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Title: Formation, regulation and evolution of 3' UTRs in Caenorhabditis elegans      
dateReleased:
12-24-2010
description:
Much of posttranscriptional mRNA regulation occurs through cis-acting sequences in mRNA 3´ untranslated regions (UTRs), which interact with specific proteins and ribonucleoprotein complexes that modulate translation, mRNA stability and subcellular localization. Studies in Caenorhabditis elegans have revealed indispensable roles for 3´UTR-mediated gene regulation, yet most C. elegans genes have lacked annotated 3´UTRs. Here we describe a high-throughput method to reliably identify 3´ ends of polyadenylated RNAs. This method, called poly(A)-position profiling by sequencing (3P-Seq), was used to determine the UTRs of C. elegans. Compared to standard methods also recently applied to C. elegans UTRs, 3P-Seq identified 8775 additional UTRs while excluding thousands of shorter UTR isoforms that do not appear to be authentic. Analysis of this expanded and corrected dataset indicated that the high A/U content of C. elegans 3´UTRs facilitated genome compaction, since the elements specifying cleavage and polyadenylation, which are A/U-rich, can more readily emerge in A/U rich regions. Indeed, 30% of the protein-coding genes have mRNAs with alternative, partially overlapping end regions that generate another 10,000 cleavage and polyadenylation sites that had gone largely unnoticed and represent potential evolutionary intermediates of progressive UTR shortening. Moreover, a third of the convergently transcribed genes utilize palindromic arrangements of bidirectional elements to specify UTRs with convergent overlap, which also contributes to genome compaction by eliminating regions between genes. Although nematode 3´UTRs have median length only one-sixth that of mammalian 3´UTRs, they have twice the density of conserved microRNA sites, in part because additional types of seed-complementary sites are preferentially conserved. These findings reveal the influence of cleavage and polyadenylation on the evolution of genome architecture and provide resources for studying posttranscriptional gene regulation. Nine samples (10 sequencing runs) from various mixed and specific stages of wild-type Caenorhabditis elegans and glp-4 mutant adults.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-24924
refinement:
raw
alternateIdentifiers:
24924
keywords:
functional genomics
dateModified:
08-21-2013
availability:
available
types:
gene expression
name:
Caenorhabditis elegans
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-24924/E-GEOD-24924.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-24924/E-GEOD-24924.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24924
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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