To assemble or not to assemble: How cis elements direct alternative splicing by modulating spliceosome assembly patterns
Eukaryotic genes are generally composed of multiple exons with intervening introns that are spliced to form mature RNA molecules. Intron removal is catalyzed by the spliceosome, a large complex of proteins and 5 RNA-protein molecules known as snRNPs. In each splicing event, snRNPs assemble anew on the transcript, distinguishing exons from introns. Alternative splicing, the process by which portions of the pre-mRNA are alternatively included from the mRNA, involves differential spliceosome assembly upon essential cis elements in the pre-mRNA: the 5’ splice site, branch point and 3’ splice site. These are partially conserved motifs that are recognized by the U1 and U2 snRNPs. Currently, there are two models for how spliceosomes recognize the appropriate splice site -intron definition, where U1 and U2 interact across the intron, and exon definition, where the U1 snRNP initially pairs with the upstream U2 snRNP across the exon, followed by a rearrangement to form interactions with the downstream U2 snRNP across the intron. Subsequent steps of splicing are thought to proceed in a standard fashion regardless of the splice site recognition mode. Additional cis elements have been reported to regulate alternative splicing by modulating the stoichiometry and interactions of splicing activators and inhibitors as well as the steric conformation and accessibility of the splice sites and branch point to block or enhance splicing at specific locations. Studies have shown that even a base pair mutation of an additional cis acting element can cause a change in the splicing outcome of a transcript, yet, it is not well understood how prevalent these elements are in a transcript and how they affect spliceosome assembly outcomes. Recently, three cases of environmentally regulated alternative splicing and hundreds of alternative splicing events were reported in S. pombe, a fission yeast with splice sites that closely match the splice site degeneracy seen in higher eukaryotes but does not have many auxiliary splicing proteins. The environmentally regulated alternative splicing of the srrm1 pre-mRNA provides the opportunity to investigate the mechanistic basis of alternative splicing by identifying and characterizing cis elements that direct differential spliceosome assembly in S. pombe. Investigating alternative splicing regulation will enhance our understanding of this important process as it pertains to diversity, gene expression, developmental processes, and disease.