Kassiopeia: a database and web application for the analysis of mutually exclusive exomes of eukaryotes

Abstract

BackgroundAlternative splicing is an important process in higher eukaryotes that allows obtaining several transcripts from one gene. A specific case of alternative splicing is mutually exclusive splicing, in which exactly one exon out of a cluster of neighbouring exons is spliced into the mature transcript. Recently, a new algorithm for the prediction of these exons has been developed based on the preconditions that the exons of the cluster have similar lengths, sequence homology, and conserved splice sites, and that they are translated in the same reading frame.DescriptionIn this contribution we introduce Kassiopeia, a database and web application for the generation, storage, and presentation of genome-wide analyses of mutually exclusive exomes. Currently, Kassiopeia provides access to the mutually exclusive exomes of twelve Drosophila species, the thale cress Arabidopsis thaliana, the flatworm Caenorhabditis elegans, and human. Mutually exclusive spliced exons (MXEs) were predicted based on gene reconstructions from Scipio. Based on the standard prediction values, with which 83.5% of the annotated MXEs of Drosophila melanogaster were reconstructed, the exomes contain surprisingly more MXEs than previously supposed and identified. The user can search Kassiopeia using BLAST or browse the genes of each species optionally adjusting the parameters used for the prediction to reveal more divergent or only very similar exon candidates.ConclusionsWe developed a pipeline to predict MXEs in the genomes of several model organisms and a web interface, Kassiopeia, for their visualization. For each gene Kassiopeia provides a comprehensive gene structure scheme, the sequences and predicted secondary structures of the MXEs, and, if available, further evidence for MXE candidates from cDNA/EST data, predictions of MXEs in homologous genes of closely related species, and RNA secondary structure predictions. Kassiopeia can be accessed at http://www.motorprotein.de/kassiopeia.

Mutually exclusive alternative splicing of pre‐mRNAs

“…In C. elegans, 389 MXEs in 138 genes were predicted, 313 of which are internal exons . Very recently, 1,399 human MXEs were predicted, 855 of which have been confirmed by transcriptomic evidence (Hatje et al, 2017). Among these 1,399 MXEs, 1,116 belong to clusters of two exons, whereas 71 clusters contain more than two exons, with a maximum of 10 MXEs detected (Hatje et al, 2017).…”

“…Afterwards, this analysis was expanded for other genomes. In C. elegans , 389 MXEs in 138 genes were predicted, 313 of which are internal exons (Hatje & Kollmar, ). Very recently, 1,399 human MXEs were predicted, 855 of which have been confirmed by transcriptomic evidence (Hatje et al, ).…”

“…A considerable number of clusters have undergone species‐specific gains and losses. For example, only 24.2% of all unique clusters are conserved in Drosophila species, while 59.2% of clusters are unique to certain species (Hatje & Kollmar, ). Moreover, the middle MXE in 14‐3‐3ξ is specific to the Drosophila simulans complex species (Yang et al, ).…”

“…, and human CD55 (Hatje et al, 2017;Figure 2). Importantly, mutually exclusive splicing offers a fascinating model that can be used to elucidate the regulatory mechanisms and significance of alternative splicing, such as those of tropomyosin (Gooding & Smith, 2008) and Dscam (Graveley, 2005).…”

“…The total number of potential isoforms is indicated on the right. Genomic organizations containing MXEs have been described in Drosophila melanogaster Dscam (Schmucker et al, 2000), D. melanogaster Mhc (Bernstein, Mogami, Donady, & Emerson, 1983), D. melanogaster multidrug resistance-associated protein 1 (MRP1) (Grailles, Brey, & Roth, 2003), Manduca sexta Spn4 (Jiang et al, 1996), Branchiostoma floridae MRP (Yue et al, 2017), and human CD55 (Hatje et al, 2017) single-cell RNA-sequencing (RNA-seq) data (Song et al, 2017). Recently, we and other researchers have indicated that the formation of long-range RNA secondary structures is involved in mutually exclusive splicing (Anastassiou, Liu, & Varadan, 2006;Graveley, 2005;May, Olson, McManus, & Graveley, 2011;Yang et al, 2011;Yue et al, 2016Yue et al, , 2017.…”