ArticleScience (New York, N.Y.)2013
Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.
Article in Science (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 543 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
543 citing papers in PubMed.
- Profiling Nascent RNA Transcription with TT-Seq.Methods in molecular biology (Clifton, N.J.) · 2027Article
- A Bioinformatic Framework for Enhancer RNAs Identification in Cancer Based on RNA-Seq and ChIP-Seq.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Lentiviral RNAi for Depletion of Enhancer RNAs in Primary Neurons.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Using BruUV-Seq to Identify Enhancer RNA Expression in Live Cells.Methods in molecular biology (Clifton, N.J.) · 2027Article
- The Mediator complex: co-transcriptional regulation and beyond.RNA biology · 2026Review
- Dysregulated AKT signaling reprograms osteosarcoma to drive selective reliance on EP300.The Journal of experimental medicine · 2026Article
- Genome-wide mapping of theiScience · 2026Article
- Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context.Cell · 2026Article
- Discrepancies between ChIP-seq and CUT&Tag histone mark profiles are explained by GC content and chromatin accessibility.bioRxiv : the preprint server for biology · 2026Article
- Directionality of transcriptional regulatory elements.Nature communications · 2026Article
- The dark genome in cardiovascular medicine.European heart journal · 2026Review
- Analysis of host and viral nascent and steady-state RNA levels in a human neuronal model of herpes simplex virus 1 infection.PLoS pathogens · 2026Article
- Genomic language model for predicting enhancers and their allele-specific activity in the human genome.Bioinformatics (Oxford, England) · 2026Article
- Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits.Animals : an open access journal from MDPI · 2026Review
- Accurate de novo transcription unit annotation from run-on and sequencing data.PLoS computational biology · 2026Article
- CDK8 Inhibition Releases the Muscle Differentiation Block in Fusion-driven Alveolar Rhabdomyosarcoma.Cancer discovery · 2026Article
- High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples.Nature biotechnology · 2026Article
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Article
- Transcriptomics Insights into Spinal Cord Injury for Therapy Development.International journal of molecular sciences · 2026Review
483 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Transcription regulation occurs frequently through promoter-associated pausing of RNA polymerase II (Pol II). We developed a precision nuclear run-on and sequencing (PRO-seq) assay to map the genome-wide distribution of transcriptionally engaged Pol II at base pair resolution. Pol II accumulates immediately downstream of promoters, at intron-exon junctions that are efficiently used for splicing, and over 3' polyadenylation sites. Focused analyses of promoters reveal that pausing is not fixed relative to initiation sites, nor is it specified directly by the position of a particular core promoter element or the first nucleosome. Core promoter elements function beyond initiation, and when optimally positioned they act collectively to dictate the position and strength of pausing. This "complex interaction" model was tested with insertional mutagenesis of the Drosophila Hsp70 core promoter.
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What OpenQuestion holds
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.