Global Approaches to Alternative Splicing and Its Regulation—Recent Advances and Open Questions

Pre-mRNA splicing is an essential RNA processing step in eukaryotes. Alternative splicing generates distinct spliced isoforms of the same gene, thereby dramatically increasing transcriptome diversity. Since most human genes undergo alternative splicing, this process contributes to a wide spectrum of biological functions in healthy and disease states. Splicing is closely regulated by various cis-regulatory elements and trans-factors. With the advent of high-throughput experimental technologies and bioinformatic algorithms, we now have powerful means to study alternative splicing globally and uncover its functional impact and regulatory mechanisms. As more RNA sequencing (RNA-Seq) data from normal and disease conditions are becoming available, many studies are underway to dissect global misregulation of splicing in diseases and develop novel splicing-targeted therapeutics. In this chapter, we first discuss the experimental and bioinformatic approaches for identification of alternative splicing, followed by a comprehensive review on the state-of-the-art methodologies to study splicing regulation. In addition, we discuss the current challenges and open questions in the RNA splicing field including gene expression kinetics, co-transcriptional splicing, and therapeutic approaches targeting splicing.