ArticleRNA biology2012
Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability.
Article in RNA biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 papers, 1 of them a synthesis that pooled it.
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Who cites it
111 citing papers in PubMed, 1 synthesis or guideline pooled it, 181 citations in OpenAlex.
- New insights into the pharmacogenomics of antidepressant response from the GENDEP and STAR*D studies: rare variant analysis and high-density imputation.The pharmacogenomics journal · 2018Pooled it
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- Half-Life as a Therapeutic Design Axis: Targeting Short-Lived lncRNAs With Antisense Oligonucleotides.IUBMB life · 2026Review
- Nonsense-mediated mRNA decay factors target short poly(A)-tailed mRNAs lacking a premature termination codon.Nature communications · 2026Article
- Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals.Genome biology · 2025Article
- Metabolic labeling of RNA using ribonucleoside analogs enables the evaluation of RNA synthesis and degradation rates.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2025Review
- SNORD80-guided 2'-O-methylation stabilizes the lncRNA GAS5 to regulate cellular stress responses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Nonsense-Mediated mRNA Decay: Mechanistic Insights and Physiological Significance.Molecular biotechnology · 2024Review
- A Comparative Overview of the Role of Human Ribonucleases in Nonsense-Mediated mRNA Decay.Genes · 2024Article
- Global impact of unproductive splicing on human gene expression.Nature genetics · 2024Article
- RNA Surveillance Factor SMG5 Is Essential for Mouse Embryonic Stem Cell Differentiation.Biomolecules · 2024Article
- Global impact of aberrant splicing on human gene expression levels.bioRxiv : the preprint server for biology · 2023Article
- Inhibition of nonsense-mediated mRNA decay reduces the tumorigenicity of human fibrosarcoma cells.NAR cancer · 2023Article
- Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression.RNA (New York, N.Y.) · 2023Article
- Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues.Genome biology · 2023Article
- Participation of ATM, SMG1, and DDX5 in a DNA Damage-Induced Alternative Splicing Pathway.Radiation research · 2023Article
- Review
- Vitamin D inhibits osteosarcoma by reprogramming nonsense-mediated RNA decay and SNAI2-mediated epithelial-to-mesenchymal transition.Frontiers in oncology · 2023Article
- Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2.Cancer research · 2022Article
- Progression of the pluripotent epiblast depends upon the NMD factor UPF2.Development (Cambridge, England) · 2022Article
51 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
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
UPF1 eliminates aberrant mRNAs harboring premature termination codons, and regulates the steady-state levels of normal physiological mRNAs. Although genome-wide studies of UPF1 targets performed, previous studies did not distinguish indirect UPF1 targets because they could not determine UPF1-dependent altered RNA stabilities. Here, we measured the decay rates of the whole transcriptome in UPF1-depleted HeLa cells using BRIC-seq, an inhibitor-free method for directly measuring RNA stability. We determined the half-lives and expression levels of 9,229 transcripts. An amount of 785 transcripts were stabilized in UPF1-depleted cells. Among these, the expression levels of 76 transcripts were increased, but those of the other 709 transcripts were not altered. RNA immunoprecipitation showed UPF1 bound to the stabilized transcripts, suggesting that UPF1 directly degrades the 709 transcripts. Many UPF1 targets in this study were newly identified. This study clearly demonstrates that direct determination of RNA stability is a powerful approach for identifying targets of RNA degradation factors.
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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.