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Volumn 9, Issue 2, 2014, Pages

Exon first nucleotide mutations in splicing: Evaluation of in silico prediction tools

Author keywords

[No Author keywords available]

Indexed keywords

BRUTON TYROSINE KINASE; POLYPYRIMIDINE TRACT BINDING PROTEIN;

EID: 84896116359     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0089570     Document Type: Article
Times cited : (17)

References (42)
  • 1
    • 0035370845 scopus 로고    scopus 로고
    • Pre-mRNA splicing in the new millennium
    • DOI 10.1016/S0955-0674(00)00212-X
    • Hastings ML, Krainer AR (2001) Pre-mRNA splicing in the new millennium. Curr Opin Cell Biol 13: 302-309. (Pubitemid 32429494)
    • (2001) Current Opinion in Cell Biology , vol.13 , Issue.3 , pp. 302-309
    • Hastings, M.L.1    Krainer, A.R.2
  • 2
    • 26944453614 scopus 로고    scopus 로고
    • Splicing in action: Assessing disease causing sequence changes
    • DOI 10.1136/jmg.2004.029538
    • Baralle D, Baralle M (2005) Splicing in action: assessing disease causing sequence changes. J Med Genet 42: 737-748. (Pubitemid 41475248)
    • (2005) Journal of Medical Genetics , vol.42 , Issue.10 , pp. 737-748
    • Baralle, D.1    Baralle, M.2
  • 3
    • 79961187826 scopus 로고    scopus 로고
    • AG-dependent 3′-splice sites are predisposed to aberrant splicing due to a mutation at the first nucleotide of an exon
    • Fu Y, Masuda A, Ito M, Shinmi J, Ohno K (2011) AG-dependent 3′-splice sites are predisposed to aberrant splicing due to a mutation at the first nucleotide of an exon. Nucleic Acids Res 39: 4396-4404.
    • (2011) Nucleic Acids Res , vol.39 , pp. 4396-4404
    • Fu, Y.1    Masuda, A.2    Ito, M.3    Shinmi, J.4    Ohno, K.5
  • 4
    • 0024808994 scopus 로고
    • The organization of 3′ splice-site sequences in mammalian introns
    • Reed R (1989) The organization of 3′ splice-site sequences in mammalian introns. Genes Dev 3: 2113-2123.
    • (1989) Genes Dev , vol.3 , pp. 2113-2123
    • Reed, R.1
  • 5
    • 0343517444 scopus 로고    scopus 로고
    • 65
    • Guth S, Martínez C, Gaur RK, Valcárcel J (1999) Evidence for substrate-specific requirement of the splicing factor U2AF(35) and for its function after polypyrimidine tract recognition by U2AF(65). Mol Cell Biol 19: 8263-8271. (Pubitemid 30414020)
    • (1999) Molecular and Cellular Biology , vol.19 , Issue.12 , pp. 8263-8271
    • Guth, S.1    Martinez, C.2    Gaur, R.K.3    Valcarcel, J.4
  • 6
    • 0033576626 scopus 로고    scopus 로고
    • Functional recognition of the 3′ splice site AG by the splicing factor U2AF35
    • Wu S, Romfo CM, Nilsen TW, Green MR (1999) Functional recognition of the 3′ splice site AG by the splicing factor U2AF35. Nature 402: 832-835.
    • (1999) Nature , vol.402 , pp. 832-835
    • Wu, S.1    Romfo, C.M.2    Nilsen, T.W.3    Green, M.R.4
  • 7
    • 0023651307 scopus 로고
    • RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression
    • Shapiro MB, Senapathy P (1987) RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res 15: 7155-7174.
    • (1987) Nucleic Acids Res , vol.15 , pp. 7155-7174
    • Shapiro, M.B.1    Senapathy, P.2
  • 8
    • 0030787520 scopus 로고    scopus 로고
    • Improved splice site detection in Genie
    • Reese MG, Eeckman FH, Kulp D, Haussler D (1997) Improved splice site detection in Genie. J Comput Biol 4: 311-323. (Pubitemid 27355870)
    • (1997) Journal of Computational Biology , vol.4 , Issue.3 , pp. 311-323
    • Reese, M.G.1
  • 9
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • DOI 10.1089/1066527041410418
    • Yeo G, Burge CB (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11: 377-394. (Pubitemid 38901668)
    • (2004) Journal of Computational Biology , vol.11 , Issue.2-3 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2
  • 10
    • 20444470310 scopus 로고    scopus 로고
    • Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation
    • DOI 10.1093/hmg/ddi164
    • Kol G, Lev-Maor G, Ast G (2005) Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation. Hum Mol Genet 14: 1559-1568. (Pubitemid 40823463)
    • (2005) Human Molecular Genetics , vol.14 , Issue.11 , pp. 1559-1568
    • Kol, G.1    Lev-Maor, G.2    Ast, G.3
  • 11
    • 38049029652 scopus 로고    scopus 로고
    • Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
    • Schwartz SH, Silva J, Burstein D, Pupko T, Eyras E, et al. (2008) Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res 18: 88-103.
    • (2008) Genome Res , vol.18 , pp. 88-103
    • Schwartz, S.H.1    Silva, J.2    Burstein, D.3    Pupko, T.4    Eyras, E.5
  • 12
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • DOI 10.1126/science.1073774
    • Fairbrother WG, Yeh RF, Sharp PA, Burge CB (2002) Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007-1013. (Pubitemid 34856033)
    • (2002) Science , vol.297 , Issue.5583 , pp. 1007-1013
    • Fairbrother, W.G.1    Yeh, R.-F.2    Sharp, P.A.3    Burge, C.B.4
  • 13
    • 2642525438 scopus 로고    scopus 로고
    • Computational definition of sequence motifs governing constitutive exon splicing
    • DOI 10.1101/gad.1195304
    • Zhang XH, Chasin LA (2004) Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev 18: 1241-1250. (Pubitemid 38720592)
    • (2004) Genes and Development , vol.18 , Issue.11 , pp. 1241-1250
    • Zhang, X.H.-F.1    Chasin, L.A.2
  • 14
    • 0042242582 scopus 로고    scopus 로고
    • ESEfinder: A web resource to identify exonic splicing enhancers
    • DOI 10.1093/nar/gkg616
    • Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR (2003) ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res 31: 3568-3571. (Pubitemid 37442199)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3568-3571
    • Cartegni, L.1    Wang, J.2    Zhu, Z.3    Zhang, M.Q.4    Krainer, A.R.5
  • 15
    • 10944256767 scopus 로고    scopus 로고
    • Systematic identification and analysis of exonic splicing silencers
    • DOI 10.1016/j.cell.2004.11.010, PII S0092867404010566
    • Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, et al. (2004) Systematic identification and analysis of exonic splicing silencers. Cell 119: 831-845. (Pubitemid 40017689)
    • (2004) Cell , vol.119 , Issue.6 , pp. 831-845
    • Wang, Z.1    Rolish, M.E.2    Yeo, G.3    Tung, V.4    Mawson, M.5    Burge, C.B.6
  • 16
    • 67849092454 scopus 로고    scopus 로고
    • SROOGLE: Webserver for integrative, user-friendly visualization of splicing signals
    • Schwartz S, Hall E, Ast G (2009) SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res 37: W189-192.
    • (2009) Nucleic Acids Res , vol.37
    • Schwartz, S.1    Hall, E.2    Ast, G.3
  • 17
    • 33745499067 scopus 로고    scopus 로고
    • Structural Basis for Polypyrimidine Tract Recognition by the Essential Pre-mRNA Splicing Factor U2AF65
    • DOI 10.1016/j.molcel.2006.05.025, PII S1097276506003406
    • Sickmier EA, Frato KE, Shen H, Paranawithana SR, Green MR, et al. (2006) Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. Mol Cell 23: 49-59. (Pubitemid 43963446)
    • (2006) Molecular Cell , vol.23 , Issue.1 , pp. 49-59
    • Sickmier, E.A.1    Frato, K.E.2    Shen, H.3    Paranawithana, S.R.4    Green, M.R.5    Kielkopf, C.L.6
  • 18
    • 79960646885 scopus 로고    scopus 로고
    • Multidomain conformational selection underlies pre-mRNA splicing regulation by U2AF
    • Mackereth CD, Madl T, Bonnal S, Simon B, Zanier K, et al. (2011) Multidomain conformational selection underlies pre-mRNA splicing regulation by U2AF. Nature 475: 408-411.
    • (2011) Nature , vol.475 , pp. 408-411
    • Mackereth, C.D.1    Madl, T.2    Bonnal, S.3    Simon, B.4    Zanier, K.5
  • 19
    • 84876046010 scopus 로고    scopus 로고
    • U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs
    • Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL (2013) U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucleic Acids Res 41: 3859-3873.
    • (2013) Nucleic Acids Res , vol.41 , pp. 3859-3873
    • Jenkins, J.L.1    Agrawal, A.A.2    Gupta, A.3    Green, M.R.4    Kielkopf, C.L.5
  • 20
    • 0032538791 scopus 로고    scopus 로고
    • A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers
    • Graveley BR, Hertel KJ, Maniatis T (1998) A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers. EMBO J 17: 6747-6756. (Pubitemid 28521808)
    • (1998) EMBO Journal , vol.17 , Issue.22 , pp. 6747-6756
    • Graveley, B.R.1    Hertel, K.J.2    Maniatis, T.3
  • 21
    • 79551539775 scopus 로고    scopus 로고
    • SMN2 exon 7 splicing is inhibited by binding of hnRNP A1 to a common ESS motif that spans the 3′ splice site
    • Doktor TK, Schroeder LD, Vested A, Palmfeldt J, Andersen HS, et al. (2011) SMN2 exon 7 splicing is inhibited by binding of hnRNP A1 to a common ESS motif that spans the 3′ splice site. Hum Mutat 32: 220-230.
    • (2011) Hum Mutat , vol.32 , pp. 220-230
    • Doktor, T.K.1    Schroeder, L.D.2    Vested, A.3    Palmfeldt, J.4    Andersen, H.S.5
  • 22
    • 0027233694 scopus 로고
    • A mutational analysis of the polypyrimidine tract of introns. Effects of sequence differences in pyrimidine tracts on splicing
    • Roscigno RF, Weiner M, Garcia-Blanco MA (1993) A mutational analysis of the polypyrimidine tract of introns. Effects of sequence differences in pyrimidine tracts on splicing. J Biol Chem 268: 11222-11229. (Pubitemid 23162315)
    • (1993) Journal of Biological Chemistry , vol.268 , Issue.15 , pp. 11222-11229
    • Roscigno, R.F.1    Weiner, M.2    Garcia-Blanco, M.A.3
  • 23
    • 0030857005 scopus 로고    scopus 로고
    • Functional analysis of the polypyrimidine tract in pre-mRNA splicing
    • Coolidge CJ, Seely RJ, Patton JG (1997) Functional analysis of the polypyrimidine tract in pre-mRNA splicing. Nucleic Acids Res 25: 888-896.
    • (1997) Nucleic Acids Res , vol.25 , pp. 888-896
    • Coolidge, C.J.1    Seely, R.J.2    Patton, J.G.3
  • 24
    • 70350569286 scopus 로고    scopus 로고
    • Mechanisms of alternative splicing regulation: Insights from molecular and genomics approaches
    • Chen M, Manley JL (2009) Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 10: 741-754.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 741-754
    • Chen, M.1    Manley, J.L.2
  • 25
    • 32344437827 scopus 로고    scopus 로고
    • Novel modes of splicing repression by PTB
    • DOI 10.1016/j.tibs.2005.12.003, PII S0968000405003476
    • Spellman R, Smith CW (2006) Novel modes of splicing repression by PTB. Trends Biochem Sci 31: 73-76. (Pubitemid 43221838)
    • (2006) Trends in Biochemical Sciences , vol.31 , Issue.2 , pp. 73-76
    • Spellman, R.1    Smith, C.W.J.2
  • 26
    • 0034743627 scopus 로고    scopus 로고
    • 65 in enhancer-dependent splicing
    • DOI 10.1017/S1355838201010317
    • Graveley BR, Hertel KJ, Maniatis T (2001) The role of U2AF35 and U2AF65 in enhancer-dependent splicing. RNA 7: 806-818. (Pubitemid 32552869)
    • (2001) RNA , vol.7 , Issue.6 , pp. 806-818
    • Graveley, B.R.1    Hertel, K.J.2    Maniatis, T.O.M.3
  • 27
    • 0029843012 scopus 로고    scopus 로고
    • Functional properties of p54, a novel SR protein active in constitutive and alternative splicing
    • Zhang WJ, Wu JY (1996) Functional properties of p54, a novel SR protein active in constitutive and alternative splicing. Mol Cell Biol 16: 5400-5408.
    • (1996) Mol Cell Biol , vol.16 , pp. 5400-5408
    • Zhang, W.J.1    Wu, J.Y.2
  • 28
    • 8644268780 scopus 로고    scopus 로고
    • A pathway of sequential Arginine-Serine-Rich Domain-Splicing signal interactions during mammalian spliceosome assembly
    • DOI 10.1016/j.molcel.2004.10.021, PII S1097276504006379
    • Shen H, Green MR (2004) A pathway of sequential arginine-serine-rich domainsplicing signal interactions during mammalian spliceosome assembly. Mol Cell 16: 363-373. (Pubitemid 39504791)
    • (2004) Molecular Cell , vol.16 , Issue.3 , pp. 363-373
    • Shen, H.1    Green, M.R.2
  • 30
    • 1242316952 scopus 로고    scopus 로고
    • Arginine-Serine-Rich Domains Bound at Splicing Enhancers Contact the Branchpoint to Promote Prespliceosome Assembly
    • DOI 10.1016/S1097-2765(04)00025-5
    • Shen H, Kan JL, Green MR (2004) Arginine-serine-rich domains bound at splicing enhancers contact the branchpoint to promote prespliceosome assembly. Mol Cell 13: 367-376. (Pubitemid 38229809)
    • (2004) Molecular Cell , vol.13 , Issue.3 , pp. 367-376
    • Shen, H.1    Kan, J.L.C.2    Green, M.R.3
  • 31
    • 0026661948 scopus 로고
    • Protein components specifically associated with prespliceosome and spliceosome complexes
    • Bennett M, Michaud S, Kingston J, Reed R (1992) Protein components specifically associated with prespliceosome and spliceosome complexes. Genes Dev 6: 1986-2000.
    • (1992) Genes Dev , vol.6 , pp. 1986-2000
    • Bennett, M.1    Michaud, S.2    Kingston, J.3    Reed, R.4
  • 32
    • 0036207384 scopus 로고    scopus 로고
    • Listening to silence and understanding nonsense: Exonic mutations that affect splicing
    • DOI 10.1038/nrg775
    • Cartegni L, Chew SL, Krainer AR (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 3: 285-298. (Pubitemid 34279797)
    • (2002) Nature Reviews Genetics , vol.3 , Issue.4 , pp. 285-298
    • Cartegni, L.1    Chew, S.L.2    Krainer, A.R.3
  • 33
    • 56749098297 scopus 로고    scopus 로고
    • Isolated growth hormone deficiency type II caused by a point mutation that alters both splice site strength and splicing enhancer function
    • Shariat N, Holladay CD, Cleary RK, Phillips JA, Patton JG (2008) Isolated growth hormone deficiency type II caused by a point mutation that alters both splice site strength and splicing enhancer function. Clin Genet 74: 539-545.
    • (2008) Clin Genet , vol.74 , pp. 539-545
    • Shariat, N.1    Holladay, C.D.2    Cleary, R.K.3    Phillips, J.A.4    Patton, J.G.5
  • 34
  • 36
    • 33749411195 scopus 로고    scopus 로고
    • In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects
    • Lastella P, Surdo NC, Resta N, Guanti G, Stella A (2006) In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects. BMC Genomics 7: 243.
    • (2006) BMC Genomics , vol.7 , pp. 243
    • Lastella, P.1    Surdo, N.C.2    Resta, N.3    Guanti, G.4    Stella, A.5
  • 37
    • 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
    • Vorechovský I (2006) Aberrant 3′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res 34: 4630-4641.
    • (2006) Nucleic Acids Res , vol.34 , pp. 4630-4641
    • Vorechovský, I.1
  • 38
    • 34547850647 scopus 로고    scopus 로고
    • Aberrant 5′ splice sites in human disease genes: Mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization
    • DOI 10.1093/nar/gkm402
    • Buratti E, Chivers M, Královicová J, Romano M, Baralle M, et al. (2007) Aberrant 5′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res 35: 4250-4263. (Pubitemid 47260233)
    • (2007) Nucleic Acids Research , vol.35 , Issue.13 , pp. 4250-4263
    • Buratti, E.1    Chivers, M.2    Kralovicova, J.3    Romano, M.4    Baralle, M.5    Krainer, A.R.6    Vorechovsky, I.7
  • 39
    • 0030911051 scopus 로고    scopus 로고
    • Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals
    • DOI 10.1016/S0092-8674(00)80221-4
    • Abovich N, Rosbash M (1997) Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89: 403-412. (Pubitemid 27220885)
    • (1997) Cell , vol.89 , Issue.3 , pp. 403-412
    • Abovich, N.1    Rosbash, M.2
  • 40
    • 0032521186 scopus 로고    scopus 로고
    • A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition
    • Berglund JA, Abovich N, Rosbash M (1998) A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition. Genes Dev 12: 858-867. (Pubitemid 28150886)
    • (1998) Genes and Development , vol.12 , Issue.6 , pp. 858-867
    • Berglund, J.A.1    Abovich, N.2    Rosbash, M.3
  • 42
    • 79952764494 scopus 로고    scopus 로고
    • Splicing mutations in glycogen-storage disease type II: Evaluation of the full spectrum of mutations and their relation to patients' phenotypes
    • Zampieri S, Buratti E, Dominissini S, Montalvo AL, Pittis MG, et al. (2011) Splicing mutations in glycogen-storage disease type II: evaluation of the full spectrum of mutations and their relation to patients' phenotypes. Eur J Hum Genet 19: 422-431.
    • (2011) Eur J Hum Genet , vol.19 , pp. 422-431
    • Zampieri, S.1    Buratti, E.2    Dominissini, S.3    Montalvo, A.L.4    Pittis, M.G.5


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