ArticleMolecular cell2021
STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts.
Article in Molecular cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 41 citations in OpenAlex.
- Review
- Transcriptional activity during seed imbibition is conserved, robust and required for germination.Nature communications · 2026Article
- Mechanisms of transcription termination across the coding and noncoding loci of the genome.Nature reviews. Molecular cell biology · 2026Review
- Regulation of RNA transcript elongation in metazoans and its relevance to disease.Nature reviews. Molecular cell biology · 2026Review
- Single-molecule imaging reveals RNA polymerase II dynamics and TAF1-dependent promoter-proximal pause release.Nature communications · 2026Article
- Transcriptional Bursting in Pluripotent Stem Cells.Biology · 2026Review
- The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate.Annual review of biochemistry · 2026Review
- Article
- Histone acetylation-dependent clustering of BRD2 instructs transcription dynamics.Nature genetics · 2026Article
- Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate.Nucleic acids research · 2026Article
- Molecular Mechanisms of Sepsis-Associated Acute Kidney Injury.Journal of the American Society of Nephrology : JASN · 2025Review
- Fast TV-PRO-seq: Accelerated and Streamlined Protocol for Timing RNA Polymerase Pausing.Bio-protocol · 2025Article
- Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite.PLoS computational biology · 2025Article
- Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition.Nature structural & molecular biology · 2025Article
- Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II.Molecular systems biology · 2025Article
- Metabolic labeling of RNA using ribonucleoside analogs enables the evaluation of RNA synthesis and degradation rates.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2025Review
- ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes.Nucleic acids research · 2025Article
- DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts.Nature communications · 2025Article
- Multiple Forms and Functions of Premature Termination by RNA Polymerase II.Journal of molecular biology · 2025Review
- Fateful Decisions of Where to Cut the Line: Pathology Associated with Aberrant 3' End Processing and Transcription Termination.Journal of molecular biology · 2025Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Despite the critical regulatory function of promoter-proximal pausing, the influence of pausing kinetics on transcriptional control remains an active area of investigation. Here, we present Start-TimeLapse-seq (STL-seq), a method that captures the genome-wide kinetics of short, capped RNA turnover and reveals principles of regulation at the pause site. By measuring the rates of release into elongation and premature termination through the inhibition of pause release, we determine that pause-release rates are highly variable, and most promoter-proximal paused RNA polymerase II molecules prematurely terminate (∼80%). The preferred regulatory mechanism upon a hormonal stimulus (20-hydroxyecdysone) is to influence pause-release rather than termination rates. Transcriptional shutdown occurs concurrently with the induction of promoter-proximal termination under hyperosmotic stress, but paused transcripts from TATA box-containing promoters remain stable, demonstrating an important role for cis-acting DNA elements in pausing. STL-seq dissects the kinetics of pause release and termination, providing an opportunity to identify mechanisms of transcriptional regulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.