ArticleRNA (New York, N.Y.)2022
Global SLAM-seq for accurate mRNA decay determination and identification of NMD targets.
Article in RNA (New York, N.Y.), 2022. 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, 25 citations in OpenAlex.
- The proportional scaling of mRNA and ribosome concentrations controls eukaryotic cell growth.Nature cell biology · 2026Article
- Nonsense-mediated mRNA decay factors target short poly(A)-tailed mRNAs lacking a premature termination codon.Nature communications · 2026Article
- P-bodies act as dynamic control hubs for RNA processing and storage.The Journal of biological chemistry · 2026Article
- Comprehensive profiling of chromatin occupancy dynamics through the cell cycle.Nucleic acids research · 2026Article
- Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex.Molecular cell · 2025Article
- New reporters for monitoring cellular NMD.RNA (New York, N.Y.) · 2025Article
- RNA degradation triggered by decapping is largely independent of initial deadenylation.The EMBO journal · 2024Article
- Transcriptome dynamics in mouse amygdala under acute and chronic stress revealed by thiol-labeled RNA sequencing.Neurobiology of stress · 2024Article
- Multiple direct and indirect roles of the Paf1 complex in transcription elongation, splicing, and histone modifications.Cell reports · 2024Article
- Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex.bioRxiv : the preprint server for biology · 2024Article
- Translation-coupled mRNA quality control mechanisms.The EMBO journal · 2023Review
- Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability.Science advances · 2023Article
- Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purification.Nucleic acids research · 2023Article
- Spatiotemporal Control of microRNA-Target Interactions.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression analysis requires accurate measurements of global RNA degradation rates, earlier problematic with methods disruptive to cell physiology. Recently, metabolic RNA labeling emerged as an efficient and minimally invasive technique applied in mammalian cells. Here, we have adapted SH-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) for a global mRNA stability study in yeast using 4-thiouracil pulse-chase labeling. We assign high-confidence half-life estimates for 67.5% of expressed ORFs, and measure a median half-life of 9.4 min. For mRNAs where half-life estimates exist in the literature, their ranking order was in good agreement with previous data, indicating that SLAM-seq efficiently classifies stable and unstable transcripts. We then leveraged our yeast protocol to identify targets of the nonsense-mediated decay (NMD) pathway by measuring the change in RNA half-lives, instead of steady-state RNA level changes. With SLAM-seq, we assign 580 transcripts as putative NMD targets, based on their measured half-lives in wild-type and
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