Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology

Holger Pillmann,Florian Odronitz,Klas Hatje,Martin Kollmar,Björn Hammesfahr

doi:10.1186/1471-2105-12-270

Holger Pillmann, Florian Odronitz + Show 3 more

Open Access

https://doi.org/10.1186/1471-2105-12-270

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Abstract

BackgroundAlternative splicing of pre-mature RNA is an important process eukaryotes utilize to increase their repertoire of different protein products. Several types of different alternative splice forms exist including exon skipping, differential splicing of exons at their 3'- or 5'-end, intron retention, and mutually exclusive splicing. The latter term is used for clusters of internal exons that are spliced in a mutually exclusive manner.ResultsWe have implemented an extension to the WebScipio software to search for mutually exclusive exons. Here, the search is based on the precondition that mutually exclusive exons encode regions of the same structural part of the protein product. This precondition provides restrictions to the search for candidate exons concerning their length, splice site conservation and reading frame preservation, and overall homology. Mutually exclusive exons that are not homologous and not of about the same length will not be found. Using the new algorithm, mutually exclusive exons in several example genes, a dynein heavy chain, a muscle myosin heavy chain, and Dscam were correctly identified. In addition, the algorithm was applied to the whole Drosophila melanogaster X chromosome and the results were compared to the Flybase annotation and an ab initio prediction. Clusters of mutually exclusive exons might be subsequent to each other and might encode dozens of exons.ConclusionsThis is the first implementation of an automatic search for mutually exclusive exons in eukaryotes. Exons are predicted and reconstructed in the same run providing the complete gene structure for the protein query of interest. WebScipio offers high quality gene structure figures with the clusters of mutually exclusive exons colour-coded, and several analysis tools for further manual inspection. The genome scale analysis of all genes of the Drosophila melanogaster X chromosome showed that WebScipio is able to find all but two of the 28 annotated mutually exclusive spliced exons and predicts 39 new candidate exons. Thus, WebScipio should be able to identify mutually exclusive spliced exons in any query sequence from any species with a very high probability. WebScipio is freely available to academics at http://www.webscipio.org.

Highlights

Alternative splicing of pre-mature RNA is an important process eukaryotes utilize to increase their repertoire of different protein products
Since the first description of alternative splicing of precursor mRNA almost 30 years ago [2,3] the suggested and verified percentage of human genes that are spliced into alternative transcripts has steadily risen
Identification of mutually exclusive spliced exons The search for mutually exclusive spliced exons is based on three criteria: (1) The lengths of the mutually exclusive exons must be very similar, because these exons are supposed to code for the same part in the resulting protein structure, including identical secondary structural elements

Summary

Introduction

Alternative splicing of pre-mature RNA is an important process eukaryotes utilize to increase their repertoire of different protein products. Several types of different alternative splice forms exist including exon skipping, differential splicing of exons at their 3’- or 5’-end, intron retention, and mutually exclusive splicing The latter term is used for clusters of internal exons that are spliced in a mutually exclusive manner. Eukaryotes can enhance their repertoire of different protein products by alternative splicing of the corresponding genes [1]. Recent analyses have shown that this mechanism might be based on intra-intronic RNA pairings that are conserved at the secondary structure level [14,15,16] These alternatively spliced exons must not be mixed up with exons that seem to be spliced in a mutually exclusive manner based on their annotation. The regulation of the splicing of these types need not be at the level of splicing

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