메뉴 건너뛰기




Volumn 12, Issue 6, 2016, Pages

Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved

Author keywords

[No Author keywords available]

Indexed keywords

GENES; STEM CELLS;

EID: 84978790868     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004964     Document Type: Article
Times cited : (19)

References (34)
  • 1
    • 0036088127 scopus 로고    scopus 로고
    • HERVd: database of human endogenous retroviruses
    • 11752294, .;():–
    • Paces J, Pavlícek A, Paces V, HERVd: database of human endogenous retroviruses. Nucleic Acids Research. 2002;30(1):205–206. doi: 10.1093/nar/30.1.20511752294
    • (2002) Nucleic Acids Research , vol.30 , Issue.1 , pp. 205-206
    • Paces, J.1    Pavlícek, A.2    Paces, V.3
  • 3
    • 84898010302 scopus 로고    scopus 로고
    • The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
    • ..;():–
    • Lu X, Sachs F, Ramsay L, Jacques PÉ, Göke J, Bourque G, et al. The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nature Structural & Molecular Biology. 2014;21(4):423–425. doi: 10.1038/nsmb.2799
    • (2014) Nature Structural & Molecular Biology , vol.21 , Issue.4 , pp. 423-425
    • Lu, X.1    Sachs, F.2    Ramsay, L.3    Jacques, P.É.4    Göke, J.5    Bourque, G.6
  • 4
    • 84922115236 scopus 로고    scopus 로고
    • Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells
    • 25317556, ..;():–
    • Wang J, Xie G, Singh M, Ghanbarian AT, Raskó T, Szvetnik A, et al. Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature. 2014;516(7531):405–409. doi: 10.1038/nature1380425317556
    • (2014) Nature , vol.516 , Issue.7531 , pp. 405-409
    • Wang, J.1    Xie, G.2    Singh, M.3    Ghanbarian, A.T.4    Raskó, T.5    Szvetnik, A.6
  • 5
    • 0036468807 scopus 로고    scopus 로고
    • Genome architecture, rearrangements and genomic disorders
    • 11818139, .;():–
    • Stankiewicz P, Lupski JR, Genome architecture, rearrangements and genomic disorders. Trends in Genetics. 2002;18(2):74–82. doi: 10.1016/S0168-9525(02)02592-111818139
    • (2002) Trends in Genetics , vol.18 , Issue.2 , pp. 74-82
    • Stankiewicz, P.1    Lupski, J.R.2
  • 6
    • 80455158263 scopus 로고    scopus 로고
    • Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses
    • .;():–
    • Subramanian RP, Wildschutte JH, Russo C, Coffin JM, Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. Retrovirology. 2011;8(1):1–22. doi: 10.1186/1742-4690-8-90
    • (2011) Retrovirology , vol.8 , Issue.1 , pp. 1-22
    • Subramanian, R.P.1    Wildschutte, J.H.2    Russo, C.3    Coffin, J.M.4
  • 7
    • 84898674273 scopus 로고    scopus 로고
    • Paleovirology: inferring viral evolution from host genome sequence data
    • .;():
    • Katzourakis A, Paleovirology: inferring viral evolution from host genome sequence data. Philosophical Transactions of the Royal Society B: Biological Sciences. 2013;368(1626):20120493. doi: 10.1098/rstb.2012.0493
    • (2013) Philosophical Transactions of the Royal Society B: Biological Sciences , vol.368 , Issue.1626 , pp. 20120493
    • Katzourakis, A.1
  • 8
    • 84908001337 scopus 로고    scopus 로고
    • Unfixed endogenous retroviral insertions in the human population
    • 24920817, .;():–
    • Marchi E, Kanapin A, Magiorkinis G, Belshaw R, Unfixed endogenous retroviral insertions in the human population. Journal of Virology. 2014;88(17):9529–9537. doi: 10.1128/JVI.00919-1424920817
    • (2014) Journal of Virology , vol.88 , Issue.17 , pp. 9529-9537
    • Marchi, E.1    Kanapin, A.2    Magiorkinis, G.3    Belshaw, R.4
  • 9
    • 33750341578 scopus 로고    scopus 로고
    • The evolutionary dynamics of human endogenous retroviral families
    • 16722807, .;:–
    • Bannert N, Kurth R, The evolutionary dynamics of human endogenous retroviral families. Annu Rev Genomics Hum Genet. 2006;7:149–173. doi: 10.1146/annurev.genom.7.080505.11570016722807
    • (2006) Annu Rev Genomics Hum Genet , vol.7 , pp. 149-173
    • Bannert, N.1    Kurth, R.2
  • 10
    • 25144501550 scopus 로고    scopus 로고
    • Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K (HML2): implications for present-day activity
    • 16160178, .;():–
    • Belshaw R, Dawson AL, Woolven-Allen J, Redding J, Burt A, Tristem M, Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K (HML2): implications for present-day activity. Journal of virology. 2005;79(19):12507–12514. doi: 10.1128/JVI.79.19.12507-12514.200516160178
    • (2005) Journal of virology , vol.79 , Issue.19 , pp. 12507-12514
    • Belshaw, R.1    Dawson, A.L.2    Woolven-Allen, J.3    Redding, J.4    Burt, A.5    Tristem, M.6
  • 11
    • 33748884192 scopus 로고    scopus 로고
    • Primate molecular divergence dates
    • 16815047, .;():–
    • Steiper ME, Young NM, Primate molecular divergence dates. Molecular Phylogenetics and Evolution. 2006;41(2):384–394. doi: 10.1016/j.ympev.2006.05.02116815047
    • (2006) Molecular Phylogenetics and Evolution , vol.41 , Issue.2 , pp. 384-394
    • Steiper, M.E.1    Young, N.M.2
  • 12
    • 0033964662 scopus 로고    scopus 로고
    • Retroviruses and primate evolution
    • 10655035, .;():–
    • Sverdlov ED, Retroviruses and primate evolution. Bioessays. 2000;(22):161–71. doi: 10.1002/(SICI)1521-1878(200002)22:2%3C161::AID-BIES7%3E3.0.CO;2-X10655035
    • (2000) Bioessays , Issue.22 , pp. 161-171
    • Sverdlov, E.D.1
  • 13
    • 84924261514 scopus 로고    scopus 로고
    • The decline of human endogenous retroviruses: extinction and survival
    • 25640971, .;():
    • Magiorkinis G, Blanco-Melo D, Belshaw R, The decline of human endogenous retroviruses: extinction and survival. Retrovirology. 2015;12(1):8. doi: 10.1186/s12977-015-0136-x25640971
    • (2015) Retrovirology , vol.12 , Issue.1 , pp. 8
    • Magiorkinis, G.1    Blanco-Melo, D.2    Belshaw, R.3
  • 14
    • 28744453801 scopus 로고    scopus 로고
    • Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome
    • 15461797, .;():
    • Pereira V, Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biology. 2004;5(10):R79. doi: 10.1186/gb-2004-5-10-r7915461797
    • (2004) Genome Biology , vol.5 , Issue.10 , pp. R79
    • Pereira, V.1
  • 16
    • 34548179537 scopus 로고    scopus 로고
    • Rate of recombinational deletion among human endogenous retroviruses
    • 17581995, ..;():–
    • Belshaw R, Watson J, Katzourakis A, Howe A, Woolven-Allen J, Burt A, et al. Rate of recombinational deletion among human endogenous retroviruses. Journal of Virology. 2007;81(17):9437–9442. doi: 10.1128/JVI.02216-0617581995
    • (2007) Journal of Virology , vol.81 , Issue.17 , pp. 9437-9442
    • Belshaw, R.1    Watson, J.2    Katzourakis, A.3    Howe, A.4    Woolven-Allen, J.5    Burt, A.6
  • 17
    • 34648822341 scopus 로고    scopus 로고
    • Effects of recombination rate on human endogenous retrovirus fixation and persistence
    • 17634225, .;():–
    • Katzourakis A, Pereira V, Tristem M, Effects of recombination rate on human endogenous retrovirus fixation and persistence. Journal of Virology. 2007;81(19):10712–10717. doi: 10.1128/JVI.00410-0717634225
    • (2007) Journal of Virology , vol.81 , Issue.19 , pp. 10712-10717
    • Katzourakis, A.1    Pereira, V.2    Tristem, M.3
  • 18
    • 84930227422 scopus 로고    scopus 로고
    • Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells
    • 25896322, ..;():–
    • Grow EJ, Flynn RA, Chavez SL, Bayless NL, Wossidlo M, Wesche DJ, et al. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature. 2015;522(7555):221–225. doi: 10.1038/nature1430825896322
    • (2015) Nature , vol.522 , Issue.7555 , pp. 221-225
    • Grow, E.J.1    Flynn, R.A.2    Chavez, S.L.3    Bayless, N.L.4    Wossidlo, M.5    Wesche, D.J.6
  • 19
    • 0030885649 scopus 로고    scopus 로고
    • Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast
    • .;():–
    • Datta A, Hendrix M, Lipsitch M, Jinks-Robertson S, Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast. Proceedings of the National Academy of Sciences. 1997;94(18):9757–9762. doi: 10.1073/pnas.94.18.9757
    • (1997) Proceedings of the National Academy of Sciences , vol.94 , Issue.18 , pp. 9757-9762
    • Datta, A.1    Hendrix, M.2    Lipsitch, M.3    Jinks-Robertson, S.4
  • 20
    • 11244260476 scopus 로고    scopus 로고
    • The effect of sequence divergence on recombination between direct repeats in Arabidopsis
    • 15611187, .;():–
    • Opperman R, Emmanuel E, Levy AA, The effect of sequence divergence on recombination between direct repeats in Arabidopsis. Genetics. 2004;168(4):2207–2215. doi: 10.1534/genetics.104.03289615611187
    • (2004) Genetics , vol.168 , Issue.4 , pp. 2207-2215
    • Opperman, R.1    Emmanuel, E.2    Levy, A.A.3
  • 21
    • 84934915470 scopus 로고    scopus 로고
    • Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split
    • .;():
    • Gemmell P, Hein J, Katzourakis A, Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split. Retrovirology. 2015;40320(5040):720.
    • (2015) Retrovirology , vol.40320 , Issue.5040 , pp. 720
    • Gemmell, P.1    Hein, J.2    Katzourakis, A.3
  • 22
    • 4344623302 scopus 로고    scopus 로고
    • Definition and variation of human endogenous retrovirus H
    • 15327901, .;():–
    • Jern P, Sperber GO, Blomberg J, Definition and variation of human endogenous retrovirus H. Virology. 2004;327(1):93–110. doi: 10.1016/j.virol.2004.06.02315327901
    • (2004) Virology , vol.327 , Issue.1 , pp. 93-110
    • Jern, P.1    Sperber, G.O.2    Blomberg, J.3
  • 23
    • 18144390153 scopus 로고    scopus 로고
    • Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H
    • 15858016, .;():–
    • Jern P, Sperber GO, Ahlsén G, Blomberg J, Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H. Journal of Virology. 2005;79(10):6325–6337. doi: 10.1128/JVI.79.10.6325-6337.200515858016
    • (2005) Journal of Virology , vol.79 , Issue.10 , pp. 6325-6337
    • Jern, P.1    Sperber, G.O.2    Ahlsén, G.3    Blomberg, J.4
  • 25
    • 84922382727 scopus 로고    scopus 로고
    • Proliferation of Endogenous Retroviruses in the Early Stages of a Host Germ Line Invasion
    • 25261407, .;():–
    • Ishida Y, Zhao K, Greenwood AD, Roca AL, Proliferation of Endogenous Retroviruses in the Early Stages of a Host Germ Line Invasion. Molecular Biology and Evolution. 2015;32(1):109–120. doi: 10.1093/molbev/msu27525261407
    • (2015) Molecular Biology and Evolution , vol.32 , Issue.1 , pp. 109-120
    • Ishida, Y.1    Zhao, K.2    Greenwood, A.D.3    Roca, A.L.4
  • 27
    • 84978846823 scopus 로고    scopus 로고
    • Smit A, Hubley R, Green P. RepeatMasker Open-3.0. 1996–2004. Institute for Systems Biology. 2004;
    • Smit A, Hubley R, Green P. RepeatMasker Open-3.0. 1996–2004. Institute for Systems Biology. 2004;.
  • 28
    • 59949092694 scopus 로고    scopus 로고
    • Automated paleontology of repetitive DNA with REANNOTATE
    • 19094224, .;():
    • Pereira V, Automated paleontology of repetitive DNA with REANNOTATE. BMC Genomics. 2008;9(1):614. doi: 10.1186/1471-2164-9-61419094224
    • (2008) BMC Genomics , vol.9 , Issue.1 , pp. 614
    • Pereira, V.1
  • 30
    • 84978846838 scopus 로고    scopus 로고
    • Retrovirus reference sequence library version 2013-12-26;. Available from:
    • Retrovirus reference sequence library version 2013-12-26;. Available from: http://tinyurl.com/odk2ukh.
  • 31
    • 84876581034 scopus 로고    scopus 로고
    • Dfam: a database of repetitive DNA based on profile hidden Markov models
    • 23203985, ..;():–
    • Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, et al. Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Research. 2013;41(D1):D70–D82. doi: 10.1093/nar/gks126523203985
    • (2013) Nucleic Acids Research , vol.41 , Issue.D1 , pp. D70-D82
    • Wheeler, T.J.1    Clements, J.2    Eddy, S.R.3    Hubley, R.4    Jones, T.A.5    Jurka, J.6
  • 32
    • 84945708555 scopus 로고
    • Programming techniques: Regular expression search algorithm
    • .;():–
    • Thompson K, Programming techniques: Regular expression search algorithm. Communications of the ACM. 1968;11(6):419–422. doi: 10.1145/363347.363387
    • (1968) Communications of the ACM , vol.11 , Issue.6 , pp. 419-422
    • Thompson, K.1
  • 33
    • 84959848780 scopus 로고
    • Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters
    • .;():–
    • Felsenstein J, Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Biology. 1973;22(3):240–249. doi: 10.1093/sysbio/22.3.240
    • (1973) Systematic Biology , vol.22 , Issue.3 , pp. 240-249
    • Felsenstein, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.