From ESTs to ESRs: Comparative analysis of mutually exclusive exons in 15 species of insects

Recent findings of extensive alternative splicing events occurring in eukaryotic organisms have provided a possible explanation for the puzzling discrepancy between the number of genes and high genome complexity. Most alternative splicing events in eukaryotic genomes are detected using sequence fragments produced by high throughput genomic technologies, such as expressed sequence tags (EST) sequencing and microarrays. Exonic splicing regulatory sequences (ESRs) are cis-acting factor binding sites that regulate constitutive and alternative splicing. In this paper, we describe an in silico analysis pipeline to extract putative ESRs from EST splicing graphs and from a multiple alignment of 15 species of insects. Our method, E2E, combines graph analysis, phylogenetic measures and a sliding window approach that extracts conserved motifs using comparative analysis and the Welch's t statistic. We studied 100% conserved motifs as well as those obtained from our E2E method. We compared our results with a recent study on the alternatively spliced N-Cadherin gene in the Drosophila melanogaster. We also looked for homologous ESTs in mouse and human genome and found that about half of the putative ESRs in common between insects and mammals have a high statistical support (p<; 0.01).