ArticleRNA (New York, N.Y.)2020
Metabolic labeling of RNA uncovers the contribution of transcription and decay rates on hypoxia-induced changes in RNA levels.
Article in RNA (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 22 citations in OpenAlex.
- The lariat RNA debranching enzyme DBR1 enhances HIF-1 signaling and chemoresistance at the expense of lariat RNA processing.The Journal of biological chemistry · 2026Article
- mRNA turnover dynamics are affected by cell differentiation and loss of the cytosine methyltransferase Nsun2.Nucleic acids research · 2025Article
- The impact of hypoxia on the cellular phenotype and proteome of KGN cells.Reproduction & fertility · 2025Article
- Inherent single-cell heterogeneity of the transcriptional response to hypoxia in cancer cells.NAR cancer · 2025Article
- Decay drives RNA abundance regulation using three distinct regulatory mechanisms.bioRxiv : the preprint server for biology · 2025Article
- The Dopaminergic Cells in the Median Raphe Region Regulate Social Behavior in Male Mice.International journal of molecular sciences · 2024Article
- Hypoxia-driven deSUMOylation of EXOSC10 promotes adaptive changes in the transcriptome profile.Cellular and molecular life sciences : CMLS · 2024Article
- Transcript accumulation rates in the earlyScience advances · 2023Article
- Formal Meta-Analysis of Hypoxic Gene Expression Profiles Reveals a Universal Gene Signature.Biomedicines · 2022Article
- Regulation of both transcription and RNA turnover contribute to germline specification.Nucleic acids research · 2022Article
- Functional RNA Dynamics Are Progressively Governed by RNA Destabilization during the Adaptation to Chronic Hypoxia.International journal of molecular sciences · 2022Review
- PABP prevents the untimely decay of select mRNA populations in human cells.The EMBO journal · 2022Article
- Systems approaches to understand oxygen sensing: how multi-omics has driven advances in understanding oxygen-based signalling.The Biochemical journal · 2022Review
- Hypoxia re-programs 2'-O-Me modifications on ribosomal RNA.iScience · 2021Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cells adapt to environmental changes, including fluctuations in oxygen levels, through the induction of specific gene expression programs. However, most transcriptomic studies do not distinguish the relative contribution of transcription, RNA processing, and RNA degradation processes to cellular homeostasis. Here we used metabolic labeling followed by massive parallel sequencing of newly transcribed and preexisting RNA fractions to simultaneously analyze RNA synthesis and decay in primary endothelial cells exposed to low oxygen tension. We found that changes in transcription rates induced by hypoxia are the major determinant of changes in RNA levels. However, degradation rates also had a significant contribution, accounting for 24% of the observed variability in total mRNA. In addition, our results indicated that hypoxia led to a reduction of the overall mRNA stability from a median half-life in normoxia of 8.7 h, to 5.7 h in hypoxia. Analysis of RNA content per cell confirmed a decrease of both mRNA and total RNA in hypoxic samples and that this effect is dependent on the EGLN/HIF/TSC2 axis. This effect could potentially contribute to fundamental global responses such as inhibition of translation in hypoxia. In summary, our study provides a quantitative analysis of the contribution of RNA synthesis and stability to the transcriptional response to hypoxia and uncovers an unexpected effect on the latter.
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