XenmiR: A resource of Xenopus microRNA expression patterns

MicroRNAs (miRNA) are short, non-coding RNAs around 22 nucleotides long. They block gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. They are involved in controlling various mechanisms during development by regulating gene expression at the post transcriptional level. Some are highly conserved amongst diverse organisms and many of them have highly specific spatio-temporal expression patterns during development. The aim of this project as part of an Industrial Partnership Agreement (IPA) with Exiqon is to determine the expression patterns of miRNAs expressed during Xenopus development using LNA oligonucleotides. These modified oligonucleotides were developed by Exiqon and bind with high affinity and high specificity to specific targets. The results will be made freely available to the scientific community. Similar studies have been done in zebrafish and chicken to the great benefit of those communities and in a broader sense to the developmental biology community as a whole. This is because it can be difficult to identify miRNAs from particular tissues. Researchers can use the expression data resources to target miRNAs to carry out functional experiments specific to their model system. Adding the complete expression patterns for Xenopus will complement the studies done in zebrafish and chick and will provide an invaluable resource for the Xenopus community. Adding Xenopus to the list of species where expression patterns are known will allow for careful analysis of similarities and differences in expression patterns and thus provide valuable comparative data. This will in turn lead to insight into the possible species specific functions of miRNAs. In addition, functional experiments such as gain of function and loss of function experiments, which are relatively easy in Xenopus, can be carried out on specific miRNAs identified from the expression database.

In Xenopus 184 miRNAs have been identified and confirmed and are registered in miRBase (http://microrna.sanger.ac.uk/). Our industrial collaborator Exiqon will produce miRCURYTM LNA oligonucleotides to these miRNAs, which we will then use to carry out in situ hybridisations on wholemount embryos and sections to determine the specific expression patterns of those miRNAs at different stages of Xenopus tropicalis and laevis development, including early development and metamorphosis. The results will be collected and made available to the scientific community in a database, which we will set up and run called XenmiR. The results will also be available via the established and widely used Xenbase and QuickImage databases.