Computational and experimental modeling of RNA Splicing

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DESCRIPTION (provided by applicant): The discovery that eukaryotic genes are "split" into exons and introns has had enormous implications for our understanding of gene expression and regulation. It is now recognized that more than half of human genes are expressed via alternative splicing, frequently in specific spatial/temporal patterns. Alternative splicing plays a fundamental role in determining the specialized properties of differentiated eukaryotic cell types during normal development, and misregulation of splicing is increasingly recognized as being responsible for many human diseases. The main goal of this project is to form a cutting-edge research team comprising computational and experimental molecular biologists to model two biologically important problems: How do c/s-elements regulate pre-mRNA splicing? How do they affect splice-site selection? To address these problems, the following specific aims are proposed. 1) To mathematically and experimentally model the dependency of pre-mRNA splicing activity upon SR protein- and hnRNP A1- dependent ESEs/ESSs in a few well defined systems. 2) To study the dependency of tissue-specific alternative splicing on c/s-elements and frans-acting splicing factors. 3) To improve and extend our web-based ESEfinder capability and service by including more enhancer and silencer motifs into the database and by implementing more computational tools for the user community. Our approach is a combination Of mathematical modeling and experimental testing, using minigene constructs and functional pre-mRNA splicing assays. This close collaboration between computational and experimental molecular biologists is expected to lead to a better understanding of the mechanism of pre- mRNA splicing regulation, as well as to improved public access to information about alternative splicing.