Nonsense-mediated mRNA decay: novel mechanistic insights and biological impact

Proteomic Analysis Reveals Branch-specific Regulation of the Unfolded Protein Response by Nonsense-mediated mRNA Decay

(2016) Jana Sieber et al.   MOLECULAR & CELLULAR PROTEOMICS

Human nonsense-mediated mRNA decay factor UPF2 interacts directly with eRF3 and the SURF complex

(2016) Andrés López-Perrote et al.   NUCLEIC ACIDS RESEARCH

The RNA helicase DHX34 functions as a scaffold for SMG1-mediated UPF1 phosphorylation

(2016) Roberto Melero et al.   Nature Communications

Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway

(2016) Zhiyun Ge et al.   eLife

Nonsense-Mediated mRNA Decay: Degradation of Defective Transcripts Is Only Part of the Story

(2015) Feng He et al.   Annual Review of Genetics

Caspases shutdown nonsense-mediated mRNA decay during apoptosis

(2015) J Jia et al.   CELL DEATH AND DIFFERENTIATION

Mechanism, factors, and physiological role of nonsense-mediated mRNA decay

(2015) Tobias Fatscher et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Smg6/Est1 licenses embryonic stem cell differentiation via nonsense-mediated mRNA decay

(2015) T. Li et al.   EMBO JOURNAL

The unfolded protein response is shaped by the NMD pathway

(2015) R. Karam et al.   EMBO REPORTS

A Combined Proteomics/Genomics Approach Links Hepatitis C Virus Infection with Nonsense-Mediated mRNA Decay

(2015) Holly R. Ramage et al.   MOLECULAR CELL

Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity

(2015) Suzanne R. Lee et al.   MOLECULAR CELL

Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes

(2015) Søren Lykke-Andersen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A network of SMG-8, SMG-9 and SMG-1 C-terminal insertion domain regulates UPF1 substrate recruitment and phosphorylation

(2015) Aurélien Deniaud et al.   NUCLEIC ACIDS RESEARCH

Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators

(2015) Qinghong Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of elements in human long 3′ UTRs that inhibit nonsense-mediated decay

(2015) Kalodiah G. Toma et al.   RNA

Attenuation of nonsense-mediated mRNA decay facilitates the response to chemotherapeutics

(2015) Maximilian W. Popp et al.   Nature Communications

Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities

(2015) Francesca Fiorini et al.   Nature Communications

Full UPF3B function is critical for neuronal differentiation of neural stem cells

(2015) Tahani Alrahbeni et al.   Molecular Brain

Nonsense-Mediated Decay Serves as a General Viral Restriction Mechanism in Plants

(2014) Damien Garcia et al.   Cell Host & Microbe

The Host Nonsense-Mediated mRNA Decay Pathway Restricts Mammalian RNA Virus Replication

(2014) Giuseppe Balistreri et al.   Cell Host & Microbe

UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome

(2014) J. Bao et al.   DEVELOPMENT

Identification and characterization of novel factors that act in the nonsense-mediated mRNA decay pathway in nematodes, flies and mammals

(2014) A. Casadio et al.   EMBO REPORTS

A post-translational regulatory switch on UPF1 controls targeted mRNA degradation

(2014) Tatsuaki Kurosaki et al.   GENES & DEVELOPMENT

Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes

(2014) Søren Lykke-Andersen et al.   GENES & DEVELOPMENT

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

A Highly Conserved Region Essential for NMD in the Upf2 N-Terminal Domain

(2014) Zaineb Fourati et al.   JOURNAL OF MOLECULAR BIOLOGY

MOV10 Is a 5′ to 3′ RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3′ UTRs

(2014) Lea H. Gregersen et al.   MOLECULAR CELL

Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells

(2014) Skye A. Schmidt et al.   NUCLEIC ACIDS RESEARCH

A novel phosphorylation-independent interaction between SMG6 and UPF1 is essential for human NMD

(2014) Pamela Nicholson et al.   NUCLEIC ACIDS RESEARCH

Phospho-dependent and phospho-independent interactions of the helicase UPF1 with the NMD factors SMG5–SMG7 and SMG6

(2014) Sutapa Chakrabarti et al.   NUCLEIC ACIDS RESEARCH

Stress-induced inhibition of nonsense-mediated RNA decay regulates intracellular cystine transport and intracellular glutathione through regulation of the cystine/glutamate exchanger SLC7A11

(2014) L Martin et al.   ONCOGENE

Eukaryotic Initiation Factor 4G Suppresses Nonsense-Mediated mRNA Decay by Two Genetically Separable Mechanisms

(2014) Raphael Joncourt et al.   PLoS One

The interaction of cytoplasmic poly(A)-binding protein with eukaryotic initiation factor 4G suppresses nonsense-mediated mRNA decay

(2014) Tobias Fatscher et al.   RNA

Structures of SMG1-UPFs Complexes: SMG1 Contributes to Regulate UPF2-Dependent Activation of UPF1 in NMD

(2014) Roberto Melero et al.   STRUCTURE

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

The RNA Helicase DHX34 Activates NMD by Promoting a Transition from the Surveillance to the Decay-Inducing Complex

(2014) Nele Hug et al.   Cell Reports

Cryoelectron Microscopic Structures of Eukaryotic Translation Termination Complexes Containing eRF1-eRF3 or eRF1-ABCE1

(2014) Anne Preis et al.   Cell Reports

Posttranscriptional Control of the Stem Cell and Neurogenic Programs by the Nonsense-Mediated RNA Decay Pathway

(2014) Chih H. Lou et al.   Cell Reports

3′ UTR Length and Messenger Ribonucleoprotein Composition Determine Endocleavage Efficiencies at Termination Codons

(2014) Volker Boehm et al.   Cell Reports

Widespread Use of Non-productive Alternative Splice Sites in Saccharomyces cerevisiae

(2014) Tadashi Kawashima et al.   PLoS Genetics

Regulation of mRNA Abundance by Polypyrimidine Tract-Binding Protein-Controlled Alternate 5′ Splice Site Choice

(2014) Fursham M. Hamid et al.   PLoS Genetics

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

Regulation of Axon Guidance by Compartmentalized Nonsense-Mediated mRNA Decay

(2013) Dilek Colak et al.   CELL

The SMG5-SMG7 heterodimer directly recruits the CCR4-NOT deadenylase complex to mRNAs containing nonsense codons via interaction with POP2

(2013) B. Loh et al.   GENES & DEVELOPMENT

An unusual arrangement of two 14-3-3-like domains in the SMG5-SMG7 heterodimer is required for efficient nonsense-mediated mRNA decay

(2013) S. Jonas et al.   GENES & DEVELOPMENT

Role of SMG-1-mediated Upf1 phosphorylation in mammalian nonsense-mediated mRNA decay

(2013) Akio Yamashita   GENES TO CELLS

Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay

(2013) J. A. Hurt et al.   GENOME RESEARCH

The UPF3B gene, implicated in intellectual disability, autism, ADHD and childhood onset schizophrenia regulates neural progenitor cell behaviour and neuronal outgrowth

(2013) Lachlan A. Jolly et al.   HUMAN MOLECULAR GENETICS

UPF1 Is Crucial for the Infectivity of Human Immunodeficiency Virus Type 1 Progeny Virions

(2013) A. K. P. Serquina et al.   JOURNAL OF VIROLOGY

Viral interference with host mRNA surveillance, the nonsense-mediated mRNA decay (NMD) pathway, through a new function of HTLV-1 Rex: implications for retroviral replication

(2013) Kazumi Nakano et al.   MICROBES AND INFECTION

Inhibition of Nonsense-Mediated RNA Decay Activates Autophagy

(2013) J. Wengrod et al.   MOLECULAR AND CELLULAR BIOLOGY

Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3′ UTRs

(2013) David Zünd et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nonsense-mediated mRNA decay occurs during eIF4F-dependent translation in human cells

(2013) Sébastien Durand et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

eIF4E-bound mRNPs are substrates for nonsense-mediated mRNA decay in mammalian cells

(2013) Simone C Rufener et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DHX34 and NBAS form part of an autoregulatory NMD circuit that regulates endogenous RNA targets in human cells, zebrafish and Caenorhabditis elegans

(2013) Dasa Longman et al.   NUCLEIC ACIDS RESEARCH

Nonsense-Mediated Decay of Alternative Precursor mRNA Splicing Variants Is a Major Determinant of the Arabidopsis Steady State Transcriptome

(2013) G. Drechsel et al.   PLANT CELL

The RNA Degradation Pathway Regulates the Function of GAS5 a Non-Coding RNA in Mammalian Cells

(2013) Hidenori Tani et al.   PLoS One

Rules that govern UPF1 binding to mRNA 3′ UTRs

(2013) Tatsuaki Kurosaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of EJC-enhanced and EJC-independent NMD in human cells reveals two partially redundant degradation pathways

(2013) S. Metze et al.   RNA

The Unfolded Protein Response in Secretory Cell Function

(2012) Kristin A. Moore et al.   Annual Review of Genetics

Testing the faux-UTR model for NMD: Analysis of Upf1p and Pab1p competition for binding to eRF3/Sup35p

(2012) Stephanie Kervestin et al.   BIOCHIMIE

Structural basis of highly conserved ribosome recycling in eukaryotes and archaea

(2012) Thomas Becker et al.   NATURE

The cryo-EM structure of the UPF–EJC complex shows UPF1 poised toward the RNA 3′ end

(2012) Roberto Melero et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tight intramolecular regulation of the human Upf1 helicase by its N- and C-terminal domains

(2012) Francesca Fiorini et al.   NUCLEIC ACIDS RESEARCH

SMG5–PNRC2 is functionally dominant compared with SMG5–SMG7 in mammalian nonsense-mediated mRNA decay

(2012) Hana Cho et al.   NUCLEIC ACIDS RESEARCH

Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability

(2012) Hidenori Tani et al.   RNA Biology

Structural Basis of the PNRC2-Mediated Link between mRNA Surveillance and Decapping

(2012) Tingfeng Lai et al.   STRUCTURE

Cancer Cell Metabolism: One Hallmark, Many Faces

(2012) Jason R. Cantor et al.   Cancer Discovery

The nonsense-mediated mRNA decay SMG-1 kinase is regulated by large-scale conformational changes controlled by SMG-8

(2011) E. Arias-Palomo et al.   GENES & DEVELOPMENT

The structure and function of the rous sarcoma virus RNA stability element

(2011) Johanna B. Withers et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and Its Regulation by Upf2

(2011) Sutapa Chakrabarti et al.   MOLECULAR CELL

RNA Homeostasis Governed by Cell Type-Specific and Branched Feedback Loops Acting on NMD

(2011) Lulu Huang et al.   MOLECULAR CELL

Identification of a MicroRNA that Activates Gene Expression by Repressing Nonsense-Mediated RNA Decay

(2011) Ivone G. Bruno et al.   MOLECULAR CELL

Transcriptome profiling of UPF3B/NMD-deficient lymphoblastoid cells from patients with various forms of intellectual disability

(2011) L S Nguyen et al.   MOLECULAR PSYCHIATRY

Dhx34 and Nbas function in the NMD pathway and are required for embryonic development in zebrafish

(2011) Corina Anastasaki et al.   NUCLEIC ACIDS RESEARCH

Interaction of PABPC1 with the translation initiation complex is critical to the NMD resistance of AUG-proximal nonsense mutations

(2011) I. Peixeiro et al.   NUCLEIC ACIDS RESEARCH

N- and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD

(2011) Yukiko Okada-Katsuhata et al.   NUCLEIC ACIDS RESEARCH

Kinetic analysis reveals the ordered coupling of translation termination and ribosome recycling in yeast

(2011) C. J. Shoemaker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosome recycling depends on a mechanistic link between the FeS cluster domain and a conformational switch of the twin-ATPase ABCE1

(2011) D. Barthelme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Autoregulation of the nonsense-mediated mRNA decay pathway in human cells

(2011) H. Yepiskoposyan et al.   RNA

mRNP quality control goes regulatory

(2011) Oliver Mühlemann et al.   TRENDS IN GENETICS

Upf1 ATPase-Dependent mRNP Disassembly Is Required for Completion of Nonsense- Mediated mRNA Decay

(2010) Tobias M. Franks et al.   CELL

Upf1 Senses 3′UTR Length to Potentiate mRNA Decay

(2010) J. Robert Hogg et al.   CELL

SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay

(2010) I. Kashima et al.   GENES & DEVELOPMENT

The Role of ABCE1 in Eukaryotic Posttermination Ribosomal Recycling

(2010) Andrey V. Pisarev et al.   MOLECULAR CELL

Characterization of SMG-9, an essential component of the nonsense-mediated mRNA decay SMG1C complex

(2010) Israel S. Fernández et al.   NUCLEIC ACIDS RESEARCH

UPF2 Is a Critical Regulator of Liver Development, Function and Regeneration

(2010) Lina A. Thoren et al.   PLoS One

Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex.

(2010) G. Buchwald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay

(2010) D. R. McIlwain et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How and where are nonsense mRNAs degraded in mammalian cells?

(2010) Oliver Mühlemann et al.   RNA Biology

Disassembly of Exon Junction Complexes by PYM

(2009) Niels H. Gehring et al.   CELL

Transforming Growth Factor type β and Smad family signaling in stem cell function

(2009) Eve Seuntjens et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Unusual bipartite mode of interaction between the nonsense-mediated decay factors, UPF1 and UPF2

(2009) Marcello Clerici et al.   EMBO JOURNAL

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) A. Yamashita et al.   GENES & DEVELOPMENT

Nonsense-Mediated mRNA Decay Effectors Are Essential for Zebrafish Embryonic Development and Survival

(2009) N. Wittkopp et al.   MOLECULAR AND CELLULAR BIOLOGY

Human Proline-Rich Nuclear Receptor Coregulatory Protein 2 Mediates an Interaction between mRNA Surveillance Machinery and Decapping Complex

(2009) Hana Cho et al.   MOLECULAR CELL

A UPF3-mediated regulatory switch that maintains RNA surveillance

(2009) Wai-Kin Chan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GTP-dependent structural rearrangement of the eRF1:eRF3 complex and eRF3 sequence motifs essential for PABP binding

(2009) A. V. Kononenko et al.   NUCLEIC ACIDS RESEARCH

The upstream open reading frame of the Arabidopsis AtMHX gene has a strong impact on transcript accumulation through the nonsense-mediated mRNA decay pathway

(2009) Helen Saul et al.   PLANT JOURNAL

Genome-Wide Identification of Alternative Splice Forms Down-Regulated by Nonsense-Mediated mRNA Decay in Drosophila

(2009) Kasper Daniel Hansen et al.   PLoS Genetics

High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans

(2009) Arun K Ramani et al.   GENOME BIOLOGY

Upf1 Phosphorylation Triggers Translational Repression during Nonsense-Mediated mRNA Decay

(2008) Olaf Isken et al.   CELL

Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay

(2008) Zoltán Kerényi et al.   EMBO JOURNAL

Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways

(2008) Pavel V Ivanov et al.   EMBO JOURNAL

NMD is essential for hematopoietic stem and progenitor cells and for eliminating by-products of programmed DNA rearrangements

(2008) J. Weischenfeldt et al.   GENES & DEVELOPMENT

Incomplete nonsense-mediated mRNA decay in Giardia lamblia

(2008) Y CHEN et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Regulation of Multiple Core Spliceosomal Proteins by Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay

(2008) A. L. Saltzman et al.   MOLECULAR AND CELLULAR BIOLOGY

SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells

(2008) Andrea B Eberle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense-mediated mRNA decay

(2008) A. L. Silva et al.   RNA

SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan

(2008) E. Huntzinger et al.   RNA

Unexpected roles for UPF1 in HIV-1 RNA metabolism and translation

(2008) L. Ajamian et al.   RNA

The meaning of nonsense

(2008) Lukas Stalder et al.   TRENDS IN CELL BIOLOGY

A Competition between Stimulators and Antagonists of Upf Complex Recruitment Governs Human Nonsense-Mediated mRNA Decay

(2008) Guramrit Singh et al.   PLOS BIOLOGY

Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region

(2008) Andrea B Eberle et al.   PLOS BIOLOGY