메뉴 건너뛰기




Volumn 15, Issue 1, 2014, Pages

RNAmotifs: Prediction of multivalent RNA motifs that control alternative splicing

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN;

EID: 84893207466     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2014-15-1-r20     Document Type: Article
Times cited : (39)

References (45)
  • 1
    • 84865270565 scopus 로고    scopus 로고
    • An exon-centric perspective
    • Blencowe BJ: An exon-centric perspective. Biochem Cell Biol 2012, 90:603-612.
    • (2012) Biochem Cell Biol , vol.90 , pp. 603-612
    • Blencowe, B.J.1
  • 3
    • 79952105381 scopus 로고    scopus 로고
    • Understanding splicing regulation through RNA splicing maps
    • Witten JT, Ule J: Understanding splicing regulation through RNA splicing maps. Trends Genet 2011, 27:89-97.
    • (2011) Trends Genet , vol.27 , pp. 89-97
    • Witten, J.T.1    Ule, J.2
  • 4
    • 72849106592 scopus 로고    scopus 로고
    • RNA processing and its regulation: global insights into biological networks
    • Licatalosi DD, Darnell RB: RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 2010, 11:75-87.
    • (2010) Nat Rev Genet , vol.11 , pp. 75-87
    • Licatalosi, D.D.1    Darnell, R.B.2
  • 5
    • 77951120000 scopus 로고    scopus 로고
    • Alternative splicing and evolution: diversification, exon definition and function
    • Keren H, Lev-Maor G, Ast G: Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 2010, 11:345-355.
    • (2010) Nat Rev Genet , vol.11 , pp. 345-355
    • Keren, H.1    Lev-Maor, G.2    Ast, G.3
  • 6
    • 84936744064 scopus 로고    scopus 로고
    • Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
    • Sugimoto Y, Konig J, Hussain S, Zupan B, Curk T, Frye M, Ule J: Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol 2012, 13:R67.
    • (2012) Genome Biol , vol.13 , pp. R67
    • Sugimoto, Y.1    Konig, J.2    Hussain, S.3    Zupan, B.4    Curk, T.5    Frye, M.6    Ule, J.7
  • 8
    • 0035369805 scopus 로고    scopus 로고
    • Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing
    • Brudno M, Gelfand MS, Spengler S, Zorn M, Dubchak I, Conboy JG: Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing. Nucleic Acids Res 2001, 29:2338-2348.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2338-2348
    • Brudno, M.1    Gelfand, M.S.2    Spengler, S.3    Zorn, M.4    Dubchak, I.5    Conboy, J.G.6
  • 9
    • 56749164864 scopus 로고    scopus 로고
    • Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines
    • Castle JC, Zhang C, Shah JK, Kulkarni AV, Kalsotra A, Cooper TA, Johnson JM: Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet 2008, 40:1416-1425.
    • (2008) Nat Genet , vol.40 , pp. 1416-1425
    • Castle, J.C.1    Zhang, C.2    Shah, J.K.3    Kulkarni, A.V.4    Kalsotra, A.5    Cooper, T.A.6    Johnson, J.M.7
  • 15
    • 51949111100 scopus 로고    scopus 로고
    • Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2
    • Zhang C, Zhang Z, Castle J, Sun S, Johnson J, Krainer AR, Zhang MQ: Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev 2008, 22:2550-2563.
    • (2008) Genes Dev , vol.22 , pp. 2550-2563
    • Zhang, C.1    Zhang, Z.2    Castle, J.3    Sun, S.4    Johnson, J.5    Krainer, A.R.6    Zhang, M.Q.7
  • 17
    • 33750222859 scopus 로고    scopus 로고
    • Sequence-specific binding of single-stranded RNA: is there a code for recognition?
    • Auweter SD, Oberstrass FC, Allain FH: Sequence-specific binding of single-stranded RNA: is there a code for recognition? Nucleic Acids Res 2006, 34:4943-4959.
    • (2006) Nucleic Acids Res , vol.34 , pp. 4943-4959
    • Auweter, S.D.1    Oberstrass, F.C.2    Allain, F.H.3
  • 18
    • 84881493949 scopus 로고    scopus 로고
    • Prediction of clustered RNA-binding protein motif sites in the mammalian genome
    • Zhang C, Lee KY, Swanson MS, Darnell RB: Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res 2013, 41:6793-6807.
    • (2013) Nucleic Acids Res , vol.41 , pp. 6793-6807
    • Zhang, C.1    Lee, K.Y.2    Swanson, M.S.3    Darnell, R.B.4
  • 19
    • 77954284248 scopus 로고    scopus 로고
    • SFmap: a web server for motif analysis and prediction of splicing factor binding sites
    • Paz I, Akerman M, Dror I, Kosti I, Mandel-Gutfreund Y: SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Res 2010, 38:W281-W285.
    • (2010) Nucleic Acids Res , vol.38 , pp. W281-W285
    • Paz, I.1    Akerman, M.2    Dror, I.3    Kosti, I.4    Mandel-Gutfreund, Y.5
  • 20
    • 0034705034 scopus 로고    scopus 로고
    • The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain
    • Jensen KB, Musunuru K, Lewis HA, Burley SK, Darnell RB: The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain. Proc Natl Acad Sci U S A 2000, 97:5740-5745.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 5740-5745
    • Jensen, K.B.1    Musunuru, K.2    Lewis, H.A.3    Burley, S.K.4    Darnell, R.B.5
  • 23
    • 0029055472 scopus 로고
    • Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins
    • Singh R, Valcarcel J, Green MR: Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. Science 1995, 268:1173-1176.
    • (1995) Science , vol.268 , pp. 1173-1176
    • Singh, R.1    Valcarcel, J.2    Green, M.R.3
  • 24
    • 79960230895 scopus 로고    scopus 로고
    • Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
    • Zhang C, Darnell RB: Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 2011, 29:607-614.
    • (2011) Nat Biotechnol , vol.29 , pp. 607-614
    • Zhang, C.1    Darnell, R.B.2
  • 30
    • 0030878682 scopus 로고    scopus 로고
    • Mutation of PTB binding sites causes misregulation of alternative 3' splice site selection in vivo
    • Perez I, Lin CH, McAfee JG, Patton JG: Mutation of PTB binding sites causes misregulation of alternative 3' splice site selection in vivo. RNA 1997, 3:764-778.
    • (1997) RNA , vol.3 , pp. 764-778
    • Perez, I.1    Lin, C.H.2    McAfee, J.G.3    Patton, J.G.4
  • 31
    • 0030027575 scopus 로고    scopus 로고
    • Individual RNA recognition motifs of TIA-1 and TIAR have different RNA binding specificities
    • Dember LM, Kim ND, Liu KQ, Anderson P: Individual RNA recognition motifs of TIA-1 and TIAR have different RNA binding specificities. J Biol Chem 1996, 271:2783-2788.
    • (1996) J Biol Chem , vol.271 , pp. 2783-2788
    • Dember, L.M.1    Kim, N.D.2    Liu, K.Q.3    Anderson, P.4
  • 34
    • 57549110044 scopus 로고    scopus 로고
    • Binding to protein surfaces by supramolecular multivalent scaffolds
    • Martos V, Castreno P, Valero J, de Mendoza J: Binding to protein surfaces by supramolecular multivalent scaffolds. Curr Opin Chem Biol 2008, 12:698-706.
    • (2008) Curr Opin Chem Biol , vol.12 , pp. 698-706
    • Martos, V.1    Castreno, P.2    Valero, J.3    de Mendoza, J.4
  • 35
    • 77954757965 scopus 로고    scopus 로고
    • Multitasking with ubiquitin through multivalent interactions
    • Liu F, Walters KJ: Multitasking with ubiquitin through multivalent interactions. Trends Biochem Sci 2010, 35:352-360.
    • (2010) Trends Biochem Sci , vol.35 , pp. 352-360
    • Liu, F.1    Walters, K.J.2
  • 36
    • 70849099495 scopus 로고    scopus 로고
    • The extracellular matrix: not just pretty fibrils
    • Hynes RO: The extracellular matrix: not just pretty fibrils. Science 2009, 326:1216-1219.
    • (2009) Science , vol.326 , pp. 1216-1219
    • Hynes, R.O.1
  • 37
    • 33745499067 scopus 로고    scopus 로고
    • Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65
    • Sickmier EA, Frato KE, Shen H, Paranawithana SR, Green MR, Kielkopf CL: Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. Mol Cell 2006, 23:49-59.
    • (2006) Mol Cell , vol.23 , 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
  • 38
    • 0034612372 scopus 로고    scopus 로고
    • A brain-enriched polypyrimidine tract-binding protein antagonizes the ability of Nova to regulate neuron-specific alternative splicing
    • Polydorides AD, Okano HJ, Yang YY, Stefani G, Darnell RB: A brain-enriched polypyrimidine tract-binding protein antagonizes the ability of Nova to regulate neuron-specific alternative splicing. Proc Natl Acad Sci U S A 2000, 97:6350-6355.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 6350-6355
    • Polydorides, A.D.1    Okano, H.J.2    Yang, Y.Y.3    Stefani, G.4    Darnell, R.B.5
  • 39
    • 84864020005 scopus 로고    scopus 로고
    • Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain
    • Licatalosi DD, Yano M, Fak JJ, Mele A, Grabinski SE, Zhang C, Darnell RB: Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain. Genes Dev 2012, 26:1626-1642.
    • (2012) Genes Dev , vol.26 , pp. 1626-1642
    • Licatalosi, D.D.1    Yano, M.2    Fak, J.J.3    Mele, A.4    Grabinski, S.E.5    Zhang, C.6    Darnell, R.B.7
  • 40
    • 79954554384 scopus 로고    scopus 로고
    • GeCo++: a C++ library for genomic features computation and annotation in the presence of variants
    • Cereda M, Sironi M, Cavalleri M, Pozzoli U: GeCo++: a C++ library for genomic features computation and annotation in the presence of variants. Bioinformatics 2011, 27:1313-1315.
    • (2011) Bioinformatics , vol.27 , pp. 1313-1315
    • Cereda, M.1    Sironi, M.2    Cavalleri, M.3    Pozzoli, U.4
  • 42
    • 84923853900 scopus 로고    scopus 로고
    • All data and software used in this study
    • All data and software used in this study. [https://bitbucket.org/rogrro/rna_motifs]


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.