Genome-Wide Analysis of mRNAs Regulated by the Nonsense-Mediated and 5′ to 3′ mRNA Decay Pathways in Yeast
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Beelman, 1996, An essential component of the decapping enzyme required for normal rates of mRNA turnover, Nature, 382, 642, 10.1038/382642a0
Cao, 2001, Computational modeling of eukaryotic mRNA turnover, RNA, 7, 1192, 10.1017/S1355838201010330
Cao, 2003, Computational modeling and experimental analysis of nonsense-mediated decay in yeast, Cell, 113, 533, 10.1016/S0092-8674(03)00353-2
Dahlseid, 2003, mRNAs encoding telomerase components and regulators are controlled by UPF genes in Saccharomyces cerevisiae, Eukaryot. Cell, 2, 134, 10.1128/EC.2.1.134-142.2003
Decker, 1993, A turnover pathway for both stable and unstable mRNAs in yeast, Genes Dev., 7, 1632, 10.1101/gad.7.8.1632
Dunckley, 1999, The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif, EMBO J., 18, 5411, 10.1093/emboj/18.19.5411
Eisen, 1998, Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. USA, 95, 14863, 10.1073/pnas.95.25.14863
Farabaugh, 1993, A novel programmed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast, Cell, 74, 93, 10.1016/0092-8674(93)90297-4
Frischmeyer, 2002, An mRNA surveillance mechanism that eliminates transcripts lacking termination codons, Science, 295, 2258, 10.1126/science.1067338
Gonzalez, 2001, Nonsense-mediated mRNA decay in Saccharomyces cerevisiae, Gene, 274, 15, 10.1016/S0378-1119(01)00552-2
Harrison, 2002, A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution, J. Mol. Biol., 316, 409, 10.1006/jmbi.2001.5343
He, 1995, Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen, Genes Dev., 9, 437, 10.1101/gad.9.4.437
He, 2001, Upf1p, Nmd2p, and Upf3p regulate the decapping and exonucleolytic degradation of both nonsense-containing mRNAs and wild-type mRNAs, Mol. Cell. Biol., 21, 1515, 10.1128/MCB.21.5.1515-1530.2001
He, 1993, Stabilization and ribosome association of unspliced pre-mRNAs in a yeast upf1- mutant, Proc. Natl. Acad. Sci. USA, 90, 7034, 10.1073/pnas.90.15.7034
He, 1997, Upf1p, Nmd2p, and Upf3p are interacting components of the yeast nonsense-mediated mRNA decay pathway, Mol. Cell. Biol., 17, 1580, 10.1128/MCB.17.3.1580
Herrick, D. (1989). Structural determinants of mRNA turnover in yeast. PhD thesis, University of Massachusetts Medical School, Worcester, Massachusetts.
Hsu, 1993, Yeast cells lacking 5′→3′ exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5′ cap structure, Mol. Cell. Biol., 13, 4826, 10.1128/MCB.13.8.4826
Jacobs Anderson, 1998, The 3′ to 5′ degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3′ to 5′ exonucleases of the exosome complex, EMBO J., 17, 1497, 10.1093/emboj/17.5.1497
Jacobson, 1996, Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells, Annu. Rev. Biochem., 65, 693, 10.1146/annurev.bi.65.070196.003401
Jacobson, 2000, Destabilization of nonsense-containing transcripts in Saccharomyces cerevisiae, 827
Leeds, 1991, The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon, Genes Dev., 5, 2303, 10.1101/gad.5.12a.2303
Lelivelt, 1999, Yeast Upf proteins required for RNA surveillance affect global expression of the yeast transcriptome, Mol. Cell. Biol., 19, 6710, 10.1128/MCB.19.10.6710
Lew, 1998, Telomere length regulation and telomeric chromatin require the nonsense-mediated mRNA decay pathway, Mol. Cell. Biol., 18, 6121, 10.1128/MCB.18.10.6121
Losson, 1979, Interference of nonsense mutations with eukaryotic messenger RNA stability, Proc. Natl. Acad. Sci. USA, 76, 5134, 10.1073/pnas.76.10.5134
Maderazo, 2000, Upf1p control of nonsense mRNA translation is regulated by Nmd2p and Upf3p, Mol. Cell. Biol., 20, 4591, 10.1128/MCB.20.13.4591-4603.2000
Maderazo, 2003, Nonsense-containing mRNAs that accumulate in the absence of a functional nonsense-mediated mRNA decay pathway are destabilized rapidly upon its restitution, Mol. Cell. Biol., 23, 842, 10.1128/MCB.23.3.842-851.2003
Mendell, 2000, Novel Upf2p orthologues suggest a functional link between translation initiation and nonsense surveillance complexes, Mol. Cell. Biol., 20, 8944, 10.1128/MCB.20.23.8944-8957.2000
Mitchell, 2003, An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3′→5′ degradation, Mol. Cell, 11, 1405, 10.1016/S1097-2765(03)00190-4
Morris, 1997, Programmed translational frameshifting in a gene required for yeast telomere replication, Curr. Biol., 7, 969, 10.1016/S0960-9822(06)00416-7
Muhlrad, 1994, Premature translational termination triggers mRNA decapping, Nature, 370, 578, 10.1038/370578a0
Muhlrad, 1999, Aberrant mRNAs with extended 3′ UTRs are substrates for rapid degradation by mRNA surveillance, RNA, 5, 1299, 10.1017/S1355838299990829
Muhlrad, 1994, Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5′→3′ digestion of the transcript, Genes Dev., 8, 855, 10.1101/gad.8.7.855
Muhlrad, 1995, Turnover mechanisms of the stable yeast PGK1 mRNA, Mol. Cell. Biol., 15, 2145, 10.1128/MCB.15.4.2145
Oliveira, 1995, The relationship between eukaryotic translation and mRNA stability. A short upstream open reading frame strongly inhibits translational initiation and greatly accelerates mRNA degradation in the yeast Saccharomyces cerevisiae, J. Biol. Chem., 270, 8936, 10.1074/jbc.270.15.8936
Page, 1999, SMG-2 is a phosphorylated protein required for mRNA surveillance in Caenorhabditis elegans and related to Upf1p of yeast, Mol. Cell. Biol., 19, 5943, 10.1128/MCB.19.9.5943
Peltz, 1993, mRNA destabilization triggered by premature translational termination depends on at least three cis-acting sequence elements and one trans-acting factor, Genes Dev., 7, 1737, 10.1101/gad.7.9.1737
Peltz, 1993, Identification of the cis-acting sequences and trans-acting factors involved in nonsense-mediated mRNA decay, 1
Pulak, 1993, mRNA surveillance by the Caenorhabditis elegans smg genes, Genes Dev., 7, 1885, 10.1101/gad.7.10.1885
Ruiz-Echevarria, 2000, The RNA binding protein Pub1 modulates the stability of transcripts containing upstream open reading frames, Cell, 101, 741, 10.1016/S0092-8674(00)80886-7
Serin, 2001, Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4), Mol. Cell. Biol., 21, 209, 10.1128/MCB.21.1.209-223.2001
Tamayo, 1999, Interpreting patterns of gene expression with self-organizing maps, Proc. Natl. Acad. Sci. USA, 96, 2907, 10.1073/pnas.96.6.2907
van Hoof, 2002, Exosome-mediated recognition and degradation of mRNAs lacking a termination codon, Science, 295, 2262, 10.1126/science.1067272
Vilela, 1998, The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability, Nucleic Acids Res., 26, 1150, 10.1093/nar/26.5.1150
Wang, 2002, Precision and functional specificity in mRNA decay, Proc. Natl. Acad. Sci. USA, 99, 5860, 10.1073/pnas.092538799
Welch, 1999, An internal open reading frame triggers nonsense-mediated decay of the yeast SPT10 mRNA, EMBO J., 18, 6134, 10.1093/emboj/18.21.6134