Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?

[1]  B. Blencowe,et al.  Regulation of Multiple Core Spliceosomal Proteins by Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay , 2008, Molecular and Cellular Biology.

[2]  A. van Hoof,et al.  Messenger RNA regulation: to translate or to degrade , 2008, The EMBO journal.

[3]  A. Visel,et al.  Ultraconservation identifies a small subset of extremely constrained developmental enhancers , 2008, Nature Genetics.

[4]  K. Uchida,et al.  Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation. , 2007, The Plant journal : for cell and molecular biology.

[5]  Michael Q. Zhang,et al.  Evolutionary impact of limited splicing fidelity in mammalian genes. , 2007, Trends in genetics : TIG.

[6]  Axel Visel,et al.  Deletion of Ultraconserved Elements Yields Viable Mice , 2007, PLoS biology.

[7]  C. Smith,et al.  Crossregulation and Functional Redundancy between the Splicing Regulator PTB and Its Paralogs nPTB and ROD1 , 2007, Molecular cell.

[8]  T. Maniatis,et al.  The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. , 2007, Molecular cell.

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

[10]  Gene W. Yeo,et al.  The EJC Factor eIF4AIII Modulates Synaptic Strength and Neuronal Protein Expression , 2007, Cell.

[11]  J. M. Izquierdo,et al.  Two Isoforms of the T-cell Intracellular Antigen 1 (TIA-1) Splicing Factor Display Distinct Splicing Regulation Activities , 2007, Journal of Biological Chemistry.

[12]  Douglas L Black,et al.  A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. , 2007, Genes & development.

[13]  L. Maquat,et al.  Staufen1 regulates diverse classes of mammalian transcripts , 2007, The EMBO journal.

[14]  Gene W. Yeo,et al.  Discovery and Analysis of Evolutionarily Conserved Intronic Splicing Regulatory Elements , 2007, PLoS Genetics.

[15]  S. Brenner,et al.  Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements , 2007, Nature.

[16]  Tyson A. Clark,et al.  Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. , 2007, Genes & development.

[17]  Alan M. Moses,et al.  In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.

[18]  R. Milo,et al.  Variability and memory of protein levels in human cells , 2006, Nature.

[19]  B. Yandell,et al.  Impact of Nonsense-Mediated mRNA Decay on the Global Expression Profile of Budding Yeast , 2006, PLoS genetics.

[20]  G. M. Wilson,et al.  Upf1/Upf2 Regulation of 3′ Untranslated Region Splice Variants of AUF1 Links Nonsense-Mediated and A+U-Rich Element-Mediated mRNA Decay , 2006, Molecular and Cellular Biology.

[21]  A. Barta,et al.  Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins , 2006, Nucleic acids research.

[22]  J. Harrow,et al.  GENCODE: producing a reference annotation for ENCODE , 2006, Genome Biology.

[23]  B. Blencowe.  Alternative Splicing: New Insights from Global Analyses , 2006, Cell.

[24]  Christopher J. Lee,et al.  Alternative splicing and RNA selection pressure — evolutionary consequences for eukaryotic genomes , 2006, Nature Reviews Genetics.

[25]  T. Hughes,et al.  Regulation of gene expression by alternative untranslated regions. , 2006, Trends in genetics : TIG.

[26]  M. L. Simpson,et al.  Gene network shaping of inherent noise spectra , 2006, Nature.

[27]  E. Hol,et al.  hUPF2 Silencing Identifies Physiologic Substrates of Mammalian Nonsense-Mediated mRNA Decay , 2006, Molecular and Cellular Biology.

[28]  B. Frey,et al.  Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. , 2006, Genes & development.

[29]  David Haussler,et al.  Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays , 2005, PLoS Comput. Biol..

[30]  M. Cuccurese,et al.  Alternative splicing and nonsense-mediated mRNA decay regulate mammalian ribosomal gene expression , 2005, Nucleic acids research.

[31]  Gil Ast,et al.  The importance of being divisible by three in alternative splicing , 2005, Nucleic acids research.

[32]  J. Raser,et al.  Noise in Gene Expression: Origins, Consequences, and Control , 2005, Science.

[33]  P. Green,et al.  Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[34]  W. Marzluff,et al.  Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1 , 2005, Nature Structural &Molecular Biology.

[35]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[36]  Juan Valcárcel,et al.  Building specificity with nonspecific RNA-binding proteins , 2005, Nature Structural &Molecular Biology.

[37]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

[38]  E. Conti,et al.  Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. , 2005, Current opinion in cell biology.

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

[40]  B. Frey,et al.  Alternative splicing of conserved exons is frequently species-specific in human and mouse. , 2005, Trends in genetics : TIG.

[41]  Luc DesGroseillers,et al.  Mammalian Staufen1 Recruits Upf1 to Specific mRNA 3′UTRs so as to Elicit mRNA Decay , 2005, Cell.

[42]  I. Rafalska,et al.  Function of alternative splicing. , 2005, Gene.

[43]  B. Frey,et al.  Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. , 2004, Molecular cell.

[44]  Klaudia Walter,et al.  Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2004, PLoS biology.

[45]  Francisco Martinez-Murillo,et al.  Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise , 2004, Nature Genetics.

[46]  D. Haussler,et al.  Ultraconserved Elements in the Human Genome , 2004, Science.

[47]  Yi Xing,et al.  Negative selection pressure against premature protein truncation is reduced by both alternative splicing and diploidy , 2004, Genome Biology.

[48]  M. Hentze,et al.  Nonsense-mediated mRNA decay: from vacuum cleaner to Swiss army knife , 2004, Genome Biology.

[49]  Stefan Stamm,et al.  Human tra2-beta1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA. , 2004, Human molecular genetics.

[50]  S. Brenner,et al.  An unappreciated role for RNA surveillance , 2004, Genome Biology.

[51]  R. Shamir,et al.  How prevalent is functional alternative splicing in the human genome? , 2004, Trends in genetics : TIG.

[52]  C. Gooding,et al.  Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. , 2004, Molecular cell.

[53]  Shuyun Dong,et al.  Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. , 2003, Molecular cell.

[54]  D. Black.  Mechanisms of alternative pre-messenger RNA splicing. , 2003, Annual review of biochemistry.

[55]  Stephen M. Mount,et al.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.

[56]  Steven E. Brenner,et al.  Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes , 2003, ISMB.

[57]  R. Sorek,et al.  Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. , 2003, Genome research.

[58]  R. Breathnach,et al.  TIA-1 or TIAR Is Required for DT40 Cell Viability* , 2003, The Journal of Biological Chemistry.

[59]  S. Brenner,et al.  Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Dan Graur,et al.  Alu-containing exons are alternatively spliced. , 2002, Genome research.

[61]  S. P. Fodor,et al.  Large-Scale Transcriptional Activity in Chromosomes 21 and 22 , 2002, Science.

[62]  L. Maquat.  Nonsense-mediated mRNA decay , 2002, Current Biology.

[63]  J. Stévenin,et al.  TIA-1 and TIAR Activate Splicing of Alternative Exons with Weak 5′ Splice Sites followed by a U-rich Stretch on Their Own Pre-mRNAs* , 2001, The Journal of Biological Chemistry.

[64]  Christopher J. Lee,et al.  Genome-wide detection of alternative splicing in expressed sequences of human genes , 2001, Nucleic Acids Res..

[65]  A Sureau,et al.  SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs , 2001, The EMBO journal.

[66]  S. Peltz,et al.  The cap-to-tail guide to mRNA turnover , 2001, Nature Reviews Molecular Cell Biology.

[67]  J. Stévenin,et al.  Alternative Splicing of Intron 3 of the Serine/Arginine-rich Protein 9G8 Gene , 2001, The Journal of Biological Chemistry.

[68]  J. Mendell,et al.  Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. , 2001, Human molecular genetics.

[69]  Q. Mitrovich,et al.  Unproductively spliced ribosomal protein mRNAs are natural targets of mRNA surveillance in C. elegans. , 2000, Genes & development.

[70]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[71]  G. M. Wilson,et al.  Regulation of AUF1 Expression via Conserved Alternatively Spliced Elements in the 3′ Untranslated Region , 1999, Molecular and Cellular Biology.

[72]  K. Apel,et al.  Circadian clock-regulated expression of an RNA-binding protein in Arabidopsis: characterisation of a minimal promoter element , 1999, Molecular and General Genetics MGG.

[73]  H. Jumaa,et al.  The splicing factor SRp20 modifies splicing of its own mRNA and ASF/SF2 antagonizes this regulation , 1997, The EMBO journal.

[74]  K. Apel,et al.  AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[75]  P. Slonimski,et al.  NAM7 nuclear gene encodes a novel member of a family of helicases with a Zn-ligand motif and is involved in mitochondrial functions in Saccharomyces cerevisiae. , 1992, Journal of molecular biology.

[76]  S. Peltz,et al.  The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. , 1991, Genes & development.

[77]  S. Lehnart,et al.  Why Do We Still Have a Maternally Inherited Mitochondrial DNA ? Insights from Evolutionary Medicine , 2007 .

[78]  F. Kaye,et al.  Evolutionary conservation of a 2-kb intronic sequence flanking a tissue-specific alternative exon in the PTBP2 gene. , 2004, Genomics.

[79]  K. Apel,et al.  The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA. , 2003, The Plant journal : for cell and molecular biology.

[80]  Terrence S. Furey,et al.  The UCSC Genome Browser Database , 2003, Nucleic Acids Res..

[81]  Christopher J. Lee,et al.  A genomic view of alternative splicing , 2002, Nature Genetics.

[82]  R. Parker,et al.  Analysis of mRNA decay pathways in Saccharomyces cerevisiae. , 1999, Methods.