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A biophysical model of supercoiling dependent transcription predicts a structural aspect to gene regulation

Overview of attention for article published in BMC Biophysics, February 2016
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (83rd percentile)

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Title
A biophysical model of supercoiling dependent transcription predicts a structural aspect to gene regulation
Published in
BMC Biophysics, February 2016
DOI 10.1186/s13628-016-0027-0
Pubmed ID
Authors

Christopher H. Bohrer, Elijah Roberts

Abstract

Transcription in Escherichia coli generates positive supercoiling in the DNA, which is relieved by the enzymatic activity of gyrase. Recently published experimental evidence suggests that transcription initiation and elongation are inhibited by the buildup of positive supercoiling. It has therefore been proposed that intermittent binding of gyrase plays a role in transcriptional bursting. Considering that transcription is one of the most fundamental cellular processes, it is desirable to be able to account for the buildup and release of positive supercoiling in models of transcription. Here we present a detailed biophysical model of gene expression that incorporates the effects of supercoiling due to transcription. By directly linking the amount of positive supercoiling to the rate of transcription, the model predicts that highly transcribed genes' mRNA distributions should substantially deviate from Poisson distributions, with enhanced density at low mRNA copy numbers. Additionally, the model predicts a high degree of correlation between expression levels of genes inside the same supercoiling domain. Our model, incorporating the supercoiling state of the gene, makes specific predictions that differ from previous models of gene expression. Genes in the same supercoiling domain influence the expression level of neighboring genes. Such structurally dependent regulation predicts correlations between genes in the same supercoiling domain. The topology of the chromosome therefore creates a higher level of gene regulation, which has broad implications for understanding the evolution and organization of bacterial genomes.

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X Demographics

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 40 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 3%
United States 1 3%
Unknown 38 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 14 35%
Researcher 9 23%
Student > Bachelor 5 13%
Student > Postgraduate 2 5%
Student > Master 2 5%
Other 4 10%
Unknown 4 10%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 21 53%
Agricultural and Biological Sciences 7 18%
Physics and Astronomy 5 13%
Engineering 2 5%
Unknown 5 13%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 9. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 01 March 2016.
All research outputs
#3,675,689
of 22,844,985 outputs
Outputs from BMC Biophysics
#12
of 69 outputs
Outputs of similar age
#66,054
of 397,355 outputs
Outputs of similar age from BMC Biophysics
#1
of 1 outputs
Altmetric has tracked 22,844,985 research outputs across all sources so far. Compared to these this one has done well and is in the 83rd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 69 research outputs from this source. They receive a mean Attention Score of 3.5. This one has done well, scoring higher than 82% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 397,355 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 83% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them