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UTRome.org: a platform for 3'UTR biology in C. elegans.

Mangone M, Macmenamin P, Zegar C, Piano F, Gunsalus KC - Nucleic Acids Res. (2007)

Bottom Line: Comprehensive and accurate genome-wide annotation of 3'UTRs and their functional elements is thus critical.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Center for Genomics and Systems Biology, New York University, 100 Washington Square East, New York, NY 10003, USA.

ABSTRACT
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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Overview of UTRome.org. The UTRome database integrates diverse information on C. elegans 3′UTRs. (A) Data on 3′UTR boundaries and predicted or experimentally validated functional elements, collected from multiple database sources or analyzed using various computational algorithms, are displayed in a series of user-friendly web pages. (B) ‘Locus Information’ page: a sample snapshot of aggregated data. (C) Results returned for the query ‘lin’ in a search limited to genes targeted by the UTRome project. (D) ‘ABI trace files’ page: a Java applet shows sequence traces for a UST including part of the polyA tail. (E) Excerpt from a ‘Gel’ page: PCR products from a 96-well cloning experiment indicate evidence for multiple 3′UTR isoforms in well H4 (automatically highlighted by a green box). (F) ‘MFOLD’ page: secondary structure prediction for a 3′UTR showing putative stem-loop structure.
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Figure 1: Overview of UTRome.org. The UTRome database integrates diverse information on C. elegans 3′UTRs. (A) Data on 3′UTR boundaries and predicted or experimentally validated functional elements, collected from multiple database sources or analyzed using various computational algorithms, are displayed in a series of user-friendly web pages. (B) ‘Locus Information’ page: a sample snapshot of aggregated data. (C) Results returned for the query ‘lin’ in a search limited to genes targeted by the UTRome project. (D) ‘ABI trace files’ page: a Java applet shows sequence traces for a UST including part of the polyA tail. (E) Excerpt from a ‘Gel’ page: PCR products from a 96-well cloning experiment indicate evidence for multiple 3′UTR isoforms in well H4 (automatically highlighted by a green box). (F) ‘MFOLD’ page: secondary structure prediction for a 3′UTR showing putative stem-loop structure.

Mentions: The UTRome database provides up-to-date information on 3′UTR structures and functional elements for every C. elegans mRNA based on combined data from public repositories such as WormBase (8,9) and continuously updated results from an ongoing high-throughput pipeline we have developed to define 3′UTRs and their isoforms (Figure 1A). Information about functional elements within 3′UTRs currently includes computationally predicted miRNA-binding sites [derived from the PicTar (19,22) and MiRanda (21) algorithms], putative PAS sites [computed based on Ref. (23)], and predicted secondary structures [using the MFOLD algorithm (24)]. For each 3′UTR, users can view or download secondary structure prediction diagrams and browse graphical coordinate-based displays illustrating gene models, 3′UTR products from our cloning pipeline, previously annotated evidence for 3′UTRs from ESTs and mRNAs, putative PAS sites and predicted or validated miRNA-binding sites. We also provide a detailed description of data produced by our cloning pipeline, including status of cloning and annotation, ABI trace files, BLAT (25) and BLAST (26) alignments to the genome, and annotated agarose gel images of RT-PCR products used for cloning. As new data become available, UTRome.org will grow substantially over time to encompass individual isoforms for the majority of genes, improved predictions for miRNA-binding sites based on updated 3′UTR annotations and additional sequenced genomes, and results from in vivo analyses of 3′UTR structure and function, including experimental characterization of specific functional sequence elements.Figure 1.


UTRome.org: a platform for 3'UTR biology in C. elegans.

Mangone M, Macmenamin P, Zegar C, Piano F, Gunsalus KC - Nucleic Acids Res. (2007)

Overview of UTRome.org. The UTRome database integrates diverse information on C. elegans 3′UTRs. (A) Data on 3′UTR boundaries and predicted or experimentally validated functional elements, collected from multiple database sources or analyzed using various computational algorithms, are displayed in a series of user-friendly web pages. (B) ‘Locus Information’ page: a sample snapshot of aggregated data. (C) Results returned for the query ‘lin’ in a search limited to genes targeted by the UTRome project. (D) ‘ABI trace files’ page: a Java applet shows sequence traces for a UST including part of the polyA tail. (E) Excerpt from a ‘Gel’ page: PCR products from a 96-well cloning experiment indicate evidence for multiple 3′UTR isoforms in well H4 (automatically highlighted by a green box). (F) ‘MFOLD’ page: secondary structure prediction for a 3′UTR showing putative stem-loop structure.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238901&req=5

Figure 1: Overview of UTRome.org. The UTRome database integrates diverse information on C. elegans 3′UTRs. (A) Data on 3′UTR boundaries and predicted or experimentally validated functional elements, collected from multiple database sources or analyzed using various computational algorithms, are displayed in a series of user-friendly web pages. (B) ‘Locus Information’ page: a sample snapshot of aggregated data. (C) Results returned for the query ‘lin’ in a search limited to genes targeted by the UTRome project. (D) ‘ABI trace files’ page: a Java applet shows sequence traces for a UST including part of the polyA tail. (E) Excerpt from a ‘Gel’ page: PCR products from a 96-well cloning experiment indicate evidence for multiple 3′UTR isoforms in well H4 (automatically highlighted by a green box). (F) ‘MFOLD’ page: secondary structure prediction for a 3′UTR showing putative stem-loop structure.
Mentions: The UTRome database provides up-to-date information on 3′UTR structures and functional elements for every C. elegans mRNA based on combined data from public repositories such as WormBase (8,9) and continuously updated results from an ongoing high-throughput pipeline we have developed to define 3′UTRs and their isoforms (Figure 1A). Information about functional elements within 3′UTRs currently includes computationally predicted miRNA-binding sites [derived from the PicTar (19,22) and MiRanda (21) algorithms], putative PAS sites [computed based on Ref. (23)], and predicted secondary structures [using the MFOLD algorithm (24)]. For each 3′UTR, users can view or download secondary structure prediction diagrams and browse graphical coordinate-based displays illustrating gene models, 3′UTR products from our cloning pipeline, previously annotated evidence for 3′UTRs from ESTs and mRNAs, putative PAS sites and predicted or validated miRNA-binding sites. We also provide a detailed description of data produced by our cloning pipeline, including status of cloning and annotation, ABI trace files, BLAT (25) and BLAST (26) alignments to the genome, and annotated agarose gel images of RT-PCR products used for cloning. As new data become available, UTRome.org will grow substantially over time to encompass individual isoforms for the majority of genes, improved predictions for miRNA-binding sites based on updated 3′UTR annotations and additional sequenced genomes, and results from in vivo analyses of 3′UTR structure and function, including experimental characterization of specific functional sequence elements.Figure 1.

Bottom Line: Comprehensive and accurate genome-wide annotation of 3'UTRs and their functional elements is thus critical.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Center for Genomics and Systems Biology, New York University, 100 Washington Square East, New York, NY 10003, USA.

ABSTRACT
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.

Show MeSH