The landscape of C. elegans 3′UTRs

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

Research output: Contribution to journalArticlepeer-review

Abstract

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 ~26,000 distinct 3′UTRs in Caenorhabditis elegans for ∼85% of the 18,328 experimentally supported protein-coding genes and revised ∼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.

Original languageEnglish (US)
Pages (from-to)432-435
Number of pages4
JournalScience
Volume329
Issue number5990
DOIs
StatePublished - Jul 23 2010

ASJC Scopus subject areas

  • General

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