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 mangone@asu.edu
Please cite Blazie et al., 2017 Genetics
The New 3'UTRome V3 is now live in GBrowse!Past publications: The UTRome website has been described in:
A comprehensive analysis of 3'UTRs in Caenorhabditis elegans
Murari E, Meadows D, Cuda N and Mangone M
Nucleic Acids Res. (2024) Jul 22;52(13):7523-7538. doi: 10.1093/nar/gkae543.
The C. elegans 3' UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3'-UTR biology, and miRNA targeting
Steber HS, Gallante C, O'Brien S, Chiu PL and Mangone M
Genome Res. (2019) Dec;29(12):2104-2116. doi: 10.1101/gr.254839.119. Epub 2019 Nov 19.
Alternative polyadenylation directs tissue specific miRNA targeting in Caenorhabditis elegans somatic tissues
Blazie S, Geissel H, Wilky H, Joshi R, Newbern J and Mangone M
Genetics (2017) https://doi.org/10.1534/genetics.116.196774 - RAW DATA
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles
Blazie S, Babb C, Wilky H, Rawls A, Park J and Mangone M
BMC Biology (2015) 13:4 doi:10.1186/s12915-015-0116-6 - RAW DATA
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) DOI: 10.1126/science.1191244
UTRome.org: a platform for 3'UTR biology in C. elegans.
Mangone M, Macmenamin P, Zegar C, Piano F, Gunsalus KC.
Nucleic Acids Res. (2008) 36, D57
Recent 3' UTR Papers
Alternative Polyadenylation Directs Tissue Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues. Genetics 2017 Genetics.116.196774. 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.
News
- July 26 2019
The new 3'UTRome V2 and the updated MiRanda target prediction have been uploaded in GBrowse
- March 18 2016
The 3'UTRome website has been moved to ASU
Funding
The UTRome Project is currently funded by the National Institute of General Medical Sciences (NIH/NIGMS R01 GM118796)