Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins

[1]  K. Peterson,et al.  The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay , 2016, Cell.

[2]  J. Persson,et al.  Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo , 2015, The Journal of cell biology.

[3]  Anne-Marie Alleaume,et al.  Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP , 2015, Nature Communications.

[4]  H. Le Hir,et al.  Transcriptome-wide modulation of splicing by the exon junction complex , 2014, Genome Biology.

[5]  Eric Nestler,et al.  ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases , 2014, BMC Genomics.

[6]  Christopher R. Sibley,et al.  iCLIP: Protein–RNA interactions at nucleotide resolution , 2014, Methods.

[7]  C. Ponting,et al.  Sequencing depth and coverage: key considerations in genomic analyses , 2014, Nature Reviews Genetics.

[8]  Lior Pachter,et al.  A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis , 2014, Nucleic acids research.

[9]  Yu Zhou,et al.  De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function , 2014, PLoS Comput. Biol..

[10]  J. Keene,et al.  Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs , 2014, Genome Biology.

[11]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[12]  H. Le Hir,et al.  EJC core component MLN51 interacts with eIF3 and activates translation , 2013, Proceedings of the National Academy of Sciences.

[13]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[14]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[15]  Can Cenik,et al.  Introns in UTRs: Why we should stop ignoring them , 2012, BioEssays : news and reviews in molecular, cellular and developmental biology.

[16]  Z. Weng,et al.  The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus , 2012, Cell.

[17]  Hugues Roest Crollius,et al.  CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex , 2012, Nature Structural &Molecular Biology.

[18]  Yutaka Suzuki,et al.  Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability , 2012, RNA biology.

[19]  Julian König,et al.  Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions , 2012, Genome Biology.

[20]  Norman E. Davey,et al.  Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins , 2012, Cell.

[21]  H. Urlaub,et al.  The cryo-EM structure of the UPF–EJC complex shows UPF1 poised toward the RNA 3′ end , 2012, Nature Structural &Molecular Biology.

[22]  A. G. Murachelli,et al.  The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex , 2012, Nature Structural &Molecular Biology.

[23]  Sherif Abou Elela,et al.  Proteins Associated with the Exon Junction Complex Also Control the Alternative Splicing of Apoptotic Regulators , 2011, Molecular and Cellular Biology.

[24]  M. Okoniewski,et al.  Autoregulation of the nonsense-mediated mRNA decay pathway in human cells. , 2011, RNA.

[25]  E. Stone,et al.  RNA homeostasis governed by cell type-specific and branched feedback loops acting on NMD. , 2011, Molecular cell.

[26]  M. Selbach,et al.  Global quantification of mammalian gene expression control , 2011, Nature.

[27]  Blaz Zupan,et al.  iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution , 2011, Journal of visualized experiments : JoVE.

[28]  M. Hentze,et al.  p38 MAPK controls prothrombin expression by regulated RNA 3' end processing. , 2011, Molecular cell.

[29]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[30]  J. Ule,et al.  iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution , 2010, Nature Structural &Molecular Biology.

[31]  Claire Basquin,et al.  Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex. , 2010, Proceedings of the National Academy of Sciences.

[32]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[33]  Gene W. Yeo,et al.  Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. , 2009, Molecular cell.

[34]  J. Gécz,et al.  A UPF3-mediated regulatory switch that maintains RNA surveillance , 2009, Nature Structural &Molecular Biology.

[35]  M. Antoniou,et al.  A physical and functional link between splicing factors promotes pre-mRNA 3′ end processing , 2009, Nucleic acids research.

[36]  M. Hentze,et al.  Disassembly of Exon Junction Complexes by PYM , 2009, Cell.

[37]  M. Hentze,et al.  The Hierarchy of Exon-Junction Complex Assembly by the Spliceosome Explains Key Features of Mammalian Nonsense-Mediated mRNA Decay , 2009, PLoS biology.

[38]  Gene W. Yeo,et al.  An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells , 2009, Nature Structural &Molecular Biology.

[39]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[40]  Nicholas J. McGlincy,et al.  Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense? , 2008, Trends in biochemical sciences.

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

[42]  M. Wilkinson,et al.  An alternative branch of the nonsense‐mediated decay pathway , 2007, The EMBO journal.

[43]  M. Hentze,et al.  A chemiluminescence-based reporter system to monitor nonsense-mediated mRNA decay. , 2006, Biochemical and biophysical research communications.

[44]  B. Séraphin,et al.  Structure of the Exon Junction Core Complex with a Trapped DEAD-Box ATPase Bound to RNA , 2006, Science.

[45]  J. Ebert,et al.  The Crystal Structure of the Exon Junction Complex Reveals How It Maintains a Stable Grip on mRNA , 2006, Cell.

[46]  O. Meyuhas,et al.  Ribosomal protein S6 phosphorylation: from protein synthesis to cell size. , 2006, Trends in biochemical sciences.

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

[48]  Christopher W. J. Smith,et al.  Novel modes of splicing repression by PTB. , 2006, Trends in biochemical sciences.

[49]  M. Moore,et al.  Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. , 2005, RNA.

[50]  M. Hentze,et al.  Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. , 2005, Molecular cell.

[51]  B. Séraphin,et al.  The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity , 2005, Nature Structural &Molecular Biology.

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

[53]  Marie-Christine Rio,et al.  Association of the Breast Cancer Protein MLN51 with the Exon Junction Complex via Its Speckle Localizer and RNA Binding Module* , 2004, Journal of Biological Chemistry.

[54]  A. Ephrussi,et al.  Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization , 2004, Nature.

[55]  M. Moore,et al.  eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay , 2004, Nature Structural &Molecular Biology.

[56]  D. Gatfield,et al.  An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay , 2004, Nature.

[57]  H. Le Hir,et al.  Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. , 2004, Genes & development.

[58]  G. Dreyfuss,et al.  Role of the Nonsense-Mediated Decay Factor hUpf3 in the Splicing-Dependent Exon-Exon Junction Complex , 2001, Science.

[59]  H. Le Hir,et al.  The exon–exon junction complex provides a binding platform for factors involved in mRNA export and nonsense‐mediated mRNA decay , 2001, The EMBO journal.

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

[61]  H. Le Hir,et al.  The spliceosome deposits multiple proteins 20–24 nucleotides upstream of mRNA exon–exon junctions , 2000, The EMBO journal.

[62]  O. Meyuhas.  Synthesis of the translational apparatus is regulated at the translational level. , 2000, European journal of biochemistry.

[63]  Michael Q. Zhang,et al.  Purification and characterization of human RNPS1: a general activator of pre‐mRNA splicing , 1999, The EMBO journal.