Analysis of cis-acting regulatory motifs involved in alternative splicing

Alternative splicing (AS) is an important posttranscriptional process in eukaryotes and contributes essentially to gene expression regulation. Cis-acting regulatory motifs play a pivotal role in alternative splicing regulation. Many human diseases involved with aberrant splicing are caused by mutations of these motifs. However, due to the short, degenerate and context-dependent nature, the prediction of cis-acting splicing motifs is a very challenging.;In this dissertation, we focus on discovery of splicing signals from sequences. This may help to reveal the integrated splicing code and to understand the regulation of gene expression on the exon level.;In chapter one, we review the up-to-date research development in alternative splicing and its regulation.;We describe a large-scale data analysis experiment to discover AS motifs in chapter two. We applied a computational framework to re-analyze ∼2,500 cassette exons. We used systematic sampling to sample potential co-regulated sequences clustered by splicing profiles and eliminated redundant motifs predicted from overlapping clusters. We conclude that these predicted motifs may be promising candidates in AS regulation by comparison to known motifs and by positional bias.;In chapter three, we describe a new ab initio approach to discover incorporating skipping rates in motif discovery. In the simulation study, we show that this approach is especially suitable to discover short and highly degenerate motifs. We discover that Nova and hnRNP A1 binding sites, as well as about ten novel motifs, are involved with AS regulation in Central Nervous System tissues specific cassette exons. Co-operation between predicted motifs are also revealed.;In chapter four, we give the present status of SPRED, a database of cis-acting splicing motif. The motifs in SPRED are compiled from literature and experimentally validated. The web interface is accompanied with query and similarity search tools. The goal of SPRED is to provide a comprehensive dictionary to facilitate the research in AS and its regulation.;Finally, we give the conclusions in chapter five. We also give the perspective for future study and briefly review the potential challenge.