NMD-degradome sequencing reveals ribosome-bound intermediates with 3′-end non-templated nucleotides

[1]  L. Maquat,et al.  Nonsense-mediated mRNA Decay and Cancer. , 2018, Current opinion in genetics & development.

[2]  O. Mühlemann,et al.  Beyond quality control: The role of nonsense-mediated mRNA decay (NMD) in regulating gene expression. , 2017, Seminars in cell & developmental biology.

[3]  V. Beneš,et al.  mRNA 3′ uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome , 2017, Nature.

[4]  M. Wilkinson,et al.  Stress and the nonsense-mediated RNA decay pathway , 2017, Cellular and Molecular Life Sciences.

[5]  F. Lejeune Nonsense-mediated mRNA decay at the crossroads of many cellular pathways , 2017, BMB reports.

[6]  Yutaka Suzuki,et al.  A GC-rich sequence feature in the 3′ UTR directs UPF1-dependent mRNA decay in mammalian cells , 2017, Genome research.

[7]  Lorenza Vitale,et al.  GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics , 2016, Database J. Biol. Databases Curation.

[8]  M. Zavolan,et al.  TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs , 2016, The EMBO journal.

[9]  R. Gregory,et al.  Dis3l2-Mediated Decay Is a Quality Control Pathway for Noncoding RNAs. , 2016, Cell reports.

[10]  J. Lykke-Andersen,et al.  Hyperphosphorylation amplifies UPF1 activity to resolve stalls in nonsense-mediated mRNA decay , 2016, Nature Communications.

[11]  David A. Brafman,et al.  Nonsense-Mediated RNA Decay Influences Human Embryonic Stem Cell Fate , 2016, Stem cell reports.

[12]  L. Maquat,et al.  Nonsense-mediated mRNA decay in humans at a glance , 2016, Journal of Cell Science.

[13]  Joshua D. Welch,et al.  EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates , 2015, RNA.

[14]  Eckart Meese,et al.  Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA microprocessor complex underlie high-risk blastemal type Wilms tumors. , 2015, Cancer cell.

[15]  Raphael Gottardo,et al.  Orchestrating high-throughput genomic analysis with Bioconductor , 2015, Nature Methods.

[16]  D. Patel,et al.  Uridylation by TUT4 and TUT7 Marks mRNA for Degradation , 2014, Cell.

[17]  J. Belasco,et al.  Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells , 2014, Nucleic acids research.

[18]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[19]  A. Sandelin,et al.  Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes , 2014, Genes & development.

[20]  L. Maquat,et al.  A post-translational regulatory switch on UPF1 controls targeted mRNA degradation , 2014, Genes & development.

[21]  O. Mühlemann,et al.  A novel phosphorylation-independent interaction between SMG6 and UPF1 is essential for human NMD , 2014, Nucleic acids research.

[22]  F. Bonneau,et al.  Phospho-dependent and phospho-independent interactions of the helicase UPF1 with the NMD factors SMG5–SMG7 and SMG6 , 2014, Nucleic acids research.

[23]  L. Joshua-Tor,et al.  Mechanism of Dis3L2 substrate recognition in the Lin28/let-7 pathway , 2014, Nature.

[24]  V. Kim,et al.  TAIL-seq: genome-wide determination of poly(A) tail length and 3' end modifications. , 2014, Molecular cell.

[25]  Joshua D. Welch,et al.  Deep sequencing shows multiple oligouridylations are required for 3' to 5' degradation of histone mRNAs on polyribosomes. , 2014, Molecular cell.

[26]  P. Park,et al.  "Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts. , 2013, Cell reports.

[27]  E. Izaurralde,et al.  The SMG5–SMG7 heterodimer directly recruits the CCR4–NOT deadenylase complex to mRNAs containing nonsense codons via interaction with POP2 , 2013, Genes & development.

[28]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[29]  D. Astuti,et al.  Perlman Syndrome: Overgrowth, Wilms Tumor Predisposition and DIS3L2 , 2013, American journal of medical genetics. Part C, Seminars in medical genetics.

[30]  R. Gregory,et al.  A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28-let-7 pathway , 2013, Nature.

[31]  L. Maquat,et al.  Temporal and spatial characterization of nonsense-mediated mRNA decay. , 2013, Genes & development.

[32]  Yunlong Liu,et al.  NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets , 2013, Bioinform..

[33]  L. Maquat,et al.  Rules that govern UPF1 binding to mRNA 3′ UTRs , 2013, Proceedings of the National Academy of Sciences.

[34]  E. Izaurralde,et al.  An unusual arrangement of two 14-3-3-like domains in the SMG5-SMG7 heterodimer is required for efficient nonsense-mediated mRNA decay. , 2013, Genes & development.

[35]  Yoon Ki Kim,et al.  SMG5–PNRC2 is functionally dominant compared with SMG5–SMG7 in mammalian nonsense-mediated mRNA decay , 2012, Nucleic acids research.

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

[37]  Michael T. McManus,et al.  Widespread RNA 3'-end oligouridylation in mammals. , 2012, RNA.

[38]  J. Opitz,et al.  Germline mutations in DIS3L2 cause the Perlman syndrome of overgrowth and Wilms tumor susceptibility , 2012, Nature Genetics.

[39]  Nicholas T. Ingolia,et al.  Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.

[40]  F. Hirahara,et al.  N- and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD , 2011, Nucleic acids research.

[41]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[42]  J. Lykke-Andersen,et al.  Upf1 ATPase-Dependent mRNP Disassembly Is Required for Completion of Nonsense- Mediated mRNA Decay , 2010, Cell.

[43]  Shimyn Slomovic,et al.  Dis3‐like 1: a novel exoribonuclease associated with the human exosome , 2010, The EMBO journal.

[44]  Wenqian Hu,et al.  Nonsense-mediated mRNA decapping occurs on polyribosomes in Saccharomyces cerevisiae , 2010, Nature Structural &Molecular Biology.

[45]  Wenqian Hu,et al.  Co-translational mRNA decay in Saccharomyces cerevisiae , 2009, Nature.

[46]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[47]  C. Norbury,et al.  Decapping is preceded by 3' uridylation in a novel pathway of bulk mRNA turnover. , 2009, Nature structural & molecular biology.

[48]  H. Hirano,et al.  SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. , 2009, Genes & development.

[49]  Yoon Ki Kim,et al.  Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex. , 2009, Molecular cell.

[50]  L. Maquat,et al.  Upf1 Phosphorylation Triggers Translational Repression during Nonsense-Mediated mRNA Decay , 2008, Cell.

[51]  M. Kiledjian,et al.  3' Terminal oligo U-tract-mediated stimulation of decapping. , 2007, RNA.

[52]  G. Pruijn,et al.  Human cell growth requires a functional cytoplasmic exosome, which is involved in various mRNA decay pathways. , 2007, RNA.

[53]  M. Hentze,et al.  The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway , 2007, Nucleic acids research.

[54]  Oleg Kikin,et al.  QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences , 2006, Nucleic Acids Res..

[55]  Tsung-Cheng Chang,et al.  Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover , 2005, Nature Structural &Molecular Biology.

[56]  J. Ebert,et al.  SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway. , 2005, Molecular cell.

[57]  E. Izaurralde,et al.  SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. , 2004, Molecular cell.

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

[59]  K. Anders,et al.  Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. , 2003, Molecular cell.

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

[61]  Y. Taya,et al.  Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. , 2001, Genes & development.

[62]  E. Petfalski,et al.  Three Novel Components of the Human Exosome* , 2001, The Journal of Biological Chemistry.

[63]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[64]  L. Maquat,et al.  Identification and Characterization of Human Orthologues to Saccharomyces cerevisiae Upf2 Protein and Upf3 Protein (Caenorhabditis elegans SMG-4) , 2001, Molecular and Cellular Biology.

[65]  L. Maquat,et al.  Identifying Cellular Nonsense-Mediated mRNA Decay (NMD) Targets: Immunoprecipitation of Phosphorylated UPF1 Followed by RNA Sequencing (p-UPF1 RIP-Seq). , 2018, Methods in molecular biology.

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

[67]  C. Norbury,et al.  The human cytoplasmic RNA terminal U-transferase ZCCHC11 targets histone mRNAs for degradation. , 2011, RNA.

[68]  L. Maquat,et al.  SMD and NMD are competitive pathways that contribute to myogenesis: effects on PAX3 and myogenin mRNAs. , 2009, Genes & development.

[69]  T. Jensen,et al.  SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells , 2009, Nature Structural &Molecular Biology.

[70]  T. Mullen,et al.  Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. , 2008, Genes & development.