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 language | English (US) |
|---|---|
| Pages (from-to) | 432-435 |
| Number of pages | 4 |
| Journal | Science |
| Volume | 329 |
| Issue number | 5990 |
| DOIs | |
| State | Published - Jul 23 2010 |
Fingerprint
All Science Journal Classification (ASJC) codes
- General
Cite this
}
The landscape of C. elegans 3′UTRs. / Mangone, Marco; Manoharan, Arun Prasad; Thierry-Mieg, Danielle; Thierry-Mieg, Jean; Han, Ting; Mackowiak, Sebastian D.; Mis, Emily; Zegar, Charles; Gutwein, Michelle R.; Khivansara, Vishal; Attie, Oliver; Salehi-Ashtiani, Kourosh; Vidal, Marc; Harkins, Timothy T.; Bouffard, Pascal; Suzuki, Yutaka; Sugano, Sumio; Kohara, Yuji; Rajewsky, Nikolaus; Piano, Fabio; Gunsalus, Kristin C.; Kim, John K.
In: Science, Vol. 329, No. 5990, 23.07.2010, p. 432-435.Research output: Contribution to journal › Article
TY - JOUR
T1 - The landscape of C. elegans 3′UTRs
AU - Mangone, Marco
AU - Manoharan, Arun Prasad
AU - Thierry-Mieg, Danielle
AU - Thierry-Mieg, Jean
AU - Han, Ting
AU - Mackowiak, Sebastian D.
AU - Mis, Emily
AU - Zegar, Charles
AU - Gutwein, Michelle R.
AU - Khivansara, Vishal
AU - Attie, Oliver
AU - Salehi-Ashtiani, Kourosh
AU - Vidal, Marc
AU - Harkins, Timothy T.
AU - Bouffard, Pascal
AU - Suzuki, Yutaka
AU - Sugano, Sumio
AU - Kohara, Yuji
AU - Rajewsky, Nikolaus
AU - Piano, Fabio
AU - Gunsalus, Kristin C.
AU - Kim, John K.
PY - 2010/7/23
Y1 - 2010/7/23
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=77954847055&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=77954847055&partnerID=8YFLogxK
U2 - https://doi.org/10.1126/science.1191244
DO - https://doi.org/10.1126/science.1191244
M3 - Article
C2 - 20522740
VL - 329
SP - 432
EP - 435
JO - Science
JF - Science
SN - 0036-8075
IS - 5990
ER -