메뉴 건너뛰기




Volumn 1, Issue 7, 2005, Pages 0585-0592

Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast

Author keywords

[No Author keywords available]

Indexed keywords

GENES; GENOME; PROTEINS; YEAST;

EID: 55449088127     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0010072.eor     Document Type: Article
Times cited : (107)

References (50)
  • 2
    • 1442329652 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae
    • Hurowitz EH, Brown PO (2003) Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol 5: R2.
    • (2003) Genome Biol , vol.5
    • Hurowitz, E.H.1    Brown, P.O.2
  • 3
    • 0035320036 scopus 로고    scopus 로고
    • MRNA localization: Message on the move
    • Jansen RP (2001) mRNA localization: Message on the move. Nat Rev Mol Cell Biol 2: 247-256.
    • (2001) Nat Rev Mol Cell Biol , vol.2 , pp. 247-256
    • Jansen, R.P.1
  • 5
    • 0036289532 scopus 로고    scopus 로고
    • Eukaryotic mRNPs may represent posttranscriptional operons
    • Keene JD, Tenenbaum SA (2002) Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell 9: 1161-1167.
    • (2002) Mol Cell , vol.9 , pp. 1161-1167
    • Keene, J.D.1    Tenenbaum, S.A.2
  • 6
    • 0037313537 scopus 로고    scopus 로고
    • Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery
    • Hieronymus H, Silver PA (2003) Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat Genet 33: 155-161.
    • (2003) Nat Genet , vol.33 , pp. 155-161
    • Hieronymus, H.1    Silver, P.A.2
  • 7
    • 19344365947 scopus 로고    scopus 로고
    • Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    • DOI: 10.1371/journal.pbio.0020079
    • Gerber AP, Herschlag D, Brown PO (2004) Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol 2: e79. DOI: 10.1371/journal.pbio.0020079
    • (2004) PLoS Biol , vol.2 , pp. 79
    • Gerber, A.P.1    Herschlag, D.2    Brown, P.O.3
  • 8
    • 0024546509 scopus 로고
    • The scanning model for translation: An update
    • Kozak M (1989) The scanning model for translation: An update. J Cell Biol 108: 229-241.
    • (1989) J Cell Biol , vol.108 , pp. 229-241
    • Kozak, M.1
  • 9
    • 0021799353 scopus 로고
    • Insertion mutagenesis to increase secondary structure within the 59 noncoding region of a eukaryotic mRNA reduces translational efficiency
    • Pelletier J, Sonenberg N (1985) Insertion mutagenesis to increase secondary structure within the 59 noncoding region of a eukaryotic mRNA reduces translational efficiency. Cell 40: 515-526.
    • (1985) Cell , vol.40 , pp. 515-526
    • Pelletier, J.1    Sonenberg, N.2
  • 10
    • 0023988840 scopus 로고
    • MRNA structures influencing translation in the yeast Saccharomyces cerevisiae
    • Baim SB, Sherman F (1988) mRNA structures influencing translation in the yeast Saccharomyces cerevisiae. Mol Cell Biol 8: 1591-1601.
    • (1988) Mol Cell Biol , vol.8 , pp. 1591-1601
    • Baim, S.B.1    Sherman, F.2
  • 11
    • 0023665902 scopus 로고
    • An analysis of 59-noncoding sequences from 699 vertebrate messenger RNAs
    • Kozak M (1987) An analysis of 59-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res 15: 8125-8148.
    • (1987) Nucleic Acids Res , vol.15 , pp. 8125-8148
    • Kozak, M.1
  • 12
    • 0024414469 scopus 로고
    • Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs
    • Kozak M (1989) Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs. Mol Cell Biol 9: 5134-5142.
    • (1989) Mol Cell Biol , vol.9 , pp. 5134-5142
    • Kozak, M.1
  • 13
    • 0028961870 scopus 로고
    • Turnover mechanisms of the stable yeast PGK1 mRNA
    • Muhlrad D, Decker CJ, Parker R (1995) Turnover mechanisms of the stable yeast PGK1 mRNA. Mol Cell Biol 15: 2145-2156.
    • (1995) Mol Cell Biol , vol.15 , pp. 2145-2156
    • Muhlrad, D.1    Decker, C.J.2    Parker, R.3
  • 14
    • 0033005239 scopus 로고    scopus 로고
    • The role of the 59 untranslated region of an mRNA in translation regulation during development
    • van der Velden AW, Thomas AAM (1999) The role of the 59 untranslated region of an mRNA in translation regulation during development. Int J Biochem Cell Biol 31: 87-106.
    • (1999) Int J Biochem Cell Biol , vol.31 , pp. 87-106
    • Van Der Velden, A.W.1    Thomas, A.A.M.2
  • 15
    • 0035032444 scopus 로고    scopus 로고
    • The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 59 secondary structure
    • Svitkin YV, Pause A, Haghighat A, Pyronnet S, Witherell G, et al. (2001) The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 59 secondary structure. RNA 7: 382-394.
    • (2001) RNA , vol.7 , pp. 382-394
    • Svitkin, Y.V.1    Pause, A.2    Haghighat, A.3    Pyronnet, S.4    Witherell, G.5
  • 16
    • 0028202495 scopus 로고
    • Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 59 to 39 digestion of the transcript
    • Muhlrad D, Decker CJ, Parker R (1994) Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 59 to 39 digestion of the transcript. Genes Dev 8: 855-866.
    • (1994) Genes Dev , vol.8 , pp. 855-866
    • Muhlrad, D.1    Decker, C.J.2    Parker, R.3
  • 18
    • 23944483135 scopus 로고    scopus 로고
    • Post-transcriptional control of gene expression: A genome-wide perspective
    • Mata J, Marguerat S, Bahler J (2005) Post-transcriptional control of gene expression: A genome-wide perspective. Trends Biochem Sci 30: 506-514.
    • (2005) Trends Biochem Sci , vol.30 , pp. 506-514
    • Mata, J.1    Marguerat, S.2    Bahler, J.3
  • 19
    • 0742288008 scopus 로고    scopus 로고
    • The enzymes and control of eukaryotic mRNA turnover
    • Parker R, Song H (2004) The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 11: 121-127.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 121-127
    • Parker, R.1    Song, H.2
  • 20
    • 0033790503 scopus 로고    scopus 로고
    • Mechanisms and control of mRNA decapping in Saccharomyces cerevisiae
    • Tucker M, Parker R (2000) Mechanisms and control of mRNA decapping in Saccharomyces cerevisiae. Annu Rev Biochem 69: 571-595.
    • (2000) Annu Rev Biochem , vol.69 , pp. 571-595
    • Tucker, M.1    Parker, R.2
  • 21
    • 0035983107 scopus 로고    scopus 로고
    • The role of the 59 untranslated region (UTR) in glucose-dependent mRNA decay
    • de la Cruz BJ, Prieto S, Scheffler IE (2002) The role of the 59 untranslated region (UTR) in glucose-dependent mRNA decay. Yeast 19: 887-902.
    • (2002) Yeast , vol.19 , pp. 887-902
    • Cruz, B.J.1    Prieto, S.2    Scheffler, I.E.3
  • 22
    • 0036021444 scopus 로고    scopus 로고
    • Emerging links between initiation of translation and human diseases
    • Kozak M (2002) Emerging links between initiation of translation and human diseases. Mamm Genome 13: 401-410.
    • (2002) Mamm Genome , vol.13 , pp. 401-410
    • Kozak, M.1
  • 23
    • 12344281782 scopus 로고    scopus 로고
    • The implications of structured 59 untranslated regions on translation and disease
    • Pickering BM, Willis AE (2005) The implications of structured 59 untranslated regions on translation and disease. Semin Cell Dev Biol 16: 39-47.
    • (2005) Semin Cell Dev Biol , vol.16 , pp. 39-47
    • Pickering, B.M.1    Willis, A.E.2
  • 24
    • 0037162469 scopus 로고    scopus 로고
    • Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
    • Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99: 9697-9702.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 9697-9702
    • Bernstein, J.A.1    Khodursky, A.B.2    Lin, P.H.3    Lin-Chao, S.4    Cohen, S.N.5
  • 26
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • Xia T, SantaLucia JJ, Burkard ME, Kierzek R, Schroeder SJ, et al. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37: 14719-14735.
    • (1998) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1    Santalucia, J.J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5
  • 27
    • 0033572893 scopus 로고    scopus 로고
    • No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
    • Workman C, Krogh A (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res 27: 4816-4822.
    • (1999) Nucleic Acids Res , vol.27 , pp. 4816-4822
    • Workman, C.1    Krogh, A.2
  • 28
    • 17844391015 scopus 로고    scopus 로고
    • Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency
    • Clote P, Ferre F, Kranakis E, Krizanc D (2005) Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA 11: 578-591.
    • (2005) RNA , vol.11 , pp. 578-591
    • Clote, P.1    Ferre, F.2    Kranakis, E.3    Krizanc, D.4
  • 29
    • 0022360113 scopus 로고
    • Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage
    • Altschul SF, Erickson BW (1985) Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage. Mol Biol Evol 2: 526-538.
    • (1985) Mol Biol e , vol.2 , pp. 526-538
    • Altschul, S.F.1    Erickson, B.W.2
  • 30
    • 0037388094 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
    • Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, et al. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100: 3889-3894.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 3889-3894
    • Arava, Y.1    Wang, Y.2    Storey, J.D.3    Liu, C.L.4    Brown, P.O.5
  • 31
    • 10944232800 scopus 로고    scopus 로고
    • Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale
    • Beyer A, Hollunder J, Nasheuer HP, Wilhelm T (2004) Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics 3: 1083-1092.
    • (2004) Mol Cell Proteomics , vol.3 , pp. 1083-1092
    • Beyer, A.1    Hollunder, J.2    Nasheuer, H.P.3    Wilhelm, T.4
  • 33
    • 0032778953 scopus 로고    scopus 로고
    • Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae
    • Schwartz DC, Parker R (1999) Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae. Mol Cell Biol 19: 5247-5256.
    • (1999) Mol Cell Biol , vol.19 , pp. 5247-5256
    • Schwartz, D.C.1    Parker, R.2
  • 35
    • 13244279520 scopus 로고    scopus 로고
    • Comparing functional annotation analyses with Catmap
    • Breslin T, Edén P, Krogh M (2004) Comparing functional annotation analyses with Catmap. BMC Bioinformatics 5: 193.
    • (2004) BMC Bioinformatics , vol.5 , pp. 193
    • Breslin, T.1    Edén, P.2    Krogh, M.3
  • 36
    • 0141519339 scopus 로고    scopus 로고
    • Widespread selection for local RNA secondary structure in coding regions of bacterial genes
    • Katz L, Burge CB (2003) Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res 13: 2042-2051.
    • (2003) Genome Res , vol.13 , pp. 2042-2051
    • Katz, L.1    Burge, C.B.2
  • 38
    • 0031832807 scopus 로고    scopus 로고
    • Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence
    • Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF (1998) Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8: 464-478.
    • (1998) Genome Res , vol.8 , pp. 464-478
    • Kim, J.M.1    Vanguri, S.2    Boeke, J.D.3    Gabriel, A.4    Voytas, D.F.5
  • 39
    • 2942561052 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors
    • Grigull J, Mnaimneh S, Pootoolal J, Robinson MD, Hughes TR (2004) Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol 24: 5534-5547.
    • (2004) Mol Cell Biol , vol.24 , pp. 5534-5547
    • Grigull, J.1    Mnaimneh, S.2    Pootoolal, J.3    Robinson, M.D.4    Hughes, T.R.5
  • 40
    • 0019433557 scopus 로고
    • Regulation of protein synthesis during heat shock
    • Lindquist S (1981) Regulation of protein synthesis during heat shock. Nature 293: 311-314.
    • (1981) Nature , vol.293 , pp. 311-314
    • Lindquist, S.1
  • 41
    • 9644275414 scopus 로고    scopus 로고
    • Translational regulation of Hsp90 mRNA. AUG-proximal 59-untranslated region elements essential for preferential heat shock translation
    • Ahmed R, Duncan RF (2004) Translational regulation of Hsp90 mRNA. AUG-proximal 59-untranslated region elements essential for preferential heat shock translation. J Biol Chem 279: 49919-49930.
    • (2004) J Biol Chem , vol.279 , pp. 49919-49930
    • Ahmed, R.1    Duncan, R.F.2
  • 42
    • 0036498828 scopus 로고    scopus 로고
    • A PUF family portrait: 39UTR regulation as a way of life
    • Wickens M, Bernstein DS, Kimble J, Parker R (2002) A PUF family portrait: 39UTR regulation as a way of life. Trends Genet 18: 150-157.
    • (2002) Trends Genet , vol.18 , pp. 150-157
    • Wickens, M.1    Bernstein, D.S.2    Kimble, J.3    Parker, R.4
  • 43
    • 0041327747 scopus 로고    scopus 로고
    • Variations in yeast 39-processing cis-elements correlate with transcript stability
    • Graber JH (2003) Variations in yeast 39-processing cis-elements correlate with transcript stability. Trends Genet 19: 473-476.
    • (2003) Trends Genet , vol.19 , pp. 473-476
    • Graber, J.H.1
  • 44
    • 0347416978 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 59 to 39 mRNA decay pathways in yeast
    • He F, Li X, Spatrick P, Casillo R, Dong S, et al. (2003) Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 59 to 39 mRNA decay pathways in yeast. Mol Cell 12: 1439-1452.
    • (2003) Mol Cell , vol.12 , pp. 1439-1452
    • He, F.1    Li, X.2    Spatrick, P.3    Casillo, R.4    Dong, S.5
  • 45
    • 0242384746 scopus 로고    scopus 로고
    • Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune sera
    • Tenenbaum SA, Carson CC, Atasoy U, Keene JD (2003) Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune sera. Gene 317: 79-87.
    • (2003) Gene , vol.317 , pp. 79-87
    • Tenenbaum, S.A.1    Carson, C.C.2    Atasoy, U.3    Keene, J.D.4
  • 46
    • 0033637153 scopus 로고    scopus 로고
    • Genomic expression programs in the response of yeast cells to environmental changes
    • Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
    • (2000) Mol Biol Cell , vol.11 , pp. 4241-4257
    • Gasch, A.P.1    Spellman, P.T.2    Kao, C.M.3    Carmel-Harel, O.4    Eisen, M.B.5
  • 47
    • 0141920354 scopus 로고    scopus 로고
    • Comparing protein abundance and mRNA expression levels on a genomic scale
    • Greenbaum D, Colangelo C, Williams K, Gerstein M (2003) Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 4: 117.
    • (2003) Genome Biol , vol.4 , pp. 117
    • Greenbaum, D.1    Colangelo, C.2    Williams, K.3    Gerstein, M.4
  • 49
    • 0033119454 scopus 로고    scopus 로고
    • MRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences
    • Seffens W, Digby D (1999) mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res 27: 1578-1584.
    • (1999) Nucleic Acids Res , vol.27 , pp. 1578-1584
    • Seffens, W.1    Digby, D.2
  • 50
    • 0030305457 scopus 로고    scopus 로고
    • R: A language for data analysis and graphics
    • Ihaka R, Gentleman R (1996) R: A language for data analysis and graphics. J Comput Grap Stat 5: 299-314.
    • (1996) J Comput Grap Stat , vol.5 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.