Genomic signatures: Tracing the origin of retroelements at the nucleotide level

Genetica

Volumn 100, Issue 1-3, 1997, Pages 271-279

  Terzian, Christophe ^a   Laprevotte, Ivan ^a   Brouillet, Sophie ^a   Hénaut, Alain ^a  

^a CNRS   (France)

Author keywords

Multivariate analysis; Oligonucleotide composition; Retrotransposons; Retroviruses

Indexed keywords

ANIMALIA; INVERTEBRATA; MAMMALIA; UNIDENTIFIED RETROVIRUS;

EID: 0031455436     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1018358301906     Document Type: Article

References (24)

1. Barrai, I., C. Scapoli, R. Barale & S. Volinia, 1990. Oligonucleotide correlations between infector and host genomes hint at evolutionary relationships. Nucleic Acids Res. 18: 3021-3025.
2. Bestor, T.H. & B. Tycko, 1996. Creation of genomic methylation patterns. Nature Genetics 12: 363-365.
3. Blaisdell, B.E., A.M. Campbell & S. Karlin, 1996. Similarities and dissimilarities of phage genomes. Proc. Natl. Acad. Sci. USA 93: 5854-5859.
4. Burge, C., A.M. Campbell & S. Karlin, 1992. Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl. Acad. Sci. USA 89: 1358-1362.
5. Capy, P., D. Anxolabéhère & T. Langin, 1994. The strange phylogenies of transposable elements: are horizontal transfers the only explanation? Trends in Genetics 10: 7-12.
6. Dombroski, B.A., S.L. Mathias, E. Nanthakumar, A.F. Scott & H.J. Kazazian, 1991. Isolation of an active human transposable element. Science 254: 1805-1808.
7. Escofier, B., 1979. Traitement simultané de variables qualitatives et quantitatives en analyse factorielle. Les Cahiers de l'Analyse des Données 4: 137-146.
8. Hancock, J.M., 1995. The contribution of slippage-like processes to genome evolution. J. Mol. Evol. 41: 1038-1047.
9. Karlin, S. & C. Burge, 1995. Dinucleotide relative abundance extremes: a genomic signature. Trends in Genetics 11: 283-290.
10. Kim, A., C. Terzian, P. Santamaria, A. Pélisson, N. Prud'homme & A. Bucheton, 1994. Retroviruses in invertebrates: the gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 91: 1285-1289.
11. Laprevotte, I., 1989. Scrambled duplications in the feline leukemia virus gag gene: a putative pattern for molecular evolution. J. Mol. Evol. 29: 135-148.
12. Laprevotte, I., 1992. Mo-MuLV nucleotide sequence exhibits three levels of oligomeric repetitions, suggesting a stepwise molecular evolution. J. Mol. Evol. 35: 420-428.
13. Laprevotte, I., S. Brouillet, C. Terzian & A. Hénaut, 1997. Retroviral oligonucleotide distributions correlate with biaised nucleotide compositions of retrovirus sequences, suggesting a duplicative stepwise molecular evolution. J. Mol. Evol. 44: 214-225.
14. Lebart, L., A. Morineau & K.A. Warwick, 1984. Multivariate Descriptive Statistical Data. John Wiley and Sons, New York.
15. Leeton, P.R. & D.R. Smyth, 1993. An abundant LINE-like ele- ment amplifies in the genome of Lilium speciosum. Mol. Gen. Genet. 237: 97-104.
16. Ohno, S. & T. Yomo, 1990. Various regulatory sequences are deprived of their uniqueness by the universal rule of TA/CG deficiency and TG/CT excess. Proc. Natl. Acad. Sci. USA 87: 1218-1222.
17. Ollivier, E., M.-O. Delorme & A. Hénaut, 1995. DosDNA occurs along yeast chromosomes, regardless of functional significance of the sequence. C.R. Acad. Sci. Paris 318: 599-608.
18. Richards, R.I. & G.R. Sutherland, 1994. Simple repeat DNA is not replicated simply. Nature Genetics 6: 114-116.
19. Shpaer, E.G. & J.I. Mullins, 1990. Selection against CpG dinucleotides in lentiviral genes: a possible role of methylation in regulation of viral expression. Nucleic Acids Res. 18: 5793-5797.
20. Springer, M.S. & R.J. Britten, 1993. Phylogenetic relationships of reverse transcriptase and RNase H sequences and aspects of genome structure in the gypsy group of retrotransposon. Mol. Biol. Evol. 10: 1370-1379.
21. Temin, H.M., 1980. Origin of retroviruses from cellular moveable genetic elements. Cell 21: 599-600.
22. Thioulouse, J., 1990. MacMul and GraphMu: two Macintosh programs for the display and analysis of multivariate data. Computers and Geosciences 16: 1235-1240.
23. Wu, W., C. Palaniappan, R.A. Bambara & P.J. Fay, 1996. Differences in mutagenesis during minus strand, plus strand and strand transfer (recombination) synthesis of the HIV-1 nef gene in vitro. Nucleic Acids Res. 24: 1710-1718.
24. Xiong, Y. & T.H. Eickbush, 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9: 3353-3362.