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Volumn 345, Issue 1 SPEC. ISS., 2005, Pages 3-12

The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: A quantitative model

Author keywords

AU rich elements; Gene expression; mRNA stability regulation; Non coding RNA; RNA secondary structure; RNA protein interactions

Indexed keywords

GENOMIC DNA; HUR PROTEIN; LIGAND; MESSENGER RNA;

EID: 13444305211     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2004.11.043     Document Type: Article
Times cited : (44)

References (42)
  • 1
    • 13444277606 scopus 로고    scopus 로고
    • Design of multi-stable nucleic acid sequences
    • H.-W. Mewes V. Heun D. Frishman S. Kramer belleville Verlag Michael Farin München, D
    • I. Abfalter, C. Flamm, and P.F. Stadler Design of multi-stable nucleic acid sequences H.-W. Mewes V. Heun D. Frishman S. Kramer Proceedings of the German Conference on Bioinformatics. GCB 2003 vol. 1 2003 belleville Verlag Michael Farin München, D 1 7
    • (2003) Proceedings of the German Conference on Bioinformatics. GCB 2003 , vol.1 , pp. 1-7
    • Abfalter, I.1    Flamm, C.2    Stadler, P.F.3
  • 3
    • 1942435249 scopus 로고    scopus 로고
    • Micromanagers of gene expression: The potentially wide-spread influence of metazoan microRNAs
    • D.P. Bartel, and C.-Z. Chen Micromanagers of gene expression: the potentially wide-spread influence of metazoan microRNAs Nat. Genet. 5 2004 396 400
    • (2004) Nat. Genet. , vol.5 , pp. 396-400
    • Bartel, D.P.1    Chen, C.-Z.2
  • 4
    • 0037090528 scopus 로고    scopus 로고
    • Life without transcriptional control? from fly to man and back again
    • C.E. Clayton Life without transcriptional control? From fly to man and back again EMBO J. 21 2002 1881 1888
    • (2002) EMBO J. , vol.21 , pp. 1881-1888
    • Clayton, C.E.1
  • 6
    • 0025663103 scopus 로고
    • Prediction of rho-independent Escherichia coli transcription terminators. a statistical analysis of their RNA stem-loop structures
    • Y. d'Aubenton Carafa, E. Brody, and C. Thermes Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures J. Mol. Biol. 216 1990 835 858
    • (1990) J. Mol. Biol. , vol.216 , pp. 835-858
    • D'Aubenton Carafa, Y.1    Brody, E.2    Thermes, C.3
  • 7
    • 3042735602 scopus 로고    scopus 로고
    • Prediction of hybridization and melting for double-stranded nucleic acids
    • R.A. Dimitrov, and M. Zuker Prediction of hybridization and melting for double-stranded nucleic acids Biophys. J. 87 2004 215 226
    • (2004) Biophys. J. , vol.87 , pp. 215-226
    • Dimitrov, R.A.1    Zuker, M.2
  • 8
    • 0346888665 scopus 로고    scopus 로고
    • A statistical sampling algorithm for RNA secondary structure prediction
    • Y. Ding, and C.E. Lawrence A statistical sampling algorithm for RNA secondary structure prediction Nucleic Acids Res. 31 2003 7180 7301
    • (2003) Nucleic Acids Res. , vol.31 , pp. 7180-7301
    • Ding, Y.1    Lawrence, C.E.2
  • 9
    • 0043285072 scopus 로고    scopus 로고
    • A partition function algorithm for nucleic acid secondary structure including pseudoknots
    • R.M. Dirks, and N.A. Pierce A partition function algorithm for nucleic acid secondary structure including pseudoknots J. Comput. Chem. 24 2003 1664 1677
    • (2003) J. Comput. Chem. , vol.24 , pp. 1664-1677
    • Dirks, R.M.1    Pierce, N.A.2
  • 10
    • 0347763700 scopus 로고    scopus 로고
    • New approaches to targeting RNA with oligonucleotides: Inhibition of group i intron self-splicing
    • M.D. Disney, J.L. Childs, and D.H. Turner New approaches to targeting RNA with oligonucleotides: inhibition of group i intron self-splicing Biopolymers 73 1 2004 151 161
    • (2004) Biopolymers , vol.73 , Issue.1 , pp. 151-161
    • Disney, M.D.1    Childs, J.L.2    Turner, D.H.3
  • 13
    • 0001477958 scopus 로고
    • RNA folding landscapes and combinatory landscapes
    • W. Fontana RNA folding landscapes and combinatory landscapes Phys. Rev., E 47 1993 2083 2099
    • (1993) Phys. Rev., e , vol.47 , pp. 2083-2099
    • Fontana, W.1
  • 14
  • 15
    • 0028881070 scopus 로고
    • Posttranscriptional regulation and RNA binding proteins in development
    • S.R. Haynes Posttranscriptional regulation and RNA binding proteins in development J. Biomed. Sci. 2 1995 293 301
    • (1995) J. Biomed. Sci. , vol.2 , pp. 293-301
    • Haynes, S.R.1
  • 16
    • 4344677175 scopus 로고    scopus 로고
    • Common logic of transcription factor and microRNA action
    • O. Hobert Common logic of transcription factor and microRNA action Trends Biochem. Sci. 29 2004 462 468
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 462-468
    • Hobert, O.1
  • 17
    • 3242708388 scopus 로고    scopus 로고
    • Computational chemistry with RNA secondary structures
    • I.L. Hofacker, C. Flamm, and P.F. Stadler Computational chemistry with RNA secondary structures Kem. Ind. 53 2004 315 322
    • (2004) Kem. Ind. , vol.53 , pp. 315-322
    • Hofacker, I.L.1    Flamm, C.2    Stadler, P.F.3
  • 19
    • 12144287461 scopus 로고    scopus 로고
    • Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
    • D. Kampa Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22 Genome Res. 14 2004 331 342
    • (2004) Genome Res. , vol.14 , pp. 331-342
    • Kampa, D.1
  • 20
    • 5644226075 scopus 로고    scopus 로고
    • Regulation of ribozyme activity with short oligonucleotides
    • Y. Komatsu Regulation of ribozyme activity with short oligonucleotides Biol. Pharm. Bull. 27 2004 457 462
    • (2004) Biol. Pharm. Bull. , vol.27 , pp. 457-462
    • Komatsu, Y.1
  • 22
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure
    • D. Mathews, J. Sabina, M. Zuker, and H. Turner Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure J. Mol. Biol. 288 1999 911 940
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.1    Sabina, J.2    Zuker, M.3    Turner, H.4
  • 23
    • 1842584883 scopus 로고    scopus 로고
    • RNA regulation: A new genetics?
    • J.S. Mattick RNA regulation: a new genetics? Nat. Genet. 5 2004 316 323
    • (2004) Nat. Genet. , vol.5 , pp. 316-323
    • Mattick, J.S.1
  • 24
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • J.S. McCaskill The equilibrium partition function and base pair binding probabilities for RNA secondary structure Biopolymers 29 1990 1105 1119
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 25
    • 5644245066 scopus 로고    scopus 로고
    • MRNA openers and closers: A methodology to modulate AU-rich element controlled mRNA stability by a molecular switch in mRNA conformation
    • N.-C. Meisner, J. Hackermüller, V. Uhl, A. Aszódi, M. Jaritz, and M. Auer mRNA openers and closers: a methodology to modulate AU-rich element controlled mRNA stability by a molecular switch in mRNA conformation ChemBioChem 5 2004 1432 1447
    • (2004) ChemBioChem , vol.5 , pp. 1432-1447
    • Meisner, N.-C.1    Hackermüller, J.2    Uhl, V.3    Aszódi, A.4    Jaritz, M.5    Auer, M.6
  • 26
    • 2442664066 scopus 로고    scopus 로고
    • Structural basis of single-stranded RNA recognition
    • A.C. Messias, and M. Sattler Structural basis of single-stranded RNA recognition Acc. Chem. Res. 37 2004 279 287
    • (2004) Acc. Chem. Res. , vol.37 , pp. 279-287
    • Messias, A.C.1    Sattler, M.2
  • 28
    • 0035929625 scopus 로고    scopus 로고
    • Temportal translation control by metastable RNA structure
    • J. Møller-Jensen, T. Franch, and K. Gerdes Temportal translation control by metastable RNA structure J. Biol. Chem. 276 2001 35707 35713
    • (2001) J. Biol. Chem. , vol.276 , pp. 35707-35713
    • Møller-Jensen, J.1    Franch, T.2    Gerdes, K.3
  • 29
    • 2542491127 scopus 로고    scopus 로고
    • Employment opportunities for non-coding RNAs
    • C. Morey, and P. Avner Employment opportunities for non-coding RNAs FEBS Lett. 567 2004 27 34
    • (2004) FEBS Lett. , vol.567 , pp. 27-34
    • Morey, C.1    Avner, P.2
  • 30
    • 3142762898 scopus 로고    scopus 로고
    • Intracellular inhibition of hepatitis C virus (HCV) internal ribosomal entry site (IRES)-dependent translation by peptide nucleic acids (PNAs) and locked nucleic acids (LNAs)
    • C.J. Nulf, and D. Corey Intracellular inhibition of hepatitis C virus (HCV) internal ribosomal entry site (IRES)-dependent translation by peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) Nucleic Acids Res. 32 2004 3792 3798
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3792-3798
    • Nulf, C.J.1    Corey, D.2
  • 32
    • 3042632236 scopus 로고    scopus 로고
    • RNA stem-loop enhanced expression of previously non-expressible genes
    • 10.1093/nar/gnh076
    • M. Paulus, M. Haslbeck, and M. Watzele RNA stem-loop enhanced expression of previously non-expressible genes Nucleic Acids Res. 32 2004 9/e78 10.1093/nar/gnh076
    • (2004) Nucleic Acids Res. , vol.32
    • Paulus, M.1    Haslbeck, M.2    Watzele, M.3
  • 33
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • M. Rehmsmeier, P. Steffn, M. Höchsmann, and R. Giegerich Fast and effective prediction of microRNA/target duplexes RNA 10 2004 1507 1517
    • (2004) RNA , vol.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffn, P.2    Höchsmann, M.3    Giegerich, R.4
  • 34
    • 0034698298 scopus 로고    scopus 로고
    • One sequence, two ribozymes: Implications for the emergence of new ribozyme folds
    • E.A. Schultes, and D.P. Bartel One sequence, two ribozymes: implications for the emergence of new ribozyme folds Science 289 2000 448 452
    • (2000) Science , vol.289 , pp. 448-452
    • Schultes, E.A.1    Bartel, D.P.2
  • 35
    • 0028196714 scopus 로고
    • From sequences to shapes and back: A case study in RNA secondary structures
    • P. Schuster, W. Fontana, P.F. Stadler, and I.L. Hofacker From sequences to shapes and back: a case study in RNA secondary structures Proc. R. Soc. Lond., B 255 1994 279 284
    • (1994) Proc. R. Soc. Lond., B , vol.255 , pp. 279-284
    • Schuster, P.1    Fontana, W.2    Stadler, P.F.3    Hofacker, I.L.4
  • 37
    • 1842453716 scopus 로고    scopus 로고
    • Controlling mRNA stability and translation with small noncoding RNAs
    • G. Storz, J.A. Opdyke, and A. Zhang Controlling mRNA stability and translation with small noncoding RNAs Curr. Opin. Microbiol. 7 2004 140 144
    • (2004) Curr. Opin. Microbiol. , vol.7 , pp. 140-144
    • Storz, G.1    Opdyke, J.A.2    Zhang, A.3
  • 38
    • 4344692339 scopus 로고    scopus 로고
    • Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs
    • M. Suzuki, and Y. Hayashizaki Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs BioEssays 26 2004 833 843
    • (2004) BioEssays , vol.26 , pp. 833-843
    • Suzuki, M.1    Hayashizaki, Y.2
  • 40
    • 0033784534 scopus 로고    scopus 로고
    • Induced fit in RNA-protein recognition
    • J.R. Williamson Induced fit in RNA-protein recognition Nat. Struct. Biol. 7 2000 834 837
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 834-837
    • Williamson, J.R.1
  • 41
    • 0038581529 scopus 로고    scopus 로고
    • Programmed DNA deletion as an RNA-guided system of genome defense
    • M.C. Yao, P. Fuller, and X. Xi Programmed DNA deletion as an RNA-guided system of genome defense Science 300 2003 1517 1518
    • (2003) Science , vol.300 , pp. 1517-1518
    • Yao, M.C.1    Fuller, P.2    Xi, X.3
  • 42
    • 4644275337 scopus 로고    scopus 로고
    • Exogenous control of mammalian gene expression through modulation of RNA self-cleavage
    • L. Yen Exogenous control of mammalian gene expression through modulation of RNA self-cleavage Nature 431 2004 471 476
    • (2004) Nature , vol.431 , pp. 471-476
    • Yen, L.1


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