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Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Overview of attention for article published in BMC Genomics, October 2015
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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 (81st percentile)
  • High Attention Score compared to outputs of the same age and source (89th percentile)

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10 X users
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1 Wikipedia page

Citations

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31 Dimensions

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56 Mendeley
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Title
Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
Published in
BMC Genomics, October 2015
DOI 10.1186/s12864-015-1993-3
Pubmed ID
Authors

Andrea M. Sass, Heleen Van Acker, Konrad U. Förstner, Filip Van Nieuwerburgh, Dieter Deforce, Jörg Vogel, Tom Coenye

Abstract

Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.

X Demographics

X Demographics

The data shown below were collected from the profiles of 10 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 56 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 2%
Unknown 55 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 17 30%
Researcher 10 18%
Student > Bachelor 4 7%
Unspecified 3 5%
Student > Master 3 5%
Other 5 9%
Unknown 14 25%
Readers by discipline Count As %
Agricultural and Biological Sciences 20 36%
Biochemistry, Genetics and Molecular Biology 10 18%
Immunology and Microbiology 4 7%
Unspecified 3 5%
Medicine and Dentistry 3 5%
Other 2 4%
Unknown 14 25%
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 30 November 2020.
All research outputs
#3,998,211
of 24,319,828 outputs
Outputs from BMC Genomics
#1,502
of 10,950 outputs
Outputs of similar age
#51,814
of 283,917 outputs
Outputs of similar age from BMC Genomics
#40
of 375 outputs
Altmetric has tracked 24,319,828 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 10,950 research outputs from this source. They receive a mean Attention Score of 4.8. This one has done well, scoring higher than 86% 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 283,917 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 81% of its contemporaries.
We're also able to compare this research output to 375 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 89% of its contemporaries.