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

BMC Biology

Research Article

Henry Wilky¹  Alan Rawls²  Stephen M Blazie³  Marco Mangone⁴  Cody Babb⁵  Jin G Park⁵ 

[1] Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA;Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA;Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA;Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA;Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA;Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA;Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA;Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA;Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA;

关键词: RNA-Seq;    Tissue-specific mRNA;    Elegans;    Promoter;    Transcription;    mRNA-tagging;    Transcriptome;    3’UTR;    miRNAs;    PAT-Seq;   

DOI  :  10.1186/s12915-015-0116-6

 received in 2014-09-29, accepted in 2015-01-12,  发布年份 2015

来源: Springer

【 摘 要 】

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 Caenorhabditis 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 approximately 20,000 tissue-specific polyadenylation sites and discovered that about 30% of transcripts in somatic cells use alternative polyadenylation in a tissue-specific manner, with their 3’UTR isoforms significantly enriched with microRNA targets.ConclusionsFor the first time, PAT-Seq allowed us 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.

【 授权许可】

Unknown   
© Blazie et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.