메뉴 건너뛰기




Volumn 460, Issue 7256, 2009, Pages 711-716

Architecture and secondary structure of an entire HIV-1 RNA genome

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS PROTEIN; VIRUS RNA;

EID: 68449092202     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature08237     Document Type: Article
Times cited : (648)

References (52)
  • 3
    • 0031711593 scopus 로고    scopus 로고
    • HIV-1: Fifteen proteins and an RNA
    • Frankel, A. D. & Young, J. A. HIV-1: fifteen proteins and an RNA. Annu. Rev. Biochem. 67, 1-25 (1998).
    • (1998) Annu. Rev. Biochem , vol.67 , pp. 1-25
    • Frankel, A.D.1    Young, J.A.2
  • 5
    • 33947379083 scopus 로고    scopus 로고
    • Host factors exploited by retroviruses
    • Goff, S. P. Host factors exploited by retroviruses. Nature Rev. Microbiol. 5, 253-263 (2007).
    • (2007) Nature Rev. Microbiol , vol.5 , pp. 253-263
    • Goff, S.P.1
  • 6
    • 40849123031 scopus 로고    scopus 로고
    • High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states
    • Wilkinson, K. A. et al. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol. 6, e96 (2008).
    • (2008) PLoS Biol , vol.6
    • Wilkinson, K.A.1
  • 7
    • 23144448275 scopus 로고    scopus 로고
    • Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: Critical role in reverse transcription and molecular mechanism
    • Levin, J. G., Guo, J., Rouzina, I. & Musier-Forsyth, K. Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. Prog. Nucleic Acid Res. Mol. Biol. 80, 217-286 (2005).
    • (2005) Prog. Nucleic Acid Res. Mol. Biol , vol.80 , pp. 217-286
    • Levin, J.G.1    Guo, J.2    Rouzina, I.3    Musier-Forsyth, K.4
  • 8
    • 0037155223 scopus 로고    scopus 로고
    • In vitro evidence for a long range pseudoknot in the 5′-untranslated and matrix coding regions of HIV-1 genomic RNA
    • Paillart, J. C., Skripkin, E., Ehresmann, B., Ehresmann, C. & Marquet, R. In vitro evidence for a long range pseudoknot in the 5′-untranslated and matrix coding regions of HIV-1 genomic RNA. J. Biol. Chem. 277, 5995-6004 (2002).
    • (2002) J. Biol. Chem , vol.277 , pp. 5995-6004
    • Paillart, J.C.1    Skripkin, E.2    Ehresmann, B.3    Ehresmann, C.4    Marquet, R.5
  • 9
    • 16244412610 scopus 로고    scopus 로고
    • RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE)
    • Merino, E. J., Wilkinson, K. A., Coughlan, J. L. & Weeks, K. M. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 127, 4223-4231 (2005).
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 4223-4231
    • Merino, E.J.1    Wilkinson, K.A.2    Coughlan, J.L.3    Weeks, K.M.4
  • 10
    • 34247162792 scopus 로고    scopus 로고
    • A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry
    • Mortimer, S. A. & Weeks, K. M. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J. Am. Chem. Soc. 129, 4144-4145 (2007).
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 4144-4145
    • Mortimer, S.A.1    Weeks, K.M.2
  • 11
    • 52949152433 scopus 로고    scopus 로고
    • Shape Finder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis
    • Vasa, S. M., Guex, N., Wilkinson, K. A., Weeks, K. M. & Giddings, M. C. Shape Finder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA 14, 1979-1990 (2008).
    • (2008) RNA , vol.14 , pp. 1979-1990
    • Vasa, S.M.1    Guex, N.2    Wilkinson, K.A.3    Weeks, K.M.4    Giddings, M.C.5
  • 12
    • 51949099863 scopus 로고    scopus 로고
    • Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA
    • Gherghe, C. M., Shajani, Z., Wilkinson, K. A., Varani, G. & Weeks, K. M. Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA. J. Am. Chem. Soc. 130, 12244-12245 (2008).
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 12244-12245
    • Gherghe, C.M.1    Shajani, Z.2    Wilkinson, K.A.3    Varani, G.4    Weeks, K.M.5
  • 13
    • 4644228621 scopus 로고    scopus 로고
    • A comparative method for finding and folding RNA secondary structures within protein-coding regions
    • Pedersen, J. S., Meyer, I. M., Forsberg, R., Simmonds, P. & Hein, J. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res. 32, 4925-4936 (2004).
    • (2004) Nucleic Acids Res , vol.32 , pp. 4925-4936
    • Pedersen, J.S.1    Meyer, I.M.2    Forsberg, R.3    Simmonds, P.4    Hein, J.5
  • 14
    • 25144458435 scopus 로고    scopus 로고
    • Theoretical Biology and Biophysics Group
    • Leitner, T. et al. HIV Sequence Compendium (Theoretical Biology and Biophysics Group, 2005).
    • (2005) HIV Sequence Compendium
    • Leitner, T.1
  • 15
    • 0027494083 scopus 로고
    • Alternative splicing of human immunodeficiency virus type 1 mRNA modulates viral protein expression, replication, and infectivity
    • Purcell, D. F. & Martin, M. A. Alternative splicing of human immunodeficiency virus type 1 mRNA modulates viral protein expression, replication, and infectivity. J. Virol. 67, 6365-6378 (1993).
    • (1993) J. Virol , vol.67 , pp. 6365-6378
    • Purcell, D.F.1    Martin, M.A.2
  • 16
    • 0032543307 scopus 로고    scopus 로고
    • Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody
    • Kwong, P. D. et al. Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 393, 648-659 (1998).
    • (1998) Nature , vol.393 , pp. 648-659
    • Kwong, P.D.1
  • 17
    • 58149199728 scopus 로고    scopus 로고
    • A pause for thought along the co-translational folding pathway
    • Komar, A. A. A pause for thought along the co-translational folding pathway. Trends Biochem. Sci. 34, 16-24 (2009).
    • (2009) Trends Biochem. Sci , vol.34 , pp. 16-24
    • Komar, A.A.1
  • 18
    • 0029870925 scopus 로고    scopus 로고
    • Programmed translational frameshifting
    • Farabaugh, P. J. Programmed translational frameshifting. Microbiol. Rev. 60, 103-134 (1996).
    • (1996) Microbiol. Rev , vol.60 , pp. 103-134
    • Farabaugh, P.J.1
  • 19
    • 41149155366 scopus 로고    scopus 로고
    • Following translation by single ribosomes one codon at a time
    • Wen, J. D. et al. Following translation by single ribosomes one codon at a time. Nature 452, 598-603 (2008).
    • (2008) Nature , vol.452 , pp. 598-603
    • Wen, J.D.1
  • 20
    • 33845899137 scopus 로고    scopus 로고
    • Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
    • Nackley, A. G. et al. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314, 1930-1933 (2006).
    • (2006) Science , vol.314 , pp. 1930-1933
    • Nackley, A.G.1
  • 21
    • 0024252185 scopus 로고
    • Extension inhibition analysis of translation initiation complexes
    • Hartz, D., McPheeters, D. S., Traut, R. & Gold, L. Extension inhibition analysis of translation initiation complexes. Methods Enzymol. 164, 419-425 (1988).
    • (1988) Methods Enzymol , vol.164 , pp. 419-425
    • Hartz, D.1    McPheeters, D.S.2    Traut, R.3    Gold, L.4
  • 22
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews, D. H. et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA 101, 7287-7292 (2004).
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 7287-7292
    • Mathews, D.H.1
  • 24
    • 13844281898 scopus 로고    scopus 로고
    • Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy
    • Kim, D. H. et al. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nature Biotechnol. 23, 222-226 (2005).
    • (2005) Nature Biotechnol , vol.23 , pp. 222-226
    • Kim, D.H.1
  • 25
    • 0025266354 scopus 로고
    • Intracellular processing of the gp160 HIV-1 envelope precursor. Endoproteolytic cleavage occurs in a cisor medial compartment of the Golgi complex
    • Stein, B. S. & Engleman, E. G. Intracellular processing of the gp160 HIV-1 envelope precursor. Endoproteolytic cleavage occurs in a cisor medial compartment of the Golgi complex. J. Biol. Chem. 265, 2640-2649 (1990).
    • (1990) J. Biol. Chem , vol.265 , pp. 2640-2649
    • Stein, B.S.1    Engleman, E.G.2
  • 26
    • 0024230701 scopus 로고
    • HIV expression strategies: Ribosomal frameshifting is directed by a short sequence in both mammalian and yeast systems
    • Wilson, W. et al. HIV expression strategies: ribosomal frameshifting is directed by a short sequence in both mammalian and yeast systems. Cell 55, 1159-1169 (1988).
    • (1988) Cell , vol.55 , pp. 1159-1169
    • Wilson, W.1
  • 27
    • 0034724565 scopus 로고    scopus 로고
    • Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting
    • Giedroc, D. P., Theimer, C. A. & Nixon, P. L. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J. Mol. Biol. 298, 167-185 (2000).
    • (2000) J. Mol. Biol , vol.298 , pp. 167-185
    • Giedroc, D.P.1    Theimer, C.A.2    Nixon, P.L.3
  • 28
    • 0842304470 scopus 로고    scopus 로고
    • The human immunodeficiency virus type 1 ribosomal frameshifting site is an invariant sequence determinant and an important target for antiviral therapy
    • Biswas, P., Jiang, X., Pacchia, A. L., Dougherty, J. P. & Peltz, S. W. The human immunodeficiency virus type 1 ribosomal frameshifting site is an invariant sequence determinant and an important target for antiviral therapy. J. Virol. 78, 2082-2087 (2004).
    • (2004) J. Virol , vol.78 , pp. 2082-2087
    • Biswas, P.1    Jiang, X.2    Pacchia, A.L.3    Dougherty, J.P.4    Peltz, S.W.5
  • 29
    • 0035082773 scopus 로고    scopus 로고
    • Ability of the V3 loop of simian immunodeficiency virus to serve as a target for antibody-mediated neutralization: Correlation of neutralization sensitivity, growth in macrophages, and decreased dependence on CD4
    • Means, R. E. et al. Ability of the V3 loop of simian immunodeficiency virus to serve as a target for antibody-mediated neutralization: correlation of neutralization sensitivity, growth in macrophages, and decreased dependence on CD4. J. Virol. 75, 3903-3915 (2001).
    • (2001) J. Virol , vol.75 , pp. 3903-3915
    • Means, R.E.1
  • 30
    • 0015847039 scopus 로고
    • A new technique for the assay of infectivity of human adenovirus 5 DNA
    • Graham, F. L. & van der Eb, A. J. A new technique for the assay of infectivity of human adenovirus 5 DNA. Virology 52, 456-467 (1973).
    • (1973) Virology , vol.52 , pp. 456-467
    • Graham, F.L.1    van der Eb, A.J.2
  • 31
    • 0022495870 scopus 로고
    • Production of acquired immunodeficiency syndrome-associated retrovirusin human and nonhuman cells transfected with an infectious molecular clone
    • Adachi, A. et al. Production of acquired immunodeficiency syndrome-associated retrovirusin human and nonhuman cells transfected with an infectious molecular clone. J. Virol. 59, 284-291 (1986).
    • (1986) J. Virol , vol.59 , pp. 284-291
    • Adachi, A.1
  • 32
    • 0036091692 scopus 로고    scopus 로고
    • Envelope glycoprotein incorporation, not shedding of surface envelope glycoprotein (gp120/SU), is the primary determinant of SU content of purified human immunodeficiency virus type 1 and simian immunodeficiency virus
    • Chertova, E. et al. Envelope glycoprotein incorporation, not shedding of surface envelope glycoprotein (gp120/SU), is the primary determinant of SU content of purified human immunodeficiency virus type 1 and simian immunodeficiency virus. J. Virol. 76, 5315-5325 (2002).
    • (2002) J. Virol , vol.76 , pp. 5315-5325
    • Chertova, E.1
  • 33
    • 0029151733 scopus 로고
    • Analysis and localization of cyclophilin A found in the virions of human immunodeficiency virus type 1 MN strain
    • Ott, D. E. et al. Analysis and localization of cyclophilin A found in the virions of human immunodeficiency virus type 1 MN strain. AIDS Res. Hum. Retroviruses 11, 1003-1006 (1995).
    • (1995) AIDS Res. Hum. Retroviruses , vol.11 , pp. 1003-1006
    • Ott, D.E.1
  • 34
    • 33747875746 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 nucleocapsid zinc-finger mutations cause defects in reverse transcription and integration
    • Thomas, J. A. et al. Human immunodeficiency virus type 1 nucleocapsid zinc-finger mutations cause defects in reverse transcription and integration. Virology 353, 41-51 (2006).
    • (2006) Virology , vol.353 , pp. 41-51
    • Thomas, J.A.1
  • 35
    • 23844524271 scopus 로고    scopus 로고
    • Highly sensitive SIV plasma viral load assay: Practical considerations, realistic performance expectations, and application to reverse engineering of vaccines for AIDS
    • Cline, A. N., Bess, J. W., Piatak, M. Jr & Lifson, J. D. Highly sensitive SIV plasma viral load assay: practical considerations, realistic performance expectations, and application to reverse engineering of vaccines for AIDS. J. Med. Primatol. 34, 303-312 (2005).
    • (2005) J. Med. Primatol , vol.34 , pp. 303-312
    • Cline, A.N.1    Bess, J.W.2    Piatak Jr, M.3    Lifson, J.D.4
  • 36
    • 0037223701 scopus 로고    scopus 로고
    • 2+ fingers are required for efficient reverse transcription, initia integration processes, and protection of newly synthesized viral DNA
    • 2+ fingers are required for efficient reverse transcription, initia integration processes, and protection of newly synthesized viral DNA. J. Virol. 77, 1469-1480 (2003).
    • (2003) J. Virol , vol.77 , pp. 1469-1480
    • Buckman, J.S.1    Bosche, W.J.2    Gorelick, R.J.3
  • 37
    • 33947720028 scopus 로고    scopus 로고
    • Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): Quantitative RNA structure analysis at single nucleotide resolution
    • Wilkinson, K. A., Merino, E. J. & Weeks, K. M. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nature Protocols 1, 1610-1616 (2006).
    • (2006) Nature Protocols , vol.1 , pp. 1610-1616
    • Wilkinson, K.A.1    Merino, E.J.2    Weeks, K.M.3
  • 38
    • 33750356022 scopus 로고    scopus 로고
    • Architecture of a gamma retroviral genomic RNA dimer
    • Badorrek, C. S. & Weeks, K. M. Architecture of a gamma retroviral genomic RNA dimer. Biochemistry 45, 12664-12672 (2006).
    • (2006) Biochemistry , vol.45 , pp. 12664-12672
    • Badorrek, C.S.1    Weeks, K.M.2
  • 39
    • 13244260785 scopus 로고    scopus 로고
    • Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
    • Dowell, R. D. & Eddy, S. R. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics 5, 71 (2004).
    • (2004) BMC Bioinformatics , vol.5 , pp. 71
    • Dowell, R.D.1    Eddy, S.R.2
  • 40
    • 0025100771 scopus 로고
    • Secondary structure is the major determinant for interaction of HIV rev protein with RNA
    • Olsen, H. S., Nelbock, P., Cochrane, A. W. & Rosen, C. A. Secondary structure is the major determinant for interaction of HIV rev protein with RNA. Science 247, 845-848 (1990).
    • (1990) Science , vol.247 , pp. 845-848
    • Olsen, H.S.1    Nelbock, P.2    Cochrane, A.W.3    Rosen, C.A.4
  • 41
    • 67649371451 scopus 로고    scopus 로고
    • Influence of nucleotide identity on ribose 2′-hydroxy reactivity in RNA
    • Wilkinson, K. A. et al. Influence of nucleotide identity on ribose 2′-hydroxy reactivity in RNA. RNA 15, 1314-1321 (2009).
    • (2009) RNA , vol.15 , pp. 1314-1321
    • Wilkinson, K.A.1
  • 42
    • 27744554044 scopus 로고    scopus 로고
    • Badorrek, C. S. & Weeks, K. M. RNA flexibility in the dimerization domain of a gamma retrovirus. Nature Chem. Biol. 1, 104-111 (2005).
    • Badorrek, C. S. & Weeks, K. M. RNA flexibility in the dimerization domain of a gamma retrovirus. Nature Chem. Biol. 1, 104-111 (2005).
  • 43
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • Knudsen, B. & Hein, J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 31, 3423-3428 (2003).
    • (2003) Nucleic Acids Res , vol.31 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 45
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein, J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376 (1981).
    • (1981) J. Mol. Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 46
    • 34547761762 scopus 로고    scopus 로고
    • Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: Subtype G is a circulating recombinant form
    • Abecasis, A. B. et al. Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. J. Virol. 81, 8543-8551 (2007).
    • (2007) J. Virol , vol.81 , pp. 8543-8551
    • Abecasis, A.B.1
  • 47
    • 68449097149 scopus 로고    scopus 로고
    • The R Development Core Team. The R Foundation for Statistical Computing (2008).
    • (2008)
  • 48
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G. & Gibson, T. J. 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, 4673-4680 (1994).
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 49
    • 48449084852 scopus 로고    scopus 로고
    • RNALogo: A new approach to display structural RNA alignment
    • Chang, T. H., Horng, J. T. & Huang, H. D. RNALogo: a new approach to display structural RNA alignment. Nucleic Acids Res. 36, W91-W96 (2008).
    • (2008) Nucleic Acids Res , vol.36
    • Chang, T.H.1    Horng, J.T.2    Huang, H.D.3
  • 50
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs
    • Xia, T. et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry 37, 14719-14735 (1998).
    • (1998) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1
  • 51
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA secondary structure
    • Mathews, D. H., Sabina, J., Zuker, M. & Turner, D. H. Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940 (1999).
    • (1999) J. Mol. Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 52
    • 0029878720 scopus 로고    scopus 로고
    • Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33-38 27-38 (1996).
    • Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33-38 27-38 (1996).


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.