The EXONerator: A silent silencer of predicted RNA exonic splice enhancer sequences

The splicing of exons is an essential step in the pre‐mRNA processing events that must occur in genes to form a functional messenger RNA (mRNA) competent for nuclear export and translation. Intron removal is catalyzed by the “spliceosome,” which interacts with cis‐acting signals in the pre‐mRNA as well as other elements such as exonic splice enhancers (ESEs) that allow differentiation between legitimate and pseudo‐splice sites. ESEs act as binding sites for SR proteins, which facilitate exon inclusion. Understanding ESE function and the factors involved in exon definition will lead to a better understanding of not only physiological alternative splicing but also aberrant splicing in disease. Computational tools such as the ESEfinder facilitate prediction of ESE sites within an exon and their expected strength of binding to SR proteins. In this work, we have created a PERL program, the EXONerator, which automates the process of mutating predicted ESE sequences to minimize their predicted strength, while simultaneously preserving the amino acid coding sequence. The EXONerator is a versatile tool that can be tailored for use as required for experimental design and greatly simplifies the process of silencing ESEs for testing their functional significance. As more information about SR proteins surfaces, the PERL coding can be easily modified to include new or refined quantitative data about RNA/protein binding.