Recent experiments have shown that the genomes of organisms such as worm, fly, human, and mouse encode hundreds of novel microRNA genes. Many of these small non-coding genes are thought to regulate the translational expression of other genes by binding to partially complementary sites in target messenger RNAs. Initial phenotypic and expression analyses suggest an important role for microRNAs in basic cellular processes such as development, viral response, and apoptosis. Furthermore, many microRNAs are conserved over large evolutionary distances. However, the biological function of most microRNAs is unknown. Although recent computational methods have made progress towards the identification of microRNA targets, no experimental high-throughput method for dissecting microRNA function exists. Our long-term goal is to create a system where bioinformatic and experimental methods are integrated to make possible the high-throughput combinatorial analysis of microRNA function. Here, we propose to setup this system. Specifically, we will (a) employ in silica methods to predict microRNA targets in five different nematode species, (b) use inhibitor oligonucleotides to knock down the function of 20 microRNAs across several nematode species in vivo, and register their loss-of-function phenotypes throughout development, (c) develop a system to validate predicted microRNA targets in vivo and test 25 computationally predicted targets. These data will generate novel insights into the biological function of microRNAs and their potential role in shaping biological diversity. This project is an intensive collaboration between a bioinformatics lab (focused on gene regulatory processes), and an experimental lab (RNAi functional genomics in nematodes) ? ?
| Mangone, Marco; Macmenamin, Philip; Zegar, Charles et al. (2008) UTRome.org: a platform for 3'UTR biology in C. elegans. Nucleic Acids Res 36:D57-62 |
