메뉴 건너뛰기




Volumn 424, Issue 5, 2012, Pages 257-269

Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing

Author keywords

deep sequencing; defective RNAs; flock house virus; virus like particles

Indexed keywords

GENOMIC RNA; NUCLEOTIDE;

EID: 84869211718     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2012.10.005     Document Type: Article
Times cited : (18)

References (52)
  • 2
    • 0030975364 scopus 로고    scopus 로고
    • Nonhomologous RNA recombination in a cell-free system: Evidence for a transesterification mechanism guided by secondary structure
    • A.B. Chetverin, H.V. Chetverina, A.A. Demidenko, and V.I. Ugarov Nonhomologous RNA recombination in a cell-free system: evidence for a transesterification mechanism guided by secondary structure Cell 88 1997 503 513
    • (1997) Cell , vol.88 , pp. 503-513
    • Chetverin, A.B.1    Chetverina, H.V.2    Demidenko, A.A.3    Ugarov, V.I.4
  • 3
    • 2642518680 scopus 로고    scopus 로고
    • RNA recombination in vivo in the absence of viral replication
    • A. Gallei, A. Pankraz, H.J. Thiel, and P. Becher RNA recombination in vivo in the absence of viral replication J. Virol. 78 2004 6271 6281
    • (2004) J. Virol. , vol.78 , pp. 6271-6281
    • Gallei, A.1    Pankraz, A.2    Thiel, H.J.3    Becher, P.4
  • 4
    • 0023017765 scopus 로고
    • The mechanism of RNA recombination in poliovirus
    • K. Kirkegaard, and D. Baltimore The mechanism of RNA recombination in poliovirus Cell 47 1986 433 443
    • (1986) Cell , vol.47 , pp. 433-443
    • Kirkegaard, K.1    Baltimore, D.2
  • 5
    • 0026602984 scopus 로고
    • RNA recombination in animal and plant viruses
    • M.M. Lai RNA recombination in animal and plant viruses Microbiol. Rev. 56 1992 61 79
    • (1992) Microbiol. Rev. , vol.56 , pp. 61-79
    • Lai, M.M.1
  • 6
    • 0027324884 scopus 로고
    • Nonhomologous RNA recombination during negative-strand synthesis of flock house virus RNA
    • Y. Li, and L.A. Ball Nonhomologous RNA recombination during negative-strand synthesis of flock house virus RNA J. Virol. 67 1993 3854 3860
    • (1993) J. Virol. , vol.67 , pp. 3854-3860
    • Li, Y.1    Ball, L.A.2
  • 7
    • 0026623162 scopus 로고
    • Poliovirus RNA recombination: Mechanistic studies in the absence of selection
    • T.C. Jarvis, and K. Kirkegaard Poliovirus RNA recombination: mechanistic studies in the absence of selection EMBO J. 11 1992 3135 3145
    • (1992) EMBO J. , vol.11 , pp. 3135-3145
    • Jarvis, T.C.1    Kirkegaard, K.2
  • 9
    • 0033594983 scopus 로고    scopus 로고
    • Widespread intra-serotype recombination in natural populations of dengue virus
    • M. Worobey, A. Rambaut, and E.C. Holmes Widespread intra-serotype recombination in natural populations of dengue virus Proc. Natl Acad. Sci. USA 96 1999 7352 7357
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 7352-7357
    • Worobey, M.1    Rambaut, A.2    Holmes, E.C.3
  • 10
    • 0033021298 scopus 로고    scopus 로고
    • Phylogenetic evidence for recombination in dengue virus
    • E.C. Holmes, M. Worobey, and A. Rambaut Phylogenetic evidence for recombination in dengue virus Mol. Biol. Evol. 16 1999 405 409
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 405-409
    • Holmes, E.C.1    Worobey, M.2    Rambaut, A.3
  • 11
    • 0141716995 scopus 로고    scopus 로고
    • SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting
    • J.S. Rest, and D.P. Mindell SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting Infect. Genet. Evol. 3 2003 219 225
    • (2003) Infect. Genet. Evol. , vol.3 , pp. 219-225
    • Rest, J.S.1    Mindell, D.P.2
  • 12
    • 0028147380 scopus 로고
    • Nonhomologous RNA recombination in tombusviruses: Generation and evolution of defective interfering RNAs by stepwise deletions
    • K.A. White, and T.J. Morris Nonhomologous RNA recombination in tombusviruses: generation and evolution of defective interfering RNAs by stepwise deletions J. Virol. 68 1994 14 24
    • (1994) J. Virol. , vol.68 , pp. 14-24
    • White, K.A.1    Morris, T.J.2
  • 13
    • 78651303213 scopus 로고    scopus 로고
    • Defective interfering RNAs: Foes of viruses and friends of virologists
    • K.B. Pathak, and P.D. Nagy Defective interfering RNAs: foes of viruses and friends of virologists Viruses 1 2009 895 919
    • (2009) Viruses , vol.1 , pp. 895-919
    • Pathak, K.B.1    Nagy, P.D.2
  • 14
    • 80052514319 scopus 로고    scopus 로고
    • Molecular characterization of Drosophila cells persistently infected with Flock House virus
    • J. Jovel, and A. Schneemann Molecular characterization of Drosophila cells persistently infected with Flock House virus Virology 419 2011 43 53
    • (2011) Virology , vol.419 , pp. 43-53
    • Jovel, J.1    Schneemann, A.2
  • 15
    • 0027273331 scopus 로고
    • Cis-Acting requirements for the replication of flock house virus RNA 2
    • L.A. Ball, and Y. Li cis-Acting requirements for the replication of flock house virus RNA 2 J. Virol. 67 1993 3544 3551
    • (1993) J. Virol. , vol.67 , pp. 3544-3551
    • Ball, L.A.1    Li, Y.2
  • 16
    • 79955778236 scopus 로고    scopus 로고
    • Defective interfering viral particles in acute dengue infections
    • D. Li, W.B. Lott, K. Lowry, A. Jones, H.M. Thu, and J. Aaskov Defective interfering viral particles in acute dengue infections PLoS One 6 2011 e19447
    • (2011) PLoS One , vol.6 , pp. 19447
    • Li, D.1    Lott, W.B.2    Lowry, K.3    Jones, A.4    Thu, H.M.5    Aaskov, J.6
  • 17
    • 84862793341 scopus 로고    scopus 로고
    • Internally deleted WNV genomes isolated from exotic birds in New Mexico: Function in cells, mosquitoes, and mice
    • K.N. Pesko, K.A. Fitzpatrick, E.M. Ryan, P.Y. Shi, B. Zhang, and N.J. Lennon Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice Virology 427 2012 10 17
    • (2012) Virology , vol.427 , pp. 10-17
    • Pesko, K.N.1    Fitzpatrick, K.A.2    Ryan, E.M.3    Shi, P.Y.4    Zhang, B.5    Lennon, N.J.6
  • 18
    • 38449106713 scopus 로고    scopus 로고
    • Penetration of nonenveloped viruses into the cytoplasm
    • B. Tsai Penetration of nonenveloped viruses into the cytoplasm Annu. Rev. Cell Dev. Biol. 23 2007 23 43
    • (2007) Annu. Rev. Cell Dev. Biol. , vol.23 , pp. 23-43
    • Tsai, B.1
  • 19
    • 79952111899 scopus 로고    scopus 로고
    • Flock house virus: A model system for understanding non-enveloped virus entry and membrane penetration
    • A. Odegard, M. Banerjee, and J.E. Johnson Flock house virus: a model system for understanding non-enveloped virus entry and membrane penetration Curr. Top. Microbiol. Immunol. 343 2010 1 22
    • (2010) Curr. Top. Microbiol. Immunol. , vol.343 , pp. 1-22
    • Odegard, A.1    Banerjee, M.2    Johnson, J.E.3
  • 21
    • 84863181640 scopus 로고    scopus 로고
    • Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus
    • A. Routh, T. Domitrovic, and J.E. Johnson Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus Proc. Natl Acad. Sci. USA 109 2012 1907 1912
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 1907-1912
    • Routh, A.1    Domitrovic, T.2    Johnson, J.E.3
  • 22
    • 0027516461 scopus 로고
    • Use of recombinant baculoviruses in synthesis of morphologically distinct viruslike particles of flock house virus, a nodavirus
    • A. Schneemann, R. Dasgupta, J.E. Johnson, and R.R. Rueckert Use of recombinant baculoviruses in synthesis of morphologically distinct viruslike particles of flock house virus, a nodavirus J. Virol. 67 1993 2756 2763
    • (1993) J. Virol. , vol.67 , pp. 2756-2763
    • Schneemann, A.1    Dasgupta, R.2    Johnson, J.E.3    Rueckert, R.R.4
  • 23
    • 34547643929 scopus 로고    scopus 로고
    • Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance
    • C. Wang, Y. Mitsuya, B. Gharizadeh, M. Ronaghi, and R.W. Shafer Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance Genome Res. 17 2007 1195 1201
    • (2007) Genome Res. , vol.17 , pp. 1195-1201
    • Wang, C.1    Mitsuya, Y.2    Gharizadeh, B.3    Ronaghi, M.4    Shafer, R.W.5
  • 25
    • 79551712478 scopus 로고    scopus 로고
    • Beyond the consensus: Dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing
    • C.F. Wright, M.J. Morelli, G. Thebaud, N.J. Knowles, P. Herzyk, and D.J. Paton Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing J. Virol. 85 2011 2266 2275
    • (2011) J. Virol. , vol.85 , pp. 2266-2275
    • Wright, C.F.1    Morelli, M.J.2    Thebaud, G.3    Knowles, N.J.4    Herzyk, P.5    Paton, D.J.6
  • 26
    • 80051507403 scopus 로고    scopus 로고
    • TopHat-Fusion: An algorithm for discovery of novel fusion transcripts
    • D. Kim, and S.L. Salzberg TopHat-Fusion: an algorithm for discovery of novel fusion transcripts Genome Biol. 12 2011 R72
    • (2011) Genome Biol. , vol.12 , pp. 72
    • Kim, D.1    Salzberg, S.L.2
  • 27
    • 79959331609 scopus 로고    scopus 로고
    • Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing
    • K. Kannan, L. Wang, J. Wang, M.M. Ittmann, W. Li, and L. Yen Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing Proc. Natl Acad. Sci. USA 108 2011 9172 9177
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 9172-9177
    • Kannan, K.1    Wang, L.2    Wang, J.3    Ittmann, M.M.4    Li, W.5    Yen, L.6
  • 28
    • 80053385552 scopus 로고    scopus 로고
    • Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
    • A.J. Bass, M.S. Lawrence, L.E. Brace, A.H. Ramos, Y. Drier, and K. Cibulskis Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion Nat. Genet. 43 2011 964 968
    • (2011) Nat. Genet. , vol.43 , pp. 964-968
    • Bass, A.J.1    Lawrence, M.S.2    Brace, L.E.3    Ramos, A.H.4    Drier, Y.5    Cibulskis, K.6
  • 30
    • 0031658922 scopus 로고    scopus 로고
    • Specific encapsidation of nodavirus RNAs is mediated through the C terminus of capsid precursor protein alpha
    • A. Schneemann, and D. Marshall Specific encapsidation of nodavirus RNAs is mediated through the C terminus of capsid precursor protein alpha J. Virol. 72 1998 8738 8746
    • (1998) J. Virol. , vol.72 , pp. 8738-8746
    • Schneemann, A.1    Marshall, D.2
  • 31
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
    • (2009) Genome Biol. , vol.10 , pp. 25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 32
    • 76249103869 scopus 로고    scopus 로고
    • Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs
    • Q. Wu, Y. Luo, R. Lu, N. Lau, E.C. Lai, W.X. Li, and S.W. Ding Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs Proc. Natl Acad. Sci. USA 107 2010 1606 1611
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 1606-1611
    • Wu, Q.1    Luo, Y.2    Lu, R.3    Lau, N.4    Lai, E.C.5    Li, W.X.6    Ding, S.W.7
  • 33
    • 80052457069 scopus 로고    scopus 로고
    • Ensuring the safety of vaccine cell substrates by massively parallel sequencing of the transcriptome
    • D. Onions, C. Cote, B. Love, B. Toms, S. Koduri, and A. Armstrong Ensuring the safety of vaccine cell substrates by massively parallel sequencing of the transcriptome Vaccine 29 2011 7117 7121
    • (2011) Vaccine , vol.29 , pp. 7117-7121
    • Onions, D.1    Cote, C.2    Love, B.3    Toms, B.4    Koduri, S.5    Armstrong, A.6
  • 34
    • 35148857107 scopus 로고    scopus 로고
    • Latent infection of a new alphanodavirus in an insect cell line
    • T.C. Li, P.D. Scotti, T. Miyamura, and N. Takeda Latent infection of a new alphanodavirus in an insect cell line J. Virol. 81 2007 10890 10896
    • (2007) J. Virol. , vol.81 , pp. 10890-10896
    • Li, T.C.1    Scotti, P.D.2    Miyamura, T.3    Takeda, N.4
  • 35
    • 18144391518 scopus 로고    scopus 로고
    • Capsid protein synthesis from replicating RNA directs specific packaging of the genome of a multipartite, positive-strand RNA virus
    • P.A. Venter, N.K. Krishna, and A. Schneemann Capsid protein synthesis from replicating RNA directs specific packaging of the genome of a multipartite, positive-strand RNA virus J. Virol. 79 2005 6239 6248
    • (2005) J. Virol. , vol.79 , pp. 6239-6248
    • Venter, P.A.1    Krishna, N.K.2    Schneemann, A.3
  • 36
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • A.L. Barabasi, and R. Albert Emergence of scaling in random networks Science 286 1999 509 512
    • (1999) Science , vol.286 , pp. 509-512
    • Barabasi, A.L.1    Albert, R.2
  • 37
    • 0242713700 scopus 로고    scopus 로고
    • The dominance of the population by a selected few: Power-law behaviour applies to a wide variety of genomic properties
    • RESEARCH0040
    • N.M. Luscombe, J. Qian, Z. Zhang, T. Johnson, and M. Gerstein The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties Genome Biol. 3 2002 RESEARCH0040
    • (2002) Genome Biol. , vol.3
    • Luscombe, N.M.1    Qian, J.2    Zhang, Z.3    Johnson, T.4    Gerstein, M.5
  • 38
    • 77956152508 scopus 로고    scopus 로고
    • The impact of PCR-generated recombination on diversity estimation of mixed viral populations by deep sequencing
    • I. Gorzer, C. Guelly, S. Trajanoski, and E. Puchhammer-Stockl The impact of PCR-generated recombination on diversity estimation of mixed viral populations by deep sequencing J. Virol. Methods 169 2010 248 252
    • (2010) J. Virol. Methods , vol.169 , pp. 248-252
    • Gorzer, I.1    Guelly, C.2    Trajanoski, S.3    Puchhammer-Stockl, E.4
  • 39
    • 2342419732 scopus 로고    scopus 로고
    • DNA replication fidelity
    • T.A. Kunkel DNA replication fidelity J. Biol. Chem. 279 2004 16895 16898
    • (2004) J. Biol. Chem. , vol.279 , pp. 16895-16898
    • Kunkel, T.A.1
  • 40
    • 0037324140 scopus 로고    scopus 로고
    • Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites
    • D. Shinde, Y. Lai, F. Sun, and N. Arnheim Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites Nucleic Acids Res. 31 2003 974 980
    • (2003) Nucleic Acids Res. , vol.31 , pp. 974-980
    • Shinde, D.1    Lai, Y.2    Sun, F.3    Arnheim, N.4
  • 43
    • 0014961824 scopus 로고
    • Defective viral particles and viral disease processes
    • A.S. Huang, and D. Baltimore Defective viral particles and viral disease processes Nature 226 1970 325 327
    • (1970) Nature , vol.226 , pp. 325-327
    • Huang, A.S.1    Baltimore, D.2
  • 44
    • 0023763122 scopus 로고
    • Biased hypermutation and other genetic changes in defective measles viruses in human brain infections
    • R. Cattaneo, A. Schmid, D. Eschle, K. Baczko, V. ter Meulen, and M.A. Billeter Biased hypermutation and other genetic changes in defective measles viruses in human brain infections Cell 55 1988 255 265
    • (1988) Cell , vol.55 , pp. 255-265
    • Cattaneo, R.1    Schmid, A.2    Eschle, D.3    Baczko, K.4    Ter Meulen, V.5    Billeter, M.A.6
  • 45
    • 30844446303 scopus 로고    scopus 로고
    • Long-term transmission of defective RNA viruses in humans and Aedes mosquitoes
    • J. Aaskov, K. Buzacott, H.M. Thu, K. Lowry, and E.C. Holmes Long-term transmission of defective RNA viruses in humans and Aedes mosquitoes Science 311 2006 236 238
    • (2006) Science , vol.311 , pp. 236-238
    • Aaskov, J.1    Buzacott, K.2    Thu, H.M.3    Lowry, K.4    Holmes, E.C.5
  • 46
    • 36048983551 scopus 로고    scopus 로고
    • Characterization of hepatitis C virus deletion mutants circulating in chronically infected patients
    • S. Noppornpanth, S.L. Smits, T.X. Lien, Y. Poovorawan, A.D. Osterhaus, and B.L. Haagmans Characterization of hepatitis C virus deletion mutants circulating in chronically infected patients J. Virol. 81 2007 12496 12503
    • (2007) J. Virol. , vol.81 , pp. 12496-12503
    • Noppornpanth, S.1    Smits, S.L.2    Lien, T.X.3    Poovorawan, Y.4    Osterhaus, A.D.5    Haagmans, B.L.6
  • 47
    • 33646162162 scopus 로고    scopus 로고
    • Interfering vaccine (defective interfering influenza A virus) protects ferrets from influenza, and allows them to develop solid immunity to reinfection
    • A. Mann, A.C. Marriott, S. Balasingam, R. Lambkin, J.S. Oxford, and N.J. Dimmock Interfering vaccine (defective interfering influenza A virus) protects ferrets from influenza, and allows them to develop solid immunity to reinfection Vaccine 24 2006 4290 4296
    • (2006) Vaccine , vol.24 , pp. 4290-4296
    • Mann, A.1    Marriott, A.C.2    Balasingam, S.3    Lambkin, R.4    Oxford, J.S.5    Dimmock, N.J.6
  • 48
    • 78651452290 scopus 로고    scopus 로고
    • Suppression of avian influenza transmission in genetically modified chickens
    • J. Lyall, R.M. Irvine, A. Sherman, T.J. McKinley, A. Nunez, and A. Purdie Suppression of avian influenza transmission in genetically modified chickens Science 331 2011 223 226
    • (2011) Science , vol.331 , pp. 223-226
    • Lyall, J.1    Irvine, R.M.2    Sherman, A.3    McKinley, T.J.4    Nunez, A.5    Purdie, A.6
  • 49
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • M. Martin Cutadapt removes adapter sequences from high-throughput sequencing reads EMBnet J 17 2011 10 12
    • (2011) EMBnet J , vol.17 , pp. 10-12
    • Martin, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.