Pre-mRNA processing is an essential control-point in the gene expression pathway of eukaryotic organisms. The budding yeast Saccharomyces cerevisiae offers a powerful opportunity to examine the regulation of this pathway. In this chapter, we will describe methods that have been developed in our lab and others to examine pre-mRNA splicing from a genome-wide perspective in yeast. Our goal is to provide all of the necessary information--from microarray design to experimental setup to data analysis--to facilitate the widespread use of this technology.
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