Google Scholar 

  122. Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genetics 9:465–476

    CAS  Google Scholar 

  123. Taft JR, Mattick JS (2003) Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding sequences. Genome Biol 5:P1

    Google Scholar 

  124. Thompson JN Jr, Woodruff RC (1980) Increased mutation in crosses between geographically separated strains of Drosophila melanogaster. Proc Natl Acad Sci USA 77:1059–1062

    PubMed  Google Scholar 

  125. Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S (2005) Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol 6:R90

    PubMed  Google Scholar 

  126. Tribolium Genome Sequencing Consortium (2008) The genome of the model beetle and pest Tribolium castaneum. Nature 452:949–955

    Google Scholar 

  127. Vagin VV, Klenov MS, Kalmykova AI, Stolyarenko AD, Kotelnikov RN and Gvozdev VA (2004) The RNA interference proteins and vasa locus are involved in the silencing of retrotransposons in the female germline of Drosophila melanogaster. RNA Biol 1:54–8

    PubMed  CAS  Google Scholar 

  128. Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, Zamore PD (2006) A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313:320–4

    PubMed  CAS  Google Scholar 

  129. Vaughn MW, Tanurdžić M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, Dedhia N, McCombie WR, Agier N, Bulski A, Colot V, Doerge RW and Martienssen RA (2007) Epigenetic Natural Variation in Arabidopsis thaliana. PLoS Biol 5:e174

    PubMed  Google Scholar 

  130. Vieira C, Biémont C (2004) Transposable element dynamics in two sibling species Drosophila melanogaster and Drosophila simulans. Genetica 120:115–123

    PubMed  CAS  Google Scholar 

  131. Vieira C, Piganeau G, Biémont C (2000) High copy numbers of multiple transposable element families in an Australian population of Drosophila simulans. Genet Res 76:117–119

    PubMed  CAS  Google Scholar 

  132. Vieira C, Lepetit D, Dumont S, Biémont C (1999) Wake up of transposable elements following Drosophila simulans worldwide colonization. Mol Biol Evol 16:1251–1255

    PubMed  CAS  Google Scholar 

  133. Vieira C, Aubry P, Lepetit D, Biémont C (1998) A temperature cline in copy number for 412 but not roo/B104 retrotransposons in populations of Drosophila simulans. Proc Biol Sci 265:1161–1165

    PubMed  CAS  Google Scholar 

  134. Vieira C, Biémont C (1997) Transposition rate of the 412 retrotransposable element is independent of copy number in natural populations of Drosophila simulans. Mol Biol Evol 14:185–188

    PubMed  CAS  Google Scholar 

  135. Vieira C, Biémont C (1996) Geographical variation in insertion site number of retrotransposon 412 in Drosophila simulans. J Mol Evol 42:443–451

    PubMed  CAS  Google Scholar 

  136. Volff JN (2006) Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 28:913–922

    PubMed  CAS  Google Scholar 

  137. Wang Y, Jorda M, Jones PL, Maleszka R, Ling X, Robertson HM, Mizzen CA, Peinado MA, Robinson GE (2006) Functional CpG methylation system in a social insect. Science 314:645–647

    PubMed  CAS  Google Scholar 

  138. Weil C, Martienssen R (2008) Epigenetic interactions between transposons and genes: lessons from plants. Curr Opin Genet Dev 18:188–192

    PubMed  CAS  Google Scholar 

  139. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982

    PubMed  CAS  Google Scholar 

  140. Wilson S, Matyunina LV, McDonald JF (1998) An enhancer region within the copia untranslated leader contains binding sites for Drosophila regulatory proteins. Gene 209:239–46

    PubMed  CAS  Google Scholar 

  141. Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, et al (2004) A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 306:1937–1940

    PubMed  Google Scholar 

  142. Zhai J, Liu J, Liu B, Li P, Meyers BC, Chen X, Cao X (2008) Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genet 4:e1000056

    PubMed  Google Scholar 

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Authors and Affiliations

  1. Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, 69622, Villeurbanne, France

    Cristina Vieira, Marie Fablet & Emmanuelle Lerat

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  1. Cristina Vieira
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  2. Marie Fablet
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  3. Emmanuelle Lerat
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Correspondence to Cristina Vieira .

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Dirk-Henner Lankenau Jean-Nicolas Volff

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Vieira, C., Fablet, M., Lerat, E. (2009). Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements. In: Lankenau, DH., Volff, JN. (eds) Transposons and the Dynamic Genome. Genome Dynamics and Stability, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/7050_2009_044

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