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Volumn 6, Issue 12, 2010, Pages 1-11

Noisy splicing drives mRNA isoform diversity in human cells

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

EID: 78650689920     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1001236     Document Type: Article
Times cited : (215)

References (61)
  • 1
    • 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
  • 2
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcriptomes
    • Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
    • (2008) Nature , vol.456 , pp. 470-476
    • Wang, E.T.1    Sandberg, R.2    Luo, S.3    Khrebtukova, I.4    Zhang, L.5
  • 3
    • 0038349624 scopus 로고    scopus 로고
    • Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome
    • Zavolan M, Kondo S, Schonbach C, Adachi J, Hume DA, et al. (2003) Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res 13: 1290-1300.
    • (2003) Genome Res , vol.13 , pp. 1290-1300
    • Zavolan, M.1    Kondo, S.2    Schonbach, C.3    Adachi, J.4    Hume, D.A.5
  • 5
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 6
    • 0036337915 scopus 로고    scopus 로고
    • A genomic view of alternative splicing
    • Modrek B, Lee C (2002) A genomic view of alternative splicing. Nat Genet 30: 13-19.
    • (2002) Nat Genet , vol.30 , pp. 13-19
    • Modrek, B.1    Lee, C.2
  • 7
    • 61649094219 scopus 로고    scopus 로고
    • Evolutionary genomics and the reach of selection
    • Hurst LD (2009) Evolutionary genomics and the reach of selection. J Biol 8: 12.
    • (2009) J Biol , vol.8 , pp. 12
    • Hurst, L.D.1
  • 8
    • 69049116283 scopus 로고    scopus 로고
    • Stochastic noise in splicing machinery
    • Melamud E, Moult J (2009) Stochastic noise in splicing machinery. Nucleic Acids Res 37: 4873-4886.
    • (2009) Nucleic Acids Res , vol.37 , pp. 4873-4886
    • Melamud, E.1    Moult, J.2
  • 9
    • 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
  • 10
    • 24644493193 scopus 로고    scopus 로고
    • Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing
    • Baek D, Green P (2005) Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc Natl Acad Sci U S A 102: 12813-12818.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 12813-12818
    • Baek, D.1    Green, P.2
  • 11
    • 1642473041 scopus 로고    scopus 로고
    • How prevalent is functional alternative splicing in the human genome?
    • Sorek R, Shamir R, Ast G (2004) How prevalent is functional alternative splicing in the human genome? Trends Genet 20: 68-71.
    • (2004) Trends Genet , vol.20 , pp. 68-71
    • Sorek, R.1    Shamir, R.2    Ast, G.3
  • 12
    • 14544277546 scopus 로고    scopus 로고
    • Identification and analysis of alternative splicing events conserved in human and mouse
    • Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB (2005) Identification and analysis of alternative splicing events conserved in human and mouse. Proc Natl Acad Sci U S A 102: 2850-2855.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 2850-2855
    • Yeo, G.W.1    van Nostrand, E.2    Holste, D.3    Poggio, T.4    Burge, C.B.5
  • 13
    • 0038617729 scopus 로고    scopus 로고
    • Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss
    • Modrek B, Lee CJ (2003) Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat Genet 34: 177-180.
    • (2003) Nat Genet , vol.34 , pp. 177-180
    • Modrek, B.1    Lee, C.J.2
  • 14
    • 38349125022 scopus 로고    scopus 로고
    • Translational control of intron splicing in eukaryotes
    • Jaillon O, Bouhouche K, Gout JF, Aury JM, Noel B, et al. (2008) Translational control of intron splicing in eukaryotes. Nature 451: 359-362.
    • (2008) Nature , vol.451 , pp. 359-362
    • Jaillon, O.1    Bouhouche, K.2    Gout, J.F.3    Aury, J.M.4    Noel, B.5
  • 15
    • 75749103383 scopus 로고    scopus 로고
    • Rate, molecular spectrum, and consequences of human mutation
    • Lynch M (2010) Rate, molecular spectrum, and consequences of human mutation. Proc Natl Acad Sci U S A 107: 961-968.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 961-968
    • Lynch, M.1
  • 17
    • 77950460661 scopus 로고    scopus 로고
    • Understanding mechanisms underlying human gene expression variation with RNA sequencing
    • Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
    • (2010) Nature , vol.464 , pp. 768-772
    • Pickrell, J.K.1    Marioni, J.C.2    Pai, A.A.3    Degner, J.F.4    Engelhardt, B.E.5
  • 18
    • 47649124124 scopus 로고    scopus 로고
    • A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    • Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
    • (2008) Science , vol.321 , pp. 956-960
    • Sultan, M.1    Schulz, M.H.2    Richard, H.3    Magen, A.4    Klingenhoff, A.5
  • 19
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
    • (2008) Genome Res , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 20
    • 33845248222 scopus 로고    scopus 로고
    • Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site
    • Dou Y, Fox-Walsh KL, Baldi PF, Hertel KJ (2006) Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site. RNA 12: 2047-2056.
    • (2006) RNA , vol.12 , pp. 2047-2056
    • Dou, Y.1    Fox-Walsh, K.L.2    Baldi, P.F.3    Hertel, K.J.4
  • 21
    • 33646491292 scopus 로고    scopus 로고
    • A simple physical model predicts small exon length variations
    • doi:10.1371/journal.pgen.0020045
    • Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, et al. (2006) A simple physical model predicts small exon length variations. PLoS Genet 2: e45. doi:10.1371/journal.pgen.0020045.
    • (2006) PLoS Genet , vol.2
    • Chern, T.M.1    van Nimwegen, E.2    Kai, C.3    Kawai, J.4    Carninci, P.5
  • 22
    • 42649130345 scopus 로고    scopus 로고
    • Widespread and subtle: Alternative splicing at shortdistance tandem sites
    • Hiller M, Platzer M (2008) Widespread and subtle: alternative splicing at shortdistance tandem sites. Trends Genet 24: 246-255.
    • (2008) Trends Genet , vol.24 , pp. 246-255
    • Hiller, M.1    Platzer, M.2
  • 25
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35: D61-65.
    • (2007) Nucleic Acids Res , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 26
    • 67650064594 scopus 로고    scopus 로고
    • The consensus coding sequence (CCDS) project: Identifying a common proteincoding gene set for the human and mouse genomes
    • Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, et al. (2009) The consensus coding sequence (CCDS) project: Identifying a common proteincoding gene set for the human and mouse genomes. Genome Res 19: 1316-1323.
    • (2009) Genome Res , vol.19 , pp. 1316-1323
    • Pruitt, K.D.1    Harrow, J.2    Harte, R.A.3    Wallin, C.4    Diekhans, M.5
  • 28
    • 77950458649 scopus 로고    scopus 로고
    • Transcriptome genetics using second generation sequencing in a caucasian population
    • Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, et al. (2010) Transcriptome genetics using second generation sequencing in a caucasian population. Nature 464: 773-777.
    • (2010) Nature , vol.464 , pp. 773-777
    • Montgomery, S.B.1    Sammeth, M.2    Gutierrez-Arcelus, M.3    Lach, R.P.4    Ingle, C.5
  • 29
    • 38649090044 scopus 로고    scopus 로고
    • Genome-wide analysis of transcript isoform variation in humans
    • Kwan T, Benovoy D, Dias C, Gurd S, Provencher C, et al. (2008) Genome-wide analysis of transcript isoform variation in humans. Nat Genet 40: 225-231.
    • (2008) Nat Genet , vol.40 , pp. 225-231
    • Kwan, T.1    Benovoy, D.2    Dias, C.3    Gurd, S.4    Provencher, C.5
  • 30
    • 63849281404 scopus 로고    scopus 로고
    • Common polymorphic transcript variation in human disease
    • Fraser HB, Xie X (2009) Common polymorphic transcript variation in human disease. Genome Res 19: 567-575.
    • (2009) Genome Res , vol.19 , pp. 567-575
    • Fraser, H.B.1    Xie, X.2
  • 31
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20: 110-121.
    • (2010) Genome Res , vol.20 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 33
    • 0033230005 scopus 로고    scopus 로고
    • Small introns tend to occur in GCrich regions in some but not all vertebrates
    • Hurst LD, Brunton CF, Smith NG (1999) Small introns tend to occur in GCrich regions in some but not all vertebrates. Trends Genet 15: 437-439.
    • (1999) Trends Genet , vol.15 , pp. 437-439
    • Hurst, L.D.1    Brunton, C.F.2    Smith, N.G.3
  • 34
    • 57649231776 scopus 로고    scopus 로고
    • Dynamic regulation of alternative splicing by silencers that modulate 59 splice site competition
    • Yu Y, Maroney PA, Denker JA, Zhang XHF, Dybkov O, et al. (2008) Dynamic regulation of alternative splicing by silencers that modulate 59 splice site competition. Cell 135: 1224-1236.
    • (2008) Cell , vol.135 , pp. 1224-1236
    • Yu, Y.1    Maroney, P.A.2    Denker, J.A.3    Zhang, X.H.F.4    Dybkov, O.5
  • 35
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • Fairbrother WG, Yeh RF, 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
  • 36
    • 42449098125 scopus 로고    scopus 로고
    • Splicing regulation: From a parts list of regulatory elements to an integrated splicing code
    • Wang Z, Burge CB (2008) Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14: 802-813.
    • (2008) RNA , vol.14 , pp. 802-813
    • Wang, Z.1    Burge, C.B.2
  • 37
    • 18344364099 scopus 로고    scopus 로고
    • Understanding alternative splicing: Towards a cellular code
    • Matlin AJ, Clark F, Smith CWJ (2005) Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6: 386-398.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 386-398
    • Matlin, A.J.1    Clark, F.2    Smith, C.W.J.3
  • 39
    • 2642525438 scopus 로고    scopus 로고
    • Computational definition of sequence motifs governing constitutive exon splicing
    • Zhang XHF, 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
  • 40
    • 10944256767 scopus 로고    scopus 로고
    • Systematic identification and analysis of exonic splicing silencers
    • 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.
    • (2004) Cell , vol.119 , pp. 831-845
    • Wang, Z.1    Rolish, M.E.2    Yeo, G.3    Tung, V.4    Mawson, M.5
  • 42
    • 70350013550 scopus 로고    scopus 로고
    • Biased chromatin signatures around polyadenylation sites and exons
    • Spies N, Nielsen CB, Padgett RA, Burge CB (2009) Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 36: 245-254.
    • (2009) Mol Cell , vol.36 , pp. 245-254
    • Spies, N.1    Nielsen, C.B.2    Padgett, R.A.3    Burge, C.B.4
  • 43
    • 69949132191 scopus 로고    scopus 로고
    • Chromatin organization marks exonintron structure
    • Schwartz S, Meshorer E, Ast G (2009) Chromatin organization marks exonintron structure. Nat Struct Mol Biol 16: 990-995.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 990-995
    • Schwartz, S.1    Meshorer, E.2    Ast, G.3
  • 45
    • 70349333201 scopus 로고    scopus 로고
    • Nucleosomes are well positioned in exons and carry characteristic histone modifications
    • Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J (2009) Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res 19: 1732-1741.
    • (2009) Genome Res , vol.19 , pp. 1732-1741
    • Andersson, R.1    Enroth, S.2    Rada-Iglesias, A.3    Wadelius, C.4    Komorowski, J.5
  • 46
    • 61349098460 scopus 로고    scopus 로고
    • Differential chromatin marking of introns and expressed exons by H3K36me3
    • Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, et al. (2009) Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41: 376-381.
    • (2009) Nat Genet , vol.41 , pp. 376-381
    • Kolasinska-Zwierz, P.1    Down, T.2    Latorre, I.3    Liu, T.4    Liu, X.S.5
  • 48
    • 44449115151 scopus 로고    scopus 로고
    • Rna landscape of evolution for optimal exon and intron discrimination
    • Zhang C, Li WH, Krainer AR, Zhang MQ (2008) Rna landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A 105: 5797-5802.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 5797-5802
    • Zhang, C.1    Li, W.H.2    Krainer, A.R.3    Zhang, M.Q.4
  • 49
    • 55549118939 scopus 로고    scopus 로고
    • The effect of intron length on exon creation ratios during the evolution of mammalian genomes
    • Roy M, Kim N, Xing Y, Lee C (2008) The effect of intron length on exon creation ratios during the evolution of mammalian genomes. RNA 14: 2261-2273.
    • (2008) RNA , vol.14 , pp. 2261-2273
    • Roy, M.1    Kim, N.2    Xing, Y.3    Lee, C.4
  • 51
    • 0345035503 scopus 로고    scopus 로고
    • Intron size and natural selection
    • Carvalho AB, Clark AG (1999) Intron size and natural selection. Nature 401: 344.
    • (1999) Nature , vol.401 , pp. 344
    • Carvalho, A.B.1    Clark, A.G.2
  • 52
    • 0037197986 scopus 로고    scopus 로고
    • Intron evolution as a population-genetic process
    • Lynch M (2002) Intron evolution as a population-genetic process. Proc Natl Acad Sci U S A 99: 6118-6123.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 6118-6123
    • Lynch, M.1
  • 53
    • 33846681383 scopus 로고    scopus 로고
    • Different levels of alternative splicing among eukaryotes
    • Kim E, Magen A, Ast G (2007) Different levels of alternative splicing among eukaryotes. Nucleic Acids Res 35: 125-131.
    • (2007) Nucleic Acids Res , vol.35 , pp. 125-131
    • Kim, E.1    Magen, A.2    Ast, G.3
  • 54
    • 77950396799 scopus 로고    scopus 로고
    • Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing
    • Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, et al. (2010) Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A.
    • (2010) Proc Natl Acad Sci U S A
    • Wu, J.Q.1    Habegger, L.2    Noisa, P.3    Szekely, A.4    Qiu, C.5
  • 55
    • 65449136284 scopus 로고    scopus 로고
    • Tophat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL (2009) Tophat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-11011.
    • (2009) Bioinformatics , vol.25 , pp. 1105-11011
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 56
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5
  • 57
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28: 503-510.
    • (2010) Nat Biotechnol , vol.28 , pp. 503-510
    • Guttman, M.1    Garber, M.2    Levin, J.Z.3    Donaghey, J.4    Robinson, J.5
  • 58
    • 77953203584 scopus 로고    scopus 로고
    • Global and unbiased detection of splice junctions from RNA-seq data
    • Ameur A, Wetterbom A, Feuk L, Gyllensten U (2010) Global and unbiased detection of splice junctions from RNA-seq data. Genome Biol 11: R34.
    • (2010) Genome Biol , vol.11
    • Ameur, A.1    Wetterbom, A.2    Feuk, L.3    Gyllensten, U.4
  • 59
    • 77955443472 scopus 로고    scopus 로고
    • Detection of splice junctions from paired-end RNA-seq data by SpliceMap
    • Au KF, Jiang H, Lin L, Xing Y, Wong WH (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res 38: 4570-4578.
    • (2010) Nucleic Acids Res , vol.38 , pp. 4570-4578
    • Au, K.F.1    Jiang, H.2    Lin, L.3    Xing, Y.4    Wong, W.H.5
  • 60
    • 62549126083 scopus 로고    scopus 로고
    • Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing
    • Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, et al. (2009) Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A 106: 3264-3269.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 3264-3269
    • Yassour, M.1    Kaplan, T.2    Fraser, H.B.3    Levin, J.Z.4    Pfiffner, J.5
  • 61
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows- Wheeler transform
    • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25: 1754-1760
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2


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