Embracing the Complexity of Pre-mRNA Splicing

NIH Public Access Author Manuscript Cell Res. Author manuscript; available in PMC 2014 February 03. NIH-PA Author Manuscript Published in final edited form as: Cell Res. 2010 August ; 20(8): 866–868. doi:10.1038/cr.2010.98. Embracing the Complexity of Pre-mRNA Splicing Peter J. Shepard and Klemens J. Hertel * Department of Microbiology & Molecular Genetics, University of California, Irvine, Irvine, CA 92697-4025, USA Keywords alternative pre-mRNA splicing; exon; intron; computation NIH-PA Author Manuscript Pre-mRNA splicing is a fundamental process required for the expression of most metazoan genes. It is carried out by the spliceosome, which catalyzes the removal of non-coding intronic sequences to assemble exons into mature mRNAs prior to export and translation. Defects in splicing lead to many human genetic diseases 1 , and splicing mutations in a number of genes involved in growth control have been implicated in multiple types of cancer 2 . Given the complexity of higher eukaryotic genes and the relatively low level of splice-site conservation, the precision of the splicing machinery in recognizing and pairing splice sites is remarkable. Introns ranging in size from less than 100 up to 100,000 bases are removed efficiently. At the same time, a large number of alternative splicing events are observed between different cell-types, developmental stages, and during other biological processes. Of the approximately 25,000 genes encoded by the human genome 3 , more than 90% are believed to produce transcripts that are alternatively spliced 4 . Thus, alternative splicing of pre-mRNAs can lead to the production of multiple protein isoforms from a single pre-mRNA, significantly enriching the proteomic diversity of higher eukaryotic organisms 5 . Because regulation of this process can determine the timing and location in which a particular protein isoform is produced, changes in alternative splicing patterns modulate many cellular activities. This extensive alternative splicing implies a significant flexibility of the spliceosome to identify and process exons within a given pre-mRNA. NIH-PA Author Manuscript Over the last few years, research from different laboratories has demonstrated that the regulation of alternative splicing depends on many different cis-acting RNA elements 6 . While most of these RNA elements appeared to have a common mechanistic goal, the initial recruitment of spliceosomal components, the sheer number of RNA sequences involved in regulating alternative splicing became more and more daunting. As a consequence, the enthusiasm to derive alternative splicing predictions based only on pre-mRNA sequence, appropriately referred to as the “splicing code”, gave way to the growing realization that alternative splicing is much more complex than initially anticipated. Computational analyses of the identified RNA elements proved to be the first efficient tools to classify and group these RNA elements, while at the same time expanding the repertoire of additional RNA sequence elements likely to be important for splicing regulation 7 . Sequence motifs that define the exon/intron boundary, the presence or absence of splicing enhancer or silencer sequences, RNA secondary structures, and the length of exons and their flanking introns are the most prominent classes of RNA elements involved in mediating efficient exon splicing 6 . While it was appreciated that the relative contribution of each of these RNA sequence elements controls how efficient splice sites are recognized and flanking introns are removed, To whom correspondence should be addressed: khertel@uci.edu.