The Landscape of <i>C. elegans</i> 3′UTRs

Marco Mangone(New York Genome Center), Arun Manoharan(Washtenaw Community College), Danielle Thierry‐Mieg(National Institutes of Health), Jean Thierry‐Mieg(National Institutes of Health), Ting Han(Washtenaw Community College), Sebastian D. Mackowiak(Max Delbrück Center), Emily K. Mis(New York Genome Center), Charles Zegar(New York Genome Center), Michelle Gutwein(New York Genome Center), Vishal Khivansara(Washtenaw Community College), Oliver Attie(New York Genome Center), Kevin Chen(Max Delbrück Center), Kourosh Salehi‐Ashtiani(Harvard University), Marc Vidal(Harvard University), Timothy T. Harkins(La Roche College), Pascal Bouffard(Enzo Life Sciences (United States)), Yutaka Suzuki(The University of Tokyo), Sumio Sugano(The University of Tokyo), Yuji Kohara(National Institute of Genetics), Nikolaus Rajewsky(Max Delbrück Center), Fabio Piano(New York University Abu Dhabi), Kristin C. Gunsalus(New York University Abu Dhabi), John K. Kim(Washtenaw Community College)
Science
June 4, 2010
10.1126/science.1191244
Cited by 262

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 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.

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