Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: Genes and pseudogenes

BMC Genomics

Volumn 6, Issue , 2005, Pages

  de Parseval, Nathalie ^a   Diop, Gora ^b   Blaise, Sandra ^a,c   Helle, Francois ^a   Vasilescu, Alexandre ^b   Matsuda, Fumihiko ^b   Heidmann, Thierry ^a  

^a INSTITUT GUSTAVE ROUSSY   (France)

^b CENTRE NATIONAL DE GÉNOTYPAGE   (France)

^c INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ENVELOPE PROTEIN; VIRUS ENVELOPE PROTEIN;

ALLELE; ARTICLE; CAUCASIAN; CELL FUSION; DISEASE PREDISPOSITION; ENVELOPE GENE; ENVFRD GENE; ENVW GENE; GENE EXPRESSION; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; GENETIC POLYMORPHISM; HUMAN; HUMAN CELL; HUMAN ENDOGENOUS RETROVIRUS; HUMAN GENOME; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; PLACENTA; PRIMATE; PROVIRUS; PSEUDOGENE; RETROVIRUS; SINGLE NUCLEOTIDE POLYMORPHISM; SYNCYTIOTROPHOBLAST; VIRUS GENOME; VIRUS PARTICLE;

HUMAN ENDOGENOUS RETROVIRUS W; HUMAN ENDOGENOUS RETROVIRUSES; PRIMATES;

EID: 25444496459     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-117     Document Type: Article

References (30)

1. Consortium IHGS: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
2. Boeke JD, Stoye JP: Retrotransposons, endogenous retroviruses, and the evolution of retroelements. In: Retroviruses. Edited by Coffin JM, Hughes SH, Varmus HE. New York: Cold Spring Harbor Laboratory Press; 1997: 343-436.
3. Bannert N, Kurth R: Retroelements and the human genome: New perspectives on an old relation. Proc Natl Acad Sci USA 2004, 13 Suppl 2:14572-14579.
4. de Parseval N, Heidmann T: Human endogenous retroviruses: from infectious elements to human genes. Cytogenet Genome Res 2005, 110:318-332.
5. Repbase update, a database of transposable elements [http://www.girinst.org]
6. de Parseval N, Lazar V, Casella JF, Benit L, Heidmann T: Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins. J Virol 2003, 77:10414-10422.
7. Best S, Le Tissier PR, Stoye JP: Endogenous retroviruses and the evolution of resistance to retroviral infection. Trends Microbiol 1997, 5:313-318.
8. Cianciolo GJ, Copeland T, Orozlan S, Snyderman R: Inhibition of lymphocyte proliferation by a synthetic peptide homologous to retroviral envelope protein. Science 1985, 230:453-455.
9. Mangeney M, Heidmann T: Tumor cells expressing a retroviral envelope escape immune rejection in vivo. Proc Natl Acad Sci USA 1998, 95:14920-14925.
10. Blond JL, Lavillette D, Cheynet V, Bouton O, Oriol G, Chapel-Fernandes S, Mandrand B, Mallet F, Cosset F-L: An envelope glycoprotein of the human endogenous retrovirus HERV-W is expressed in the human placenta and fuses cells expressing the type D mammalian retrovirus receptor. J Virol 2000, 74:3321-3329.
11. Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, Keith JCJ, McCoy JM: Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 2000, 403:785-788.
12. Blaise S, de Parseval N, Bénit L, Heidmann T: Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. Proc Natl Acad Sci USA 2003, 100:13013-13018.
13. Frendo JL, Olivier D, Cheynet V, Blond JL, Bouton O, Vidaud M, Rabreau M, Evain-Brion D, Mallet F: Direct involvement of HERV-W Env glycoprotein in human trophoblast cell fusion and differentiation. Mol Cell Biol 2003, 23:3566-3574.
14. de Parseval N, Heidmann T: Physiological knock-out of the envelope gene of the single copy ERV-3 human endogenous retrovirus in a fraction of the caucasian population. J Virol 1998, 72:3442-3445.
15. Turner G, Barbulescu M, Su M, Jensen-Seaman MI, Kidd KK, Lenz J: Insertional polymorphisms of full-length endogenous retroviruses in humans. Curr Biol 2001, 11:1531-1535.
16. Hughes JF, Coffin JM: Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: implications for human and viral evolution. Proc Natl Acad Sci U S A 2004, 101:1668-1672.
17. Zhao Z, Fu YX, Hewett-Emmett D, Boerwinkle E: Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene 2003, 312:207-213.
18. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, Duan J, Carr JL, Lee MS, Koshy B, Kumar AM, Zhang G, Newell WR, Windemuth A, Xu C, Kalbfleisch TS, Shaner SL, Arnold K, Schulz V, Drysdale CM, Nandabalan K, Judson RS, Ruano G, Vovis GF: Haplotype variation and linkage disequilibrium in 313 human genes. Science 2001, 293:489-493.
19. Mallet F, Bouton O, Prudhomme S, Cheynet V, Oriol G, Bonnaud B, Lucotte G, Duret L, Mandrand B: The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology. Proc Natl Acad Sci U S A 2004, 101:1731-1736.
20. Laird N: Computational Statistic: the EM algorithm. In: Handbook of Statistics. Edited by Rao CR, vol. 9. Amsterdam: Elsevier Science Publishers; 1993: 509-520.
21. Blaise S, Ruggieri A, Dewannieux M, Cosset F-L, Heidmann T: Identification of an envelope protein from the FRD family of Human Endogenous Retroviruses (HERVFRD) conferring infectivity on retroviral particles and functional conservation among simians. J Virol 2004, 78:1050-1054.
22. Herve CA, Forrest G, Lower R, Griffiths DJ, Venables PJ: Conservation and loss of the ERV3 open reading frame in primates. Genomics 2004, 83:940-943.
23. Benit L, Calteau A, Heidmann T: Characterization of the low-copy HERV-Fc family: evidence for recent integrations in primates of elements with coding envelope genes. Virology 2003, 312:159-168.
24. de Parseval N, Casella JF, Gressin L, Heidmann T: Characterization of the three HERV-H proviruses with an open envelope reading frame encompassing the immunosuppressive domain and evolutionary history in primates. Virology 2001, 279:558-569.
25. Fay JC, Wu CI: Sequence divergence, functional constraint, and selection in protein evolution. Annu Rev Genomics Hum Genet 2003, 4:213-235.
26. Bonnaud B, Bouton O, Oriol G, Cheynet V, Duret L, Mallet F: Evidence of selection on the domesticated ERVWE1 env retroviral element involved in placentation. Mol Biol Evol 2004, 21:1895-1901.
27. Zhang J, Webb DM: Evolutionary deterioration of the vomeronasal pheromone transduction pathway in catarrhine primates. Proc Natl Acad Sci U S A 2003, 100:8337-8341.
28. Belshaw R, Pereira V, Katzourakis A, Talbot G, Paces J, Burt A, Tristem M: Long-term reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci U S A 2004, 25:4894-4899.
29. Takahashi M, Matsuda F, Margetic N, Lathrop M: Automated identification of single nucleotide polymorphisms from sequencing data. In: J Bioinf Computat Biol Proc, IEEE CS Bioinformatics Conference: 2002; 2002: pp 87-96.
30. Devlin B, Risch N: A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995, 29:311-322.