What is the worm 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 and alternative polyadenylation for all protein-coding mRNAs, and includes annotations extracted from other databases (such as WormBase and PicTar) as well as new annotations generated by others.
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).
For questions, please contact Marco Mangone at firstname.lastname@example.org
Please cite Blazie et al., 2015 BMC Biology
Past publications: 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.
Nature 2009 Jun 18;459(7249):927-30.
Recent 3' UTR Papers
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles. BMC Biology 2015 Jan 20
Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3'-end-seq. Nucleic Acids Res. 2012 Jul 40(13):6304-18
Regulation of mRNA translation and stability by microRNAs Annu Rev Biochem. 2010;79:351-79.
- March 18 2016
The 3'UTRome website has been moved to ASU
The UTRome v1 was initially developed at NYU in 2011 by Marco Mangone, Kris Gunsalus and Fabio Piano for the modENCODE Consortium. The server was recently moved to the School of Life Sciences at Arizona State University, and is now maintained by Marco Mangone's group at ASU
The UTRome Project is currently funded by the School of Life Sciences at Arizona State University