TY - JOUR
T1 - UTRome.org
T2 - A platform for 3′UTR biology in C. elegans
AU - Mangone, Marco
AU - Macmenamin, Philip
AU - Zegar, Charles
AU - Piano, Fabio
AU - Gunsalus, Kristin C.
N1 - Funding Information:
We thank Danielle and Jean Thierry-Mieg for sharing statistics on alternative transcript isoforms and insightful discussions on sequence curation, Ravi Sachidanandam for kindly providing us with the TraceView Java applet, Michael Zuker for suggestions on how to install and configure MFOLD, Victor Chistyakov for help with the AJAX auto-suggest feature, Nikolaus Rajewsky and his research group for fruitful collaborations on 30UTR biology, Kevin Chen for helpful comments on the manuscript, and the modENCODE Consortium for propelling this project forward. This work was supported by grants from the National Human Genome Research Institute (R21HG003971 and 1U01HG004276). Funding to pay the Open Access publication charges for this article was provided by NHGRI award 1U01HG004276.
PY - 2008/1
Y1 - 2008/1
N2 - 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 http://www.UTRome.org, to provide a rich and comprehensive resource for 3′UTR biology in the well-characterized, experimentally tractable model system Caenorhabditis elegans. UTRome.org 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. UTRome.org 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.
AB - 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 http://www.UTRome.org, to provide a rich and comprehensive resource for 3′UTR biology in the well-characterized, experimentally tractable model system Caenorhabditis elegans. UTRome.org 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. UTRome.org 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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U2 - 10.1093/nar/gkm946
DO - 10.1093/nar/gkm946
M3 - Article
C2 - 17986455
AN - SCOPUS:38549153757
SN - 0305-1048
VL - 36
SP - D57-D62
JO - Nucleic acids research
JF - Nucleic acids research
IS - SUPPL. 1
ER -