Large-scale Discovery of Regulatory Motifs Involved in Alternative Splicing

Alternative splicing is a highly important process in many eukaryotic organisms, but surprisingly little is known about its regulation. Often, this process involves cis-regulatory DNA motifs located within the alternative spliced exons or the flanking introns. To discover such regulatory motifs, we reanalyzed a dataset containing ~3000 skipped exons and their relative expression levels in ten mouse tissues provided by Pan and colleagues [1]. We clustered the skipped exons by their expression profiles and applied MEME (multiple Em for motif elicitation) to build a motif dictionary from each cluster. The discovered motifs were validated by comparing with known regulatory elements and by examining positional bias. By incorporating the levels of alternative splicing, our study provides not only solid targets for further experiments, but also a computational framework applicable in other organisms. The motif dictionary is available at http://www4.ncsu.edu/~szhao3/ ASMotif.html.