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The Landscape of C. elegans 3'UTRs

Mangone, Marco, Manoharan, Arun Prasad, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Han, Ting, Mackowiak, Sebastian D., Mis, Emily, Zegar, Charles, Gutwein, Michelle R., Khivansara, Vishal, Attie, Oliver, Chen, Kevin, Salehi-Ashtiani, Kourosh, Vidal, Marc, Harkins, Timothy T., Bouffard, Pascal, Suzuki, Yutaka, Sugano, Sumio, Kohara, Yuji, Rajewsky, Nikolaus, Piano, Fabio, Gunsalus, Kristin C., Kim, John K.
Science 2010 v.329 no.5990 pp. 432-435
3' untranslated regions, Caenorhabditis elegans, animal age, complementary DNA, gene expression regulation, genes, histones, microRNA, models, sequence analysis
Three-prime untranslated regions (3'UTRs) of metazoan messenger RNAs (mRNAs) contain numerous regulatory elements, yet remain largely uncharacterized. Using polyA capture, 3' rapid amplification of complementary DNA (cDNA) ends, full-length cDNAs, and RNA-seq, we defined approximately 26,000 distinct 3'UTRs in Caenorhabditis elegans for approximately 85% of the 18,328 experimentally supported protein-coding genes and revised approximately 40% of gene models. Alternative 3'UTR isoforms are frequent, often differentially expressed during development. Average 3'UTR length decreases with animal age. Surprisingly, no polyadenylation signal (PAS) was detected for 13% of polyadenylation sites, predominantly among shorter alternative isoforms. Trans-spliced (versus non-trans-spliced) mRNAs possess longer 3'UTRs and frequently contain no PAS or variant PAS. We identified conserved 3'UTR motifs, isoform-specific predicted microRNA target sites, and polyadenylation of most histone genes. Our data reveal a rich complexity of 3'UTRs, both genome-wide and throughout development.