SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle

Haiyue Liu, Roberto Arsiè, Daniel Schwabe, Marcel Schilling, Igor Minia, Jonathan Alles, Anastasiya Boltengagen, Christine Kocks, Martin Falcke, Nir Friedman, Markus Landthaler*, Nikolaus Rajewsky*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


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.

Original languageAmerican English
Article numbere11427
JournalMolecular Systems Biology
Issue number10
StatePublished - 12 Oct 2023

Bibliographical note

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© 2023 The Authors. Published under the terms of the CC BY 4.0 license.


  • cell cycle
  • mRNA kinetics
  • single cells
  • temporal regulation
  • transcription and degradation


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