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STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts
Joshua T Zimmer1, Nicolle A Rosa-Mercado2, Daniele Canzio3
1Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA.
New Start-TimeLapse-seq (STL-seq) reveals most paused RNA polymerase II terminates prematurely. Hormonal stimuli regulate pause release, not termination, highlighting transcription control mechanisms.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Promoter-proximal pausing is crucial for transcriptional regulation.
- Understanding pausing kinetics is key to deciphering gene expression control.
Purpose of the Study:
- To introduce Start-TimeLapse-seq (STL-seq) for measuring genome-wide RNA turnover kinetics at pause sites.
- To investigate the regulation of transcription initiation and termination.
Main Methods:
- Developed Start-TimeLapse-seq (STL-seq) to capture short, capped RNA turnover kinetics.
- Measured pause release and premature termination rates by inhibiting pause release.
- Analyzed transcriptional responses to hormonal stimulus (20-hydroxyecdysone) and hyperosmotic stress.
Main Results:
- Most promoter-proximal paused RNA polymerase II molecules prematurely terminate (~80%).
- Pause release rates are highly variable across the genome.
- Hormonal stimuli primarily affect pause release rates, not termination rates.
- Hyperosmotic stress induces promoter-proximal termination, while TATA box-containing promoters show stable paused transcripts.
Conclusions:
- STL-seq provides a novel method to dissect transcription pause release and termination kinetics.
- Transcriptional regulation involves differential control of pause release versus termination.
- Cis-acting DNA elements, like TATA boxes, play a significant role in pausing stability.
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