The landscape of C. elegans 3'UTRs.
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.
Mangone
Marco
M
Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, New York, NY 10003, USA.
Manoharan
Arun Prasad
AP
Thierry-Mieg
Danielle
D
Thierry-Mieg
Jean
J
Han
Ting
T
Mackowiak
Sebastian D
SD
Mis
Emily
E
Zegar
Charles
C
Gutwein
Michelle R
MR
Khivansara
Vishal
V
Attie
Oliver
O
Chen
Kevin
K
Salehi-Ashtiani
Kourosh
K
Vidal
Marc
M
Harkins
Timothy T
TT
Bouffard
Pascal
P
Suzuki
Yutaka
Y
Sugano
Sumio
S
Kohara
Yuji
Y
Rajewsky
Nikolaus
N
Piano
Fabio
F
Gunsalus
Kristin C
KC
Kim
John K
JK
D020413:3' Untranslated Regions; D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000196:embryology / Q000235:genetics* / Q000254:growth & development; D019295:Computational Biology; D017124:Conserved Sequence; D012734:Disorders of Sex Development; D018507:Gene Expression Regulation, Developmental; D015723:Gene Library; D017238:Genes, Helminth; D015801:Helminth Proteins / Q000235:genetics; D006657:Histones / Q000235:genetics; D008297:Male; D035683:MicroRNAs / Q000378:metabolism; D009876:Operon; D011061:Poly A / Q000378:metabolism; D026723:Polyadenylation; D018510:RNA, Helminth / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D020040:Trans-Splicing
D020413:3' Untranslated Regions; D015801:Helminth Proteins; D006657:Histones; D035683:MicroRNAs; D018510:RNA, Helminth; D012333:RNA, Messenger; D011061:Poly A