The Landscape of C. elegans 3′UTRs

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Science  03 Jun 2010:
DOI: 10.1126/science.1191244


Three-prime untranslated regions (3′UTRs) of metazoan mRNAs contain numerous regulatory elements, yet remain largely uncharacterized. Using polyA capture, 3′RACE, full-length cDNAs, and RNA-seq, we define ~26,000 distinct 3′UTRs in Caenorhabditis elegans for ~85% of the 18,328 experimentally supported protein coding genes and revise ~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) is detected for 13% of polyA sites, predominantly among shorter alternative isoforms. Trans-spliced (vs. non-trans-spliced) mRNAs possess longer 3′UTRs and frequently contain no PAS or variant PAS. We identify 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 genome-wide and throughout development.