Related Experiment Video
Updated: Apr 19, 2026
Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains
Published on: December 13, 2014
Nonsense-mediated mRNA decay factors target short poly(A)-tailed mRNAs lacking a premature termination codon
Toni Gouhier1,2,3, Cosmin Saveanu4,5, Gwenael Badis6,7
1Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS UMR8197, INSERM, PSL Research University, Paris, France.
Abstract:
Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance pathway known to degrade mRNAs containing premature termination codons (PTCs). mRNA recognition by the Upf1, Upf2 and Upf3 NMD factors is favoured by long distances between the stop codon and the poly(A)-binding protein (Pab1) binding site. Using Nanopore direct RNA sequencing, we now show that PTC-containing NMD targets account for only 6% of Upf1-associated RNA and have long poly(A) tails, indicating that Upf1-binding occurs prior to their deadenylation. Conversely, most Upf1-associated mRNAs have short poly(A) tails, lack a PTC and correspond to highly expressed genes. A short poly(A) tail is thus an important feature of a new class of Upf1 targets, redefining the scope of the NMD RNA degradation pathway. Recognition of short poly(A)-tailed mRNAs by Upf1, Upf2 and Upf3 (the NMD machinery) triggers their decapping, uncovering a hitherto unknown role of the NMD machinery in the degradation of these transcripts.
Insights
Nonsense-mediated mRNA decay (NMD) surveillance degrades faulty mRNAs. New findings reveal NMD machinery also targets normal mRNAs with short poly(A) tails, expanding its known functions in RNA degradation.
Area of Science:
- Molecular Biology
- RNA Biology
- Gene Regulation
Background:
- Nonsense-mediated mRNA decay (NMD) is a crucial eukaryotic surveillance pathway.
- NMD degrades messenger RNAs (mRNAs) harboring premature termination codons (PTCs).
- Recognition of NMD targets typically involves Upf1, Upf2, and Upf3 proteins and is influenced by the distance between the stop codon and poly(A)-binding protein (Pab1).
Purpose of the Study:
- To investigate the full scope of Upf1-associated RNAs.
- To characterize the features of NMD targets beyond those with PTCs.
- To redefine the role of the NMD pathway in RNA degradation.
Main Methods:
- Utilized Nanopore direct RNA sequencing.
- Analyzed Upf1-associated RNA populations.
- Characterized poly(A) tail lengths and presence of PTCs in target mRNAs.
Main Results:
- PTC-containing NMD targets represent only 6% of Upf1-associated RNA and possess long poly(A) tails.
- The majority of Upf1-associated mRNAs lack PTCs and have short poly(A) tails, correlating with highly expressed genes.
- Short poly(A) tails are identified as a key feature for a novel class of Upf1 targets.
Conclusions:
- The NMD pathway's scope extends beyond PTC-containing mRNAs.
- Short poly(A) tails define a new category of Upf1 targets.
- The NMD machinery plays a previously unrecognized role in degrading short poly(A)-tailed mRNAs via decapping.
More Related Videos
09:26Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
Published on: July 10, 2019
09:04Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
Published on: September 21, 2017
Related Concept Videos
02:27Nonsense-mediated mRNA Decay
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
02:27Nonsense-mediated mRNA Decay
02:31Nuclear Export of mRNA
02:31Nuclear Export of mRNA
02:51mRNA Stability and Gene Expression
Cis-acting Elements involved in mRNA stability
02:51mRNA Stability and Gene Expression