ArticleGenome research2013
Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 188 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
188 citing papers in PubMed, 303 citations in OpenAlex.
- A systems perspective on monoallelic inborn errors of immunity.Nature genetics · 2026Review
- Beyond quality control: biological roles of nonsense-mediated RNA decay.The EMBO journal · 2026Review
- predNMD: prediction of nonsense-mediated mRNA decay for improved clinical variant pathogenicity classification.bioRxiv : the preprint server for biology · 2026Article
- Nonsense-mediated mRNA decay factors target short poly(A)-tailed mRNAs lacking a premature termination codon.Nature communications · 2026Article
- Article
- Synergistic Methods to Investigate Eukaryotic Translation and Its Quality Control.Journal of molecular biology · 2025Review
- Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals.Genome biology · 2025Article
- Nonsense-Mediated mRNA Decay in Human Health and Diseases: Current Understanding, Regulatory Mechanisms and Future Perspectives.Molecular biotechnology · 2025Review
- Coordinated expression of retained introns and poison exons in renal cell carcinoma.Cell reports · 2025Article
- Review
- Cytoplasmic mRNA decay and quality control machineries in eukaryotes.Nature reviews. Genetics · 2025Review
- Mechanisms suppressing noncoding translation.Trends in cell biology · 2025Review
- Cell type- and factor-specific nonsense-mediated RNA decay.Nucleic acids research · 2025Article
- Sex-Biased Gene Expression of RNAi Pathway Components in the Sea Lice Caligus rogercresseyi.Marine biotechnology (New York, N.Y.) · 2025Article
- Retroviral adapters hijack the RNA helicase UPF1 in a CRM1/XPO1-dependent manner and reveal proviral roles of UPF1.Nucleic acids research · 2025Article
- Article
- The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus.Nature reviews. Genetics · 2025Review
- RNA anchoring of Upf1 facilitates recruitment of Dcp2 in the NMD decapping complex.Nucleic acids research · 2025Article
- Sequence-dependent and -independent effects of intron-mediated enhancement learned from thousands of random introns.Nucleic acids research · 2025Article
- Messenger RNA Surveillance: Current Understanding, Regulatory Mechanisms, and Future Implications.Molecular biotechnology · 2025Review
128 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
UPF1 is a DNA/RNA helicase with essential roles in nonsense-mediated mRNA decay (NMD) and embryonic development. How UPF1 regulates target abundance and the relationship between NMD and embryogenesis are not well understood. To explore how NMD shapes the embryonic transcriptome, we integrated genome-wide analyses of UPF1 binding locations, NMD-regulated gene expression, and translation in murine embryonic stem cells (mESCs). We identified over 200 direct UPF1 binding targets using crosslinking/immunoprecipitation-sequencing (CLIP-seq) and revealed a repression pathway that involves 3' UTR binding by UPF1 and translation but is independent of canonical targeting features involving 3' UTR length and stop codon placement. Interestingly, NMD targeting of this set of mRNAs occurs in other mouse tissues and is conserved in human. We also show, using ribosome footprint profiling, that actively translated upstream open reading frames (uORFs) are enriched in transcription factor mRNAs and predict mRNA repression by NMD, while poorly translated mRNAs escape repression. Together, our results identify novel NMD determinants and targets and provide context for understanding the impact of UPF1 and NMD on the mESC transcriptome.
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What OpenQuestion holds
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.