A combined computational-experimental approach predicts human microRNA targets

Marianthi Kiriakidou; Peter T. Nelson; Andrei Kouranov; Petko Fitziev; Costas Bouyioukos; Zissimos Mourelatos; Artemis Hatzigeorgiou

doi:10.1101/gad.1184704

A combined computational-experimental approach predicts human microRNA targets

Departments of ¹Pathology, ²Medicine, and ³Genetics, School of Medicine, ⁴Center for Bioinformatics, and ⁵Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

Abstract

A new paradigm of gene expression regulation has emerged recently with the discovery of microRNAs (miRNAs). Most, if not all, miRNAs are thought to control gene expression, mostly by base pairing with miRNA-recognition elements (MREs) found in their messenger RNA (mRNA) targets. Although a large number of human miRNAs have been reported, many of their mRNA targets remain unknown. Here we used a combined bioinformatics and experimental approach to identify important rules governing miRNA-MRE recognition that allow prediction of human miRNA targets. We describe a computational program, “DIANA-microT”, that identifies mRNA targets for animal miRNAs and predicts mRNA targets, bearing single MREs, for human and mouse miRNAs.

Keywords

Footnotes

Supplemental material is available at http://www.genesdev.org.
Article published online ahead of print. Article and publication date are at http://www.genesdev.org/cgi/doi/10.1101/gad.1184704.
↵6 Present address: Department of Computer Science, Free University of Berlin, Berlin 14195, Germany.
Corresponding authors.
↵7 E-MAIL mourelaz{at}uphs.upenn.edu; FAX (215) 746-0285.
↵8 E-MAIL artemis{at}uphs.upenn.edu; FAX (215) 573-2326.
- Accepted April 6, 2004.
- Received January 8, 2004.
Cold Spring Harbor Laboratory Press