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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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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.

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Geographical breakdown

Country Count As %
Netherlands 2 2%
United States 2 2%
Chile 1 <1%
Belgium 1 <1%
Unknown 122 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 43 34%
Researcher 20 16%
Student > Doctoral Student 13 10%
Student > Master 12 9%
Student > Bachelor 9 7%
Other 16 13%
Unknown 15 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 48 38%
Biochemistry, Genetics and Molecular Biology 46 36%
Neuroscience 8 6%
Pharmacology, Toxicology and Pharmaceutical Science 2 2%
Environmental Science 2 2%
Other 3 2%
Unknown 19 15%