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Volumn 17, Issue 6, 2009, Pages 759-765

Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; DINUCLEOTIDE; GUANINE; MESSENGER RNA PRECURSOR; THYMINE;

EID: 67349134700     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2008.257     Document Type: Article
Times cited : (58)

References (38)
  • 1
    • 10044274340 scopus 로고    scopus 로고
    • Influence of RNA secondary structure on the pre-mRNA splicing process
    • Buratti E, Baralle FE: Influence of RNA secondary structure on the pre-mRNA splicing process. Mol Cell Biol 2004; 24: 10505-10514.
    • (2004) Mol Cell Biol , vol.24 , pp. 10505-10514
    • Buratti, E.1    Baralle, F.E.2
  • 2
    • 37349056702 scopus 로고    scopus 로고
    • Pre-mRNA secondary structures influence exon recognition
    • Hiller M, Zhang Z, Backofen R, Stamm S: Pre-mRNA secondary structures influence exon recognition. PLoS Genet 2007; 3: E204.
    • (2007) PLoS Genet , vol.3
    • Hiller, M.1    Zhang, Z.2    Backofen, R.3    Stamm, S.4
  • 3
    • 0032128255 scopus 로고    scopus 로고
    • Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins
    • Liu HX, Zhang M, Krainer AR: Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev 1998; 12: 1998-2012.
    • (1998) Genes Dev , vol.12 , pp. 1998-2012
    • Liu, H.X.1    Zhang, M.2    Krainer, A.R.3
  • 4
    • 0033552901 scopus 로고    scopus 로고
    • SR proteins are 'locators' of the RNA splicing machinery
    • Graveley BR, Hertel KJ, Maniatis T: SR proteins are 'locators' of the RNA splicing machinery. Curr Biol 1999; 9: R6-R7.
    • (1999) Curr Biol , vol.9
    • Graveley, B.R.1    Hertel, K.J.2    Maniatis, T.3
  • 5
    • 0026660025 scopus 로고
    • HnRNP I, the polypyrimidine tract-binding protein: Distinct nuclear localization and association with hnRNAs
    • Ghetti A, Pinol-Roma S, Michael WM, Morandi C, Dreyfuss G: HnRNP I, the polypyrimidine tract-binding protein: Distinct nuclear localization and association with hnRNAs. Nucleic Acids Res 1992; 20: 3671-3678.
    • (1992) Nucleic Acids Res , vol.20 , pp. 3671-3678
    • Ghetti, A.1    Pinol-Roma, S.2    Michael, W.M.3    Morandi, C.4    Dreyfuss, G.5
  • 6
    • 0028356054 scopus 로고
    • The hnRNP F protein: Unique primary structure, nucleic acid-binding properties, and subcellular localization
    • Matunis MJ, XinU J, Dreyfuss G: The hnRNP F protein: unique primary structure, nucleic acid-binding properties, and subcellular localization. Nucleic Acids Res 1994; 22: 1059-1067.
    • (1994) Nucleic Acids Res , vol.22 , pp. 1059-1067
    • Matunis, M.J.1    XinU, J.2    Dreyfuss, G.3
  • 7
    • 0028215301 scopus 로고
    • RNA bindinS specificity of hnRNP A1: Significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing
    • Burd CG, Dreyfuss G: RNA bindinS specificity of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing. EMBO J 1994; 13: 1197-1204.
    • (1994) EMBO J , vol.13 , pp. 1197-1204
    • Burd, C.G.1    Dreyfuss, G.2
  • 8
    • 0035941211 scopus 로고    scopus 로고
    • Determination of the RNA binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H/H'/F/2H9 family
    • Caputi M, Zahler AM: Determination of the RNA binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H/H'/F/2H9 family. J Biol Chem 2001; 276: 43850-43859.
    • (2001) J Biol Chem , vol.276 , pp. 43850-43859
    • Caputi, M.1    Zahler, A.M.2
  • 9
    • 0033019048 scopus 로고    scopus 로고
    • Selection and characterization of pre-mRNA splicing enhancers: Identification of novel SR protein-specific enhancer sequences
    • Schaal TD, Maniatis T: Selection and characterization of pre-mRNA splicing enhancers: Identification of novel SR protein-specific enhancer sequences. Mol Cell Biol 1999; 19: 1705-1719.
    • (1999) Mol Cell Biol , vol.19 , pp. 1705-1719
    • Schaal, T.D.1    Maniatis, T.2
  • 10
    • 3342938228 scopus 로고    scopus 로고
    • In vivo selection reveals combinatorial controls that define a critical exon in the spinal muscular atrophy genes
    • Singh NN, Androphy EJ, Singh RN: In vivo selection reveals combinatorial controls that define a critical exon in the spinal muscular atrophy genes. RNA 2004; 10: 1291-1305.
    • (2004) RNA , vol.10 , pp. 1291-1305
    • Singh, N.N.1    Androphy, E.J.2    Singh, R.N.3
  • 11
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • Fairbrother WG, Yeh RF, Sharp PA, Burge CB: Predictive identification of exonic splicing enhancers in human genes. Science 2002; 297: 1007-1013.
    • (2002) Science , vol.297 , pp. 1007-1013
    • Fairbrother, W.G.1    Yeh, R.F.2    Sharp, P.A.3    Burge, C.B.4
  • 12
    • 2642525438 scopus 로고    scopus 로고
    • Computational definition of sequence motifs governing constitutive exon splicing
    • Zhang XH, Chasin LA: Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev 2004; 18: 1241-1250.
    • (2004) Genes Dev , vol.18 , pp. 1241-1250
    • Zhang, X.H.1    Chasin, L.A.2
  • 13
    • 10944256767 scopus 로고    scopus 로고
    • Systematic identification and analysis of exonic splicing silencers
    • Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB: Systematic identification and analysis of exonic splicing silencers. Cell 2004; 119: 831-845.
    • (2004) Cell , vol.119 , pp. 831-845
    • Wang, Z.1    Rolish, M.E.2    Yeo, G.3    Tung, V.4    Mawson, M.5    Burge, C.B.6
  • 15
    • 33745207758 scopus 로고    scopus 로고
    • Comparative analysis identifies exonic splicing regulatory sequences-the complex definition of enhancers and silencers
    • Goren A, Ram O, Amit M et al: Comparative analysis identifies exonic splicing regulatory sequences-the complex definition of enhancers and silencers. Mol Cell 2006; 22: 769-781.
    • (2006) Mol Cell , vol.22 , pp. 769-781
    • Goren, A.1    Ram, O.2    Amit, M.3
  • 16
    • 34248338233 scopus 로고    scopus 로고
    • Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5′ splice-site disruption
    • Wimmer K, Roca X, Beiglbock H et al: Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5′ splice-site disruption. Hum Mutat 2007; 28 599-612.
    • (2007) Hum Mutat , vol.28 , pp. 599-612
    • Wimmer, K.1    Roca, X.2    Beiglbock, H.3
  • 17
    • 36248977122 scopus 로고    scopus 로고
    • Global control of aberrant splice site activation by auxiliary splicing sequences: Evidence for a gradient in exon and intron definition
    • Kralovicova J, Vorechovsky I: Global control of aberrant splice site activation by auxiliary splicing sequences: Evidence for a gradient in exon and intron definition. Nucleic Acids Res 2007; 35: 6399-6413.
    • (2007) Nucleic Acids Res , vol.35 , pp. 6399-6413
    • Kralovicova, J.1    Vorechovsky, I.2
  • 18
    • 33745501015 scopus 로고    scopus 로고
    • General and specific functions of exonic splicing silencers in splicing control
    • Wang Z, Xiao X, Van Nostrand E, Burge CB: General and specific functions of exonic splicing silencers in splicing control. Mol Cell 2006; 23: 61-70.
    • (2006) Mol Cell , vol.23 , pp. 61-70
    • Wang, Z.1    Xiao, X.2    Van Nostrand, E.3    Burge, C.B.4
  • 19
    • 0033966774 scopus 로고    scopus 로고
    • Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1
    • Ars E, Serra E, Garcia J et al: Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1. Hum Mol Genet 2000; 9: 237-247.
    • (2000) Hum Mol Genet , vol.9 , pp. 237-247
    • Ars, E.1    Serra, E.2    Garcia, J.3
  • 20
    • 0039108539 scopus 로고    scopus 로고
    • Splicing defects in the ataxia-telangiectasia gene, ATM: Underlying mutations and consequences
    • Teraoka SN, Telatar M, Becker-Catania S et al: Splicing defects in the ataxia-telangiectasia gene, ATM: Underlying mutations and consequences. Am J Hum Genet 1999; 64: 1617-1631.
    • (1999) Am J Hum Genet , vol.64 , pp. 1617-1631
    • Teraoka, S.N.1    Telatar, M.2    Becker-Catania, S.3
  • 22
    • 0023651307 scopus 로고
    • RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression
    • Shapiro MB, Senapathy P: RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression. Nucleic Acids Res 1987; 15: 7155-7174.
    • (1987) Nucleic Acids Res , vol.15 , pp. 7155-7174
    • Shapiro, M.B.1    Senapathy, P.2
  • 23
    • 33750142512 scopus 로고    scopus 로고
    • Aberrant 3′ splice sites in human disease genes: Mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization
    • Vorechovsky I: Aberrant 3′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res 2006; 34: 4630-4641.
    • (2006) Nucleic Acids Res , vol.34 , pp. 4630-4641
    • Vorechovsky, I.1
  • 24
    • 34547850647 scopus 로고    scopus 로고
    • Aberrant 5′ splice sites in human disease genes: Mutation pattern, nucletide structure and comparison of computational tools that predict their utilization
    • Buratti E, Chivers MC, Kralovicova J et al: Aberrant 5′ splice sites in human disease genes: Mutation pattern, nucletide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res 2007; 35: 4250-4263.
    • (2007) Nucleic Acids Res , vol.35 , pp. 4250-4263
    • Buratti, E.1    Chivers, M.C.2    Kralovicova, J.3
  • 26
    • 33747891736 scopus 로고    scopus 로고
    • An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers
    • Smith PJ, Zhang C, Wang J, Chew SL, Zhang MQ, Krainer AR: An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet 2006; 15: 2490-2508.
    • (2006) Hum Mol Genet , vol.15 , pp. 2490-2508
    • Smith, P.J.1    Zhang, C.2    Wang, J.3    Chew, S.L.4    Zhang, M.Q.5    Krainer, A.R.6
  • 28
    • 44449115151 scopus 로고    scopus 로고
    • RNA landscape of evolution for optimal exon and intron discrimination
    • Zhang C, Li WH, Krainer AR, Zhang MQ: RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci USA 2008; 105: 5797-5802.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 5797-5802
    • Zhang, C.1    Li, W.H.2    Krainer, A.R.3    Zhang, M.Q.4
  • 30
    • 1842607847 scopus 로고    scopus 로고
    • Team RDC:, Vienna, Austria: R Foundation for Statistical Computing: ISBN 3-900051-07-0 2007
    • Team RDC: R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing: ISBN 3-900051-07-0 2007.
    • R: A Language and Environment for Statistical Computing
  • 31
    • 46749098393 scopus 로고    scopus 로고
    • Evaluation of in silico splice tools for decision-making in molecular diagnosis
    • Houdayer C, Dehainault C, Mattler C et al: Evaluation of in silico splice tools for decision-making in molecular diagnosis. Hum Mutat 2008; 29: 975-982.
    • (2008) Hum Mutat , vol.29 , pp. 975-982
    • Houdayer, C.1    Dehainault, C.2    Mattler, C.3
  • 32
    • 1942469356 scopus 로고    scopus 로고
    • Comparative analysis detects dependencies among the 5′ splice-site positions
    • Carmel I, Tal S, Vig I, Ast G: Comparative analysis detects dependencies among the 5′ splice-site positions. RNA 2004; 10: 828-840.
    • (2004) RNA , vol.10 , pp. 828-840
    • Carmel, I.1    Tal, S.2    Vig, I.3    Ast, G.4
  • 33
    • 10944245056 scopus 로고    scopus 로고
    • Alternative splicing of conserved exons is frequently species-specific in human and mouse
    • Pan Q, Bakowski MA, Morris Q et al: Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet 2005; 21: 73-77.
    • (2005) Trends Genet , vol.21 , pp. 73-77
    • Pan, Q.1    Bakowski, M.A.2    Morris, Q.3
  • 34
    • 66749167094 scopus 로고    scopus 로고
    • Disease-causing mutations improving the branch site and polypyrimidine tract: Pseudoexon activation of LINE-2 and antisense Alu lacking the poly(T)-tail
    • in press
    • Meili D, Kralovicova J, Zagalak J et al: Disease-causing mutations improving the branch site and polypyrimidine tract: Pseudoexon activation of LINE-2 and antisense Alu lacking the poly(T)-tail. Hum Mutat 2009; (in press).
    • (2009) Hum Mutat
    • Meili, D.1    Kralovicova, J.2    Zagalak, J.3
  • 35
    • 0024808994 scopus 로고
    • The organization of 3′ splice-site sequences in mammalian introns
    • Reed R: The organization of 3′ splice-site sequences in mammalian introns. Genes Dev 1989; 3: 2113-2123.
    • (1989) Genes Dev , vol.3 , pp. 2113-2123
    • Reed, R.1
  • 36
    • 0030743391 scopus 로고    scopus 로고
    • G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection
    • McCullough AJ, Berget SM: G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol Cell Biol 1997; 17: 4562-4571.
    • (1997) Mol Cell Biol , vol.17 , pp. 4562-4571
    • McCullough, A.J.1    Berget, S.M.2
  • 37
    • 21844480060 scopus 로고    scopus 로고
    • A combinatorial code for splicing silencing: UAGG and GGGG motifs
    • Han K, Yeo G, An P, Burge CB, Grabowski PJ: A combinatorial code for splicing silencing: UAGG and GGGG motifs. PLoS Biol 2005; 3: e158.
    • (2005) PLoS Biol , vol.3
    • Han, K.1    Yeo, G.2    An, P.3    Burge, C.B.4    Grabowski, P.J.5
  • 38
    • 32044475140 scopus 로고    scopus 로고
    • Position-dependent repression and promotion of DQB1 intron 3 splicing by GGGG motifs
    • Kralovicova J, Vorechovsky I: Position-dependent repression and promotion of DQB1 intron 3 splicing by GGGG motifs. J Immunol 2006; 176: 2381-2388.
    • (2006) J Immunol , vol.176 , pp. 2381-2388
    • Kralovicova, J.1    Vorechovsky, I.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.