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The Landscape of C. elegans 3′UTRs

2010; American Association for the Advancement of Science; Volume: 329; Issue: 5990 Linguagem: Inglês

10.1126/science.1191244

1095-9203

Marco Mangone, Arun Manoharan, Danielle Thierry‐Mieg, Jean Thierry‐Mieg, Ting Han, Sebastian D. Mackowiak, Emily K. Mis, Charles Zegar, Michelle Gutwein, Vishal Khivansara, Oliver Attie, Kevin Chen, Kourosh Salehi‐Ashtiani, Marc Vidal, Timothy T. Harkins, Pascal Bouffard, Yutaka Suzuki, Sumio Sugano, Yuji Kohara, Nikolaus Rajewsky, Fabio Piano, Kristin C. Gunsalus, John K. Kim,

MicroRNA in disease regulation

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.