Definition and variation of human endogenous retrovirus H

Virology

Volumn 327, Issue 1, 2004, Pages 93-110

  Jern, Patric ^a   Sperber, Göran O ^a   Blomberg, Jonas ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Evolution; HERV F; HERV H; Human endogenous retrovirus; Phylogeny; Polymorphism; RGH2; RTVLH2; Transposable element

Indexed keywords

ARTICLE; GEL ELECTROPHORESIS; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN ENDOGENOUS RETROVIRUS H; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETROVIRUS; SINGLE NUCLEOTIDE POLYMORPHISM; VIRAL GENETICS;

AMINO ACID SEQUENCE; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA TRANSPOSABLE ELEMENTS; ELECTROPHORESIS; ENDOGENOUS RETROVIRUSES; EVOLUTION, MOLECULAR; GENES, POL; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; TEMPERATURE; VARIATION (GENETICS);

HUMAN ENDOGENOUS RETROVIRUS; HUMAN ENDOGENOUS RETROVIRUS H; UNIDENTIFIED RETROVIRUS;

EID: 4344623302     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virol.2004.06.023     Document Type: Article

References (41)

1. S. Anderssen, E. Sjottem, G. Svineng, and T. Johansen Comparative analyses of LTRs of the ERV-H family of primate-specific retrovirus-like elements isolated from marmoset. African green monkey, and man Virology 234 1 1997 14 30
2. M.A. Batzer, P.L. Deininger, U. Hellmann-Blumberg, J. Jurka, D. Labuda, C.M. Rubin, C.W. Schmid, E. Zietkiewicz, and E. Zuckerkandl Standardized nomenclature for Alu repeats J. Mol. Evol. 42 1 1996 3 6
3. L. Benit, P. Dessen, and T. Heidmann Identification, phylogeny, and evolution of retroviral elements based on their envelope genes J. Virol. 75 23 2001 11709 11719
4. L. Benit, A. Calteau, and T. Heidmann Characterization of the low-copy HERV-Fc family: evidence for recent integrations in primates of elements with coding envelope genes Virology 312 1 2003 159 168
5. S. Blaise, N. de Parseval, L. Benit, and T. Heidmann Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution Proc. Natl. Acad. Sci. U.S.A. 100 22 2003 13013 13018
6. S. Blaise, A. Ruggieri, M. Dewannieux, F.L. Cosset, and T. Heidmann Identification of an envelope protein from the FRD family of human endogenous retroviruses (HERV-FRD) conferring infectivity and functional conservation among simians J. Virol. 78 2 2004 1050 1054
7. M. Bock, and J.P. Stoye Endogenous retroviruses and the human germline Curr. Opin. Genet. Dev. 10 6 2000 651 655
8. G.J. Cianciolo, T.D. Copeland, S. Oroszlan, and R. Snyderman Inhibition of lymphocyte proliferation by a synthetic peptide homologous to retroviral envelope proteins Science 230 4724 1985 453 455
9. J.E. Clough, J.A. Foster, M. Barnett, and H.A. Wichman Computer simulation of transposable element evolution: random template and strict master models J. Mol. Evol. 42 1 1996 52 58
10. P.L. Deininger, M.A. Batzer, C.A. Hutchison III, and M.H. Edgell Master genes in mammalian repetitive DNA amplification Trends Genet. 8 9 1992 307 311
11. N. de Parseval, and T. Heidmann Physiological knockout of the envelope gene of the single-copy ERV-3 human endogenous retrovirus in a fraction of the Caucasian population J. Virol. 72 4 1998 3442 3445
12. N. de Parseval, J. Casella, L. Gressin, and T. Heidmann Characterization of the three HERV-H proviruses with an open envelope reading frame encompassing the immunosuppressive domain and evolutionary history in primates Virology 279 2 2001 558 569
13. N. de Parseval, V. Lazar, J.F. Casella, L. Benit, and T. Heidmann Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins J. Virol. 77 19 2003 10414 10422
14. C.A. Dunn, P. Medstrand, and D.L. Mager An endogenous retroviral long terminal repeat is the dominant promoter for human {beta}1,3- galactosyltransferase 5 in the colon Proc. Natl. Acad. Sci. U.S.A. 100 22 2003 12841 12846
15. C. Fraser, R.K. Humphries, and D.L. Mager Chromosomal distribution of the RTVL-H family of human endogenous retrovirus-like sequences Genomics 2 4 1988 280 287
16. P. Jern, M. Lindeskog, D. Karlsson, and J. Blomberg Full-length HERV-H elements with env SU open reading frames in the human genome AIDS Res. Hum. Retroviruses 18 9 2002 671 676
17. J. Jurka Repbase update: a database and an electronic journal of repetitive elements Trends Genet. 16 9 2000 418 420
18. V. Kapitonov, and J. Jurka The age of Alu subfamilies J. Mol. Evol. 42 1 1996 59 65
19. S. Kumar, K. Tamura, I.B. Jakobsen, and M. Nei MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 12 2001 1244 1245
20. M. Lindeskog, and J. Blomberg Spliced human endogenous retroviral HERV-H env transcripts in T-cell leukaemia cell lines and normal leukocytes: alternative splicing pattern of HERV-H transcripts J. Gen. Virol. 78 Pt. 10 1997 2575 2585
21. M. Lindeskog, D.L. Mager, and J. Blomberg Isolation of a human endogenous retroviral HERV-H element with an open env reading frame Virology 258 2 1999 441 450
22. D.L. Mager, and J.D. Freeman HERV-H endogenous retroviruses: presence in the New World branch but amplification in the Old World primate lineage Virology 213 2 1995 395 404
23. D.L. Mager, and P.S. Henthorn Identification of a retrovirus-like repetitive element in human DNA Proc. Natl. Acad. Sci. U.S.A. 81 23 1984 7510 7514
24. M. Mangeney, and T. Heidmann Tumor cells expressing a retroviral envelope escape immune rejection in vivo Proc. Natl. Acad. Sci. U.S.A. 95 25 1998 14920 14925
25. M. Mangeney, N. de Parseval, G. Thomas, and T. Heidmann The full-length envelope of an HERV-H human endogenous retrovirus has immunosuppressive properties J. Gen. Virol. 82 Pt. 10 2001 2515 2518
26. P. Medstrand, and J. Blomberg Characterization of novel reverse transcriptase encoding human endogenous retroviral sequences similar to type A and type B retroviruses: differential transcription in normal human tissues J. Virol. 67 11 1993 6778 6787
27. S. Mi, X. Lee, X. Li, G.M. Veldman, H. Finnerty, L. Racie, E. LaVallie, X.Y. Tang, P. Edouard, S. Howes, J.C. Keith Jr., and J.M. McCoy Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis Nature 403 6771 2000 785 789
28. T. Muster, A. Waltenberger, A. Grassauer, S. Hirschl, P. Caucig, I. Romirer, D. Fodinger, H. Seppele, O. Schanab, C. Magin-Lachmann, R. Lower, B. Jansen, H. Pehamberger, and K. Wolff An endogenous retrovirus derived from human melanoma cells Cancer Res. 63 24 2003 8735 8741
29. J. Paces, A. Pavlicek, and V. Paces HERVd: database of human endogenous retroviruses Nucleic Acids Res. 30 1 2002 205 206
30. J. Paces, A. Pavlicek, R. Zika, V.V. Kapitonov, J. Jurka, and V. Paces HERVd: the human endogenous retroviruses database: update Nucleic Acids Res. 32 D50 2004 (Database issue)
31. R.D. Page TreeView: an application to display phylogenetic trees on personal computers Comput. Appl. Biosci. 12 4 1996 357 358
32. D. Riesner, G. Steger, R. Zimmat, R.A. Owens, M. Wagenhofer, W. Hillen, S. Vollbach, and K. Henco Temperature-gradient gel electrophoresis of nucleic acids: analysis of conformational transitions, sequence variations, and proteinâ€"nucleic acid interactions Electrophoresis 10 5â€"6 1989 377 389
33. A.M. Schulte, S. Lai, A. Kurtz, F. Czubayko, A.T. Riegel, and A. Wellstein Human trophoblast and choriocarcinoma expression of the growth factor pleiotrophin attributable to germ-line insertion of an endogenous retrovirus Proc. Natl. Acad. Sci. U.S.A. 93 25 1996 14759 14764
34. V.C. Sheffield, D.R. Cox, L.S. Lerman, and R.M. Myers Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes Proc. Natl. Acad. Sci. U.S.A. 86 1 1989 232 236
35. G. Steger Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction Nucleic Acids Res. 22 14 1994 2760 2768
36. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 22 1994 4673 4680
37. J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 25 24 1997 4876 4882
38. C.N. Ting, M.P. Rosenberg, C.M. Snow, L.C. Samuelson, and M.H. Meisler Endogenous retroviral sequences are required for tissue-specific expression of a human salivary amylase gene Genes Dev. 6 8 1992 1457 1465
39. M. Tristem Identification and characterization of novel human endogenous retrovirus families by phylogenetic screening of the human genome mapping project database J. Virol. 74 8 2000 3715 3730
40. B. Widegren, C. Kjellman, S. Aminoff, L.G. Sahlford, and H.O. Sjogren The structure and phylogeny of a new family of human endogenous retroviruses J. Gen. Virol. 77 Pt. 8 1996 1631 1641
41. D.A. Wilkinson, D.L. Mager, and J.C. Leong Endogenous human retroviruses J. Levy The Retroviridae 1994 Plenum Press New York 465 535