Analysis of nonsense-mediated mRNA decay in mammalian cells. (Q54303567)

27 May 2018

title

Analysis of nonsense-mediated mRNA decay in mammalian cells. (English)

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27 May 2018

3

Oliver Mühlemann

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27 May 2018

Pamela Nicholson

1

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27 May 2018

Raphael Joncourt

series ordinal

2

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27 May 2018

publication date

1 June 2012

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27 May 2018

Current protocols in cell biology

published in

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27 May 2018

volume

Chapter 27

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27 May 2018

page(s)

Unit27.4

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27 May 2018

Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets

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

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MicroRNAs: target recognition and regulatory functions

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Role for a bidentate ribonuclease in the initiation step of RNA interference

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Localization of ASH1 mRNA particles in living yeast

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

21 January 2018

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Nonsense-mediated mRNA decay (NMD) mechanisms

21 January 2018

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A system for stable expression of short interfering RNAs in mammalian cells

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

21 January 2018

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Efficient downregulation of immunoglobulin mu mRNA with premature translation-termination codons requires the 5'-half of the VDJ exon

21 January 2018

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Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays

21 January 2018

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Real-time, fluorescence-based quantitative PCR: a snapshot of current procedures and preferences

21 January 2018

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

21 January 2018

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beta 0 thalassemia, a nonsense mutation in man

21 January 2018

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The nonsense-mediated decay RNA surveillance pathway

21 January 2018

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Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex

21 January 2018

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microRNA/Argonaute 2 regulates nonsense-mediated messenger RNA decay

21 January 2018

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Ago2/miRISC-mediated inhibition of CBP80/20-dependent translation and thereby abrogation of nonsense-mediated mRNA decay require the cap-associating activity of Ago2

21 January 2018

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Single-Step Method of RNA Isolation by Acid Guanidinium Thiocyanate–Phenol–Chloroform Extraction

21 January 2018

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The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on

21 January 2018

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

21 January 2018

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Tethered function assays using 3' untranslated regions.

21 January 2018

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mRNA stabilization by poly(A) binding protein is independent of poly(A) and requires translation.

21 January 2018

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In vivo dynamics of RNA polymerase II transcription.

21 January 2018

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Translation driven by an eIF4G core domain in vivo

21 January 2018

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Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein

21 January 2018

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Cotranscriptional effect of a premature termination codon revealed by live-cell imaging.

21 January 2018

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RNA quality control in eukaryotes

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

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

21 January 2018

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SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells

21 January 2018

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High-throughput RNAi screening in cultured cells: a user's guide.

21 January 2018

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RNA interference is mediated by 21- and 22-nucleotide RNAs

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

RNA integrity and the effect on the real-time qRT-PCR performance

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

A novel mode of RBD-protein recognition in the Y14–Mago complex

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Nonsense-mediated mRNA decay in health and disease

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Y14 and hUpf3b form an NMD-activating complex

21 January 2018

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

21 January 2018

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A novel method for real time quantitative RT-PCR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex

21 January 2018

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Arginine/serine-rich domains of SR proteins can function as activators of pre-mRNA splicing.

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Multiple portions of poly(A)-binding protein stimulate translation in vivo

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

A co-repressor assembly nucleated by Sex-lethal in the 3'UTR mediates translational control of Drosophila msl-2 mRNA

21 January 2018

1 reference

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Kinetic analysis of the RNAi enzyme complex

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Real time quantitative PCR

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

The Argonaute protein family

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Nonsense-mediated decay approaches the clinic

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase

21 January 2018

1 reference

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CBP80 promotes interaction of Upf1 with Upf2 during nonsense-mediated mRNA decay in mammalian cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Real-time RT-PCR normalisation; strategies and considerations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Upf1 phosphorylation triggers translational repression during nonsense-mediated mRNA decay

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

A three-dimensional view of the molecular machinery of RNA interference

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Tethering of proteins to RNAs by bacteriophage proteins

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Nonsense-mediated mRNA decay modulates clinical outcome of genetic disease

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

The real-time polymerase chain reaction

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Applying nonsense-mediated mRNA decay research to the clinic: progress and challenges

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Real-time observation of transcription initiation and elongation on an endogenous yeast gene

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Conditional RNAi: towards a silent gene therapy

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Improved quantitative real-time RT-PCR for expression profiling of individual cells

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Interference of nonsense mutations with eukaryotic messenger RNA stability

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Real-time PCR in virology

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

A conserved role of a DEAD box helicase in mRNA masking

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Splicing enhances translation in mammalian cells: an additional function of the exon junction complex

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Structural and functional modules in RNA interference

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Functional immunoglobulin M production after transfection of cloned immunoglobulin heavy and light chain genes into lymphoid cells

21 January 2018

1 reference

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Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

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

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

A new mathematical model for relative quantification in real-time RT-PCR

21 January 2018

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Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Execution of nonsense-mediated mRNA decay: what defines a substrate?

21 January 2018

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Protein RNA and protein protein interactions mediate association of human EST1A/SMG6 with telomerase

21 January 2018

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The RNA binding protein Pub1 modulates the stability of transcripts containing upstream open reading frames

21 January 2018

1 reference

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Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4)

21 January 2018

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

21 January 2018

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Imaging of gene expression in living cells and tissues

21 January 2018

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On the road to reading the RNA-interference code

21 January 2018

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Proteins binding to 5' untranslated region sites: a general mechanism for translational regulation of mRNAs in human and yeast cells

21 January 2018

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A mutated human homologue to yeast Upf1 protein has a dominant-negative effect on the decay of nonsense-containing mRNAs in mammalian cells

21 January 2018

1 reference

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Inhibition of real-time RT-PCR quantification due to tissue-specific contaminants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

SMG7 acts as a molecular link between mRNA surveillance and mRNA decay

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Cooperative binding of R17 coat protein to RNA

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Real-time PCR for mRNA quantitation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

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

21 January 2018

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An efficient one-step site-directed and site-saturation mutagenesis protocol

21 January 2018

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Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Nonsense-mediated mRNA decay: target genes and functional diversification of effectors

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Localization and anchoring of mRNA in budding yeast

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471143030.CB2704S55

Crystal structure of an RNA bacteriophage coat protein–operator complex

21 January 2018

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10.1002/0471143030.CB2704S55

21 January 2018

Identifiers

DOI

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27 May 2018

PubMed ID

22733442

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27 May 2018