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

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. Researchers at the Max Delbrück Center for Molecular Medicine have developed 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, the researchers 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 they 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. This 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.

A novel approach (SLAM-Drop-seq) is coupled to a robust computational analysis method (Eskrate) to discriminate new and preexisting transcripts in single cells and to calculate their time-dependent kinetic rates of synthesis and decay during the cell cycle.