Alternative RNA splicing is used by diverse organisms, including plants, to produce multiple proteins per gene. This project will develop information about the global regulation of alternative RNA splicing, using the model plant Arabidopsis thaliana to elaborate a "splicing code" that describes how DNA sequences specify splicing outcomes in plant species. First, a large number of short sequences will be systematically tested to see how they affect splicing. Then, a microarray platform for studying the alternative splicing of many genes in Arabidopsis will be developed. A relatively small set of developmental and environmental variables will be used to validate the platform. Then, data on alternative splicing from the microarray platform will be used to predict defined discrete regulatory splicing signals that will then be tested using the in planta assay.
Systematic studies of gene expression in Arabidopsis, like those in other organisms, have focused on the overall abundance of RNA without regard to the relative abundance of alternatively spliced isoforms that may encode distinct protein isoforms. The Arabidopsis research community as a whole will benefit from the availability of a microarray platform for studying alternative splicing, and it is likely that the existence of this alternative splicing platform will promote the discovery of regulation at the level of RNA processing that would have otherwise gone without notice. Similarly, continued development of the SEE ESE web server (www.tigr.org/software/SeeEse/eseF.html), which identifies sequences involved in the regulation of splicing, will provide the Arabidopsis community with a resource for evaluating the potential impact of specific mutations on splicing. Students working on this project will be exposed to research and will have a valuable hands-on laboratory experience. The University of Maryland is a large state University that serves a diverse population and undergraduates who were exposed to research in the Mount laboratory have gone on to Ph.D. programs at top research universities.
