ArticleGenes & development2015
Stably paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor triptolide.
Article in Genes & development, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Acidic transcription factors position the genome at nuclear speckles through transcription-dependent and -independent mechanisms.Molecular cell · 2026Article
- Mechanisms of transcription termination across the coding and noncoding loci of the genome.Nature reviews. Molecular cell biology · 2026Review
- The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate.Annual review of biochemistry · 2026Review
- PAF1C restores transcription after DNA damage independently of promoting histone mark deposition.EMBO reports · 2026Article
- A single cluster of RNA Polymerase II molecules is stably associated with active genes.Nature communications · 2026Article
- Evolution of promoter-proximal pausing enabled a new layer of transcription control.Nature structural & molecular biology · 2026Article
- Defective RNA processing and ELOA-mediated transcriptional elongation in reversible cellular senescence suggest aging by transcription.Molecular cell · 2025Article
- Identification of human RNA Polymerase II interactors at early stages of transcription.bioRxiv : the preprint server for biology · 2025Article
- A single cluster of RNA Polymerase II molecules is stably associated with active genes.bioRxiv : the preprint server for biology · 2025Article
- DSS1 is required for proper Integrator-PP2A function.Nature communications · 2025Article
- Domain acquisition enabled functional expansion of the TFIIS transcription factor family.Cell & bioscience · 2025Review
- Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition.Nature structural & molecular biology · 2025Article
- Pharmacological, computational, and mechanistic insights into triptolide's role in targeting drug-resistant cancers.Naunyn-Schmiedeberg's archives of pharmacology · 2025Review
- CRL3Molecular cell · 2024Article
- Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA polymerase II productive elongation.Cell reports · 2024Article
- Increased transcriptional elongation and RNA stability of GPCR ligand binding genes unveiled via RNA polymerase II degradation.Nucleic acids research · 2024Article
- Enhancers associated with unstable RNAs are rare in plants.Nature plants · 2024Article
- Predicting RNA polymerase II transcriptional elongation pausing and associated histone code.Briefings in bioinformatics · 2024Article
- Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules.Nucleic acids research · 2024Article
- Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity.PLoS genetics · 2024Article
32 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Transcription by RNA polymerase II (Pol II) in metazoans is regulated in several steps, including preinitiation complex (PIC) formation, initiation, Pol II escape, productive elongation, cotranscriptional RNA processing, and termination. Genome-wide studies have demonstrated that the phenomenon of promoter-bound Pol II pausing is widespread, especially for genes involved in developmental and stimulus-responsive pathways. However, a mechanistic understanding of the paused Pol II state at promoters is limited. For example, at a global level, it is unclear to what extent the engaged paused Pol II is stably tethered to the promoter or undergoes rapid cycles of initiation and termination. Here we used the small molecule triptolide (TPL), an XPB/TFIIH inhibitor, to block transcriptional initiation and then measured Pol II occupancy by chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-seq). This inhibition of initiation enabled us to investigate different states of paused Pol II. Specifically, our global analysis revealed that most genes with paused Pol II, as defined by a pausing index, show significant clearance of Pol II during the period of TPL treatment. Our study further identified a group of genes with unexpectedly stably paused Pol II, with unchanged Pol II occupancy even after 1 h of inhibition of initiation. This group of genes constitutes a small portion of all paused genes defined by the conventional criterion of pausing index. These findings could pave the way for evaluating the contribution of different elongation/pausing factors on different states of Pol II pausing in developmental and other stimulus-responsive pathways.
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