Defining Pre-mRNA cis Elements that Regulate Cell-Specific Splicing

A large number of genes express multiple mRNAs that encode diverse protein isoforms via alternative pre-mRNA splicing. For many genes, alternative splicing is regulated according to cell-specific patterns (in this chapter, cell-specific is used as a general term to refer to regulation according to differentiated cell type, developmental stage, gender, or in response to an external stimulus). In many cases, the same pre-mRNA transcript is processed differently in different cells, indicating that elements within the pre-mRNA direct cell-specific splicing via interactions with cell-specific factors or a cell-specific combination of ubiquitous factors. Results from a large number of vertebrate experimental systems have identified elements that affect splice site choice; however, only a few of these have been shown to direct cell-specific splicing (1 ,4 ,5 ,7 ,14 ,15 ,19 ). While ubiquitously recognized elements are likely to participate in cell-specific splicing events, this chapter focuses on experimental strategies to identify cis elements that promote cell-specific splicing in vertebrates and to distinguish cell-specific and general splicing elements.