(Q37588098)

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

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Europe PubMed Central

PMC publication ID

21 August 2017

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

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Europe PubMed Central

PMC publication ID

21 August 2017

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Joël Bourquin

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Oliver Mühlemann

5

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Oliver Mühlemann

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Europe PubMed Central

PMC publication ID

21 August 2017

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Martino Colombo

1

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Europe PubMed Central

PMC publication ID

21 August 2017

Evangelos D Karousis

2

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Europe PubMed Central

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21 August 2017

Joël Bourquin

3

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Europe PubMed Central

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21 August 2017

Rémy Bruggmann

4

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Europe PubMed Central

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21 August 2017

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18 November 2016

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Europe PubMed Central

PMC publication ID

21 August 2017

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Europe PubMed Central

PMC publication ID

21 August 2017

23

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Europe PubMed Central

PMC publication ID

21 August 2017

2

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Europe PubMed Central

PMC publication ID

21 August 2017

189-201

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Detecting actively translated open reading frames in ribosome profiling data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Trimmomatic: a flexible trimmer for Illumina sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

The RNA degradation pathway regulates the function of GAS5 a non-coding RNA in mammalian cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

How and where are nonsense mRNAs degraded in mammalian cells?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Detection of nonneutral substitution rates on mammalian phylogenies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

The meaning of nonsense

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Posttranscriptional gene regulation by spatial rearrangement of the 3' untranslated region

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Association of yeast Upf1p with direct substrates of the NMD pathway.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Saccharomyces cerevisiae Ebs1p is a putative ortholog of human Smg7 and promotes nonsense-mediated mRNA decay

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Caenorhabditis elegans SMG-2 selectively marks mRNAs containing premature translation termination codons

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

An alternative branch of the nonsense-mediated decay pathway

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

A GFP-based reporter system to monitor nonsense-mediated mRNA decay

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

Interference of nonsense mutations with eukaryotic messenger RNA stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

6 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

6 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

6 September 2017

Rules that govern UPF1 binding to mRNA 3' UTRs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

6 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

6 September 2017

Upf1 senses 3'UTR length to potentiate mRNA decay

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

14 September 2017

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

14 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

28 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

28 September 2017

A regulatory mechanism that detects premature nonsense codons in T-cell receptor transcripts in vivo is reversed by protein synthesis inhibitors in vitro

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

28 September 2017

The host nonsense-mediated mRNA decay pathway restricts Mammalian RNA virus replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

25 June 2018

Nonsense-mediated decay serves as a general viral restriction mechanism in plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

25 June 2018

UPF1 association with the cap-binding protein, CBP80, promotes nonsense-mediated mRNA decay at two distinct steps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

25 June 2018

Binary specification of nonsense codons by splicing and cytoplasmic translation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

25 June 2018

3' UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

1 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

1 September 2018

Analysis of nonsense-mediated mRNA decay in mammalian cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

1 September 2018

EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3' UTR length.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

1 September 2018

hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

1 September 2018

mRNA surveillance of expressed pseudogenes in C. elegans.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

1 September 2018

A faux 3'-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5238794

1 September 2018

RETRACTED: A mathematical model explains saturating axon guidance responses to molecular gradients.

1 reference

https://api.crossref.org/works/10.1261%2FRNA.059055.116

21 January 2018

Contextual interactions determine whether the Drosophila homeodomain protein, Vnd, acts as a repressor or activator

1 reference

https://api.crossref.org/works/10.1261%2FRNA.059055.116

21 January 2018

Positive outcomes influence the rate and time to publication, but not the impact factor of publications of clinical trial results

1 reference

https://api.crossref.org/works/10.1261%2FRNA.059055.116

21 January 2018

mRNP quality control goes regulatory

1 reference

https://api.crossref.org/works/10.1261%2FRNA.059055.116

21 January 2018

Unstable β-globin mRNA in mRNA-deficient β0 thalassemia

1 reference

https://pubmed.ncbi.nlm.nih.gov/27864472

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1261/RNA.059055.116

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

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