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Volumn 38, Issue 10, 2010, Pages 3318-3327

Overlapping splicing regulatory motifs-combinatorial effects on splicing

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; BIOINFORMATICS; EUKARYOTE; GENE EXPRESSION REGULATION; GENE SEQUENCE; HUMAN; MATHEMATICAL ANALYSIS; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING; ANIMAL; BIOLOGY; EXON; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; REGULATORY RNA SEQUENCE;

EID: 77953700980     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq005     Document Type: Article
Times cited : (15)

References (45)
  • 1
    • 0013394889 scopus 로고    scopus 로고
    • Mechanisms of alternative pre-messenger RNA splicing
    • Black,D.L. (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem., 72, 291-336.
    • (2003) Annu. Rev. Biochem. , vol.72 , pp. 291-336
    • Black, D.L.1
  • 4
    • 33745860086 scopus 로고    scopus 로고
    • Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions
    • Deckert,J., Hartmuth,K., Boehringer,D., Behzadnia,N., Will,C.L., Kastner,B., Stark,H., Urlaub,H. and Luhrmann,R. (2006) Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions. Mol. Cell Biol., 26, 5528-5543.
    • (2006) Mol. Cell Biol. , vol.26 , pp. 5528-5543
    • Deckert, J.1    Hartmuth, K.2    Boehringer, D.3    Behzadnia, N.4    Will, C.L.5    Kastner, B.6    Stark, H.7    Urlaub, H.8    Luhrmann, R.9
  • 6
    • 0042671357 scopus 로고    scopus 로고
    • Pre-mRNA splicing: awash in a sea of proteins
    • Jurica,M.S. and Moore,M.J. (2003) Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell, 12, 5-14.
    • (2003) Mol. Cell , vol.12 , pp. 5-14
    • Jurica, M.S.1    Moore, M.J.2
  • 7
    • 0037068447 scopus 로고    scopus 로고
    • Comprehensive proteomic analysis of the human spliceosome
    • Zhou,Z., Licklider,L.J., Gygi,S.P. and Reed,R. (2002) Comprehensive proteomic analysis of the human spliceosome. Nature, 419, 182-185.
    • (2002) Nature , vol.419 , pp. 182-185
    • Zhou, Z.1    Licklider, L.J.2    Gygi, S.P.3    Reed, R.4
  • 8
    • 0028895417 scopus 로고
    • Exon recognition in vertebrate splicing
    • Berget,S.M. (1995) Exon recognition in vertebrate splicing. J. Biol. Chem., 270, 2411-2414.
    • (1995) J. Biol. Chem. , vol.270 , pp. 2411-2414
    • Berget, S.M.1
  • 9
    • 0035252410 scopus 로고    scopus 로고
    • Alternative splicing: increasing diversity in the proteomic world
    • Graveley,B.R. (2001) Alternative splicing: increasing diversity in the proteomic world. Trends Genet., 17, 100-107.
    • (2001) Trends Genet. , vol.17 , pp. 100-107
    • Graveley, B.R.1
  • 10
    • 0035949674 scopus 로고    scopus 로고
    • A computational analysis of sequence features involved in recognition of short introns
    • Lim,L.P. and Burge,C.B. (2001) A computational analysis of sequence features involved in recognition of short introns. Proc. Natl Acad. Sci. USA, 98, 11193-11198.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 11193-11198
    • Lim, L.P.1    Burge, C.B.2
  • 11
    • 38049029652 scopus 로고    scopus 로고
    • Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
    • Schwartz,S.H., Silva,J., Burstein,D., Pupko,T., Eyras,E. and Ast,G. (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    Ast, G.6
  • 12
    • 0034161419 scopus 로고    scopus 로고
    • Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases
    • Blencowe,B.J. (2000) Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem. Sci., 25, 106-110.
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 106-110
    • Blencowe, B.J.1
  • 13
    • 0036534129 scopus 로고    scopus 로고
    • Alternative splicing: multiple control mechanisms and involvement in human disease
    • Caceres,J.F. and Kornblihtt,A.R. (2002) Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet., 18, 186-193.
    • (2002) Trends Genet. , vol.18 , pp. 186-193
    • Caceres, J.F.1    Kornblihtt, A.R.2
  • 14
    • 0036207384 scopus 로고    scopus 로고
    • Listening to silence and understanding nonsense: exonic mutations that affect splicing
    • Cartegni,L., Chew,S.L. and Krainer,A.R. (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev. Genet., 3, 285-298.
    • (2002) Nat. Rev. Genet. , vol.3 , pp. 285-298
    • Cartegni, L.1    Chew, S.L.2    Krainer, A.R.3
  • 15
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • Fairbrother,W.G., Yeh,R.F., Sharp,P.A. and Burge,C.B. (2002) Predictive identification of exonic splicing enhancers in human genes. Science, 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
  • 16
    • 0033835333 scopus 로고    scopus 로고
    • Sorting out the complexity of SR protein functions
    • Graveley,B.R. (2000) Sorting out the complexity of SR protein functions. RNA, 6, 1197-1211.
    • (2000) RNA , vol.6 , pp. 1197-1211
    • Graveley, B.R.1
  • 19
    • 26944489645 scopus 로고    scopus 로고
    • Building specificity with nonspecific RNA-binding proteins
    • Singh,R. and Valcarcel,J. (2005) Building specificity with nonspecific RNA-binding proteins. Nat. Struct. Mol. Biol., 12, 645-653.
    • (2005) Nat. Struct. Mol. Biol. , vol.12 , pp. 645-653
    • Singh, R.1    Valcarcel, J.2
  • 20
    • 0030279439 scopus 로고    scopus 로고
    • Directing alternative splicing: cast and scenarios
    • Chabot,B. (1996) Directing alternative splicing: cast and scenarios. Trends Genet., 12, 472-478.
    • (1996) Trends Genet. , vol.12 , pp. 472-478
    • Chabot, B.1
  • 21
    • 0037062982 scopus 로고    scopus 로고
    • Alternative pre-mRNA splicing and proteome expansion in metazoans
    • Maniatis,T. and Tasic,B. (2002) Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature, 418, 236-243.
    • (2002) Nature , vol.418 , pp. 236-243
    • Maniatis, T.1    Tasic, B.2
  • 22
    • 0034256020 scopus 로고    scopus 로고
    • Alternative pre-mRNA splicing: the logic of combinatorial control
    • Smith,C.W. and Valcarcel,J. (2000) Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci., 25, 381-388.
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 381-388
    • Smith, C.W.1    Valcarcel, J.2
  • 23
    • 60849108914 scopus 로고    scopus 로고
    • Splicing of designer exons reveals unexpected complexity in pre-mRNA splicing
    • Zhang,X.H., Arias,M.A., Ke,S. and Chasin,L.A. (2009) Splicing of designer exons reveals unexpected complexity in pre-mRNA splicing. RNA, 15, 367-376.
    • (2009) RNA , vol.15 , pp. 367-376
    • Zhang, X.H.1    Arias, M.A.2    Ke, S.3    Chasin, L.A.4
  • 24
    • 64849109747 scopus 로고    scopus 로고
    • A computational approach for genome-wide mapping of splicing factor binding sites
    • Akerman,M., David-Eden,H., Pinter,R.Y. and Mandel-Gutfreund,Y. (2009) A computational approach for genome-wide mapping of splicing factor binding sites. Genome Biol., 10, R30.
    • (2009) Genome Biol. , vol.10
    • Akerman, M.1    David-Eden, H.2    Pinter, R.Y.3    Mandel-Gutfreund, Y.4
  • 25
    • 0025777044 scopus 로고
    • Functional significance of an overlapping consensus binding motif for Sp1 and Zif268 in the murine adenosine deaminase gene promoter
    • Ackerman,S.L., Minden,A.G., Williams,G.T., Bobonis,C. and Yeung,C.Y. (1991) Functional significance of an overlapping consensus binding motif for Sp1 and Zif268 in the murine adenosine deaminase gene promoter. Proc. Natl Acad. Sci. USA, 88, 7523-7527.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 7523-7527
    • Ackerman, S.L.1    Minden, A.G.2    Williams, G.T.3    Bobonis, C.4    Yeung, C.Y.5
  • 26
    • 0027198067 scopus 로고
    • Overlapping binding sites of two different transcription factors in the promoter of the human gene for the Alzheimer amyloid precursor protein
    • Pollwein,P. (1993) Overlapping binding sites of two different transcription factors in the promoter of the human gene for the Alzheimer amyloid precursor protein. Biochem. Biophys. Res. Commun., 190, 637-647.
    • (1993) Biochem. Biophys. Res. Commun. , vol.190 , pp. 637-647
    • Pollwein, P.1
  • 27
    • 0030656245 scopus 로고    scopus 로고
    • Overlapping DNA recognition motifs between Sp1 and a novel trans-acting factor within the wt1 tumour suppressor gene promoter
    • Discenza,M.T., Dehbi,M. and Pelletier,J. (1997) Overlapping DNA recognition motifs between Sp1 and a novel trans-acting factor within the wt1 tumour suppressor gene promoter. Nucleic Acids Res., 25, 4314-4322.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4314-4322
    • Discenza, M.T.1    Dehbi, M.2    Pelletier, J.3
  • 28
    • 0035808433 scopus 로고    scopus 로고
    • Transcription factors recognizing overlapping C1-A2 binding sites positively regulate insulin gene expression
    • Harrington,R.H. and Sharma,A. (2001) Transcription factors recognizing overlapping C1-A2 binding sites positively regulate insulin gene expression. J. Biol. Chem., 276, 104-113.
    • (2001) J. Biol. Chem. , vol.276 , pp. 104-113
    • Harrington, R.H.1    Sharma, A.2
  • 31
    • 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
  • 32
    • 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
  • 33
    • 33747891736 scopus 로고    scopus 로고
    • An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers
    • Smith,P.J., Zhang,C., Wang,J., Chew,S.L., Zhang,M.Q. and Krainer,A.R. (2006) An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum. Mol. Genet., 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
  • 34
  • 35
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc., 57, 289-300.
    • (1995) J. R. Stat. Soc. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 36
    • 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., Keren,H., Lev-Maor,G., Vig,I., Pupko,T. and Ast,G. (2006) Comparative analysis identifies exonic splicing regulatory sequences-The complex definition of enhancers and silencers. Mol. Cell, 22, 769-781.
    • (2006) Mol. Cell , vol.22 , pp. 769-781
    • Goren, A.1    Ram, O.2    Amit, M.3    Keren, H.4    Lev-Maor, G.5    Vig, I.6    Pupko, T.7    Ast, G.8
  • 37
    • 2642525438 scopus 로고    scopus 로고
    • Computational definition of sequence motifs governing constitutive exon splicing
    • Zhang,X.H. and Chasin,L.A. (2004) Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev., 18, 1241-1250.
    • (2004) Genes Dev. , vol.18 , pp. 1241-1250
    • Zhang, X.H.1    Chasin, L.A.2
  • 38
    • 19344367734 scopus 로고    scopus 로고
    • Single nucleotide polymorphism-based validation of exonic splicing enhancers
    • Fairbrother,W.G., Holste,D., Burge,C.B. and Sharp,P.A. (2004) Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol., 2, E268.
    • (2004) PLoS Biol. , vol.2
    • Fairbrother, W.G.1    Holste, D.2    Burge, C.B.3    Sharp, P.A.4
  • 39
    • 30744469841 scopus 로고    scopus 로고
    • Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
    • Parmley,J.L., Chamary,J.V. and Hurst,L.D. (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol. Biol. Evol., 23, 301-309.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 301-309
    • Parmley, J.L.1    Chamary, J.V.2    Hurst, L.D.3
  • 40
    • 5044222204 scopus 로고    scopus 로고
    • How did alternative splicing evolve?
    • Ast,G. (2004) How did alternative splicing evolve? Nat. Rev. Genet., 5, 773-782.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 773-782
    • Ast, G.1
  • 41
    • 43249117483 scopus 로고    scopus 로고
    • Multifactorial interplay controls the splicing profile of Alu-derived exons
    • Ram,O., Schwartz,S. and Ast,G. (2008) Multifactorial interplay controls the splicing profile of Alu-derived exons. Mol. Cell Biol., 28, 3513-3525.
    • (2008) Mol. Cell Biol. , vol.28 , pp. 3513-3525
    • Ram, O.1    Schwartz, S.2    Ast, G.3
  • 42
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • Yeo,G. and Burge,C.B. (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol., 11, 377-394.
    • (2004) J. Comput. Biol. , vol.11 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2
  • 43
    • 0036911605 scopus 로고    scopus 로고
    • Distribution and characterization of regulatory elements in the human genome
    • Majewski,J. and Ott,J. (2002) Distribution and characterization of regulatory elements in the human genome. Genome Res., 12, 1827-1836.
    • (2002) Genome Res. , vol.12 , pp. 1827-1836
    • Majewski, J.1    Ott, J.2
  • 44
    • 0030988942 scopus 로고    scopus 로고
    • Identification of a new class of exonic splicing enhancers by in vivo selection
    • Coulter,L.R., Landree,M.A. and Cooper,T.A. (1997) Identification of a new class of exonic splicing enhancers by in vivo selection. Mol. Cell Biol., 17, 2143-2150.
    • (1997) Mol. Cell Biol. , vol.17 , pp. 2143-2150
    • Coulter, L.R.1    Landree, M.A.2    Cooper, T.A.3
  • 45
    • 30044440197 scopus 로고    scopus 로고
    • Chromatin, transcript elongation and alternative splicing
    • Kornblihtt,A.R. (2006) Chromatin, transcript elongation and alternative splicing. Nat. Struct. Mol. Biol., 13, 5-7.
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 5-7
    • Kornblihtt, A.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.