title: Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles.
abstract: BACKGROUND
  Tissue-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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  For 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.
authors.affiliation: Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA. Stephen.Blazie@asu.edu.|Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA. Stephen.Blazie@asu.edu.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Blazie
authors.affiliation: Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA. Cody.Babb@asu.edu.
authors.forename: Cody
authors.initials: C
authors.lastname: Babb
authors.affiliation: Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA. Henry.Wilky@asu.edu.
authors.forename: Henry
authors.initials: H
authors.lastname: Wilky
authors.affiliation: Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA. Alan.Rawls@asu.edu.|Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA. Alan.Rawls@asu.edu.
authors.forename: Alan
authors.initials: A
authors.lastname: Rawls
authors.affiliation: Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA. Jin.Park.1@asu.edu.
authors.forename: Jin G
authors.initials: JG
authors.lastname: Park
authors.affiliation: Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA. mangone@asu.edu.|Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA. mangone@asu.edu.|Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA. mangone@asu.edu.
authors.forename: Marco
authors.initials: M
authors.lastname: Mangone
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D007413:Intestinal Mucosa / Q000378:metabolism*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D009132:Muscles / Q000378:metabolism*; D009928:Organ Specificity / Q000235:genetics; D010614:Pharynx / Q000378:metabolism; D011061:Poly A / Q000378:metabolism; D026723:Polyadenylation / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs; D020033:Protein Isoforms; D012333:RNA, Messenger; D011061:Poly A