메뉴 건너뛰기




Volumn 154, Issue 2, 2000, Pages 909-921

Comparative sequence analysis and patterns of covariation in RNA secondary structures

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RIBONUCLEASE P; RIBOSOME RNA; RNA; RNA 5S; TRANSFER RNA;

EID: 0033980890     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (75)

References (50)
  • 1
    • 0024022215 scopus 로고
    • Tlie role of localization of bicoid RN'A in organizing the anterior pattern of the Drosophila embryo
    • BERLETH, T., M. BURRI, G. TIIOMA, D. Borr, S. RICHSTF.IN et al, 1988 Tlie role of localization of bicoid RN'A in organizing the anterior pattern of the Drosophila embryo. EMBOJ. 7: 1749-175G.
    • (1988) EMBOJ. , vol.7
    • Berleth, T.1    Burri, M.2    Tiioma, G.3    Borr, D.4    Richstfin, S.5
  • 2
    • 0031841911 scopus 로고    scopus 로고
    • The rihonuclease P database
    • BROWN, J. W., 1998 The rihonuclease P database. Nucleic Acids Res. 26: 351-352.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 351-352
    • Brown, J.W.1
  • 4
    • 0023677769 scopus 로고
    • A gradient of bicoid protein in Drosophila embryos
    • DRIEVER, W., and C. NüSSLEIN-VOLHARD, 1988 A gradient of bicoid protein in Drosophila embryos. Cell 54: 83-93.
    • (1988) Cell , vol.54 , pp. 83-93
    • Driever, W.1    Nüsslein-Volhard, C.2
  • 5
    • 0029832218 scopus 로고    scopus 로고
    • RNA-catalysed RN'A polymerization using nucleosidc triphosphatcs
    • EKLANU, E. II., and D. P. BARTF.I., 1996 RNA-catalysed RN'A polymerization using nucleosidc triphosphatcs. Nature 382: 373-376.
    • (1996) Nature , vol.382 , pp. 373-376
    • Eklanu, E.1    Bartfi, D.P.2
  • 6
    • 0030939498 scopus 로고    scopus 로고
    • RNA-RNA interaction is required for the formation of specific bicoid niRNA 3' UTR-STAUFEN ribonncleoprotein particles
    • FF.RRANDON, D., I. KOCH, E. WF.STIIOFF and C. NüSSLEIN-VOLHARD, 1997 RNA-RNA interaction is required for the formation of specific bicoid niRNA 3' UTR-STAUFEN ribonncleoprotein particles. EMBOJ. 16: 1751-1758.
    • (1997) EMBOJ. , vol.16 , pp. 1751-1758
    • Ffrrandon, D.1    Koch, I.2    Wfstiioff, E.3    Nüsslein-Volhard, C.4
  • 7
    • 0016792988 scopus 로고
    • 5S RNA secondary structure
    • Fox, G. E., and C. R. WOF.SE, 1975 5S RNA secondary structure. Nature 256: 505-507.
    • (1975) Nature , vol.256 , pp. 505-507
    • Fox, G.E.1    Wofse, C.R.2
  • 8
    • 36849148382 scopus 로고
    • The RNA world
    • GILBERT, W., 1986 The RNA world. Nature 319: 618.
    • (1986) Nature , vol.319 , pp. 618
    • Gilbert, W.1
  • 9
    • 0001657535 scopus 로고
    • Using maximum likelihood to infer selection from phytogenies
    • edited by B. Goi.niNG. Chapman Hall, New York
    • GOI.DI.NO, B., 1994 Using maximum likelihood to infer selection from phytogenies, pp. 126-139 in Non-neulral Evolution: Thrones and Molecular Data, edited by B. Goi.niNG. Chapman Hall, New York.
    • (1994) Non-neulral Evolution: Thrones and Molecular Data , pp. 126-139
    • Goidino, B.1
  • 10
    • 0024637355 scopus 로고
    • Molecular phlogeny of the kingdoms Animalia, Plantae, and Fungi
    • Gouv, M.,and W.-H. LI, 1989 Molecular ph)logeny of the kingdoms Animalia, Plantae, and Fungi. Mol. Biol. Evol. 6: 109-122.
    • (1989) Mol. Biol. Evol. , vol.6 , pp. 109-122
    • Li, W.-H.1
  • 11
    • 0021013526 scopus 로고
    • The RNA moiety of riboiuiclcasc P is the catalytic snbunit of the enzyme
    • GUERRIER-TAKADA, C., K. GARDINF.R, T. MARSH, N. PACF. and S. ALTMAN, 1983 The RNA moiety of riboiuiclcasc P is the catalytic snbunit of the enzyme. Cell 35: 849-857.
    • (1983) Cell , vol.35 , pp. 849-857
    • Guerrier-Takada, C.1    Gardinfr, K.2    Marsh, T.3    Pacf, N.4    Altman, S.5
  • 13
    • 0027221959 scopus 로고
    • Prediction of common folding structures of homologous RNAs
    • HAN, K., and H.-J. KIM, 1993 Prediction of common folding structures of homologous RNAs. Nucleic Acids Res. 21: 1251-1207.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 1251-11207
    • Han, K.1    Kim, H.-J.2
  • 14
    • 0025361553 scopus 로고
    • Predicting optimal and suboptimal secondary structure for UNA, pp. 281-306 in Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences (Methods in Enzymology, Vol. 52), edited by R
    • JAEGER, J. A., D. H. TURNER and M. ZUKER, 1990 Predicting optimal and suboptimal secondary structure for UNA, pp. 281-306 in Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences (Methods in Enzymology, Vol. 52), edited by R. F. DooLITTI.E. Academic Près, San Diego.
    • (1990) F. DooLITTI.E. Academic Près, San Diego.
    • Jaeger, J.A.1    Turner, D.H.2    Zuker, M.3
  • 15
    • 0024286617 scopus 로고
    • The secondary stnicture of ribomtclease P RNA, the catalytic element of a ribonuclcoprotcin enzyme
    • JAMES, B. D., G.J. OI.SEN, J. I.iu and N. R. PACE, 1988 The secondary stnicture of ribomtclease P RNA, the catalytic element of a ribonuclcoprotcin enzyme. Cell 52: 19-26.
    • (1988) Cell , vol.52 , pp. 19-26
    • James, B.D.1    Oisen, G.J.2    Iiu, J.3    Pace, N.R.4
  • 17
    • 0016146021 scopus 로고
    • Three-dimensional tertiär' structure of yeast phcnylalaninc transfer RNA
    • KIM, S. H., F. L. SUIWATII, G.J. Q.UIGI.EV, A. McPiiERSON, J. L. SUSSMAN el a., 1974 Three-dimensional tertiär)' structure of yeast phcnylalaninc transfer RNA. Science 185: 435-140.
    • (1974) Science , vol.185 , pp. 435-1140
    • Kim, S.H.1    Suiwatii, F.L.2    Quigiev, G.J.3    McPiierson, A.4    Sussman, J.L.5
  • 18
    • 52449148668 scopus 로고
    • The role of compensator- Neutral mutations in molecular evolution
    • KIMURA, M., 1985 The role of compensator)- neutral mutations in molecular evolution. J. Genet. 64: 7-19.
    • (1985) J. Genet. , vol.64 , pp. 7-19
    • Kimura, M.1
  • 19
    • 0029026878 scopus 로고
    • Maintenance of prc-mRNA secondary structure by epistatic selection
    • KIRIIY, D. A., S. V. MUSE and W. STEPHAN, 1995 Maintenance of prc-mRNA secondary structure by epistatic selection. Proc. Nail. Acad. Sci. USA 92: 9047-9051.
    • (1995) Proc. Nail. Acad. Sci. USA , vol.92 , pp. 9047-9051
    • Kiriiy, D.A.1    Muse, S.V.2    Stephan, W.3
  • 20
    • 0029348884 scopus 로고
    • A comparison of tliermodynamic foldings with comparatively derived structures of 1GS and IGS-likc rRNAs
    • KONINGS, D. A. M., andR. R. GUTEM., 1995 A comparison of tliermodynamic foldings with comparatively derived structures of 1GS and IGS-likc rRNAs. RNA 1: 559-574.
    • (1995) RNA , vol.1 , pp. 559-574
    • Konings, D.A.M.1    Gutem, A.R.2
  • 21
    • 0020417286 scopus 로고
    • Self-splicing RNA: Autocxcision and autocyclization of the ribosomal RNA intervening sequence of Tctrahymcna
    • KKûGEK, K., P.J. GKAISOWSKI, A.J. ZAUG.J. SANDS, D. E. GOTTSCIIUNC: et al., 1982 Self-splicing RNA: autocxcision and autocyclization of the ribosomal RNA intervening sequence of Tctrahymcna. Cell 31: 147-157.
    • (1982) Cell , vol.31 , pp. 147-157
    • Kkûgek, K.1    Gkaisowski, P.J.2    Zaug, A.J.3    Sands, J.4    Gottsciiunc, D.E.5
  • 22
    • 0029876868 scopus 로고    scopus 로고
    • 199G Evolutionär- Relationships of enkaryotic kingdoms
    • KUMAR, S., and A. RZHF.TSKY, 199G Evolutionär)- relationships of enkaryotic kingdoms. J. Mol. Evol. 42: 183-193.
    • J. Mol. Evol. , vol.42 , pp. 183-193
    • Kumar, S.1    Rzhftsky, A.2
  • 23
    • 0017780432 scopus 로고
    • The genetic analysis of meiosis in female urosolihila mclanogasler
    • LINDSLEY, D. L., and L. SANDLER, 1977 The genetic analysis of meiosis in female urosolihila mclanogasler. Philos. Trans. R. Soc. Lond. B 277: 295-312.
    • (1977) Philos. Trans. R. Soc. Lond. B , vol.277 , pp. 295-312
    • Lindsley, D.L.1    Sandler, L.2
  • 24
    • 0025074179 scopus 로고
    • RNA localization signal: Phylogenctic conservation of function and RNA secondary structure
    • MACDONAI.D, P. M., 1990 bicoid mRNA localization signal: phylogenctic conservation of function and RNA secondary structure. Development 110: 1G1-171.
    • (1990) Development , vol.110
    • Macdonaid, P.M.1
  • 25
    • 0031806104 scopus 로고    scopus 로고
    • Mutational analysis of an RNA recognition element that mediates localization of bicoid mRNA
    • MACDONALD, P. M., and K. KF.RR, 1998 Mutational analysis of an RNA recognition element that mediates localization of bicoid mRNA. Mol. Cell. Biol. 18: 3788-3795.
    • (1998) Mol. Cell. Biol. , vol.18 , pp. 3788-3795
    • Macdonald, P.M.1    Kfrr, K.2
  • 26
    • 0024282180 scopus 로고
    • Cw-acting sequences responsible for anterior localization of bicoid mRNA in Drosopihila embryos
    • MACDONALD, P. M., and G. STRUIII, 1988 Cw-acting sequences responsible for anterior localization of bicoid mRNA in Drosopihila embryos. Nature 336: 595-598.
    • (1988) Nature , vol.336 , pp. 595-598
    • Macdonald, P.M.1    Struiii, G.2
  • 28
    • 0024276911 scopus 로고
    • A stem-loop in the 3' untranslated region mediates iron-dependent regulation of transferrin receptor mRNA stability in the cytoplasm
    • MULLNER, E. W., and L. C. Kui IN, 1988 A stem-loop in the 3' untranslated region mediates iron-dependent regulation of transferrin receptor mRNA stability in the cytoplasm. Cell 53: 815-825.
    • (1988) Cell , vol.53 , pp. 815-825
    • Mullner, E.W.1    Kuiin, L.C.2
  • 29
    • 0028900996 scopus 로고
    • Evolutionär' analyses of DNA sequences subject to constraints on secondary stnicture
    • MUSE, S. V., 1995 Evolutionär)' analyses of DNA sequences subject to constraints on secondary stnicture. Genetics 139: 1429-1439.
    • (1995) Genetics , vol.139 , pp. 1429-1439
    • Muse, S.V.1
  • 30
    • 0025075436 scopus 로고
    • Synthesis and NMR study of ribo-oligonucleotidcs forming a hammcrhcacl-lypc RNA cnzrnc system
    • OIJAI, O., H. KODAMA, H. HIROAKI, T. SAKATA, T. TANAKA el al., 1990 Synthesis and NMR study of ribo-oligonucleotidcs forming a hammcrhcacl-lypc RNA cnz)rnc system. Nucleic Acids Res. 18: 5955-5960.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 5955-5960
    • Oijai, O.1    Kodama, H.2    Hiroaki, H.3    Sakata, T.4    Tanaka, T.5
  • 31
    • 0033151862 scopus 로고    scopus 로고
    • The environment of 5S rRNA in the ribosomc: Cross-links to 23S rRNA from sites within helices II and III of the 5S molecule
    • OSSWAI.D, M., and R. BRIMACOMBE, 1999 The environment of 5S rRNA in the ribosomc: cross-links to 23S rRNA from sites within helices II and III of the 5S molecule. Nucleic Acids Res. 11: 2283-2290.
    • (1999) Nucleic Acids Res. , vol.11 , pp. 2283-2290
    • Osswaid, M.1    Brimacombe, R.2
  • 32
    • 0025253318 scopus 로고
    • Kibonnclcasc P: Function and variation
    • PACE, N. R., and D. SMITH, 1990 Kibonnclcasc P: function and variation. J. Biol. Chcm. 265: 3587-3590.
    • (1990) J. Biol. Chcm. , vol.265 , pp. 3587-3590
    • Pace, N.R.1    Smith, D.2
  • 33
    • 0024416246 scopus 로고
    • Phylogcnctic comparative analysis and the secondary structure of ribonncleasc-a review
    • PACE, N. R., D. K. SMITH, G.J. OLSEN and B. D.JAMES, 1989 Phylogcnctic comparative analysis and the secondary structure of ribonncleasc-a review. Gene 82: 65-75.
    • (1989) Gene , vol.82 , pp. 65-75
    • Pace, N.R.1    Smith, D.K.2    Olsen, G.J.3    Djames, B.4
  • 34
    • 0028218876 scopus 로고
    • Point mutations in the stem-loop at the 3' end of mouse histone mRNA reduce expression by reducing the efficiency of 3' end formation
    • PANDEY, N. B., A. S. WILLIAMS, J. II. SUN, V. D. BROWN, U. BOND et al., 1994 Point mutations in the stem-loop at the 3' end of mouse histone mRNA reduce expression by reducing the efficiency of 3' end formation. Mol. Cell. Biol. 14: 1709-1720.
    • (1994) Mol. Cell. Biol. , vol.14 , pp. 1709-1720
    • Pandey, N.B.1    Williams, A.S.2    Sun, J.3    Brown, V.D.4    Bond, U.5
  • 35
    • 0031017384 scopus 로고    scopus 로고
    • Site-directed mutations reveal long-range compensator' interactions in the Adh gene of Drosophila melanogaster
    • PARSCII.J., S. TANDA and W. STEPHAN, 1997 Site-directed mutations reveal long-range compensator)' interactions in the Adh gene of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 94: 928-933.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 928-933
    • Parsciij1    Tanda, S.2    Stephan, W.3
  • 36
    • 0028063567 scopus 로고
    • Three-dimensional structure of a hammerhead ribozymc
    • PI.EY, II. W., K. M. FI.AIIERTY and D. B. McKAY, 1994 Three-dimensional structure of a hammerhead ribozymc. Nature 372: 68-74.
    • (1994) Nature , vol.372 , pp. 68-74
    • Fiaiierty, K.M.1    McKay, D.B.2
  • 37
    • 0029091043 scopus 로고
    • Estimating substitution rates in ribosomal RNA genes
    • RZHETSKY, A., 1995 Estimating substitution rates in ribosomal RNA genes. Genetics 141: 771-783.
    • (1995) Genetics , vol.141 , pp. 771-783
    • Rzhetsky, A.1
  • 38
    • 0028512129 scopus 로고
    • A stochastic model for the evolution of autocorrclated D N'A sequences
    • SCIIöXIGF.R, M., and A. vox HAE.SF.I.ER, 1994 A stochastic model for the evolution of autocorrclated D N'A sequences. Mol. Pliylogenet. Evol. 3: 240-247.
    • (1994) Mol. Pliylogenet. Evol. , vol.3 , pp. 240-247
    • Sciiöxigfr, M.1    Vox Haesfier, A.2
  • 39
    • 0029073091 scopus 로고
    • The crystal structure of an all-RNA hammerhead ribozymc: A proposed mechanism for RNA catalytic cleavage
    • SCOTT, W. G., J. T. Fixen and A. KLUG, 1995 The crystal structure of an all-RNA hammerhead ribozymc: a proposed mechanism for RNA catalytic cleavage. Cell 81: 991-1002.
    • (1995) Cell , vol.81 , pp. 991-1002
    • Scott, W.G.1    Fixen, J.T.2    Klug, A.3
  • 40
    • 0025041799 scopus 로고
    • Molecular analysis of the bifoid gene from Dmsofthila pseudoobsamr. identification of conserved domains within coding and noncoding regions of the faVwrf inRNA
    • SEEGF.R, M. A., and T. C. KAUFMAN, 1990 Molecular analysis of the bifoid gene from Dmsofthila pseudoobsamr. identification of conserved domains within coding and noncoding regions of the faVwrf inRNA. EMBOJ. 9: 2977-2987.
    • (1990) EMBOJ. , vol.9 , pp. 2977-2987
    • Seegfr, M.A.1    Kaufman, T.C.2
  • 41
    • 0025869710 scopus 로고
    • Compilation of 5S rRNA and öS rRNA gene sequences
    • SPECHT, T., J. WOLTF.RS and V. A. ERDMANN, 1991 Compilation of 5S rRNA and öS rRNA gene sequences. Nucleic Acids Res. 19: 2189-2191.
    • (1991) Nucleic Acids Res. , vol.19 , pp. 2189-2191
    • Specht, T.1    Woltfrs, J.2    Erdmann, V.A.3
  • 43
    • 0029784930 scopus 로고    scopus 로고
    • The rate of compensator' evolution
    • STEPHAX, W., 1996 The rate of compensator)' evolution. Genetics 144: 419-426.
    • (1996) Genetics , vol.144 , pp. 419-426
    • Stephax, W.1
  • 44
    • 0027164566 scopus 로고
    • RNA folding in Drosophila shows a distance effect for compensator' fitness interactions
    • STEPHAX, W., and D. A. KIRBY, 1993 RNA folding in Drosophila shows a distance effect for compensator)' fitness interactions. Genetics 135: 97-103.
    • (1993) Genetics , vol.135 , pp. 97-103
    • Stephax, W.1    Kirby, D.A.2
  • 45
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • THOMPSON,J. D., T.J. GIKSON, F. PLEWNIAK, F.JEANMOUGIN and D. G. HIGGINS, 1997 The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 487G-4882.
    • (1997) Nucleic Acids Res. , vol.25
    • Thompson, J.D.1    Gikson F Plewniak, T.J.2    Jeanmougin, F.3    Higgins, D.G.4
  • 46
    • 0028874337 scopus 로고
    • Ncighborjoining and maximum likelihood with RNA sequences: Addressing interdependence of sites
    • TILUEK, E. R. M., and R. A. COLLINS, 1995 Ncighborjoining and maximum likelihood with RNA sequences: addressing interdependence of sites. Mol. Biol. Evol. 12: 7-15.
    • (1995) Mol. Biol. Evol. 12 , pp. 7-15
    • Tiluek, E.R.M.1    Collins, R.A.2
  • 47
    • 33847534603 scopus 로고    scopus 로고
    • RNA-catalysed nucleotidc synthesis
    • UNRAU, P. J-, and D. P. BARTEL, 1998 RNA-catalysed nucleotidc synthesis. Nature 395: 2GO-2G3.
    • (1998) Nature , vol.395
    • Bartel, D.P.1
  • 49
    • 0001271789 scopus 로고
    • I'hylogenetic structure of the prokaryotic domain: The primär' kingdoms
    • WOESE, C. R., and G. E. Fox, 1977 I'hylogenetic structure of the prokaryotic domain: the primär)' kingdoms. Proc. Natl. Acad. Sci. USA 74: 5088-5090.
    • (1977) Proc. Natl. Acad. Sci. USA , vol.74 , pp. 5088-5090
    • Woese, C.R.1    Fox, G.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.