ArticleNucleic acids research2014
Road rules for traffic on DNA-systematic analysis of transcriptional roadblocking in vivo.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 46 citations in OpenAlex.
- Engineering Dual-Input Glucose- and Temperature-Sensitive Lysis Circuits inMicroorganisms · 2025Article
- When push comes to shove - RNA polymerase and DNA-bound protein roadblocks.Biophysical reviews · 2023Review
- The Growth Dependent Design Constraints of Transcription-Factor-Based Metabolite Biosensors.ACS synthetic biology · 2022Article
- Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops.Nucleic acids research · 2022Article
- Highly tunable TetR-dependent target gene expression in the acetic acid bacterium Gluconobacter oxydans.Applied microbiology and biotechnology · 2021Article
- Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.Transcription · 2021Article
- Macromolecular assemblies supporting transcription-translation coupling.Transcription · 2021Review
- The loopometer: a quantitative in vivo assay for DNA-looping proteins.Nucleic acids research · 2021Article
- Programming Escherichia coli to function as a digital display.Molecular systems biology · 2020Article
- Synthetic Biology Enables Programmable Cell-Based Biosensors.Chemphyschem : a European journal of chemical physics and physical chemistry · 2020Review
- Transcription of Bacterial Chromatin.Journal of molecular biology · 2019Review
- RNA polymerase pausing at a protein roadblock can enhance transcriptional interference by promoter occlusion.FEBS letters · 2019Article
- Programmable DNA looping using engineered bivalent dCas9 complexes.Nature communications · 2017Article
- Proteins mediating DNA loops effectively block transcription.Protein science : a publication of the Protein Society · 2017Article
- Directing traffic on DNA-How transcription factors relieve or induce transcriptional interference.Transcription · 2017Article
- Mfd Protein and Transcription-Repair Coupling in Escherichia coli.Photochemistry and photobiology · 2017Review
- Aspects of protein-DNA interactions: a review of quantitative thermodynamic theory for modelling synthetic circuits utilising LacI and CI repressors, IPTG and the reporter gene lacZ.Biophysical reviews · 2016Review
- The role of repressor kinetics in relief of transcriptional interference between convergent promoters.Nucleic acids research · 2016Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic DNA is bound by many proteins that could potentially impede elongation of RNA polymerase (RNAP), but the factors determining the magnitude of transcriptional roadblocking in vivo are poorly understood. Through systematic experiments and modeling, we analyse how roadblocking by the lac repressor (LacI) in Escherichia coli cells is controlled by promoter firing rate, the concentration and affinity of the roadblocker protein, the transcription-coupled repair protein Mfd, and promoter-roadblock spacing. Increased readthrough of the roadblock at higher RNAP fluxes requires active dislodgement of LacI by multiple RNAPs. However, this RNAP cooperation effect occurs only for strong promoters because roadblock-paused RNAP is quickly terminated by Mfd. The results are most consistent with a single RNAP also sometimes dislodging LacI, though we cannot exclude the possibility that a single RNAP reads through by waiting for spontaneous LacI dissociation. Reducing the occupancy of the roadblock site by increasing the LacI off-rate (weakening the operator) increased dislodgement strongly, giving a stronger effect on readthrough than decreasing the LacI on-rate (decreasing LacI concentration). Thus, protein binding kinetics can be tuned to maintain site occupation while reducing detrimental roadblocking.
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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.