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Volumn 14, Issue 12, 2008, Pages 2478-2488

Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene

Author keywords

Covariation; HIV 1 pol gene; RNA secondary structure; SHAPE; Synonymous variability; Thermodynamic prediction

Indexed keywords

PROTEINASE; RNA;

EID: 57049152936     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1252608     Document Type: Article
Times cited : (21)

References (45)
  • 1
    • 0038176532 scopus 로고    scopus 로고
    • A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon
    • Abbink, T.E. and Berkhout, B. 2003. A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon. J. Biol. Chem. 278: 11601-11611.
    • (2003) J. Biol. Chem , vol.278 , pp. 11601-11611
    • Abbink, T.E.1    Berkhout, B.2
  • 2
    • 84972545970 scopus 로고
    • A survey of exact inference for contingency tables
    • Agresti, A. 1992. A survey of exact inference for contingency tables. Stat. Sci. 7: 131-177.
    • (1992) Stat. Sci , vol.7 , pp. 131-177
    • Agresti, A.1
  • 3
    • 27744554044 scopus 로고    scopus 로고
    • RNA flexibility in the dimerization domain of a g retrovirus
    • Badorrek, C.S. and Weeks, K.M. 2005. RNA flexibility in the dimerization domain of a g retrovirus. Nat. Chem. Biol. 1: 104-111.
    • (2005) Nat. Chem. Biol , vol.1 , pp. 104-111
    • Badorrek, C.S.1    Weeks, K.M.2
  • 4
    • 0026528771 scopus 로고
    • Structural features in TAR RNA of human and simian immunodeficiency viruses: A phylogenetic analysis
    • Berkhout, B. 1992. Structural features in TAR RNA of human and simian immunodeficiency viruses: A phylogenetic analysis. Nucleic Acids Res. 20: 27-31.
    • (1992) Nucleic Acids Res , vol.20 , pp. 27-31
    • Berkhout, B.1
  • 6
    • 1842509978 scopus 로고    scopus 로고
    • Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase
    • Chen, L., Perlina, A., and Lee, C.J. 2004. Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase. J. Virol. 78: 3722-3732.
    • (2004) J. Virol , vol.78 , pp. 3722-3732
    • Chen, L.1    Perlina, A.2    Lee, C.J.3
  • 9
    • 13944278373 scopus 로고    scopus 로고
    • SAFA: Semiautomated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
    • Das, R., Laederach, A., Pearlman, S.M., Herschlag, D., and Altman, R.B. 2005. SAFA: Semiautomated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 11: 344-354.
    • (2005) RNA , vol.11 , pp. 344-354
    • Das, R.1    Laederach, A.2    Pearlman, S.M.3    Herschlag, D.4    Altman, R.B.5
  • 10
    • 57049131652 scopus 로고    scopus 로고
    • Fisher, R.A. 1922. On the interpretation of χ(2) from contingency tables, and the calculation of P. J. R. Stat. Soc. [Ser A] 85: 87-94.
    • Fisher, R.A. 1922. On the interpretation of χ(2) from contingency tables, and the calculation of P. J. R. Stat. Soc. [Ser A] 85: 87-94.
  • 11
    • 4344592441 scopus 로고    scopus 로고
    • The structure of HIV-1 genomic RNA in the gp120 gene determines a recombination hot spot in vivo
    • Galetto, R., Moumen, A., Giacomoni, V., Veron, M., Charneau, P., and Negroni, M. 2004. The structure of HIV-1 genomic RNA in the gp120 gene determines a recombination hot spot in vivo. J. Biol. Chem. 279: 36625-36632.
    • (2004) J. Biol. Chem , vol.279 , pp. 36625-36632
    • Galetto, R.1    Moumen, A.2    Giacomoni, V.3    Veron, M.4    Charneau, P.5    Negroni, M.6
  • 12
    • 33646374954 scopus 로고    scopus 로고
    • Dissection of a circumscribed recombination hot spot in HIV-1 after a single infectious cycle
    • Galetto, R., Giacomoni, V., Veron, M., and Negroni, M. 2006. Dissection of a circumscribed recombination hot spot in HIV-1 after a single infectious cycle. J. Biol. Chem. 281: 2711-2720.
    • (2006) J. Biol. Chem , vol.281 , pp. 2711-2720
    • Galetto, R.1    Giacomoni, V.2    Veron, M.3    Negroni, M.4
  • 14
    • 34547556305 scopus 로고    scopus 로고
    • The RNAz web server: Prediction of thermodynamically stable and evolutionarily conserved RNA structures
    • Gruber, A.R., Neubock, R., Hofacker, I.L., and Washietl, S. 2007. The RNAz web server: Prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res. 35: W335-W338.
    • (2007) Nucleic Acids Res , vol.35
    • Gruber, A.R.1    Neubock, R.2    Hofacker, I.L.3    Washietl, S.4
  • 16
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker, I.L., Fekete, M., and Stadler, P.F. 2002. Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319: 1059-1066.
    • (2002) J. Mol. Biol , vol.319 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.F.3
  • 17
    • 3543051101 scopus 로고    scopus 로고
    • Conserved RNA secondary structures in viral genomes: A survey
    • Hofacker, I.L., Stadler, P.F., and Stocsits, R.R. 2004. Conserved RNA secondary structures in viral genomes: A survey. Bioinformatics 20: 1495-1499.
    • (2004) Bioinformatics , vol.20 , pp. 1495-1499
    • Hofacker, I.L.1    Stadler, P.F.2    Stocsits, R.R.3
  • 18
    • 0141519339 scopus 로고    scopus 로고
    • Widespread selection for local RNA secondary structure in coding regions of bacterial genes
    • Katz, L. and Burge, C.B. 2003. Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res. 13: 2042-2051.
    • (2003) Genome Res , vol.13 , pp. 2042-2051
    • Katz, L.1    Burge, C.B.2
  • 19
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • Knudsen, B. and Hein, J. 2003. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 31: 3423-3428.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 20
    • 0024518918 scopus 로고
    • The HIV-1 rev trans-activator acts through a structured target sequence to activate nuclear export of unspliced viral mRNA
    • Malim, M.H., Hauber, J., Le, S.Y., Maizel, J.V., and Cullen, B.R. 1989. The HIV-1 rev trans-activator acts through a structured target sequence to activate nuclear export of unspliced viral mRNA. Nature 338: 254-257.
    • (1989) Nature , vol.338 , pp. 254-257
    • Malim, M.H.1    Hauber, J.2    Le, S.Y.3    Maizel, J.V.4    Cullen, B.R.5
  • 21
    • 33744790273 scopus 로고    scopus 로고
    • Prediction of RNA secondary structure by free energy minimization
    • Mathews, D.H. and Turner, D.H. 2006. Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol. 16: 270-278.
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 270-278
    • Mathews, D.H.1    Turner, D.H.2
  • 22
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill, J.S. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 23
    • 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., and Weeks, K.M. 2005. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 127: 4223-4231.
    • (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
  • 24
    • 0024819449 scopus 로고
    • Synthesis of small RNAs using T7 RNA polymerase
    • Milligan, J.F. and Uhlenbeck, O.C. 1989. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180: 51-62.
    • (1989) Methods Enzymol , vol.180 , pp. 51-62
    • Milligan, J.F.1    Uhlenbeck, O.C.2
  • 25
    • 0035883822 scopus 로고    scopus 로고
    • The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination
    • Moumen, A., Polomack, L., Roques, B., Buc, H., and Negroni, M. 2001. The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination. Nucleic Acids Res. 29: 3814-3821.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3814-3821
    • Moumen, A.1    Polomack, L.2    Roques, B.3    Buc, H.4    Negroni, M.5
  • 27
    • 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., and Marquet, R. 2002. 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) J. Biol. Chem , vol.277 , pp. 5995-6004
    • Paillart, J.C.1    Skripkin, E.2    Ehresmann, B.3    Ehresmann, C.4    Marquet, R.5
  • 29
    • 0026717107 scopus 로고
    • Human immunodeficiency virus type 1 gag-pol frameshifting is dependent on downstream mRNA secondary structure: Demonstration by expression in vivo
    • Parkin, N.T., Chamorro, M., and Varmus, H.E. 1992. Human immunodeficiency virus type 1 gag-pol frameshifting is dependent on downstream mRNA secondary structure: Demonstration by expression in vivo. J. Virol. 66: 5147-5151.
    • (1992) J. Virol , vol.66 , pp. 5147-5151
    • Parkin, N.T.1    Chamorro, M.2    Varmus, H.E.3
  • 30
    • 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., and Hein, J. 2004. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res. 32: 4925-4936.
    • (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
  • 31
    • 0036375092 scopus 로고    scopus 로고
    • RNA secondary structure and squence conservation in C1 region of human immunodeficiency virus type 1 env gene
    • Peleg, O., Brunak, S., Trifonov, E.N., Nevo, E., and Bolshoy, A. 2002. RNA secondary structure and squence conservation in C1 region of human immunodeficiency virus type 1 env gene. AIDS Res. Hum. Retroviruses 18: 867-878.
    • (2002) AIDS Res. Hum. Retroviruses , vol.18 , pp. 867-878
    • Peleg, O.1    Brunak, S.2    Trifonov, E.N.3    Nevo, E.4    Bolshoy, A.5
  • 32
    • 0242349119 scopus 로고    scopus 로고
    • Hidden messages in the nef gene of human immunodeficiency virus type 1 suggest a novel RNA secondary structure
    • Peleg, O., Trifonov, E.N., and Bolshoy, A. 2003. Hidden messages in the nef gene of human immunodeficiency virus type 1 suggest a novel RNA secondary structure. Nucleic Acids Res. 31: 4192-4200.
    • (2003) Nucleic Acids Res , vol.31 , pp. 4192-4200
    • Peleg, O.1    Trifonov, E.N.2    Bolshoy, A.3
  • 34
    • 14844357223 scopus 로고    scopus 로고
    • Analysis of full-length human immunodeficiency virus type 1 genome reveals a variable spectrum of subtypes B and f recombinants in Sao Paulo, Brazil
    • Sa Filho, D.J., Sanabani, S., Diaz, R.S., Munerato, P., Brunstein, A., Fusuma, E., Sabino, E.C., and Janini, L.M. 2005. Analysis of full-length human immunodeficiency virus type 1 genome reveals a variable spectrum of subtypes B and f recombinants in Sao Paulo, Brazil. AIDS Res. Hum. Retroviruses 21: 145-151.
    • (2005) AIDS Res. Hum. Retroviruses , vol.21 , pp. 145-151
    • Sa Filho, D.J.1    Sanabani, S.2    Diaz, R.S.3    Munerato, P.4    Brunstein, A.5    Fusuma, E.6    Sabino, E.C.7    Janini, L.M.8
  • 35
    • 0027952970 scopus 로고
    • Antiviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase occur in specific RNA structural regions
    • Schinazi, R.F., Lloyd Jr., R.M., Ramanathan, C.S., and Taylor, E.W. 1994. Antiviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase occur in specific RNA structural regions. Antimicrob. Agents Chemother. 38: 268-274.
    • (1994) Antimicrob. Agents Chemother , vol.38 , pp. 268-274
    • Schinazi, R.F.1    Lloyd Jr., R.M.2    Ramanathan, C.S.3    Taylor, E.W.4
  • 36
    • 0033039492 scopus 로고    scopus 로고
    • Structural constraints on RNA virus evolution
    • Simmonds, P. and Smith, D.B. 1999. Structural constraints on RNA virus evolution. J. Virol. 73: 5787-5794.
    • (1999) J. Virol , vol.73 , pp. 5787-5794
    • Simmonds, P.1    Smith, D.B.2
  • 37
    • 4344619191 scopus 로고    scopus 로고
    • Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence
    • Simmonds, P., Tuplin, A., and Evans, D.J. 2004. Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence. RNA 10: 1337-1351.
    • (2004) RNA , vol.10 , pp. 1337-1351
    • Simmonds, P.1    Tuplin, A.2    Evans, D.J.3
  • 38
    • 33746555576 scopus 로고    scopus 로고
    • HIV/AIDS epidemiology, pathogenesis, prevention, and treatment
    • Simon, V., Ho, D.D., and Abdool Karim, Q. 2006. HIV/AIDS epidemiology, pathogenesis, prevention, and treatment. Lancet 368: 489-504.
    • (2006) Lancet , vol.368 , pp. 489-504
    • Simon, V.1    Ho, D.D.2    Abdool Karim, Q.3
  • 39
    • 0029057423 scopus 로고
    • The tendency of lentiviral open reading frames to become A-rich: Constraints imposed by viral genome organization and cellular tRNA availability
    • van Hemert, F.J. and Berkhout, B. 1995. The tendency of lentiviral open reading frames to become A-rich: Constraints imposed by viral genome organization and cellular tRNA availability. J. Mol. Evol. 41: 132-140.
    • (1995) J. Mol. Evol , vol.41 , pp. 132-140
    • van Hemert, F.J.1    Berkhout, B.2
  • 40
    • 41049099009 scopus 로고    scopus 로고
    • Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase
    • doi: 10.1371/journal.pone. 0000814
    • Wang, Q. and Lee, C. 2007. Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase. PLoS One 2: e814. doi: 10.1371/journal.pone. 0000814.
    • (2007) PLoS One , vol.2
    • Wang, Q.1    Lee, C.2
  • 41
    • 16344370497 scopus 로고    scopus 로고
    • RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts
    • Wilkinson, K.A., Merino, E.J., and Weeks, K.M. 2005. RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts. J. Am. Chem. Soc. 127: 4659-4667.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 4659-4667
    • Wilkinson, K.A.1    Merino, E.J.2    Weeks, K.M.3
  • 42
    • 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., and Weeks, K.M. 2006. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): Quantitative RNA structure analysis at single nucleotide resolution. Nat. Protocols 1: 1610-1616.
    • (2006) Nat. Protocols , vol.1 , pp. 1610-1616
    • Wilkinson, K.A.1    Merino, E.J.2    Weeks, K.M.3
  • 43
    • 33644853819 scopus 로고    scopus 로고
    • Can RNA selection pressure distort the measurement of Ka/Ks?
    • Xing, Y. and Lee, C. 2006. Can RNA selection pressure distort the measurement of Ka/Ks? Gene 370: 1-5.
    • (2006) Gene , vol.370 , pp. 1-5
    • Xing, Y.1    Lee, C.2
  • 45
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1


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