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Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles

Overview of attention for article published in BMC Biology, January 2015
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (90th percentile)

Mentioned by

blogs
1 blog
twitter
15 tweeters
facebook
1 Facebook page

Citations

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59 Dimensions

Readers on

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117 Mendeley
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Title
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles
Published in
BMC Biology, January 2015
DOI 10.1186/s12915-015-0116-6
Pubmed ID
Authors

Stephen M Blazie, Cody Babb, Henry Wilky, Alan Rawls, Jin G Park, Marco Mangone

Abstract

BackgroundTissue-specific RNA plasticity broadly impacts the development, tissue identity and adaptability of all organisms, but changes in composition, expression levels and its impact on gene regulation in different somatic tissues are largely unknown. Here we developed a new method, polyA-tagging and sequencing (PAT-Seq) to isolate high-quality tissue-specific mRNA from C. elegans intestine, pharynx, and body muscle tissues and study changes in their tissue-specific transcriptomes, and 3¿UTRomes.ResultsWe have identified thousands of novel genes and isoforms differentially expressed between these three tissues. The intestine transcriptome is expansive, expressing over 30% of C. elegans mRNAs, while muscle transcriptomes are smaller but contain characteristic unique gene signatures. Active promoter regions in all three tissues reveal both known and novel enriched tissue-specific elements, along with putative transcription factors, suggesting novel tissue-specific modes of transcription initiation. We have precisely mapped ~20,000 tissue-specific polyadenylation sites, and discovered that ~30% of transcripts in somatic cells use alternative polyadenylation in a tissue-specific manner, with their 3¿UTR isoforms significantly enriched with microRNA targets.ConclusionsPAT-Seq allowed for the first time to directly study tissue specific gene expression changes in an in vivo setting and compare these changes between three somatic tissues from the same organism at single-base resolution within the same experiment. We pinpoint precise tissue-specific transcriptome rearrangements and for the first time link tissue-specific alternative polyadenylation to miRNA regulation, suggesting novel and unexplored tissue-specific post-transcriptional regulatory networks in somatic cells.

Twitter Demographics

The data shown below were collected from the profiles of 15 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 117 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Netherlands 2 2%
United States 2 2%
Chile 1 <1%
Belgium 1 <1%
Unknown 111 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 43 37%
Researcher 19 16%
Student > Doctoral Student 12 10%
Student > Master 9 8%
Student > Bachelor 8 7%
Other 16 14%
Unknown 10 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 48 41%
Biochemistry, Genetics and Molecular Biology 44 38%
Neuroscience 7 6%
Environmental Science 2 2%
Immunology and Microbiology 1 <1%
Other 2 2%
Unknown 13 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 14. 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 03 April 2015.
All research outputs
#1,978,257
of 21,224,592 outputs
Outputs from BMC Biology
#583
of 1,819 outputs
Outputs of similar age
#30,596
of 321,728 outputs
Outputs of similar age from BMC Biology
#1
of 1 outputs
Altmetric has tracked 21,224,592 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 90th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,819 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 20.0. This one has gotten more attention than average, scoring higher than 68% of its peers.
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