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Volumn 34, Issue 17, 2006, Pages

Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN; SINGLE STRANDED RNA; RNA;

EID: 33750212480     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl544     Document Type: Article
Times cited : (131)

References (34)
  • 2
    • 2442664066 scopus 로고    scopus 로고
    • Structural basis of single-stranded RNA recognition
    • Messias,A.C. and Sattler,M. (2004) Structural basis of single-stranded RNA recognition. Acc. Chem. Res., 37, 279-287.
    • (2004) Acc. Chem. Res. , vol.37 , pp. 279-287
    • Messias, A.C.1    Sattler, M.2
  • 3
    • 0036600739 scopus 로고    scopus 로고
    • RNA-protein interactions
    • Hall,K.B. (2002) RNA-protein interactions. Curr. Opin. Struct. Biol., 12, 283-288.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 283-288
    • Hall, K.B.1
  • 4
    • 13744252668 scopus 로고    scopus 로고
    • The RNA ligands for mouse proline-rich RNA-binding protein (mouse Prrp) contain two consensus sequences in separate loop structure
    • Hori,T., Taguchi,Y., Uesugi,S. and Kurihara,Y. (2005) The RNA ligands for mouse proline-rich RNA-binding protein (mouse Prrp) contain two consensus sequences in separate loop structure. Nucleic Acids Res., 33, 190-200.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 190-200
    • Hori, T.1    Taguchi, Y.2    Uesugi, S.3    Kurihara, Y.4
  • 5
    • 0035907317 scopus 로고    scopus 로고
    • Optimized RNA targets of two closely related triple KH domain proteins, heterogeneous nuclear ribonucleoprotein K and alphaCP-2KL, suggest distinct modes of RNA recognition
    • Thisted,T., Lyakhov,D.L. and Liebhaber,S.A. (2001) Optimized RNA targets of two closely related triple KH domain proteins, heterogeneous nuclear ribonucleoprotein K and alphaCP-2KL, suggest distinct modes of RNA recognition. J. Biol. Chem., 276, 17484-17496.
    • (2001) J. Biol. Chem. , vol.276 , pp. 17484-17496
    • Thisted, T.1    Lyakhov, D.L.2    Liebhaber, S.A.3
  • 6
    • 0030992812 scopus 로고    scopus 로고
    • The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo
    • Buckanovich,R.J. and Darnell,R.B. (1997) The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo. Mol. Cell. Biol., 17, 3194-3201.
    • (1997) Mol. Cell. Biol. , vol.17 , pp. 3194-3201
    • Buckanovich, R.J.1    Darnell, R.B.2
  • 7
    • 0032128255 scopus 로고    scopus 로고
    • Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins
    • Liu,H.X., Zhang,M. and Krainer,A.R. (1998) Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev., 12, 1998-2012.
    • (1998) Genes Dev. , vol.12 , pp. 1998-2012
    • Liu, H.X.1    Zhang, M.2    Krainer, A.R.3
  • 8
    • 0033963336 scopus 로고    scopus 로고
    • Exonic splicing enhancer motif recognized by human SC35 under splicing conditions
    • Liu,H.X., Chew,S.L., Cartegni,L., Zhang,M.Q. and Krainer,A.R. (2000) Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. Mol. Cell. Biol., 20, 1063-1071.
    • (2000) Mol. Cell. Biol. , vol.20 , pp. 1063-1071
    • Liu, H.X.1    Chew, S.L.2    Cartegni, L.3    Zhang, M.Q.4    Krainer, A.R.5
  • 9
    • 25844493154 scopus 로고    scopus 로고
    • RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction
    • Dubey,A.K., Baker,C.S., Romeo,T. and Babitzke,P. (2005) RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction. RNA, 11, 1579-1587.
    • (2005) RNA , vol.11 , pp. 1579-1587
    • Dubey, A.K.1    Baker, C.S.2    Romeo, T.3    Babitzke, P.4
  • 10
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey,T. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.2 , pp. 28-36
    • Bailey, T.1    Elkan, C.2
  • 11
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using EM
    • Bailey,T.L. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using EM. Machine Learning, 21, 51-80.
    • (1995) Machine Learning , vol.21 , pp. 51-80
    • Bailey, T.L.1    Elkan, C.2
  • 12
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence,C., Altschul,S., Boguski,M., Liu,J., Neuwald,A. and Wootton,J. (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.1    Altschul, S.2    Boguski, M.3    Liu, J.4    Neuwald, A.5    Wootton, J.6
  • 13
    • 5644245066 scopus 로고    scopus 로고
    • mRNA openers and closers: Modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure
    • Meisner,N.-C., Hackermuller,J., Uhl,V., Aszodi,A., Jaritz,M. and Auer,M. (2004) mRNA openers and closers: Modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure. Chembiochem, 5, 1432-1447.
    • (2004) Chembiochem , vol.5 , pp. 1432-1447
    • Meisner, N.-C.1    Hackermuller, J.2    Uhl, V.3    Aszodi, A.4    Jaritz, M.5    Auer, M.6
  • 14
    • 13444305211 scopus 로고    scopus 로고
    • The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: A quantitative model
    • Hackermuller,J., Meisner,N.-C., Auer,M., Jaritz,M. and Stadler,P.F. (2005) The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: A quantitative model. Gene, 345, 3-12.
    • (2005) Gene , vol.345 , pp. 3-12
    • Hackermuller, J.1    Meisner, N.-C.2    Auer, M.3    Jaritz, M.4    Stadler, P.F.5
  • 16
    • 2942694026 scopus 로고    scopus 로고
    • RNAProfile: An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
    • Pavesi,G., Mauri,G., Stefani,M. and Pesole,G. (2004) RNAProfile: An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. Nucleic Acids Res., 32, 3258-3269.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3258-3269
    • Pavesi, G.1    Mauri, G.2    Stefani, M.3    Pesole, G.4
  • 17
    • 25444512062 scopus 로고    scopus 로고
    • A method for aligning RNA secondary structures and its application to RNA motif detection
    • Liu,J., Wang,J.T.L., Hu,J. and Tian,B. (2005) A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics, 6, 89.
    • (2005) BMC Bioinformatics , vol.6 , pp. 89
    • Liu, J.1    Wang, J.T.L.2    Hu, J.3    Tian, B.4
  • 18
    • 32544452741 scopus 로고    scopus 로고
    • CMfinder-a covariance model based RNA motif finding algorithm
    • Yao,Z., Weinberg,Z. and Ruzzo,W.L. (2006) CMfinder-a covariance model based RNA motif finding algorithm. Bioinformatics, 22, 445-452.
    • (2006) Bioinformatics , vol.22 , pp. 445-452
    • Yao, Z.1    Weinberg, Z.2    Ruzzo, W.L.3
  • 19
    • 2942544566 scopus 로고    scopus 로고
    • RSEARCH: Finding homologs of single structured RNA sequences
    • Klein,R.J. and Eddy,S.R. (2003) RSEARCH: Finding homologs of single structured RNA sequences. BMC Bioinformatics, 4, 44.
    • (2003) BMC Bioinformatics , vol.4 , pp. 44
    • Klein, R.J.1    Eddy, S.R.2
  • 20
    • 24044519380 scopus 로고    scopus 로고
    • MARNA: Multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
    • Siebert,S. and Backofen,R. (2005) MARNA: Multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics, 21, 3352-3359.
    • (2005) Bioinformatics , vol.21 , pp. 3352-3359
    • Siebert, S.1    Backofen, R.2
  • 21
    • 10944234965 scopus 로고    scopus 로고
    • Local sequence-structure motifs in RNA
    • Backofen,R. and Will,S. (2004) Local sequence-structure motifs in RNA. J. Bioinform. Comput. Biol., 2(4), 681-698.
    • (2004) J. Bioinform. Comput. Biol. , vol.2 , Issue.4 , pp. 681-698
    • Backofen, R.1    Will, S.2
  • 24
    • 0013014211 scopus 로고
    • Discovering motifs in DNA and protein sequences: The approximate common substring problem
    • PhD thesis. University of California San Diego
    • Bailey,T.L. (1995) Discovering motifs in DNA and protein sequences: The approximate common substring problem. PhD thesis. University of California San Diego.
    • (1995)
    • Bailey, T.L.1
  • 26
    • 0030570466 scopus 로고    scopus 로고
    • Nucleolin is a sequence-specific RNA-binding protein: Characterization of targets on pre-ribosomal RNA
    • Ghisolfi-Nieto,L., Joseph,G., Puvion-Dutilleul,F., Amalric,F. and Bouvet,P. (1996) Nucleolin is a sequence-specific RNA-binding protein: characterization of targets on pre-ribosomal RNA. J. Mol. Biol., 260, 34-53.
    • (1996) J. Mol. Biol. , vol.260 , pp. 34-53
    • Ghisolfi-Nieto, L.1    Joseph, G.2    Puvion-Dutilleul, F.3    Amalric, F.4    Bouvet, P.5
  • 27
    • 0030953470 scopus 로고    scopus 로고
    • A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52
    • Shi,H., Hoffman,B.E. and Lis,J.T. (1997) A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52. Mol. Cell. Biol., 17, 2649-2657.
    • (1997) Mol. Cell. Biol. , vol.17 , pp. 2649-2657
    • Shi, H.1    Hoffman, B.E.2    Lis, J.T.3
  • 28
    • 0029758487 scopus 로고    scopus 로고
    • Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress
    • Hentze,M.W. and Kuhn,L.C. (1996) Molecular control of vertebrate iron metabolism: MRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. Proc. Natl Acad. Sci. USA, 93, 8175-8182.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 8175-8182
    • Hentze, M.W.1    Kuhn, L.C.2
  • 29
    • 0034070741 scopus 로고    scopus 로고
    • The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein
    • Varani,L., Gunderson,S.I., Mattaj,I.W., Kay,L.E., Neuhaus,D. and Varani,G. (2000) The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein. Nature Struct. Biol., 7, 329-335.
    • (2000) Nature Struct. Biol. , vol.7 , pp. 329-335
    • Varani, L.1    Gunderson, S.I.2    Mattaj, I.W.3    Kay, L.E.4    Neuhaus, D.5    Varani, G.6
  • 30
    • 0037150091 scopus 로고    scopus 로고
    • Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-Tat-TAR ternary complex formation
    • Richter,S., Cao,H. and Rana,T.M. (2002) Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-Tat-TAR ternary complex formation. Biochemistry, 41, 6391-6397.
    • (2002) Biochemistry , vol.41 , pp. 6391-6397
    • Richter, S.1    Cao, H.2    Rana, T.M.3
  • 31
    • 0037062495 scopus 로고    scopus 로고
    • TAR RNA loop: A scaffold for the assembly of a regulatory switch in HIV replication
    • Richter,S., Ping,Y.-H. and Rana,T.M. (2002) TAR RNA loop: A scaffold for the assembly of a regulatory switch in HIV replication. Proc. Natl Acad. Sci. USA, 99, 7928-7933.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 7928-7933
    • Richter, S.1    Ping, Y.-H.2    Rana, T.M.3
  • 32
    • 0036183551 scopus 로고    scopus 로고
    • RNA destabilization by the granulocyte colony-stimulating factor stem-loop destabilizing element involves a single stem-loop that promotes deadenylation
    • Putland,R.A., Sassinis,T.A., Harvey,J.S., Diamond,P., Coles,L.S., Brown,C.Y. and Goodall,G.J. (2002) RNA destabilization by the granulocyte colony-stimulating factor stem-loop destabilizing element involves a single stem-loop that promotes deadenylation. Mol. Cell. Biol., 22, 1664-1673.
    • (2002) Mol. Cell. Biol. , vol.22 , pp. 1664-1673
    • Putland, R.A.1    Sassinis, T.A.2    Harvey, J.S.3    Diamond, P.4    Coles, L.S.5    Brown, C.Y.6    Goodall, G.J.7
  • 33
    • 33745087121 scopus 로고    scopus 로고
    • Complete probabilistic analysis of RNA shapes
    • Voss,B., Giegerich,R. and Rehmsmeier,M. (2006) Complete probabilistic analysis of RNA shapes. BMC Biol., 4, 5.
    • (2006) BMC Biol. , vol.4 , pp. 5
    • Voss, B.1    Giegerich, R.2    Rehmsmeier, M.3
  • 34
    • 0033563512 scopus 로고    scopus 로고
    • The biology of eukaryotic promoter prediction-a review
    • Pedersen,A.G., Baldi,P., Chauvin,Y. and Brunak,S. (1999) The biology of eukaryotic promoter prediction-a review. Comput. Chem., 23, 191-207.
    • (1999) Comput. Chem. , vol.23 , pp. 191-207
    • Pedersen, A.G.1    Baldi, P.2    Chauvin, Y.3    Brunak, S.4


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