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


  • H. Liu
  • R. Arsiè
  • D. Schwabe
  • M. Schilling
  • I. Minia
  • J. Alles
  • A. Boltengagen
  • C. Kocks
  • M. Falcke
  • N. Friedman
  • M. Landthaler
  • N. Rajewsky


  • Molecular Systems Biology


  • Mol Syst Biol 19 (10): e11427


  • 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.