메뉴 건너뛰기




Volumn 105, Issue 15, 2008, Pages 5797-5802

RNA landscape of evolution for optimal exon and intron discrimination

Author keywords

DNA strand asymmetry; Exon and intron recognition; Exon identity elements; Intron identity elements; Splicing regulatory elements

Indexed keywords

GENOMIC RNA; NUCLEOTIDE; RNA;

EID: 44449115151     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0801692105     Document Type: Article
Times cited : (97)

References (32)
  • 1
    • 0036207384 scopus 로고    scopus 로고
    • Listening to silence and understanding nonsense: Exonic mutations that affect splicing
    • Cartegni L, Chew SL, Krainer AR (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
  • 2
    • 0013394889 scopus 로고    scopus 로고
    • Mechanisms of alternative pre-messenger RNA splicing
    • Black DL (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
  • 3
    • 0030988942 scopus 로고    scopus 로고
    • Identification of a new class of exonic splicing enhancers by in vivo selection
    • Coulter LR, Landree MA, Cooper TA (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
  • 4
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • Fairbrother WG, Yeh R-F, Sharp, PA, Burge CB (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
  • 5
    • 33745207758 scopus 로고    scopus 로고
    • Comparative analysis identifies exonic splicing regulatory sequences-the complex definition of enhancers and silencers
    • Goren A, et al. (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
  • 6
    • 33747891736 scopus 로고    scopus 로고
    • An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers
    • Smith PJ, et al. (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
  • 7
    • 0028805223 scopus 로고
    • Selection of novel exon recognition elements from a pool of random sequences
    • Tian H, Kole R (1995) Selection of novel exon recognition elements from a pool of random sequences. Mol Cell Biol 15:6291-6298.
    • (1995) Mol Cell Biol , vol.15 , pp. 6291-6298
    • Tian, H.1    Kole, R.2
  • 8
    • 10944256767 scopus 로고    scopus 로고
    • Systematic identification and analysis of exonic splicing silencers
    • Wang ZF, et al. (2004) Systematic identification and analysis of exonic splicing silencers. Cell 119:831-845.
    • (2004) Cell , vol.119 , pp. 831-845
    • Wang, Z.F.1
  • 9
    • 2642525438 scopus 로고    scopus 로고
    • Computational definition of sequence motifs governing constitutive exon splicing
    • Zhang XH-F Chasin LA (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.-F.1    Chasin, L.A.2
  • 10
    • 1842635464 scopus 로고    scopus 로고
    • Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression
    • Zheng Z-M (2004) Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression. J Biomed Sci 11:278-294.
    • (2004) J Biomed Sci , vol.11 , pp. 278-294
    • Zheng, Z.-M.1
  • 11
    • 17044427579 scopus 로고    scopus 로고
    • Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers
    • Ibrahim EC, Schaal TD, Hertel KJ, Reed R, Maniatis T (2005) Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers. Proc Natl Acad Sci USA 102:5002-5007.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 5002-5007
    • Ibrahim, E.C.1    Schaal, T.D.2    Hertel, K.J.3    Reed, R.4    Maniatis, T.5
  • 12
    • 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 (1997) G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol Cell Biol 17:4562-4571.
    • (1997) Mol Cell Biol , vol.17 , pp. 4562-4571
    • McCullough, A.J.1    Berget, S.M.2
  • 13
    • 0038486897 scopus 로고    scopus 로고
    • Intronic sequences flanking alternatively spliced exons are conserved between human and mouse
    • Sorek R, Ast G (2003) Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res 13:1631-1637.
    • (2003) Genome Res , vol.13 , pp. 1631-1637
    • Sorek, R.1    Ast, G.2
  • 14
    • 31144465926 scopus 로고    scopus 로고
    • Hearing silence: Non-neutral evolution at synonymous sites in mammals
    • Chamary JV, Parmley JL, Hurst LD (2006) Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7:98-108.
    • (2006) Nat Rev Genet , vol.7 , pp. 98-108
    • Chamary, J.V.1    Parmley, J.L.2    Hurst, L.D.3
  • 15
    • 0014218036 scopus 로고
    • On denaturation of deoxyribonucleic acid. 2. Effects of concentration
    • Lin HJ, Chargaff E (1967) On denaturation of deoxyribonucleic acid. 2. Effects of concentration. Biochim Biophys Acta 145:398-409.
    • (1967) Biochim Biophys Acta , vol.145 , pp. 398-409
    • Lin, H.J.1    Chargaff, E.2
  • 16
    • 33845214633 scopus 로고    scopus 로고
    • Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions
    • Albrecht-Buehler G (2006) Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions. Proc Natl Acad Sci USA 103:17828-17833.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 17828-17833
    • Albrecht-Buehler, G.1
  • 17
    • 0036363646 scopus 로고    scopus 로고
    • Mechanisms of transcription-coupled DNA repair
    • Svejstrup JQ (2002) Mechanisms of transcription-coupled DNA repair. Nature Rev Mol Cell Biol 3:21-29.
    • (2002) Nature Rev Mol Cell Biol , vol.3 , pp. 21-29
    • Svejstrup, J.Q.1
  • 18
    • 0037380022 scopus 로고    scopus 로고
    • Transcription-associated mutational asymmetry in mammalian evolution
    • Green P, et al. (2003) Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 33:514-517.
    • (2003) Nat Genet , vol.33 , pp. 514-517
    • Green, P.1
  • 19
    • 4644246096 scopus 로고    scopus 로고
    • Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes
    • Touchon M, Arneodo A, d'Aubenton -Carafa Y, Thermes C (2004) Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucleic Acids Res 32:4969-4978.
    • (2004) Nucleic Acids Res , vol.32 , pp. 4969-4978
    • Touchon, M.1    Arneodo, A.2    d'Aubenton -Carafa, Y.3    Thermes, C.4
  • 20
    • 0024117031 scopus 로고
    • RNA-binding specificity of hnRNA proteins-a subset bind to the 3′ end of introns
    • Swanson MS, Dreyfuss G (1988) RNA-binding specificity of hnRNA proteins-a subset bind to the 3′ end of introns. EMBO J 7:3519-3529.
    • (1988) EMBO J , vol.7 , pp. 3519-3529
    • Swanson, M.S.1    Dreyfuss, G.2
  • 21
    • 0029064220 scopus 로고
    • The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities
    • Tacke R, Manley JL (1995) The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J 14:3540-3551.
    • (1995) EMBO J , vol.14 , pp. 3540-3551
    • Tacke, R.1    Manley, J.L.2
  • 22
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 23
    • 30744432134 scopus 로고    scopus 로고
    • Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
    • Chamary JV, Hurst L (2005) Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol 6:R75.
    • (2005) Genome Biol , vol.6
    • Chamary, J.V.1    Hurst, L.2
  • 24
    • 19344367734 scopus 로고    scopus 로고
    • Single nucleotide polymorphism - based validation of exonic splicing enhancers
    • Fairbrother WG, Holste D, Burge CB, Sharp PA (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
  • 26
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
    • (2007) Nature , vol.447 , pp. 799-816
  • 27
    • 34848893914 scopus 로고    scopus 로고
    • Evolutionary impact of limited splicing fidelity in mammalian genes
    • Zhang C, Krainer AR, Zhang MQ (2007) Evolutionary impact of limited splicing fidelity in mammalian genes. Trends Genet 23:484-488.
    • (2007) Trends Genet , vol.23 , pp. 484-488
    • Zhang, C.1    Krainer, A.R.2    Zhang, M.Q.3
  • 28
    • 34347406537 scopus 로고    scopus 로고
    • Identification of candidate regulatory sequences in mammalian 3′ UTRs by statistical analysis of oligonucleotide distributions
    • Cora D, Di Cunto F, Caselle M, Provero P (2007) Identification of candidate regulatory sequences in mammalian 3′ UTRs by statistical analysis of oligonucleotide distributions. BMC Bioinformatics 8:174.
    • (2007) BMC Bioinformatics , vol.8 , pp. 174
    • Cora, D.1    Di Cunto, F.2    Caselle, M.3    Provero, P.4
  • 29
    • 41649093631 scopus 로고    scopus 로고
    • Positive selection acting on splicing motifs reflects compensatory evolution
    • 10.1101/gr.070268.107
    • Ke S, Zhang XHF, Chasin LA (2008) Positive selection acting on splicing motifs reflects compensatory evolution. Genome Res 10.1101/gr.070268.107.
    • (2008) Genome Res
    • Ke, S.1    Zhang, X.H.F.2    Chasin, L.A.3
  • 30
    • 33847032203 scopus 로고    scopus 로고
    • The genetic code is nearly optimal for allowing additional information within protein-coding sequences
    • Itzkovitz S, Alon U (2007) The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res 17:405-412.
    • (2007) Genome Res , vol.17 , pp. 405-412
    • Itzkovitz, S.1    Alon, U.2
  • 31
    • 0342614926 scopus 로고    scopus 로고
    • Codon usage tabulated from international DNA sequence databases: Status for the year 2000
    • Nakamura Y, Gojobori T, Ikemura T (2000) Codon usage tabulated from international DNA sequence databases: Status for the year 2000. Nucleic Acids Res 28:292.
    • (2000) Nucleic Acids Res , vol.28 , pp. 292
    • Nakamura, Y.1    Gojobori, T.2    Ikemura, T.3
  • 32
    • 0036677661 scopus 로고    scopus 로고
    • Why are complementary DNA strands symmetric?
    • Baisnee P-F, Hampson S, Baldi P (2002) Why are complementary DNA strands symmetric? Bioinformatics 18:1021-1033.
    • (2002) Bioinformatics , vol.18 , pp. 1021-1033
    • Baisnee, P.-F.1    Hampson, S.2    Baldi, P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.