What is the 3'UTRome?3'UTRs are important portions of mRNAs required for post-transcriptional regulation by interacting with proteins or non-coding RNAs (e.g. microRNAs). To study the role of 3'UTRs we are building a 3'UTR database for C. elegans.
The UTRome.org database is intended as a comprehensive resource for 3'UTR biology in C. elegans. The database provides detailed information on 3'UTR structures for all protein-coding mRNAs, and includes annotations extracted from other databases (such as WormBase and PicTar) as well as new annotations generated as part of the NYU 3'UTRome project (including preliminary characterization of 3'UTR clones, USTs (UTR sequence tags), curated sequences, and computational and experimental analysis of functional elements).
Examples of functional elements within 3'UTRs include predicted and validated microRNA (miRNA) binding sites (responsible for post-transcriptional gene regulation), putative consensus signals for polyA addition, and predicted secondary structures (which may influence the biological activity of 3'UTRs).
The 3'UTRome project is part of the modENCODE Consortium, an NIH initiative to characterize at a genomic scale functional sequence elements encoded in the worm (C. elegans) and fly (D.melanogaster) genomes.
The UTRome website has been described in:
Integrative Analysis of the C. elegans Genome by the modENCODE Project.
Science DOI: 10.1126/science.1196914 (2010)
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 2010 Jul 23;329(5990):432-5.
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.
Nature 2009 Jun 18;459(7249):927-30.
Recent 3' UTR Papers
Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation Cell 2010 Dec 10;143(6):1018-29.
Regulation of mRNA translation and stability by microRNAs Annu Rev Biochem. 2010;79:351-79.
- Jan 24 2011
We have implemented a new tool that you can use to improve the annotation. At the bottom of the gene-page there is now a new panel named 'comments'; there you can input text and share your annotation with others.
- Jan 21 2011
For those interested in ordering 3'UTR clones: The ordering page is not yet online. We are in contact with several distributors to release the library in the next few months. At that point the ordering page will be available. Please be patient. Contact us for more details.
- Nov 17 2010
We have included in our GBrowse a new 3'UTR dataset from Jan et al., 2010.
The 3'UTRome Project is funded by NHGRI