ArticleGenome biology2015
Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed, 98 citations in OpenAlex.
- ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition.bioRxiv : the preprint server for biology · 2026Article
- RNAP-seq:bioRxiv : the preprint server for biology · 2026Article
- Heterogeneous template-dependent transcription dynamics of T7 RNAP revealed by single-molecule imaging.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Structure of the 30S translation initiation complex coupled to paused RNA polymerase and its potential for riboregulation.Nature communications · 2025Article
- Nascent RNA profiling reveals genome-wide productive reiterative initiation regulating gene transcription in bacteria.Nucleic acids research · 2025Article
- Applying the brakes to transcription: regulation of gene expression by RNA polymerase pausing.Journal of bacteriology · 2025Review
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.Nucleic acids research · 2025Article
- Differential impact of divalent metals on native elongating transcript sequencing (NET-seq) protocols for RNA polymerases I and II.PloS one · 2025Article
- Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations.Nucleic acids research · 2024Article
- Precision run-on sequencing (PRO-seq) for microbiome transcriptomics.Nature microbiology · 2024Article
- DNA-sequence and epigenomic determinants of local rates of transcription elongation.bioRxiv : the preprint server for biology · 2023Article
- Robust regulation of transcription pausing inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- 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
- Structural and mechanistic basis of σ-dependent transcriptional pausing.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome.Nucleic acids research · 2022Article
- Transcriptome-Wide Effects of NusA on RNA Polymerase Pausing in Bacillus subtilis.Journal of bacteriology · 2022Article
- Site-specific photolabile roadblocks for the study of transcription elongation in biologically complex systems.Communications biology · 2022Article
- Investigating the role of RNA structures in transcriptional pausing using in vitro assays and in silico analyses.RNA biology · 2022Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundTranscription elongation is frequently interrupted by pausing signals in DNA, with downstream effects on gene expression. Transcription errors also induce prolonged pausing, which can lead to a destabilized genome by interfering with DNA replication. Mechanisms of pausing associated with translocation blocks and misincorporation have been characterized in vitro, but not in vivo.
resultsWe investigate the pausing pattern of RNA polymerase (RNAP) in Escherichia coli by a novel approach, combining native elongating transcript sequencing (NET-seq) with RNase footprinting of the transcripts (RNET-seq). We reveal that the G-dC base pair at the 5' end of the RNA-DNA hybrid interferes with RNAP translocation. The distance between the 5' G-dC base pair and the 3' end of RNA fluctuates over a three-nucleotide width. Thus, the G-dC base pair can induce pausing in post-translocated, pre-translocated, and backtracked states of RNAP. Additionally, a CpG sequence of the template DNA strand spanning the active site of RNAP inhibits elongation and induces G-to-A errors, which leads to backtracking of RNAP. Gre factors efficiently proofread the errors and rescue the backtracked complexes. We also find that pausing events are enriched in the 5' untranslated region and antisense transcription of mRNA genes and are reduced in rRNA genes.
conclusionsIn E. coli, robust transcriptional pausing involves RNAP interaction with G-dC at the upstream end of the RNA-DNA hybrid, which interferes with translocation. CpG DNA sequences induce transcriptional pausing and G-to-A errors.
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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.