RNA Quality Control in Eukaryotes

Eukaryotic cells contain numerous RNA quality-control systems that are important for shaping the transcriptome of eukaryotic cells. These systems not only prevent accumulation of nonfunctional RNAs but also regulate normal mRNAs, repress viral and parasitic RNAs, and potentially contribute to the evolution of new RNAs and hence proteins. These quality-control circuits can be viewed as a series of kinetic competitions between steps in normal RNA biogenesis or function and RNA degradation pathways. These RNA quality-control circuits depend on specific adaptor proteins that target aberrant RNAs for degradation as well as the coupling of individual steps in mRNA biogenesis and function.

[1]  JamesC . Anderson,et al.  Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA. , 2006, RNA.

[2]  T. Tuschl,et al.  Mechanisms of gene silencing by double-stranded RNA , 2004, Nature.

[3]  G. Dreyfuss,et al.  Messenger-RNA-binding proteins and the messages they carry , 2002, Nature Reviews Molecular Cell Biology.

[4]  Rune Thomsen,et al.  Dissecting mechanisms of nuclear mRNA surveillance in THO/sub2 complex mutants , 2007, The EMBO journal.

[5]  P. Mitchell,et al.  Degradation of ribosomal RNA precursors by the exosome. , 2000, Nucleic acids research.

[6]  Marc Dreyfus,et al.  The Poly(A) Tail of mRNAs Bodyguard in Eukaryotes, Scavenger in Bacteria , 2002, Cell.

[7]  M. Ares,et al.  Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[8]  D. Tollervey,et al.  Identification of a Regulated Pathway for Nuclear Pre-mRNA Turnover , 2000, Cell.

[9]  F. Clark,et al.  Understanding alternative splicing: towards a cellular code , 2005, Nature Reviews Molecular Cell Biology.

[10]  F. Sherman,et al.  Mutant LYS2 mRNAs retained and degraded in the nucleus of Saccharomyces cerevisiae. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[11]  M. Moore From Birth to Death: The Complex Lives of Eukaryotic mRNAs , 2005, Science.

[12]  J. Steitz,et al.  Identification of a rapid mammalian deadenylation-dependent decay pathway and its inhibition by a viral RNA element. , 2006, Molecular cell.

[13]  J. Butler,et al.  A Nuclear 3′-5′ Exonuclease Involved in mRNA Degradation Interacts with Poly(A) Polymerase and the hnRNA Protein Npl3p , 2000, Molecular and Cellular Biology.

[14]  S. Wolin,et al.  A possible role for the 60-kD Ro autoantigen in a discard pathway for defective 5S rRNA precursors. , 1994, Genes & development.

[15]  Alan G Hinnebusch,et al.  Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae. , 2004, Genes & development.

[16]  Roy Parker,et al.  Exosome-Mediated Recognition and Degradation of mRNAs Lacking a Termination Codon , 2002, Science.

[17]  U. Nehrbass,et al.  Quality control of messenger ribonucleoprotein particles in the nucleus and at the pore. , 2005, Current opinion in cell biology.

[18]  R. Parker,et al.  Effects of mutations in the Saccharomyces cerevisiae RNA14, RNA15, and PAP1 genes on polyadenylation in vivo , 1995, Molecular and cellular biology.

[19]  R. Parker,et al.  Defects in the mRNA export factors Rat7p, Gle1p, Mex67p, and Rat8p cause hyperadenylation during 3'-end formation of nascent transcripts. , 2001, RNA.

[20]  Yukihide Tomari,et al.  piRNAs--the ancient hunters of genome invaders. , 2007, Genes & development.

[21]  J. Butler,et al.  Degradation of Normal mRNA in the Nucleus of Saccharomyces cerevisiae , 2003, Molecular and Cellular Biology.

[22]  C. Norbury,et al.  Requirement of Fission Yeast Cid14 in Polyadenylation of rRNAs , 2006, Molecular and Cellular Biology.

[23]  G. Chanfreau,et al.  RNAse III-mediated degradation of unspliced pre-mRNAs and lariat introns. , 2003, Molecular cell.

[24]  L. Maquat,et al.  Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. , 2007, Genes & development.

[25]  S. Wolin,et al.  The trials and travels of tRNA. , 1999, Genes & development.

[26]  D. Tollervey,et al.  Surveillance of nuclear‐restricted pre‐ribosomes within a subnucleolar region of Saccharomyces cerevisiae , 2006, The EMBO journal.

[27]  D. J. Van Horn,et al.  A misfolded form of 5S rRNA is complexed with the Ro and La autoantigens. , 1996, RNA.

[28]  Letian Kuai,et al.  Polyadenylation of rRNA in Saccharomyces cerevisiae. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[29]  R. Reed,et al.  Human mRNA Export Machinery Recruited to the 5′ End of mRNA , 2006, Cell.

[30]  W. Keller,et al.  A New Yeast Poly(A) Polymerase Complex Involved in RNA Quality Control , 2005, PLoS biology.

[31]  D. Tollervey,et al.  Processing of 3'-extended read-through transcripts by the exosome can generate functional mRNAs. , 2002, Molecular cell.

[32]  Gabriele Fuchs,et al.  Structural Insights into RNA Quality Control: The Ro Autoantigen Binds Misfolded RNAs via Its Central Cavity , 2005, Cell.

[33]  C. Kane,et al.  Promoting elongation with transcript cleavage stimulatory factors. , 2002, Biochimica et biophysica acta.

[34]  M. Rosbash,et al.  Quality control of mRNA 3′-end processing is linked to the nuclear exosome , 2001, Nature.

[35]  A. Klungland,et al.  Repair of methyl lesions in DNA and RNA by oxidative demethylation , 2007, Neuroscience.

[36]  S. Grewal,et al.  Heterochromatin revisited , 2007, Nature Reviews Genetics.

[37]  H. Jungwirth,et al.  Diazaborine Treatment of Baker's Yeast Results in Stabilization of Aberrant mRNAs* , 2001, The Journal of Biological Chemistry.

[38]  T. Inada,et al.  Translation of aberrant mRNAs lacking a termination codon or with a shortened 3′‐UTR is repressed after initiation in yeast , 2005, The EMBO journal.

[39]  M. Rosbash,et al.  Localization of nuclear retained mRNAs in Saccharomyces cerevisiae. , 2003, RNA.

[40]  S. Wolin,et al.  Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen , 2006, Nature Structural &Molecular Biology.

[41]  G. Carmichael,et al.  Retention and repression: fates of hyperedited RNAs in the nucleus. , 2005, Current opinion in cell biology.

[42]  J. Butler,et al.  Rat1p and Rai1p function with the nuclear exosome in the processing and degradation of rRNA precursors. , 2005, RNA.

[43]  M. Moore,et al.  A late-acting quality control process for mature eukaryotic rRNAs. , 2006, Molecular cell.

[44]  L. Maquat,et al.  Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. , 2003, Molecular cell.

[45]  David Tollervey,et al.  RNA-quality control by the exosome , 2006, Nature Reviews Molecular Cell Biology.

[46]  Andrés Aguilera,et al.  Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. , 2003, Molecular cell.

[47]  R. Parker,et al.  Cytoplasmic Decay of Intergenic Transcripts in Saccharomyces cerevisiae , 2006, Molecular and Cellular Biology.

[48]  R. Silverman,et al.  Small self-RNA generated by RNase L amplifies antiviral innate immunity , 2007, Nature.

[49]  J. Mendell,et al.  When the Message Goes Awry Disease-Producing Mutations that Influence mRNA Content and Performance , 2001, Cell.

[50]  D. Tollervey,et al.  The exosome subunit Rrp44 plays a direct role in RNA substrate recognition. , 2007, Molecular cell.

[51]  M. Rosbash,et al.  A block to mRNA nuclear export in S. cerevisiae leads to hyperadenylation of transcripts that accumulate at the site of transcription. , 2001, Molecular cell.

[52]  R. Flavell,et al.  Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3 , 2001, Nature.

[53]  E. Hurt,et al.  The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans , 2000, Nature.

[54]  V. Kim MicroRNA biogenesis: coordinated cropping and dicing , 2005, Nature Reviews Molecular Cell Biology.

[55]  Jian Kong,et al.  A cell type–restricted mRNA surveillance pathway triggered by ribosome extension into the 3′ untranslated region , 2007, Nature Structural &Molecular Biology.

[56]  B. Séraphin,et al.  Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase , 2005, Cell.

[57]  P. Legrain,et al.  Some cis- and trans-acting mutants for splicing target pre-mRNA to the cytoplasm , 1989, Cell.

[58]  M. Serrano,et al.  Antiviral action of the tumor suppressor ARF , 2006, The EMBO journal.

[59]  G. Chanfreau,et al.  Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. , 2006, RNA.

[60]  C R Cantor,et al.  In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[61]  D. Tollervey,et al.  Roles of the HEAT repeat proteins Utp10 and Utp20 in 40S ribosome maturation. , 2007, RNA.

[62]  Weifeng Gu,et al.  Rapid tRNA decay can result from lack of nonessential modifications. , 2006, Molecular cell.

[63]  E. Petfalski,et al.  RNA Degradation by the Exosome Is Promoted by a Nuclear Polyadenylation Complex , 2005, Cell.

[64]  R. Nazar Ribosomal RNA Processing and Ribosome Biogenesis in Eukaryotes , 2004, IUBMB life.

[65]  Meenal Patel,et al.  PTC124 targets genetic disorders caused by nonsense mutations , 2007, Nature.

[66]  Steven P. Gygi,et al.  RNAi-Dependent and -Independent RNA Turnover Mechanisms Contribute to Heterochromatic Gene Silencing , 2007, Cell.

[67]  D. Morris,et al.  Silencing the transcriptome's dark matter: mechanisms for suppressing translation of intergenic transcripts. , 2006, Molecular cell.

[68]  J. Gécz,et al.  Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation , 2007, Nature Genetics.

[69]  A. Podtelejnikov,et al.  The yeast exosome and human PM-Scl are related complexes of 3' --> 5' exonucleases. , 1999, Genes & development.

[70]  Kathryn A. O’Donnell,et al.  An mRNA Surveillance Mechanism That Eliminates Transcripts Lacking Termination Codons , 2002, Science.

[71]  G. Gao,et al.  The zinc-finger antiviral protein recruits the RNA processing exosome to degrade the target mRNA , 2007, Proceedings of the National Academy of Sciences.

[72]  Kuniaki Saito,et al.  Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. , 2006, Genes & development.

[73]  J. Butler,et al.  5-Fluorouracil Enhances Exosome-Dependent Accumulation of Polyadenylated rRNAs , 2004, Molecular and Cellular Biology.

[74]  R. Parker,et al.  Yeast Exosome Mutants Accumulate 3′-Extended Polyadenylated Forms of U4 Small Nuclear RNA and Small Nucleolar RNAs , 2000, Molecular and Cellular Biology.

[75]  Judith L Campbell,et al.  Contribution of Trf4/5 and the Nuclear Exosome to Genome Stability Through Regulation of Histone mRNA Levels in Saccharomyces cerevisiae , 2007, Genetics.

[76]  Jennifer Hesson,et al.  Untemplated Oligoadenylation Promotes Degradation of RISC-Cleaved Transcripts , 2006, Science.

[77]  S. Shuman,et al.  Accelerated mRNA decay in conditional mutants of yeast mRNA capping enzyme. , 1998, Nucleic acids research.

[78]  F. Grosveld,et al.  Inefficient processing impairs release of RNA from the site of transcription , 1999, The EMBO journal.

[79]  M. Rosbash,et al.  Interactions between mRNA Export Commitment, 3′-End Quality Control, and Nuclear Degradation , 2002, Molecular and Cellular Biology.

[80]  R. Reed,et al.  TREX, SR proteins and export of mRNA. , 2005, Current opinion in cell biology.

[81]  Zuo Zhang,et al.  The Fate of dsRNA in the Nucleus A p54nrb-Containing Complex Mediates the Nuclear Retention of Promiscuously A-to-I Edited RNAs , 2001, Cell.

[82]  L. Maquat Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics , 2004, Nature Reviews Molecular Cell Biology.

[83]  Haiwei Song,et al.  The enzymes and control of eukaryotic mRNA turnover , 2004, Nature Structural &Molecular Biology.

[84]  S. Lindquist,et al.  Hsp90 as a capacitor for morphological evolution , 1998, Nature.

[85]  R. Parker,et al.  Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation , 2006, Nature.

[86]  R. Parker,et al.  Cytoplasmic degradation of splice-defective pre-mRNAs and intermediates. , 2003, Molecular cell.