ArticleNucleic acids research2021
Conserved DNA sequence features underlie pervasive RNA polymerase pausing.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 46 citations in OpenAlex.
- Structural basis for P-TEFb association with BRD4.bioRxiv : the preprint server for biology · 2026Article
- Mfd interacts with RNA polymerase to modulate flagellum-dependent motility, chemotaxis, and population heterogeneity in the stationary phase ofJournal of bacteriology · 2026Article
- The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate.Annual review of biochemistry · 2026Review
- RNAP-seq:bioRxiv : the preprint server for biology · 2026Article
- Cell-free genomics reveals fundamental regulatory principles of the Mycobacterium tuberculosis transcription cycle.Molecular cell · 2026Article
- Massively parallel assay of human splice variants reveals cis-regulatory drivers of disease-associated and cell type-specific splicing regulation.bioRxiv : the preprint server for biology · 2025Article
- A transcription coupling model for how enhancers communicate with their target genes.Nature structural & molecular biology · 2025Review
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.Nucleic acids research · 2025Article
- NusG-Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression.Journal of molecular biology · 2025Review
- Bacteroides expand the functional versatility of a conserved transcription factor and transcribed DNA to program capsule diversity.Nature communications · 2024Article
- A Compendium of G-Flipon Biological Functions That Have Experimental Validation.International journal of molecular sciences · 2024Review
- Predicting RNA polymerase II transcriptional elongation pausing and associated histone code.Briefings in bioinformatics · 2024Article
- RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations.Nucleic acids research · 2024Article
- Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing.Molecular cell · 2024Article
- DNA-sequence and epigenomic determinants of local rates of transcription elongation.bioRxiv : the preprint server for biology · 2023Article
- High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription.Nature communications · 2023Article
- Structural and functional basis of the universal transcription factor NusG pro-pausing activity in Mycobacterium tuberculosis.Molecular cell · 2023Article
- Butt-seq: a new method for facile profiling of transcription.Genes & development · 2023Article
- Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures.Nucleic acids research · 2023Article
- An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pausing of transcribing RNA polymerase is regulated and creates opportunities to control gene expression. Research in metazoans has so far mainly focused on RNA polymerase II (Pol II) promoter-proximal pausing leaving the pervasive nature of pausing and its regulatory potential in mammalian cells unclear. Here, we developed a pause detecting algorithm (PDA) for nucleotide-resolution occupancy data and a new native elongating transcript sequencing approach, termed nested NET-seq, that strongly reduces artifactual peaks commonly misinterpreted as pausing sites. Leveraging PDA and nested NET-seq reveal widespread genome-wide Pol II pausing at single-nucleotide resolution in human cells. Notably, the majority of Pol II pauses occur outside of promoter-proximal gene regions primarily along the gene-body of transcribed genes. Sequence analysis combined with machine learning modeling reveals DNA sequence properties underlying widespread transcriptional pausing including a new pause motif. Interestingly, key sequence determinants of RNA polymerase pausing are conserved between human cells and bacteria. These studies indicate pervasive sequence-induced transcriptional pausing in human cells and the knowledge of exact pause locations implies potential functional roles in gene expression.
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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.