ArticleProceedings of the National Academy of Sciences of the United States of America2013
RNA polymerase approaches its promoter without long-range sliding along DNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed, 68 citations in OpenAlex.
- A mechanism of synergistic Mediator recruitment in RNA polymerase II transcription activation revealed by single-molecule fluorescence.Molecular cell · 2025Article
- Recent advances in mycobacterial transcription: insights beyond the general pathway.Journal of bacteriology · 2025Review
- Single-molecule analysis of transcription activation: dynamics of SAGA coactivator recruitment.Nature structural & molecular biology · 2025Article
- Single-molecule visualization of sequence-specific RNA binding by a designer PPR protein.Nucleic acids research · 2024Article
- The structural mechanism for transcription activation by Caulobacter crescentus GcrA.Nucleic acids research · 2023Article
- Impact ofInternational journal of molecular sciences · 2022Review
- Molecular Origins of Transcriptional Heterogeneity in Diazotrophic Klebsiella oxytoca.mSystems · 2022Article
- Bayesian machine learning analysis of single-molecule fluorescence colocalization images.eLife · 2022Article
- Analytical kinetic model of native tandem promoters in E. coli.PLoS computational biology · 2022Article
- Anticipating response function in gene regulatory networks.Journal of the Royal Society, Interface · 2021Article
- Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription.International journal of molecular sciences · 2021Article
- Transcription activation by a sliding clamp.Nature communications · 2021Article
- Alternative transcription cycle for bacterial RNA polymerase.Nature communications · 2020Article
- Transcription of Bacterial Chromatin.Journal of molecular biology · 2019Review
- Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli.Nucleic acids research · 2019Article
- Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription.eLife · 2019Article
- Gene transcription in bursting: a unified mode for realizing accuracy and stochasticity.Biological reviews of the Cambridge Philosophical Society · 2019Article
- Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World.Chemical reviews · 2018Review
- Processive searching ability varies among members of the gap-filling DNA polymerase X family.The Journal of biological chemistry · 2017Article
- Studying transcription initiation by RNA polymerase with diffusion-based single-molecule fluorescence.Protein science : a publication of the Protein Society · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Sequence-specific DNA binding proteins must quickly bind target sequences, despite the enormously larger amount of nontarget DNA present in cells. RNA polymerases (or associated general transcription factors) are hypothesized to reach promoter sequences by facilitated diffusion (FD). In FD, a protein first binds to nontarget DNA and then reaches the target by a 1D sliding search. We tested whether Escherichia coli σ(54)RNA polymerase reaches a promoter by FD using the colocalization single-molecule spectroscopy (CoSMoS) multiwavelength fluorescence microscopy technique. Experiments directly compared the rates of initial polymerase binding to and dissociation from promoter and nonpromoter DNAs measured in the same sample under identical conditions. Binding to a nonpromoter DNA was much slower than binding to a promoter-containing DNA of the same length, indicating that the detected nonspecific binding events are not on the pathway to promoter binding. Truncating one of the DNA segments flanking the promoter to a length as short as 7 bp or lengthening it to ~3,000 bp did not alter the promoter-specific binding rate. These results exclude FD over distances corresponding to the length of the promoter or longer from playing any significant role in accelerating promoter search. Instead, the data support a direct binding mechanism, in which σ(54)RNA polymerase reaches the local vicinity of promoters by 3D diffusion through solution, and suggest that binding may be accelerated by atypical structural or dynamic features of promoter DNA. Direct binding explains how polymerase can quickly reach a promoter, despite occupancy of promoter-flanking DNA by bound proteins that would impede FD.
Indexed as
Identifiers
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.