Abstracts
Résumé
Les SINE (short interspersed repetitive elements) sont des éléments mobiles de l’ADN dérivés principalement des ARN de transfert ou de l’ARN cytoplasmique 7SL. Ils forment une composante majeure du génome des eucaryotes, puisque leur nombre peut atteindre plus de 104 copies par génome. Aucune fonction évidente n’est encore aujourd’hui attribuée à ces éléments. Récemment, ces « ADN égoïstes » se sont révélés être des outils très efficaces en systématique moléculaire: en effet, l’insertion d’un SINE à un site donné est un événement unique et non réversible à l’échelle des génomes. Les SINE se révèlent ainsi des outils phylogénétiques « parfaits ». L’étude de la présence ou de l’absence de sites d’insertion de ces éléments transposables a récemment conduit à des résultats phylogénétiques inattendus. Les qualités et les limites de ce nouvel outil phylogénétique sont présentées dans cet article.
Summary
SINE (short interspersed repetitive elements) are retroposons derived from tRNA or 7SL RNA. These repetitive sequences represent a large part of the eukaryotic genome. Their copy number can reach more than 104 per genome. However, no evident function is recognized to these elements. Recently, these « selfish DNAs » appear as a powerful tool in molecular systematic. SINE retroposons have the ability to duplicate and to be reincorporated many times into the genome. Their insertions have two major characteristics: first, a SINE has a negligible probability to be inserted twice at a specific genomic location, second, the chance that a deletion at one insertion site matches exactly the boundaries of the SINE is also insignificant. For these reasons, the analysis of SINE insertions is a source of phylogenetic information, free of convergence and reversal. SINEs thus appear as « perfect » phylogenetic characters and the study of their insertion site has recently led to unexpected phylogenetic results. The advantages and limits of this new phylogenetic method are presented here.
Appendices
Références
- 1. Jaeger JJ. Rodent phylogeny: new data and old problems. In: Benton MJ, ed. The phylogeny and classification of the Tetrapods. Oxford: Clarendon Press, 1988 : 177-99.
- 2. Shedlock AM, Okada N. SINE insertions: powerful tools for molecular systematics. BioEssays 2000; 22: 148-60.
- 3. Shedlock AM, Milinkovitch MC, Okada N. SINE evolution, missing data, and the origine of whales. Syst Biol 2000; 49: 808-17.
- 4. Hamdi H, Nishio H, Zielinski R, Dugaiczyk A. Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates. J Mol Biol 1999; 289: 861-71.
- 5. Tatout C, Warwick S, Lenoir A, Deragon JM. SINE insertions as clade markers for wild crucifer species. Mol Biol Evol 1999; 16: 1614-21.
- 6. Batzer MA, Stoneking M, Alegria-Hartman M, et al. African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci USA 1994; 91: 12288-92.
- 7. Novick GE, Novick CC, Yunis J, et al. Polymorphic alu insertions and the Asian origin of native American populations. Hum Biol 1998; 70: 23-39.
- 8. De Pancorbo MM, Lopez-Martinez M, Martinez-Bouzas C, et al. The Basques according to polymorphic Alu insertions. Hum Genet 2001; 109: 224-33.
- 9. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001; 409: 860-921.
- 10. Makalowski W. SINEs as a genomic scrap yard: an essay on genomic evolution. In: Maraia RJ, ed. The impact of short interspersed elements (SINEs) on the host genome. Austin: R.G. Landes Company, 1995 : 81-104.
- 11. Okada N. SINEs: short interspersed repeated elements of the eukaryotic genome. Trends Ecol Evol 1991; 6: 358-61.
- 12. Borodulina OR, Kramerov DA. Wide distribution of short interspersed elements among eukaryotic genomes. FEBS Lett 1999; 457: 409-13.
- 13. Lenoir A, Lavie L, Prieto JL, et al. The evolutionary origin and genomic organization of SINEs in Arabidopsis thaliana. Mol Biol Evol 2001; 18: 2315-22
- 14. Okada N, Hamada M, Ogiwara I, Ohshima K. SINEs and LINEs share common 3’ sequences: a review. Gene 1997; 205: 229-43.
- 15. Jurka J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci USA 1997; 94: 1872-7.
- 16. Tatout C, Lavie L, Deragon JM. Similar target site selection occurs in integration of plant and mammalian retroposons. J Mol Evol 1998; 47: 463-70.
- 17. Endoh H, Okada N. Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. Proc Natl Acad Sci USA 1986; 83: 251-5.
- 18. Nikaido M, Rooney AP, Okada N. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: hippopotamuses are the closest extant relatives of whales. Proc Natl Acad Sci USA 1999; 96: 10261-6.
- 19. Philippe H, Laurent J. How good are deep phylogenetic trees? Curr Opin Genet Dev 1998; 8: 616-23.
- 20. Mooers AØ, Holmes EC. The evolution of base composition and phylogenetic inference. Trends Ecol Evol 2000; 15: 365-9.
- 21. Sullivan J, Swofford DL. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J Mammal Evol 1997; 4: 77-86.
- 22. Shimamura M, Yasue H, Ohshima K, et al. Molecular evidence from retroposon that whales form a clade within even-toed Ungulata. Nature 1997; 388: 666-70.
- 23. McKenna MC, Bell SK. Classification of mammals above the species level. New York: Columbia University Press, 1997 : 632 p.
- 24. Montgelard C, Ducroq S, Douzery E. What is a suiforme (Artiodactyla)? Mol Phylogenet Evol 1998; 9: 528-32.
- 25. Nikaido M, Matsuno F, Hamilton H, et al. Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins. Proc Natl Acad Sci USA 2001; 98: 7384-9.