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

Hurt, Jessica A.; Robertson, Alex D.; Burge, Christopher B.

doi:10.1101/gr.157354.113

Cited by 241 publications

(345 citation statements)

References 79 publications

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“…16,20,103 Apart from reduced translation downstream, the presence of uORFs also correlates with reduced steady-state levels of transcripts, 16 which is indicative of reduced stability of uORF-containing transcripts. Consistently, uORF-containing transcripts have been shown to be enriched in targets of nonsense-mediated mRNA decay (NMD), 21,92,94,[104][105][106][107] which induces rapid degradation of transcripts with premature termination codons.…”

Section: Uorfs As Widespread Repressive Genetic Elementsmentioning

confidence: 89%

Decoding sORF translation – from small proteins to gene regulation

2016

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Translation is best known as the fundamental mechanism by which the ribosome converts a sequence of nucleotides into a string of amino acids. Extensive research over many years has elucidated the key principles of translation, and the majority of translated regions were thought to be known. The recent discovery of wide-spread translation outside of annotated protein-coding open reading frames (ORFs) came therefore as a surprise, raising the intriguing possibility that these newly discovered translated regions might have unrecognized protein-coding or gene-regulatory functions. Here, we highlight recent findings that provide evidence that some of these newly discovered translated short ORFs (sORFs) encode functional, previously missed small proteins, while others have regulatory roles. Based on known examples we will also speculate about putative additional roles and the potentially much wider impact that these translated regions might have on cellular homeostasis and gene regulation.

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Section: Uorfs As Widespread Repressive Genetic Elementsmentioning

confidence: 89%

Decoding sORF translation – from small proteins to gene regulation

2016

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“…Indeed, SMG6 and the SMG5-SMG7 complex are only recruited to NMD targets upon UPF1 phosphorylation, enabling the sequential assembly of the surveillance complex and step-wise recruitment of decay factors. In this context, it is important to note that UPF1 also associates with mRNAs that are not destined for degradation by NMD (Hogg and Goff 2010;Hurt et al 2013;Kurosaki and Maquat 2013;Zü nd et al 2013), and thus a tight regulation of UPF1 phosphorylation and the subsequent recruitment of decay factors are required to prevent unscheduled degradation. In contrast, in yeast, UPF1 is not phosphorylated and is thought to recruit decay factors to the target mRNA Swisher and Parker 2011).…”

Section: Role Of Decapping In Nmdmentioning

confidence: 99%

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

2013

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Nonsense-mediated mRNA decay (NMD) is a eukaryotic quality control mechanism that detects aberrant mRNAs containing nonsense codons and induces their rapid degradation. This degradation is mediated by SMG6, an NMDspecific endonuclease, as well as the SMG5 and SMG7 proteins, which recruit general mRNA decay enzymes. However, it remains unknown which specific decay factors are recruited and whether this recruitment is direct. Here, we show that SMG7 binds directly to POP2, a catalytic subunit of the CCR4-NOT deadenylase complex, and elicits deadenylation-dependent decapping and 59-to-39 decay of NMD targets. Accordingly, a catalytically inactive POP2 mutant partially suppresses NMD in human cells. The SMG7-POP2 interaction is critical for NMD in cells depleted of SMG6, indicating that SMG7 and SMG6 act redundantly to promote the degradation of NMD targets. We further show that UPF1 provides multiple binding sites for decapping factors. These data unveil a missing direct physical link between NMD and the general mRNA decay machinery and indicate that NMD employs diverse and partially redundant mechanisms to ensure robust degradation of aberrant mRNAs.

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“…We developed a computational pipeline to assemble transcripts containing known and novel cassette exons using RNA-seq reads from control and Rbfox2 knockdown as well as control and Upf-1 knockdown and control and cycloheximide-treated mESCs (data from Hurt et al 2013). Each of these transcripts was then translated in silico, assigning reading frames using Ensembl start codon annotations.…”

Section: Widespread Regulation Of As-nmd By Rbfox2 Controls Gene Exprmentioning

confidence: 99%

“…For gene expression analysis, mapped reads were aligned using Cufflinks 2.1.1 (Trapnell et al 2012) to a custom annotation file generated from annotated and novel junctions called by TopHat from the RNA-seq performed in this study as well as that from Hurt et al (2013). For splicing analysis, reads were aligned to annotated mouse splicing events using the MISO algorithm (Katz et al 2010).…”

Section: Rna-seq Analysismentioning

confidence: 99%

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Rbfox2 controls autoregulation in RNA-binding protein networks

Boutz²,

et al. 2014

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The tight regulation of splicing networks is critical for organismal development. To maintain robust splicing patterns, many splicing factors autoregulate their expression through alternative splicing-coupled nonsensemediated decay (AS-NMD). However, as negative autoregulation results in a self-limiting window of splicing factor expression, it is unknown how variations in steady-state protein levels can arise in different physiological contexts. Here, we demonstrate that Rbfox2 cross-regulates AS-NMD events within RNA-binding proteins to alter their expression. Using individual nucleotide-resolution cross-linking immunoprecipitation coupled to highthroughput sequencing (iCLIP) and mRNA sequencing, we identified >200 AS-NMD splicing events that are bound by Rbfox2 in mouse embryonic stem cells. These ''silent'' events are characterized by minimal apparent splicing changes but appreciable changes in gene expression upon Rbfox2 knockdown due to degradation of the NMDinducing isoform. Nearly 70 of these AS-NMD events fall within genes encoding RNA-binding proteins, many of which are autoregulated. As with the coding splicing events that we found to be regulated by Rbfox2, silent splicing events are evolutionarily conserved and frequently contain the Rbfox2 consensus UGCAUG. Our findings uncover an unexpectedly broad and multilayer regulatory network controlled by Rbfox2 and offer an explanation for how autoregulatory splicing networks are tuned.

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

Cited by 241 publications

References 79 publications

Decoding sORF translation – from small proteins to gene regulation

Decoding sORF translation – from small proteins to gene regulation

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

Rbfox2 controls autoregulation in RNA-binding protein networks

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