ArticleMethods (San Diego, Calif.)2017
Metabolic labeling and recovery of nascent RNA to accurately quantify mRNA stability.
Article in Methods (San Diego, Calif.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 73 citations in OpenAlex.
- Spatial mapping of RNA turnover kinetics in the mouse brain.Nature neuroscience · 2026Article
- Cap 2'-O-methyltransferase CMTR2 regulates male meiosis independent of its methyltransferase activity.Nucleic acids research · 2026Article
- Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain.bioRxiv : the preprint server for biology · 2026Article
- mRNA turnover dynamics are affected by cell differentiation and loss of the cytosine methyltransferase Nsun2.Nucleic acids research · 2025Article
- Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos.Nucleic acids research · 2025Article
- RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks.Bioinformatics (Oxford, England) · 2025Article
- New reporters for monitoring cellular NMD.RNA (New York, N.Y.) · 2025Article
- RNA Decay Assay: 5-Ethynyl-Uridine Labeling and Chasing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A Method for Rapid Inducible RNA Decay.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics.NAR genomics and bioinformatics · 2024Article
- A rapid inducible RNA decay system reveals fast mRNA decay in P-bodies.Nature communications · 2024Article
- Article
- Coordination of rhythmic RNA synthesis and degradation orchestrates 24- and 12-h RNA expression patterns in mouse fibroblasts.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics.bioRxiv : the preprint server for biology · 2023Article
- Coordination of rhythmic RNA synthesis and degradation orchestrates 24-hour and 12-hour RNA expression patterns in mouse fibroblasts.bioRxiv : the preprint server for biology · 2023Article
- Computational insights into mRNA and protein dynamics underlying synaptic plasticity rules.Molecular and cellular neurosciences · 2023Review
- A selective and sensitive detection system for 4-thiouridine modification in RNA.RNA (New York, N.Y.) · 2023Article
- Global SLAM-seq for accurate mRNA decay determination and identification of NMD targets.RNA (New York, N.Y.) · 2022Article
- Enhancers regulate 3' end processing activity to control expression of alternative 3'UTR isoforms.Nature communications · 2022Article
- Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment.BMC bioinformatics · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Changes in the rate of mRNA decay are closely coordinated with transcriptional changes and together these events have profound effects on gene expression during development and disease. Traditional approaches to assess mRNA decay have relied on inhibition of transcription, which can alter mRNA decay rates and confound interpretation. More recently, metabolic labeling combined with chemical modification and fractionation of labeled RNAs has allowed the isolation of nascent transcripts and the subsequent calculation of mRNA decay rates. This approach has been widely adopted for measuring mRNA half-lives on a global scale, but has proven challenging to use for analysis of single genes. We present a series of normalization and quality assurance steps to be used in combination with 4-thiouridine pulse labeling of cultured eukaryotic cells. Importantly, we demonstrate how the relative amount of 4sU-labeled nascent RNA influences accurate quantification. The approach described facilitates reproducible measurement of individual mRNA half-lives using 4-thiouridine and could be adapted for use with other nucleoside analogs.
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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.