ArticleNucleic acids research2018
Directed hydroxyl radical probing reveals Upf1 binding to the 80S ribosomal E site rRNA at the L1 stalk.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
15 citing papers in PubMed, 20 citations in OpenAlex.
- Synergistic Methods to Investigate Eukaryotic Translation and Its Quality Control.Journal of molecular biology · 2025Review
- Translation stalling in neurons: a critical mechanism for timely protein delivery to distal cellular processes.Biochemical Society transactions · 2025Article
- Cytoplasmic mRNA decay and quality control machineries in eukaryotes.Nature reviews. Genetics · 2025Review
- RNA anchoring of Upf1 facilitates recruitment of Dcp2 in the NMD decapping complex.Nucleic acids research · 2025Article
- Nonsense-mediated mRNA decay pathway in plants under stress: general gene regulatory mechanism and advances.Planta · 2024Review
- UPF1-From mRNA Degradation to Human Disorders.Cells · 2023Review
- Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance.RNA (New York, N.Y.) · 2022Article
- Features and factors that dictate if terminating ribosomes cause or counteract nonsense-mediated mRNA decay.The Journal of biological chemistry · 2022Review
- A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production.Nature communications · 2022Article
- Inhibition of post-termination ribosome recycling at premature termination codons in UPF1 ATPase mutants.eLife · 2020Article
- UPF1-Mediated RNA Decay-Danse Macabre in a Cloud.Biomolecules · 2020Review
- Nonsense-mediated mRNA decay: The challenge of telling right from wrong in a complex transcriptome.Wiley interdisciplinary reviews. RNA · 2019Review
- Quality and quantity control of gene expression by nonsense-mediated mRNA decay.Nature reviews. Molecular cell biology · 2019Review
- Assaying RNA structure with LASER-Seq.Nucleic acids research · 2019Article
- New insights into the interplay between the translation machinery and nonsense-mediated mRNA decay factors.Biochemical Society transactions · 2018Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Upf1 is an SF1-family RNA helicase that is essential for the nonsense-mediated decay (NMD) process in eukaryotes. While Upf1 has been shown to interact with 80S ribosomes, the molecular details of this interaction were unknown. Using purified recombinant proteins and high-throughput sequencing combined with Fe-BABE directed hydroxyl radical probing (HTS-BABE) we have characterized the interaction between Upf1 and the yeast 80S ribosome. We identify the 1C domain of Upf1, an alpha-helical insertion in the RecA helicase core, to be essential for ribosome binding, and determine that the L1 stalk of 25S rRNA is the binding site for Upf1 on the ribosome. Using the cleavage sites identified by hydroxyl radical probing and high-resolution structures of both yeast Upf1 and the human 80S ribosome, we provide a model of a Upf1:80S structure. Our model requires that the L1 stalk adopt an open configuration as adopted by an un-rotated, or classical-state, ribosome. Our results shed light on the interaction between Upf1 and the ribosome, and suggest that Upf1 may specifically engage a classical-state ribosome during translation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.