Evidence map›Paper›PMID 27026687›Full record

ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2016

Dissecting the stochastic transcription initiation process in live Escherichia coli.

Jason Lloyd-Price, Sofia Startceva, Vinodh Kandavalli, Jerome G Chandraseelan, Nadia Goncalves, Samuel M D Oliveira, Antti Häkkinen, Andre S Ribeiro

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
3.1field-weighted citation impact, top 8% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed, 38 citations in OpenAlex.

  1. Thermal Shifts Dominate Single-Gene Responses to Transcription-Targeting Antibiotics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
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  11. Chromosome and plasmid-borne PScientific reports · 2019
    Article
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  13. Article
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  15. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 1 institution in 1 country.

Jason Lloyd-PriceLaboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland.
Sofia StartcevaLaboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland.
Vinodh KandavalliLaboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland.
Jerome G ChandraseelanLaboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland.
Nadia GoncalvesLaboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland.
Samuel M D OliveiraLaboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland.
Antti HäkkinenLaboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland.
Andre S RibeiroLaboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland andre.ribeiro@tut.fi.
Tampere University · FI

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We investigate the hypothesis that, in Escherichia coli, while the concentration of RNA polymerases differs in different growth conditions, the fraction of RNA polymerases free for transcription remains approximately constant within a certain range of these conditions. After establishing this, we apply a standard model-fitting procedure to fully characterize the in vivo kinetics of the rate-limiting steps in transcription initiation of the Plac/ara-1 promoter from distributions of intervals between transcription events in cells with different RNA polymerase concentrations. We find that, under full induction, the closed complex lasts ∼788 s while subsequent steps last ∼193 s, on average. We then establish that the closed complex formation usually occurs multiple times prior to each successful initiation event. Furthermore, the promoter intermittently switches to an inactive state that, on average, lasts ∼87 s. This is shown to arise from the intermittent repression of the promoter by LacI. The methods employed here should be of use to resolve the rate-limiting steps governing the in vivo dynamics of initiation of prokaryotic promoters, similar to established steady-state assays to resolve the in vitro dynamics.

Indexed as

Models, GeneticTranscription Initiation, GeneticDNA-Directed RNA PolymerasesEscherichia coliEscherichia coli ProteinsLac RepressorsPromoter Regions, GeneticProtein BindingStochastic ProcessesDNA-Directed RNA PolymerasesEscherichia coli ProteinsLacI protein, E coliLac Repressorsfree RNA polymerasein vivo transcription dynamicsrate-limiting stepsrepressor binding dynamicsreversible closed complex formation

Identifiers

PMID27026687
PMCPMC4909308
OpenAlexW2323834851

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

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.