Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways

PABP enhances release factor recruitment and stop codon recognition during translation termination

(2016) Alexandr Ivanov et al.   NUCLEIC ACIDS RESEARCH

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

(2016) Joana Carlevaro-Fita et al.   RNA

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

(2016) Evangelos D. Karousis et al.   Wiley Interdisciplinary Reviews-RNA

A mathematical model explains saturating axon guidance responses to molecular gradients

(2016) Huyen Nguyen 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

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

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

(2015) Kalodiah G. Toma et al.   RNA

Quality control of transcription start site selection by nonsense-mediated-mRNA decay

(2015) Christophe Malabat et al.   eLife

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

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

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

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

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

(2014) Volker Boehm et al.   Cell Reports

Nonsense-mediated mRNA decay — Mechanisms of substrate mRNA recognition and degradation in mammalian cells

(2013) Christoph Schweingruber et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

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

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

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

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

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

Positive Outcomes Influence the Rate and Time to Publication, but Not the Impact Factor of Publications of Clinical Trial Results

(2013) Pilar Suñé 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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

(2012) Hidenori Tani et al.   RNA Biology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

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

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 Senses 3′UTR Length to Potentiate mRNA Decay

(2010) J. Robert Hogg et al.   CELL

A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness

(2010) A. M. Burroughs et al.   GENOME RESEARCH

UPF1 Association with the Cap-Binding Protein, CBP80, Promotes Nonsense-Mediated mRNA Decay at Two Distinct Steps

(2010) Jungwook Hwang et al.   MOLECULAR CELL

How and where are nonsense mRNAs degraded in mammalian cells?

(2010) Oliver Mühlemann et al.   RNA Biology

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

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

(2009) Kasper Daniel Hansen et al.   PLoS Genetics

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

The multiple lives of NMD factors: balancing roles in gene and genome regulation

(2008) Olaf Isken et al.   NATURE REVIEWS GENETICS

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

The meaning of nonsense

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