ArticleMolecular systems biology2023
SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle.
Article in Molecular systems biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Regulation of mRNA decay and translation during the mammalian cell cycle.RNA (New York, N.Y.) · 2026Review
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- A convenient single-cell assay for the newly synthesized transcriptome reveals FLI1 regulon downregulation during T cell activation.Cell reports methods · 2026Article
- Fundamental errors in RNA velocity arising from the omission of cell growth.bioRxiv : the preprint server for biology · 2025Article
- Review
- Fragile X messenger ribonucleoprotein 1 (FMRP) regulates glycolytic gene expression under chronic hypoxia in HCT116 cells.Scientific reports · 2025Article
- Transcriptome and Temporal Transcriptome Analyses in Single Cells.International journal of molecular sciences · 2024Review
- Development of Non-Invasive miRNA Markers for Assessing the Quality of Human Induced Pluripotent Stem Cell-Derived Retinal Organoids.International journal of molecular sciences · 2024Article
- A dynamical perspective: moving towards mechanism in single-cell transcriptomics.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Single-Cell RNA-Sequencing of RVFV Infection.Methods in molecular biology (Clifton, N.J.) · 2024Article
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12 authors.
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Abstract
RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation. To date, little is known about time‐dependent kinetic rates during dynamic processes. Here, we present SLAM‐Drop‐seq, a method that combines RNA metabolic labeling and alkylation of modified nucleotides in methanol‐fixed cells with droplet‐based sequencing to detect newly synthesized and preexisting mRNAs in single cells. As a first application, we sequenced 7280 HEK293 cells and calculated gene‐specific kinetic rates during the cell cycle using the novel package Eskrate. Of the 377 robust‐cycling genes that we identified, only a minor fraction is regulated solely by either dynamic transcription or degradation (6 and 4%, respectively). By contrast, the vast majority (89%) exhibit dynamically regulated transcription and degradation rates during the cell cycle. Our study thus shows that temporally regulated mRNA degradation is fundamental for the correct expression of a majority of cycling genes. SLAM‐Drop‐seq, combined with Eskrate, is a powerful approach to understanding the underlying mRNA kinetics of single‐cell gene expression dynamics in continuous biological processes.
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