Genomic Measurement of Alternative Splicing by DNA Array

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Alternative splicing is a key process in the control of mammalian gene expression and a major source of protein diversity. Errors in splicing regulation are implicated in many disease processes including cancer, but the cellular circuitry involved in this regulation is mostly unknown. Gene expression profiling using DNA microarrays has led to major advances in our understanding of gene regulatory systems on a genome wide scale. However, none of the commonly available systems of microarray analysis can detect changes in splicing and instead give information on the overall transcript abundance from each gene. These methods provide information on the first layer of gene regulation but miss many important changes in gene product caused by alterations in splicing pattern. The project proposed here will enable three groups to collaborate on establishing a new type of DNA microarray that allows the parallel analysis of multiple alternative splicing patterns. Each of the labs in this collaboration has unique expertise in the study of splicing. We will design and produce arrays of oligonucleotides that detect and measure splicing events in the mouse. This microarray method is well established for yeast splicing, and recent results demonstrate its ability to detect alternative splicing in more complex human cell lines and tissues. The proposal here is to apply it to specific systems of regulation in the mouse, including the nervous system and the heart. The goals of the project are to move the study of splicing regulation to the level of the whole genome, to comprehensively search for genes subject to specific splicing regulatory pathways, and to provide greater precision to gene expression profiling.