메뉴 건너뛰기




Volumn 48, Issue 10, 2016, Pages 1112-1118

The rules and impact of nonsense-mediated mRNA decay in human cancers

Author keywords

[No Author keywords available]

Indexed keywords

HEMOGLOBIN BETA CHAIN; POLYADENYLIC ACID BINDING PROTEIN; RNA BINDING PROTEIN; TRANSCRIPTOME; STOP CODON;

EID: 84987641578     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3664     Document Type: Article
Times cited : (329)

References (49)
  • 1
    • 0029330286 scopus 로고
    • When cells stop making sense: Effects of nonsense codons on RNA metabolism in vertebrate cells
    • Maquat, L. E. When cells stop making sense: effects of nonsense codons on RNA metabolism in vertebrate cells. RNA 1, 453-465 (1995).
    • (1995) RNA , vol.1 , pp. 453-465
    • Maquat, L.E.1
  • 2
    • 6944256813 scopus 로고    scopus 로고
    • Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise
    • Mendell, J. T., Sharifi, N. A., Meyers, J. L., Martinez-Murillo, F. & Dietz, H. C. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36, 1073-1078 (2004).
    • (2004) Nat. Genet. , vol.36 , pp. 1073-1078
    • Mendell, J.T.1    Sharifi, N.A.2    Meyers, J.L.3    Martinez-Murillo, F.4    Dietz, H.C.5
  • 3
    • 0032837376 scopus 로고    scopus 로고
    • Nonsense-mediated mRNA decay in health and disease
    • Frischmeyer, P. A. & Dietz, H. C. Nonsense-mediated mRNA decay in health and disease. Hum. Mol. Genet. 8, 1893-1900 (1999).
    • (1999) Hum. Mol. Genet. , vol.8 , pp. 1893-1900
    • Frischmeyer, P.A.1    Dietz, H.C.2
  • 4
    • 0028344092 scopus 로고
    • Nonsense codon mutations in the terminal exon of the '-globin gene are not associated with a reduction in '-mRNA accumulation: A mechanism for the phenotype of dominant ?-thalassemia
    • Hall, G. W. & Thein, S. Nonsense codon mutations in the terminal exon of the ?-globin gene are not associated with a reduction in ?-mRNA accumulation: a mechanism for the phenotype of dominant ?-thalassemia. Blood 83, 2031-2037 (1994).
    • (1994) Blood , vol.83 , pp. 2031-2037
    • Hall, G.W.1    Thein, S.2
  • 5
    • 0035168526 scopus 로고    scopus 로고
    • Long mutant dystrophins and variable phenotypes: Evasion of nonsense-mediated decay?
    • Kerr, T. P., Sewry, C. A., Robb, S. A. & Roberts, R. G. Long mutant dystrophins and variable phenotypes: evasion of nonsense-mediated decay? Hum. Genet. 109, 402-407 (2001).
    • (2001) Hum. Genet. , vol.109 , pp. 402-407
    • Kerr, T.P.1    Sewry, C.A.2    Robb, S.A.3    Roberts, R.G.4
  • 6
    • 0031840487 scopus 로고    scopus 로고
    • At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: A possible link between nuclear splicing and cytoplasmic translation
    • Zhang, J., Sun, X., Qian, Y., LaDuca, J. P. & Maquat, L. E. At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: a possible link between nuclear splicing and cytoplasmic translation. Mol. Cell. Biol. 18, 5272-5283 (1998).
    • (1998) Mol. Cell. Biol. , vol.18 , pp. 5272-5283
    • Zhang, J.1    Sun, X.2    Qian, Y.3    LaDuca, J.P.4    Maquat, L.E.5
  • 7
    • 0032526946 scopus 로고    scopus 로고
    • Binary specification of nonsense codons by splicing and cytoplasmic translation
    • Thermann, R. et al. Binary specification of nonsense codons by splicing and cytoplasmic translation. EMBO J. 17, 3484-3494 (1998).
    • (1998) EMBO J. , vol.17 , pp. 3484-3494
    • Thermann, R.1
  • 8
    • 0035801373 scopus 로고    scopus 로고
    • The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay
    • Le Hir, H., Gatfield, D., Izaurralde, E. & Moore, M. J. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 20, 4987-4997 (2001).
    • (2001) EMBO J. , vol.20 , pp. 4987-4997
    • Le Hir, H.1    Gatfield, D.2    Izaurralde, E.3    Moore, M.J.4
  • 9
    • 37849005006 scopus 로고    scopus 로고
    • NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity
    • Chamieh, H., Ballut, L., Bonneau, F. & Le Hir, H. NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity. Nat. Struct. Mol. Biol. 15, 85-93 (2008).
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 85-93
    • Chamieh, H.1    Ballut, L.2    Bonneau, F.3    Le Hir, H.4
  • 10
    • 59649124310 scopus 로고    scopus 로고
    • Nonsense-mediated mRNA decay (NMD) mechanisms
    • Brogna, S. & Wen, J. Nonsense-mediated mRNA decay (NMD) mechanisms. Nat. Struct. Mol. Biol. 16, 107-113 (2009).
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 107-113
    • Brogna, S.1    Wen, J.2
  • 11
    • 0036205348 scopus 로고    scopus 로고
    • Boundary-independent polar nonsense-mediated decay
    • Wang, J., Gudikote, J. P., Olivas, O. R. & Wilkinson, M. F. Boundary-independent polar nonsense-mediated decay. EMBO Rep. 3, 274-279 (2002).
    • (2002) EMBO Rep. , vol.3 , pp. 274-279
    • Wang, J.1    Gudikote, J.P.2    Olivas, O.R.3    Wilkinson, M.F.4
  • 12
    • 3042796497 scopus 로고    scopus 로고
    • Efficient downregulation of immunoglobulin ' mRNA with premature translation-termination codons requires the 5'-half of the VDJ exon
    • Bühler, M., Paillusson, A. & Mühlemann, O. Efficient downregulation of immunoglobulin ' mRNA with premature translation-termination codons requires the 5'-half of the VDJ exon. Nucleic Acids Res. 32, 3304-3315 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3304-3315
    • Bühler, M.1    Paillusson, A.2    Mühlemann, O.3
  • 13
    • 43249093760 scopus 로고    scopus 로고
    • Posttranscriptional gene regulation by spatial rearrangement of the 3' untranslated region
    • Eberle, A. B., Stalder, L., Mathys, H., Orozco, R. Z. & Mühlemann, O. Posttranscriptional gene regulation by spatial rearrangement of the 3? untranslated region. PLoS Biol. 6, e92 (2008).
    • (2008) PLoS Biol. , vol.6 , pp. e92
    • Eberle, A.B.1    Stalder, L.2    Mathys, H.3    Orozco, R.Z.4    Mühlemann, O.5
  • 14
    • 0038487811 scopus 로고    scopus 로고
    • Poly(A)-binding proteins: Multifunctional scaffolds for the post-transcriptional control of gene expression
    • Mangus, D. A., Evans, M. C. & Jacobson, A. Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol. 4, 223 (2003).
    • (2003) Genome Biol. , vol.4 , pp. 223
    • Mangus, D.A.1    Evans, M.C.2    Jacobson, A.3
  • 15
    • 0042025014 scopus 로고    scopus 로고
    • Nonsense-mediated mRNA decay in Drosophila: At the intersection of the yeast and mammalian pathways
    • Gatfield, D., Unterholzner, L., Ciccarelli, F. D., Bork, P. & Izaurralde, E. Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. EMBO J. 22, 3960-3970 (2003).
    • (2003) EMBO J. , vol.22 , pp. 3960-3970
    • Gatfield, D.1    Unterholzner, L.2    Ciccarelli, F.D.3    Bork, P.4    Izaurralde, E.5
  • 17
    • 0031046735 scopus 로고    scopus 로고
    • Evidence that translation reinitiation abrogates nonsense-mediated mRNA decay in mammalian cells
    • Zhang, J. & Maquat, L. E. Evidence that translation reinitiation abrogates nonsense-mediated mRNA decay in mammalian cells. EMBO J. 16, 826-833 (1997).
    • (1997) EMBO J. , vol.16 , pp. 826-833
    • Zhang, J.1    Maquat, L.E.2
  • 18
    • 0034667531 scopus 로고    scopus 로고
    • Nonsense mutations in the human ?-globin gene lead to unexpected levels of cytoplasmic mRNA accumulation
    • Romão, L. et al. Nonsense mutations in the human ?-globin gene lead to unexpected levels of cytoplasmic mRNA accumulation. Blood 96, 2895-2901 (2000).
    • (2000) Blood , vol.96 , pp. 2895-2901
    • Romão, L.1
  • 19
    • 40449131535 scopus 로고    scopus 로고
    • Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense-mediated mRNA decay
    • Silva, A. L., Ribeiro, P., Inácio, A., Liebhaber, S. A. & Romão, L. Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense-mediated mRNA decay. RNA 14, 563-576 (2008).
    • (2008) RNA , vol.14 , pp. 563-576
    • Silva, A.L.1    Ribeiro, P.2    Inácio, A.3    Liebhaber, S.A.4    Romão, L.5
  • 20
    • 84885645853 scopus 로고    scopus 로고
    • Transcriptome and genome sequencing uncovers functional variation in humans
    • Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506-511 (2013).
    • (2013) Nature , vol.501 , pp. 506-511
    • Lappalainen, T.1
  • 21
    • 84929015299 scopus 로고    scopus 로고
    • Effect of predicted protein-truncating genetic variants on the human transcriptome
    • Rivas, M. A. et al. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348, 666-669 (2015).
    • (2015) Science , vol.348 , pp. 666-669
    • Rivas, M.A.1
  • 22
    • 84942236803 scopus 로고    scopus 로고
    • Somatic mutation in cancer and normal cells
    • Martincorena, I. & Campbell, P. J. Somatic mutation in cancer and normal cells. Science 349, 1483-1489 (2015).
    • (2015) Science , vol.349 , pp. 1483-1489
    • Martincorena, I.1    Campbell, P.J.2
  • 23
    • 84906885914 scopus 로고    scopus 로고
    • A post-translational regulatory switch on UPF1 controls targeted mRNA degradation
    • Kurosaki, T. et al. A post-translational regulatory switch on UPF1 controls targeted mRNA degradation. Genes Dev. 28, 1900-1916 (2014).
    • (2014) Genes Dev , vol.28 , pp. 1900-1916
    • Kurosaki, T.1
  • 24
    • 43249084802 scopus 로고    scopus 로고
    • A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay
    • Singh, G., Rebbapragada, I. & Lykke-Andersen, J. A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay. PLoS Biol. 6, e111 (2008).
    • (2008) PLoS Biol , vol.6 , pp. e111
    • Singh, G.1    Rebbapragada, I.2    Lykke-Andersen, J.3
  • 25
    • 84873828345 scopus 로고    scopus 로고
    • Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability
    • Tani, H. et al. Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability. RNA Biol. 9, 1370-1379 (2012).
    • (2012) RNA Biol. , vol.9 , pp. 1370-1379
    • Tani, H.1
  • 26
    • 34848914038 scopus 로고    scopus 로고
    • Capturing heterogeneity in gene expression studies by surrogate variable analysis
    • Leek, J. T. & Storey, J. D. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 3, 1724-1735 (2007).
    • (2007) PLoS Genet. , vol.3 , pp. 1724-1735
    • Leek, J.T.1    Storey, J.D.2
  • 27
    • 84936805108 scopus 로고    scopus 로고
    • Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities
    • Fiorini, F., Bagchi, D., Le Hir, H. & Croquette, V. Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities. Nat. Commun. 6, 7581 (2015).
    • (2015) Nat. Commun. , vol.6 , pp. 7581
    • Fiorini, F.1    Bagchi, D.2    Le Hir, H.3    Croquette, V.4
  • 28
    • 84880427394 scopus 로고    scopus 로고
    • A compendium of RNA-binding motifs for decoding gene regulation
    • Ray, D. et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499, 172-177 (2013).
    • (2013) Nature , vol.499 , pp. 172-177
    • Ray, D.1
  • 29
    • 78650647972 scopus 로고    scopus 로고
    • Nonsense-mediated decay targets have multiple sequence-related features that can inhibit translation
    • Zhang, Z. et al. Nonsense-mediated decay targets have multiple sequence-related features that can inhibit translation. Mol. Syst. Biol. 6, 442 (2010).
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 442
    • Zhang, Z.1
  • 30
    • 77954147818 scopus 로고    scopus 로고
    • Translational selection is ubiquitous in prokaryotes
    • Supek, F., Skunca, N., Repar, J., Vlahovicek, K. & Smuc, T. Translational selection is ubiquitous in prokaryotes. PLoS Genet. 6, e1001004 (2010).
    • (2010) PLoS Genet. , vol.6 , pp. e1001004
    • Supek, F.1    Skunca, N.2    Repar, J.3    Vlahovicek, K.4    Smuc, T.5
  • 31
    • 33750356583 scopus 로고    scopus 로고
    • Nonsense-mediated mRNA decay: Target genes and functional diversification of effectors
    • Rehwinkel, J., Raes, J. & Izaurralde, E. Nonsense-mediated mRNA decay: target genes and functional diversification of effectors. Trends Biochem. Sci. 31, 639-646 (2006).
    • (2006) Trends Biochem. Sci. , vol.31 , pp. 639-646
    • Rehwinkel, J.1    Raes, J.2    Izaurralde, E.3
  • 32
    • 84859934498 scopus 로고    scopus 로고
    • Mediation of Drosophila autosomal dosage effects and compensation by network interactions
    • Malone, J. H. et al. Mediation of Drosophila autosomal dosage effects and compensation by network interactions. Genome Biol. 13, r28 (2012).
    • (2012) Genome Biol. , vol.13 , pp. r28
    • Malone, J.H.1
  • 33
    • 84964308876 scopus 로고    scopus 로고
    • Gene expression analysis identifies global gene dosage sensitivity in cancer
    • Fehrmann, R. S. et al. Gene expression analysis identifies global gene dosage sensitivity in cancer. Nat. Genet. 47, 115-125 (2015).
    • (2015) Nat. Genet. , vol.47 , pp. 115-125
    • Fehrmann, R.S.1
  • 34
    • 84994324806 scopus 로고    scopus 로고
    • Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer
    • Ju, Y. S. et al. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife 3, e02935 (2014).
    • (2014) ELife , vol.3 , pp. e02935
    • Ju, Y.S.1
  • 36
    • 0033527061 scopus 로고    scopus 로고
    • Haploinsufficiency for the neurofibromatosis 1 (NF1) tumor suppressor results in increased astrocyte proliferation
    • Gutmann, D. H. et al. Haploinsufficiency for the neurofibromatosis 1 (NF1) tumor suppressor results in increased astrocyte proliferation. Oncogene 18, 4450-4459 (1999).
    • (1999) Oncogene , vol.18 , pp. 4450-4459
    • Gutmann, D.H.1
  • 37
    • 84887992179 scopus 로고    scopus 로고
    • Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome
    • Davoli, T. et al. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell 155, 948-962 (2013).
    • (2013) Cell , vol.155 , pp. 948-962
    • Davoli, T.1
  • 38
    • 84908032938 scopus 로고    scopus 로고
    • Tug-of-war between driver and passenger mutations in cancer and other adaptive processes
    • McFarland, C. D., Mirny, L. A. & Korolev, K. S. Tug-of-war between driver and passenger mutations in cancer and other adaptive processes. Proc. Natl. Acad. Sci. USA 111, 15138-15143 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 15138-15143
    • McFarland, C.D.1    Mirny, L.A.2    Korolev, K.S.3
  • 39
    • 84946040120 scopus 로고    scopus 로고
    • COSMIC: Exploring the world's knowledge of somatic mutations in human cancer
    • Forbes, S. A. et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805-D811 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. D805-D811
    • Forbes, S.A.1
  • 40
    • 84905274395 scopus 로고    scopus 로고
    • Measuring error rates in genomic perturbation screens: Gold standards for human functional genomics
    • Hart, T., Brown, K. R., Sircoulomb, F., Rottapel, R. & Moffat, J. Measuring error rates in genomic perturbation screens: gold standards for human functional genomics. Mol. Syst. Biol. 10, 733 (2014).
    • (2014) Mol. Syst. Biol. , vol.10 , pp. 733
    • Hart, T.1    Brown, K.R.2    Sircoulomb, F.3    Rottapel, R.4    Moffat, J.5
  • 41
    • 84863541457 scopus 로고    scopus 로고
    • Recurrent hemizygous deletions in cancers may optimize proliferative potential
    • Solimini, N. L. et al. Recurrent hemizygous deletions in cancers may optimize proliferative potential. Science 337, 104-109 (2012).
    • (2012) Science , vol.337 , pp. 104-109
    • Solimini, N.L.1
  • 42
    • 84879488128 scopus 로고    scopus 로고
    • Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene
    • Gonzàlez-Porta, M., Frankish, A., Rung, J., Harrow, J. & Brazma, A. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Genome Biol. 14, R70 (2013).
    • (2013) Genome Biol. , vol.14 , pp. R70
    • Gonzàlez-Porta, M.1    Frankish, A.2    Rung, J.3    Harrow, J.4    Brazma, A.5
  • 43
    • 84941725069 scopus 로고    scopus 로고
    • Assessing allele-specific expression across multiple tissues from RNA-seq read data
    • Pirinen, M. et al. Assessing allele-specific expression across multiple tissues from RNA-seq read data. Bioinformatics 31, 2497-2504 (2015).
    • (2015) Bioinformatics , vol.31 , pp. 2497-2504
    • Pirinen, M.1
  • 44
    • 77955505742 scopus 로고    scopus 로고
    • A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies
    • Stegle, O., Parts, L., Durbin, R. & Winn, J. A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLoS Comput. Biol. 6, e1000770 (2010).
    • (2010) PLoS Comput. Biol. , vol.6 , pp. e1000770
    • Stegle, O.1    Parts, L.2    Durbin, R.3    Winn, J.4
  • 45
    • 84896366070 scopus 로고    scopus 로고
    • Synonymous mutations frequently act as driver mutations in human cancers
    • Supek, F., Miñana, B., Valcárcel, J., Gabaldón, T. & Lehner, B. Synonymous mutations frequently act as driver mutations in human cancers. Cell 156, 1324-1335 (2014).
    • (2014) Cell , vol.156 , pp. 1324-1335
    • Supek, F.1    Miñana, B.2    Valcárcel, J.3    Gabaldón, T.4    Lehner, B.5
  • 46
    • 73049097101 scopus 로고    scopus 로고
    • Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
    • Friedel, C. C., Dölken, L., Ruzsics, Z., Koszinowski, U. H. & Zimmer, R. Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res. 37, e115 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. e115
    • Friedel, C.C.1    Dölken, L.2    Ruzsics, Z.3    Koszinowski, U.H.4    Zimmer, R.5
  • 47
    • 84860575639 scopus 로고    scopus 로고
    • Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals
    • Tani, H. et al. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res. 22, 947-956 (2012).
    • (2012) Genome Res. , vol.22 , pp. 947-956
    • Tani, H.1
  • 48
    • 84996773946 scopus 로고    scopus 로고
    • Translation of 5' leaders is pervasive in genes resistant to eIF2 repression
    • Andreev, D. E. et al. Translation of 5' leaders is pervasive in genes resistant to eIF2 repression. eLife 4, e03971 (2015).
    • (2015) ELife , vol.4 , pp. e03971
    • Andreev, D.E.1
  • 49
    • 84946023145 scopus 로고    scopus 로고
    • The GOA database: Gene ontology annotation updates for 2015
    • Huntley, R. P. et al. The GOA database: gene ontology annotation updates for 2015. Nucleic Acids Res. 43, D1057-D1063 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. D1057-D1063
    • Huntley, R.P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.