SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle.
Mol Syst Biol
; 19(10): 1-23, 2023 10.
Article
in En
| MEDLINE
| ID: mdl-38778223
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 timedependent kinetic rates during dynamic processes. Here, we present SLAMDropseq, a method that combines RNA metabolic labeling and alkylation of modified nucleotides in methanolfixed cells with dropletbased sequencing to detect newly synthesized and preexisting mRNAs in single cells. As a first application, we sequenced 7280 HEK293 cells and calculated genespecific kinetic rates during the cell cycle using the novel package Eskrate. Of the 377 robustcycling 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. SLAMDropseq, combined with Eskrate, is a powerful approach to understanding the underlying mRNA kinetics of singlecell gene expression dynamics in continuous biological processes.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
RNA, Messenger
/
Cell Cycle
Limits:
Humans
Language:
En
Journal:
Mol Syst Biol
Journal subject:
BIOLOGIA MOLECULAR
/
BIOTECNOLOGIA
Year:
2023
Document type:
Article
Affiliation country:
Alemania
Country of publication:
Alemania