Insights into the regulation of AS have come predominantly from the molecular dissection of individual genes (reviewed in [1,12]). Prominent examples include the tissue-specific splicing of the c-src N1 exon [13], cancer-associated splicing of the CD44 gene [14] and the alternative splicing cascade involved in Drosophila melanogaster sex determination [15]. Biochemical studies of these and other genes have described important classes of trans-acting splicing-regulatory factors, implicating members of the ubiquitously expressed serine/arginine-rich protein (SR protein) and heterogeneous nuclear ribonucleoprotein (hnRNP) families, and tissue-specific factors including members of the CELF [16] and NOVA [17] families of proteins, as well as other proteins and protein families, in control of specific splicing events. A number of cis-regulatory elements in exons or introns that play key regulatory roles have also been identified, using a variety of methods including site-directed mutagenesis, systematic evolution of ligands by exponential enrichment (SELEX) and computational approaches [18-22]. In addition, DNA microarrays and polymerase colony approaches have been developed for higher-throughput analysis of alternative mRNA isoforms [23-26] and a cross-linking/immunoprecipitation strategy (CLIP) has been developed for systematic detection of the
