Article a platform for 3′UTR biology in C. elegans

Department of Biology and Center for Genomics and Systems Biology, New York University, 100 Washington Square East, New York, NY 10003, USA.
Nucleic Acids Research (Impact Factor: 9.11). 02/2008; 36(Database issue):D57-62. DOI: 10.1093/nar/gkm946
Source: PubMed


Three-prime untranslated regions (3′UTRs) are widely recognized as important post-transcriptional regulatory regions of mRNAs.
RNA-binding proteins and small non-coding RNAs such as microRNAs (miRNAs) bind to functional elements within 3′UTRs to influence
mRNA stability, translation and localization. These interactions play many important roles in development, metabolism and
disease. However, even in the most well-annotated metazoan genomes, 3′UTRs and their functional elements are not well defined.
Comprehensive and accurate genome-wide annotation of 3′UTRs and their functional elements is thus critical. We have developed
an open-access database, available at, to provide a rich and comprehensive resource for 3′UTR biology in the well-characterized, experimentally tractable model
system Caenorhabditis elegans. combines data from public repositories and a large-scale effort we are undertaking to characterize 3′UTRs and
their functional elements in C. elegans, including 3′UTR sequences, graphical displays, predicted and validated functional elements, secondary structure predictions
and detailed data from our cloning pipeline. will grow substantially over time to encompass individual 3′UTR isoforms
for the majority of genes, new and revised functional elements, and in vivo data on 3′UTR function as they become available. The UTRome database thus represents a powerful tool to better understand
the biology of 3′UTRs.

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    • "TRome: a collection of predicted and experimentally validated functional elements in 3 -UTRs of Caenorhabditis elegans. It also contains isoforms and their expression profiles in the various stages of the organism Mangone et al. (2008) "
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