TY - JOUR
T1 - Alternative polyadenylation directs tissue-specific miRNA targeting in Caenorhabditis elegans somatic tissues
AU - Blazie, Stephen M.
AU - Geissel, Heather C.
AU - Wilky, Henry
AU - Joshi, Rajan
AU - Newbern, Jason
AU - Mangone, Marco
N1 - Funding Information:
We thank the Alison Frand laboratory for the pAF207 plasmid containing the PEST degron tag sequence used in our experiments. We also thank Justin Wolter and Kausen Kotagama for their review of the manuscript. This work was supported by National Institutes of Health (NIH) grants 1R21CA179144 and 1R01GM118796.
Publisher Copyright:
© 2017 Blazie et al.
PY - 2017/6
Y1 - 2017/6
N2 - mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3‘untranslated region (3‘UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3‘UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3‘UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis.
AB - mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3‘untranslated region (3‘UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3‘UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3‘UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis.
KW - Alternative polyadenylation
KW - C. elegans
KW - Transcriptome
KW - miRNA
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U2 - 10.1534/genetics.116.196774
DO - 10.1534/genetics.116.196774
M3 - Article
C2 - 28348061
AN - SCOPUS:85020688342
SN - 0016-6731
VL - 206
SP - 757
EP - 774
JO - Genetics
JF - Genetics
IS - 2
ER -