Polymorphic integrations of an endogenous gammaretrovirus in the mule deer genome

Journal of Virology

Volumn 86, Issue 5, 2012, Pages 2787-2796

  Elleder, Daniel ^a   Kim, Oekyung ^a   Padhi, Abinash ^a   Bankert, Jason G ^a   Simeonov, Ivan ^a   Schuster, Stephan C ^a   Wittekindt, Nicola E ^a,d   Motameny, Susanne ^b   Poss, Mary ^a,c  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF COLOGNE   (Germany)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DEER; DEMOGRAPHY; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC TRANSCRIPTION; HOST; NONHUMAN; NUCLEOTIDE SEQUENCE; ODOCOILEUS HEMIONUS; OPEN READING FRAME; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROVIRUS; RETROVIRUS; SHEEP; SWINE; WHITE TAILED DEER;

ANIMALS; DEER; ENDOGENOUS RETROVIRUSES; GAMMARETROVIRUS; GENE DOSAGE; GENOME; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; VIRUS INTEGRATION;

CERVIDAE; CERVUS CANADENSIS; GAMMARETROVIRUS; MAMMALIA; MUNTIACUS; MUNTIACUS MUNTJAK; ODOCOILEUS HEMIONUS; ODOCOILEUS VIRGINIANUS; OVIS ARIES; SUIDAE;

EID: 84857859279     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.06859-11     Document Type: Article

References (53)

1. Aaronson SA, Tronick SR, Stephenson JR. 1976. Endogenous type C RNA virus of Odocoileus hemionus, a mammalian species of New World origin. Cell 9:489-494.
2. Adelson DL, Raison JM, Edgar RC. 2009. Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome. Proc. Natl. Acad. Sci. U. S. A. 106:12855-12860.
3. Anderson MM, Lauring AS, Burns CC, Overbaugh J. 2000. Identification of a cellular cofactor required for infection by feline leukemia virus. Science 287:1828-1830.
4. Armezzani A, et al. 2011. The signal peptide of a recently integrated endogenous sheep betaretrovirus envelope plays a major role in eluding gag-mediated late restriction. J. Virol. 85:7118-7128.
5. Arnaud F, et al. 2007. A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses. PLoS Pathog. 3:e170.
6. Balada E, Vilardell-Tarres M, Ordi-Ros J. 2010. Implication of human endogenous retroviruses in the development of autoimmune diseases. Int. Rev. Immunol. 29:351-370.
7. Belshaw R, et al. 2005. Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K(HML2): implications for present-day activity. J. Virol. 79: 12507-12514.
8. Belshaw R, et al. 2007. Rate of recombinational deletion among human endogenous retroviruses. J. Virol. 81:9437-9442.
9. Blikstad V, Benachenhou F, Sperber GO, Blomberg J. 2008. Evolution of human endogenous retroviral sequences: a conceptual account. Cell. Mol. Life Sci. 65:3348-3365.
10. Brown PO. 1997. Integration. In Coffin JM, Hughes SH, Varmus HE (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, New York, NY.
11. Carr SM, Ballinger SW, Derr JN, Blankenship LH, Bickham JW. 1986. Mitochondrial DNA analysis of hybridization between sympatric whitetailed deer and mule deer in west Texas. Proc. Natl. Acad. Sci. U. S. A. 83:9576-9580.
12. Chessa B, et al. 2009. Revealing the history of sheep domestication using retrovirus integrations. Science 324:532-536.
13. Cohen CJ, Lock WM, Mager DL. 2009. Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Gene 448:105-114.
14. Demirov DG, Freed EO. 2004. Retrovirus budding. Virus Res. 106:87-102.
15. Elleder D, Pavlíček A, Pačes J, Hejnar J. 2002. Preferential integration of human immunodeficiency virus type 1 into genes, cytogenetic R bands and GC-rich DNA regions: insight from the human genome sequence. FEBS Lett. 517:285-286.
16. Ferreri GC, et al. 2011. Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere. J. Virol. 85:4761-4771.
17. Gilbert C, Ropiquet A, Hassanin A. 2006. Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): systematics, morphology, and biogeography. Mol. Phylogenet. Evol. 40:101-117.
18. Gorelick RJ, Henderson LE, Hanser JP, Rein A. 1988. Point mutants of Moloney murine leukemia virus that fail to package viral RNA: evidence for specific RNA recognition by a "zinc finger-like" protein sequence. Proc. Natl. Acad. Sci. U. S. A. 85:8420-8424.
19. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
20. Hedges SB, Dudley J, Kumar S. 2006. TimeTree: a public knowledgebase of divergence times among organisms. Bioinformatics 22:2971-2972.
21. Jha AR, et al. 2011. Human endogenous retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans. PLoS One 6:e20234.
22. Johnson WE, Coffin JM. 1999. Constructing primate phylogenies from ancient retrovirus sequences. Proc. Natl. Acad. Sci. U. S. A. 96:10254-10260.
23. Klymiuk N, Muller M, Brem G, Aigner B. 2003. Characterization of endogenous retroviruses in sheep. J. Virol. 77:11268-11273.
24. Klymiuk N, Muller M, Brem G, Aigner B. 2002. Characterization of porcine endogenous retrovirus gamma pro-pol nucleotide sequences. J. Virol. 76:11738-11743.
25. Lander ES, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
26. Lewinski MK, Bushman FD. 2005. Retroviral DNA integration- mechanism and consequences. Adv. Genet. 55:147-181.
27. Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18:1851-1858.
28. Macfarlane C, Simmonds P. 2004. Allelic variation of HERV-K(HML-2) endogenous retroviral elements in human populations. J. Mol. Evol. 59: 642-656.
29. Mager DL, Freeman JD. 1995. HERV-H endogenous retroviruses: presence in the New World branch but amplification in the Old World primate lineage. Virology 213:395-404.
30. Maksakova IA, et al. 2006. Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line. PLoS Genet. 2:e2.
31. Merza M, Larsson E, Steen M, Morein B. 1994. Association of a retrovirus with a wasting condition in the Swedish moose. Virology 202:956-961.
32. Mi S, et al. 2000. Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 403:785-789.
33. Mitchell RS, et al. 2004. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol. 2:E234.
34. Moyes D, Griffiths DJ, Venables PJ. 2007. Insertional polymorphisms: a new lease of life for endogenous retroviruses in human disease. Trends Genet. 23:326-333.
35. O'Neill RJ, O'Neill MJ, Graves JA. 1998. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 393:68-72.
36. Oliveira NM, Satija H, Kouwenhoven IA, Eiden MV. 2007. Changes in viral protein function that accompany retroviral endogenization. Proc. Natl. Acad. Sci. U. S. A. 104:17506-17511.
37. Overbaugh J, Riedel N, Hoover EA, Mullins JI. 1988. Transduction of endogenous envelope genes by feline leukaemia virus in vitro. Nature 332:731-734.
38. Paul TA, et al. 2006. Identification and characterization of an exogenous retrovirus from Atlantic salmon swim bladder sarcomas. J. Virol. 80: 2941-2948.
39. Roca AL, Nash WG, Menninger JC, Murphy WJ, O'Brien SJ. 2005. Insertional polymorphisms of endogenous feline leukemia viruses. J. Virol. 79:3979-3986.
40. Roca AL, Pecon-Slattery J, O'Brien SJ. 2004. Genomically intact endogenous feline leukemia viruses of recent origin. J. Virol. 78:4370 - 4375.
41. Rosenberg N, Jolicoeur P. 1997. Retroviral pathogenesis. In Coffin JM, Hughes SH, Varmus HE (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, New York, NY.
42. Ruprecht K, Mayer J, Sauter M, Roemer K, Mueller-Lantzsch N. 2008. Endogenous retroviruses and cancer. Cell. Mol. Life Sci. 65: 3366-3382.
43. Seabury CM, et al. 2011. Genome-wide polymorphism and comparative analyses in the white-tailed deer (Odocoileus virginianus): a model for conservation genomics. PLoS One 6:e15811.
44. Shimamura M, Abe H, Nikaido M, Ohshima K, Okada N. 1999. Genealogy of families of SINEs in cetaceans and artiodactyls: the presence of a huge superfamily of tRNA(Glu)-derived families of SINEs. Mol. Biol. Evol. 16:1046-1060.
45. Swanstrom R, Wills JW. 1997. Synthesis, assembly, and processing of viral proteins. In Coffin JM, Hughes SH, Varmus HE (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, New York, NY.
46. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
47. Tandon R, et al. 2011. Identification of human endogenous retrovirusspecific T cell responses in vertically HIV-1-infected subjects. J. Virol. 85:11526-11531.
48. Tarlinton RE, Meers J, Young PR. 2006. Retroviral invasion of the koala genome. Nature 442:79-81.
49. Turner G, et al. 2001. Insertional polymorphisms of full-length endogenous retroviruses in humans. Curr. Biol. 11:1531-1535.
50. Untergasser A, et al. 2007. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 35:W71-W74.
51. Waterston RH, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
52. Wittekindt NE, et al. 2010. Nodeomics: pathogen detection in vertebrate lymph nodes using meta-transcriptomics. PLoS One 5:e13432.
53. Zhang Y, Maksakova IA, Gagnier L, van de Lagemaat LN, Mager DL. 2008. Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PLoS Genet. 4:e1000007.