The sRNA Workbench

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RNA silencing is a complex and highly conserved regulatory mechanism that is now known to be involved in diverse processes such as development, pathogen control, genome maintenance and response to environmental change. Since its recent discovery, RNA silencing has become a fast moving area of research of great importance in both plant and animal molecular biology. Its discovery has not only been a major breakthrough for our understanding of complex regulatory processes in living cells, but has also opened the door to the development of novel therapeutics for human diseases. The importance of these findings was highlighted by the award of the Nobel prize for medicine in 2006 for the discovery of RNA interference. Small RNA molecules (sRNAs) play a crucial role in the RNA silencing machinery in that they can interact with other nucleic acids in a sequence specific manner to mark them as targets for inactivation. To learn more about this mechanism and its implications, researchers employ cutting-edge sequencing technologies to obtain large datasets of sRNA sequences (typically between 1-10 million sequences about 20-30 nucleotides in length) from a number of organisms. With these technologies becoming more accessible and affordable it is now possible to obtain multiple large-scale data sets which allow the analysis of changes in the sRNA population. These changes can indicate the involvement of RNA silencing pathways in the biological process of interest, such as regulation of key developmental stages in an organism. However, there is a lack of software tools for the analysis of such experiments, which presents a major bottleneck to the exploitation of the technology, especially for biologists without direct bioinformatics support. In this project, we will build on our existing publicly available software tools for sRNA analysis, with the aim of providing an easy to use, downloadable workbench to provide a complete solution for the analysis of plant and animal sRNA datasets. This will provide biologists with a much needed resource to identify novel sRNAs and their function as part of wet-lab studies.