About The UTRome

The UTRome database contains data from three major groups. Fabio Piano laboratory in New York University, John Kim Laboratory in Michigan University and Yuji Kohara Laboratory in Tokyo.
This work is supported by grants from the National Human Genome Research Institute (R21HG003971 and 1U01HG004276).

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 this open-access database, 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.

The UTRome website has been described in:

The Landscape of C. elegans 3'UTRs.
Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak S, Mis E, Zegar C, Gutwein MR, Khivansara V, Attie O, Chen K, Salehi-Ashtiani K, Vidal M, Harkins TT, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F, Gunsalus KC, Kim JK.
Science DOI: 10.1126/science.1191244 (2010)

UTRome.org: a platform for 3'UTR biology in C. elegans.
Mangone M, Macmenamin P, Zegar C, Piano F, Gunsalus KC.
Nucleic Acids Res. 36, D57 (2008)

Unlocking the secrets of the genome.
modENCODE Consortium
Nature 2009 Jun 18;459(7249):927-30.

We have recently moved the website from NYU to ASU, and incorporated tissue-specific transcriptome and 3'UTRome data from several groups. Tissue-specific RNA plasticity broadly impacts the development, tissue identity and adaptability of all organisms, but changes in composition, expression levels and its impact on gene regulation in different somatic tissues are largely unknown. We developed a new method, polyA-tagging and sequencing (PAT-Seq) to isolate high-quality tissue-specific mRNA from C. elegans intestine, pharynx, and body muscle tissues and study changes in their tissue-specific transcriptomes, exomes and 3′UTRomes.

We have identified thousands of novel genes and isoforms differentially expressed between these three tissues, and created a website to display our results.

The UTRome is a useful online resource for scientists interested in 3'UTR biology and Alternative polyadenylation (APA). The UTRome.org site uses an Apache web server and several custom-made Perl scripts that query a dedicated MySQL database. It is currently hosted in the Biodesign Institute at Arizona State University, and offers a simple and well-integrated interactive user interface to query gene records and 3'UTR isoform data, access to a dedicated gBrowse installation specifically designed to study APA in worms. This database displays tracks for each tissue transcriptome, including tissue-specific APA, as well as curated 3'UTR data from previously published studies. For questions, please contact Marco Mangone at mangone@asu.edu

© The Biodesign Institute at Arizona State University - PO Box 875001, Tempe, AZ 85287-5001