메뉴 건너뛰기




Volumn 160, Issue 6, 2015, Pages 1111-1124

Codon optimality is a major determinant of mRNA stability

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PROTEIN; CODON; FUNGAL RNA;

EID: 84924567669     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.02.029     Document Type: Article
Times cited : (694)

References (38)
  • 1
    • 0028220048 scopus 로고
    • Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
    • H. Akashi Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy Genetics 136 1994 927 935
    • (1994) Genetics , vol.136 , pp. 927-935
    • Akashi, H.1
  • 2
    • 0027198406 scopus 로고
    • A small segment of the MAT alpha 1 transcript promotes mRNA decay in Saccharomyces cerevisiae: A stimulatory role for rare codons
    • G. Caponigro, D. Muhlrad, and R. Parker A small segment of the MAT alpha 1 transcript promotes mRNA decay in Saccharomyces cerevisiae: a stimulatory role for rare codons Mol. Cell. Biol. 13 1993 5141 5148
    • (1993) Mol. Cell. Biol. , vol.13 , pp. 5141-5148
    • Caponigro, G.1    Muhlrad, D.2    Parker, R.3
  • 3
    • 84875465945 scopus 로고    scopus 로고
    • Positively charged residues are the major determinants of ribosomal velocity
    • C.A. Charneski, and L.D. Hurst Positively charged residues are the major determinants of ribosomal velocity PLoS Biol. 11 2013 e1001508
    • (2013) PLoS Biol. , vol.11 , pp. e1001508
    • Charneski, C.A.1    Hurst, L.D.2
  • 5
    • 25144482816 scopus 로고    scopus 로고
    • General translational repression by activators of mRNA decapping
    • J. Coller, and R. Parker General translational repression by activators of mRNA decapping Cell 122 2005 875 886
    • (2005) Cell , vol.122 , pp. 875-886
    • Coller, J.1    Parker, R.2
  • 6
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • D.A. Drummond, and C.O. Wilke Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution Cell 134 2008 341 352
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 7
    • 84894131718 scopus 로고    scopus 로고
    • Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast
    • J.V. Geisberg, Z. Moqtaderi, X. Fan, F. Ozsolak, and K. Struhl Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast Cell 156 2014 812 824
    • (2014) Cell , vol.156 , pp. 812-824
    • Geisberg, J.V.1    Moqtaderi, Z.2    Fan, X.3    Ozsolak, F.4    Struhl, K.5
  • 8
    • 84857770525 scopus 로고    scopus 로고
    • RNA decay modulates gene expression and controls its fidelity
    • S. Ghosh, and A. Jacobson RNA decay modulates gene expression and controls its fidelity Wiley Interdiscip. Rev. RNA 1 2010 351 361
    • (2010) Wiley Interdiscip. Rev. RNA , vol.1 , pp. 351-361
    • Ghosh, S.1    Jacobson, A.2
  • 10
    • 33846954393 scopus 로고    scopus 로고
    • PUF protein-mediated deadenylation is catalyzed by Ccr4p
    • A.C. Goldstrohm, D.J. Seay, B.A. Hook, and M. Wickens PUF protein-mediated deadenylation is catalyzed by Ccr4p J. Biol. Chem. 282 2007 109 114
    • (2007) J. Biol. Chem. , vol.282 , pp. 109-114
    • Goldstrohm, A.C.1    Seay, D.J.2    Hook, B.A.3    Wickens, M.4
  • 12
    • 0023394968 scopus 로고
    • Codon replacement in the PGK1 gene of Saccharomyces cerevisiae: Experimental approach to study the role of biased codon usage in gene expression
    • A. Hoekema, R.A. Kastelein, M. Vasser, and H.A. de Boer Codon replacement in the PGK1 gene of Saccharomyces cerevisiae: experimental approach to study the role of biased codon usage in gene expression Mol. Cell. Biol. 7 1987 2914 2924
    • (1987) Mol. Cell. Biol. , vol.7 , pp. 2914-2924
    • Hoekema, A.1    Kastelein, R.A.2    Vasser, M.3    De Boer, H.A.4
  • 13
    • 70249141564 scopus 로고    scopus 로고
    • Co-translational mRNA decay in Saccharomyces cerevisiae
    • W. Hu, T.J. Sweet, S. Chamnongpol, K.E. Baker, and J. Coller Co-translational mRNA decay in Saccharomyces cerevisiae Nature 461 2009 225 229
    • (2009) Nature , vol.461 , pp. 225-229
    • Hu, W.1    Sweet, T.J.2    Chamnongpol, S.3    Baker, K.E.4    Coller, J.5
  • 14
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • N.T. Ingolia, S. Ghaemmaghami, J.R.S. Newman, and J.S. Weissman Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling Science 324 2009 218 223
    • (2009) Science , vol.324 , pp. 218-223
    • Ingolia, N.T.1    Ghaemmaghami, S.2    Newman, J.R.S.3    Weissman, J.S.4
  • 15
    • 84899077335 scopus 로고    scopus 로고
    • Inferring gene function from evolutionary change in signatures of translation efficiency
    • A. Krisko, T. Copic, T. Gabaldón, B. Lehner, and F. Supek Inferring gene function from evolutionary change in signatures of translation efficiency Genome Biol. 15 2014 R44
    • (2014) Genome Biol. , vol.15 , pp. R44
    • Krisko, A.1    Copic, T.2    Gabaldón, T.3    Lehner, B.4    Supek, F.5
  • 16
    • 0033055772 scopus 로고    scopus 로고
    • The cis acting sequences responsible for the differential decay of the unstable MFA2 and stable PGK1 transcripts in yeast include the context of the translational start codon
    • T. LaGrandeur, and R. Parker The cis acting sequences responsible for the differential decay of the unstable MFA2 and stable PGK1 transcripts in yeast include the context of the translational start codon RNA 5 1999 420 433
    • (1999) RNA , vol.5 , pp. 420-433
    • Lagrandeur, T.1    Parker, R.2
  • 17
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 18
    • 84884418135 scopus 로고    scopus 로고
    • Emerging roles for ribonucleoprotein modification and remodeling in controlling RNA fate
    • S.R. Lee, and J. Lykke-Andersen Emerging roles for ribonucleoprotein modification and remodeling in controlling RNA fate Trends Cell Biol. 23 2013 504 510
    • (2013) Trends Cell Biol. , vol.23 , pp. 504-510
    • Lee, S.R.1    Lykke-Andersen, J.2
  • 20
    • 0026441426 scopus 로고
    • Mutations affecting stability and deadenylation of the yeast MFA2 transcript
    • D. Muhlrad, and R. Parker Mutations affecting stability and deadenylation of the yeast MFA2 transcript Genes Dev. 6 1992 2100 2111
    • (1992) Genes Dev. , vol.6 , pp. 2100-2111
    • Muhlrad, D.1    Parker, R.2
  • 21
    • 0028961870 scopus 로고
    • Turnover mechanisms of the stable yeast PGK1 mRNA
    • D. Muhlrad, C.J. Decker, and R. Parker Turnover mechanisms of the stable yeast PGK1 mRNA Mol. Cell. Biol. 15 1995 2145 2156
    • (1995) Mol. Cell. Biol. , vol.15 , pp. 2145-2156
    • Muhlrad, D.1    Decker, C.J.2    Parker, R.3
  • 22
    • 0023143706 scopus 로고
    • Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis
    • M. Nonet, C. Scafe, J. Sexton, and R. Young Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis Mol. Cell. Biol. 7 1987 1602 1611
    • (1987) Mol. Cell. Biol. , vol.7 , pp. 1602-1611
    • Nonet, M.1    Scafe, C.2    Sexton, J.3    Young, R.4
  • 23
    • 84867732569 scopus 로고    scopus 로고
    • Speeding with control: Codon usage, tRNAs, and ribosomes
    • E.M. Novoa, and L. Ribas de Pouplana Speeding with control: codon usage, tRNAs, and ribosomes Trends Genet. 28 2012 574 581
    • (2012) Trends Genet. , vol.28 , pp. 574-581
    • Novoa, E.M.1    Ribas De Pouplana, L.2
  • 24
    • 0034388021 scopus 로고    scopus 로고
    • The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast
    • W. Olivas, and R. Parker The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast EMBO J. 19 2000 6602 6611
    • (2000) EMBO J. , vol.19 , pp. 6602-6611
    • Olivas, W.1    Parker, R.2
  • 25
    • 84873570699 scopus 로고    scopus 로고
    • Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
    • S. Pechmann, and J. Frydman Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding Nat. Struct. Mol. Biol. 20 2013 237 243
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 237-243
    • Pechmann, S.1    Frydman, J.2
  • 26
    • 84878113615 scopus 로고    scopus 로고
    • The DHH1/RCKp54 family of helicases: An ancient family of proteins that promote translational silencing
    • V. Presnyak, and J. Coller The DHH1/RCKp54 family of helicases: an ancient family of proteins that promote translational silencing Biochim. Biophys. Acta 1829 2013 817 823
    • (2013) Biochim. Biophys. Acta , vol.1829 , pp. 817-823
    • Presnyak, V.1    Coller, J.2
  • 27
    • 84859219968 scopus 로고    scopus 로고
    • Balanced codon usage optimizes eukaryotic translational efficiency
    • W. Qian, J.R. Yang, N.M. Pearson, C. Maclean, and J. Zhang Balanced codon usage optimizes eukaryotic translational efficiency PLoS Genet. 8 2012 e1002603
    • (2012) PLoS Genet. , vol.8 , pp. e1002603
    • Qian, W.1    Yang, J.R.2    Pearson, N.M.3    Maclean, C.4    Zhang, J.5
  • 28
    • 4644280499 scopus 로고    scopus 로고
    • Solving the riddle of codon usage preferences: A test for translational selection
    • M. dos Reis, R. Savva, and L. Wernisch Solving the riddle of codon usage preferences: a test for translational selection Nucleic Acids Res 32 2004 5036 5044
    • (2004) Nucleic Acids Res , vol.32 , pp. 5036-5044
    • Dos Reis, M.1    Savva, R.2    Wernisch, L.3
  • 29
    • 84861841297 scopus 로고    scopus 로고
    • Translation drives mRNA quality control
    • C.J. Shoemaker, and R. Green Translation drives mRNA quality control Nat. Struct. Mol. Biol. 19 2012 594 601
    • (2012) Nat. Struct. Mol. Biol. , vol.19 , pp. 594-601
    • Shoemaker, C.J.1    Green, R.2
  • 30
    • 84863688029 scopus 로고    scopus 로고
    • The DEAD-box protein Dhh1 promotes decapping by slowing ribosome movement
    • T. Sweet, C. Kovalak, and J. Coller The DEAD-box protein Dhh1 promotes decapping by slowing ribosome movement PLoS Biol. 10 2012 e1001342
    • (2012) PLoS Biol. , vol.10 , pp. e1001342
    • Sweet, T.1    Kovalak, C.2    Coller, J.3
  • 34
    • 67649356943 scopus 로고    scopus 로고
    • Translationally optimal codons associate with structurally sensitive sites in proteins
    • T. Zhou, M. Weems, and C.O. Wilke Translationally optimal codons associate with structurally sensitive sites in proteins Mol. Biol. Evol. 26 2009 1571 1580
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 1571-1580
    • Zhou, T.1    Weems, M.2    Wilke, C.O.3
  • 36
    • 0024266139 scopus 로고
    • New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites
    • R.D. Gietz, and A. Sugino New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites Gene 74 1988 527 534
    • (1988) Gene , vol.74 , pp. 527-534
    • Gietz, R.D.1    Sugino, A.2
  • 38
    • 9444225935 scopus 로고    scopus 로고
    • Java Treeview - Extensible visualization of microarray data
    • A.J. Saldanha Java Treeview - extensible visualization of microarray data Bioinformatics 20 2004 3246 3248
    • (2004) Bioinformatics , vol.20 , pp. 3246-3248
    • Saldanha, A.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.