SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle
Autor/innen
- H. Liu
- R. Arsiè
- D. Schwabe
- M. Schilling
- I. Minia
- J. Alles
- A. Boltengagen
- C. Kocks
- M. Falcke
- N. Friedman
- M. Landthaler
- N. Rajewsky
Journal
- Molecular Systems Biology
Quellenangabe
- Mol Syst Biol 19 (10): e11427
Zusammenfassung
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.