link.springer.com

Allelic Variation of HERV-K(HML-2) Endogenous Retroviral Elements in Human Populations - Journal of Molecular Evolution

  • ️Simmonds, Peter
  • ️Mon Nov 01 2004

  • SB Akopov LG Nikolaev PP Khil YB Lebedev ED Sverdlov (1998) ArticleTitleLong terminal repeats of human endogenous retrovirus K family (HERV-K) specifically bind host cell nuclear proteins FEES Lett 421 229–233

    Google Scholar 

  • M Barbulescu G Turner MI Seaman AS Deinard KK Kidd J Lenz (1999) ArticleTitleMany human endogenous retrovirus K (HERV-K) proviruses are unique to humans Curr Biol 9 861–868

    Google Scholar 

  • E Bosch MA Jobling (2003) ArticleTitleDuplications of the AZFa region of the human Y chromosome are mediated by homologous recombination between HERVs and are compatible with male fertility Hum Mol Genet 12 341–347

    Google Scholar 

  • A Buzdin K Khodosevich I Mamedov T Vinogradova Y Lebedev G Hunsmann E Sverdlov (2002) ArticleTitleA technique for genome-wide identification of differences in the interspersed repeats integrations between closely related genomes and its application to detection of human-specific integrations of HERV-K LTRs Genomics 79 413–422

    Google Scholar 

  • A Buzdin S Ustyugova K Khodosevich I Mamedov Y Lebedev G Hunsmann E Sverdlov (2003) ArticleTitleHuman-specific subfamilies of HERV-K (HML-2) long terminal repeats: three master genes were active simultaneously during branching of hominoid lineages Genomics 81 149–156

    Google Scholar 

  • FC Chen WH Li (2001) ArticleTitleGenomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees Am J Hum Genet 68 444–456 Occurrence Handle10.1086/318206 Occurrence Handle1:CAS:528:DC%2BD3MXhtl2lsLg%3D Occurrence Handle11170892

    Article  CAS  PubMed  Google Scholar 

  • J Costas (2001) ArticleTitleEvolutionary dynamics of the human endogenous retro virus family HERV-K inferred from full-length proviral genomes J Mol Evol 53 237–243

    Google Scholar 

  • AW Dangel BJ Baker AR Mendoza CY Yu (1995) ArticleTitleComplement component C4 gene intron 9 as a phylogenetic marker for primates: Long terminal repeats of the endogenous retrovirus ERV-K(C4) are a molecular clock of evolution Immunogenetics 42 41–52 Occurrence Handle1:CAS:528:DyaK2MXnt1Chsrk%3D Occurrence Handle7797267

    CAS  PubMed  Google Scholar 

  • PL Deininger MA Batzer (2002) ArticleTitleMammalian retroelements Genome Res 12 1455–1465

    Google Scholar 

  • AN Domansky EP Kopantzev EV Snezhkov YB Lebedev C Leib-Mosch ED Sverdlov (2000) ArticleTitleSolitary HERV-K LTRs possess bi-directional promoter activity and contain a negative regulatory element in the U5 region FEES Lett 472 191–195

    Google Scholar 

  • M Faerman D Filon G Kahila CL Greenblatt P Smith A Oppenheim (1995) ArticleTitleSex identification of archaeological human remains based on amplification of the X and Y amelogenin alleles Gene 167 327–332

    Google Scholar 

  • KA Frazer X Chen DA Hinds PV Pant N Patil DR Cox (2003) ArticleTitleGenomic DNA insertions and deletions occur frequently between humans and nonhuman primates Genome Res 13 341–346

    Google Scholar 

  • NL Goodchild JD Freeman DL Mager (1995) ArticleTitleSpliced HERV-H endogenous retroviral sequences in human genomic DNA: Evidence for amplification via retrotransposition Virology 206 164–173

    Google Scholar 

  • R Horton D Niblett S Milne S Palmer B Tubby J Trowsdale S Beck (1998) ArticleTitleLarge-scale sequence comparisons reveal unusually high levels of variation in the HLA-DQB1 locus in the class II region of the human MHC J Mol Biol 282 71–97

    Google Scholar 

  • JF Hughes JM Coffin (2001) ArticleTitleEvidence for genomic rearrangements mediated by human endogenous retroviruses during primate evolution Nat Genet 29 487–489

    Google Scholar 

  • JW Huh KW Hong JM Yi TH Kirn O Takenaka WH Lee HS Kim (2003) ArticleTitleMolecular phylogeny and evolution of the human endogenous retrovirus HERV-W LTR family in hominoid primates Mol Cells 15 122–126

    Google Scholar 

  • InstitutionalAuthorNameInternational Human Genome Sequencing Consortium (2001) ArticleTitleInitial sequencing and analysis of the human genome Nature 409 860–921

    Google Scholar 

  • WE Johnson JM Coffin (1999) ArticleTitleConstructing primate phylogenies from ancient retrovirus sequences Proc Natl Acad Sci USA 96 10254–10260

    Google Scholar 

  • DH Kass MA Batzer PL Deninger (1995) ArticleTitleGene conversion as a secondary mechanism in SINE evolution Mol Cell Biol 15 19–25

    Google Scholar 

  • SG Kurdyukov YB Lebedev II Artamonova TN Gorodentseva AV Batrak IZ Mamedov TL Azhikina SP Legchilina IG Efimenko K Gardiner ED Sverdlov (2001) ArticleTitleFull-sized HERV-K (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locations and evolutionary history Gene 273 51–61

    Google Scholar 

  • AV Lapuk PP Khil IV Lavrentieva YB Lebedev ED Sverdlov (1999) ArticleTitleA human endogenous retrovirus-like (HERV) LTR formed more than 10 million years ago due to an insertion of HERV-H LTR into the 5′ LTR of HERV-K is situated on human chromosomes 10, 19 and Y J Gen Virol 80 835–839

    Google Scholar 

  • I Lavrentieva P Khil T Vinogradova A Akhmedov A Lapuk O Shakhova Y Lebedev G Monastyrskaya ED Sverdlov (1998) ArticleTitleSubfamilies and nearest-neighbour dendrogram for the LTRs of human endogenous retroviruses HERV-K mapped on human chromosome 19: Physical neighbourhood does not correlate with identity level Hum Genet 102 107–116

    Google Scholar 

  • YB Lebedev OS Belonovitch NV Zybrova PP Khil SG Kurdyukov TV Vinogradova G Hunsmann ED Sverdlov (2000) ArticleTitleDifferences in HERV-K LTR insertions in orthologous loci of humans and great apes Gene 247 265–277

    Google Scholar 

  • D Liao T Pavelitz AM Weiner (1998) ArticleTitleCharacterization of a novel class of interspersed LTR elements in primate genomes: Structure, genomic distribution, and evolution J Mol Evol 46 649–660

    Google Scholar 

  • G Liu S Zhao JA Bailey SC Sahinalp C Alkan E Tuzun ED Green EE Eichler (2003) ArticleTitleAnalysis of primate genomic variation reveals a repeat-driven expansion of the human genome Genome Res 13 358–368

    Google Scholar 

  • DP Locke R Segraves L Carbone N Archidiacono DG Albertson D Pinkel EE Eichler (2003) ArticleTitleLarge-scale variation among human and great ape genomes determined by array comparative genomic hybridization Genome Res 13 347–357

    Google Scholar 

  • R Lower J Lower R Kurth (1996) ArticleTitleThe viruses in all of us: Characteristics and biological significance of human endogenous retrovirus sequences Proc Natl Acad Sci USA 93 5177–5184 Occurrence Handle10.1073/pnas.93.11.5177 Occurrence Handle1:STN:280:BymB38visFI%3D Occurrence Handle8643549

    Article  CAS  PubMed  Google Scholar 

  • DL Mager DJ Freeman (1995) ArticleTitleHERV-H endogenous retroviruses: Presence in the new world branch but amplification in the old world primate lineage Virology 213 395–404

    Google Scholar 

  • DL Mager NL Goodchild (1989) ArticleTitleHomologous recombination between the LTRs of a human retrovirus-like element causes a 5-kb deletion in two siblings Am J Hum Genet 45 848–854

    Google Scholar 

  • I Mamedov A Batrak A Buzdin E Arzumanyan Y Lebedev ED Sverdlov (2002) ArticleTitleGenome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes Nucleic Acids Res 30 e71

    Google Scholar 

  • J Mayer E Meese N Mueller-Lantzsch (1997a) ArticleTitleChromosomal assignment of human endogenous retrovirus K (HERV-K) env open reading frames Cytogenet Cell Genet 79 157–161

    Google Scholar 

  • J Mayer E Meese N Mueller-Lantzsch (1997b) ArticleTitleMultiple human endogenous retrovirus (HERV-K) loci with gag open reading frames in the human genome Cytogenet Cell Genet 78 1–5

    Google Scholar 

  • J Mayer E Meese N Mueller-Lantzsch (1998) ArticleTitleHuman endogenous retrovirus K homologous sequences and their coding capacity in Old World primates J Virol 72 1870–1875

    Google Scholar 

  • P Medstrand J Blomberg (1993) ArticleTitleCharacterization 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 6778–6787

    Google Scholar 

  • P Medstrand DL Mager (1998) ArticleTitleHuman-specific integrations of the HERV-K endogenous retrovirus family J Virol 72 9782–9787

    Google Scholar 

  • JS Myers BJ Vincent H Udall WS Watkins TA Morrish GE Kilroy GD Swergold J Henke L Henke JV Moran LB Jorde MA Batzer (2002) ArticleTitleA comprehensive analysis of recently integrated human Ta L1 elements Am J Hum Genet 71 312–326

    Google Scholar 

  • EV Nadezhdin YB Lebedev DV Glazkova D Bornholdt IP Arman KH Grzeschik G Hunsmann ED Sverdlov (2001) ArticleTitleIdentification of paralogous HERV-K LTRs on human chromosomes 3, 4, 7 and 11 in regions containing clusters of olfactory receptor genes Mol Genet Genomics 265 820–825

    Google Scholar 

  • M Ono T Yasunaga T Miyata H Ushikubo (1986) ArticleTitleNucleotide sequence of human endogenous retrovirus genome related to the mouse mammary tumor virus genome J Virol 60 589–598 Occurrence Handle1:CAS:528:DyaL2sXmtF2jtQ%3D%3D Occurrence Handle3021993

    CAS  PubMed  Google Scholar 

  • EM Ostertag JL Goodier Y Zhang HH Kazazian (2003) ArticleTitleSVA elements are nonautonomous retrotransposons that cause disease in humans Am J Hum Genet 73 1444–1451

    Google Scholar 

  • C Patience DA Wilkinson RA Weiss (1997) ArticleTitleOur retroviral heritage Trends Genet 13 116–120

    Google Scholar 

  • K Reus J Mayer M Sauter D Scherer N Muller-Lantzsch E Meese (200la) ArticleTitleGenomic organization of the human endogenous retrovirus HERV-K(HML-2.HOM) (ERVK6) on chromosome 7 Genomics 72 314–320

    Google Scholar 

  • K Reus J Mayer M Sauter H Zischler N Muller-Lantzsch E Meese (2001b) ArticleTitleHERV-K (OLD): Ancestor sequences of the human endogenous retrovirus family HERV-K (HML-2) J Virol 75 8917–8926

    Google Scholar 

  • AM Roy-Engel ML Carroll M El-Sawy A Salem RK Garger SV Nguyen PL Deininger MA Batzer (2002) ArticleTitleNon-traditional Alu evolution and primate genomic diversity J Mol Biol 316 1033–1040

    Google Scholar 

  • W Seifarth C Baust A Murr H Skladny F Krieg-Schneider J Blusch T Werner R Hehlmann C Leib-Mosch (1998) ArticleTitleProviral structure, chromosomal location, and expression of HERV-K- T47D, a novel human endogenous retrovirus derived from T47D particles J Virol 72 8384–8391

    Google Scholar 

  • L Shen LC Wu S Sanlioglu R Chen AR Mendoza AW Dangel MC Carroll WB Zipf CY Yu (1994) ArticleTitleStructure and genetics of the partially duplicated gene RP located immediately upstream of the complement C4A and C4B genes in the HLA class III region: Molecular cloning, exon-intron structure, composite retroposon, and breakpoint of gene duplication J Biol Chem 269 8466–8476

    Google Scholar 

  • A Shih EE Coutavas MG Rush (1991) ArticleTitleEvolutionary implications of primate endogenous retroviruses Virology 185 495–502

    Google Scholar 

  • P Simmonds DB Smith (1999) ArticleTitleStructural constraints on RNA virus evolution J Virol 73 5787–5794

    Google Scholar 

  • GR Simpson C Patience R Lower RR Tonjes HD Moore RA Weiss MT Boyd (1996) ArticleTitleEndogenous D-type (HERV-K) related sequences are packaged into retroviral particles in the placenta and possess open reading frames for reverse transcriptase Virology 222 451–456

    Google Scholar 

  • P Stankiewicz JR Lupski (2002) ArticleTitleMolecular-evolutionary mechanisms for genomic disorders Curr Opin Genet Dev 12 312–319

    Google Scholar 

  • C Stringer (2002) ArticleTitleModern human origins: progress and prospects Philos Trans R Soc Lond B Biol Sci 357 563–579

    Google Scholar 

  • J Sugimoto N Matsuura Y Kinjo N Takasu T Oda Y Jinno (2001) ArticleTitleTranscriptionally active HERV-K genes: Identification, isolation, and chromosomal mapping Genomics 72 137–144

    Google Scholar 

  • C Sun H Skaletsky S Rozen J Gromoll E Nieschlag R Oates DC Page (2000) ArticleTitleDeletion of azoospermia factor a (AZFa) region of human Y chromosome caused by recombination between HERV15 proviruses Hum Mol Genet 9 2291–2296

    Google Scholar 

  • ED Sverdlov (2000) ArticleTitleRetroviruses and primate evolution Bioessays 22 161–171 Occurrence Handle10.1002/(SICI)1521-1878(200002)22:2<161::AID-BIES7>3.0.CO;2-X Occurrence Handle1:CAS:528:DC%2BD3MXmslSht7s%3D Occurrence Handle10655035

    Article  CAS  PubMed  Google Scholar 

  • RR Tonjes F Czauderna R Kurth (1999) ArticleTitleGenome-wide screening, cloning, chromosomal assignment, and expression of full-length human endogenous retrovirus type K J Virol 73 9187–9195

    Google Scholar 

  • EM Towler SV Gulnik TN Bhat D Xie E Gustschina TR Sumpter N Robertson C Jones M Sauter N Mueller-Lantzsch C Debouck JW Erickson (1998) ArticleTitleFunctional characterization of the protease of human endogenous retrovirus, K10: Can it complement HIV-1 protease? Biochemistry 37 17137–17144

    Google Scholar 

  • M Tristem (2000) ArticleTitleIdentification and characterization of novel human endogenous retrovirus families by phylogenetic screening of the human genome mapping project database J Virol 74 3715–3730

    Google Scholar 

  • G Turner M Barbulescu M Su MI Jensen-Seaman KK Kidd J Lenz (2001) ArticleTitleInsertional polymorphisms of full-length endogenous retroviruses in humans Curr Biol 11 1531–1535

    Google Scholar 

  • HB Urnovitz WH Murphy (1996) ArticleTitleHuman endogenous retroviruses: nature, occurrence, and clinical implications in human disease Clin Microbiol Rev 9 72–99 Occurrence Handle1:CAS:528:DyaK28XhtFyksLY%3D Occurrence Handle8665478

    CAS  PubMed  Google Scholar 

  • TV Vinogradova LP Leppik LG Nikolaev SB Akopov AM Kleiman NB Senyuta ED Sverdlov (2001) ArticleTitleSolitary human endogenous retroviruses-K LTRs retain transcriptional activity in vivo, the mode of which is different in different cell types Virology 290 83–90

    Google Scholar 

  • ZB Zhu B Jian JE Volanakis (1994) ArticleTitleAncestry of SINE-R.C2 a human-specific retroposon Hum Genet 93 545–551

    Google Scholar 

  • J Zsiros MF Jebbink VV Lukashov PA Voute B Berkhout (1998) ArticleTitleEvolutionary relationships within a subgroup of HERV-K-related human endogenous retroviruses J Gen Virol 79 61–70

    Google Scholar 

  • J Zsiros MF Jebbink VV Lukashov PA Voute B Berkhout (1999) ArticleTitleBiased nucleotide composition of the genome of HERV-K related endogenous retroviruses and its evolutionary implications J Mol Evol 48 102–111

    Google Scholar