Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function.
BACKGROUND
Alternative splicing often occurs in the coding sequence and alters protein structure and function. It is mainly carried out in two ways: by skipping exons that encode a certain protein feature and by introducing a frameshift that changes the downstream protein sequence. These mechanisms are widespread and well investigated.


RESULTS
Here, we propose an additional mechanism of alternative splicing to modulate protein function. This mechanism creates a protein feature by putting together two non-consecutive exons or destroys a feature by inserting an exon in its body. In contrast to other mechanisms, the individual parts of the feature are present in both splice variants but the feature is only functional in the splice form where both parts are merged. We provide evidence for this mechanism by performing a genome-wide search with four protein features: transmembrane helices, phosphorylation and glycosylation sites, and Pfam domains.


CONCLUSIONS
We describe a novel type of event that creates or removes a protein feature by alternative splicing. Current data suggest that these events are rare. Besides the four features investigated here, this mechanism is conceivable for many other protein features, especially for small linear protein motifs. It is important for the characterization of functional differences of two splice forms and should be considered in genome-wide annotation efforts. Furthermore, it offers a novel strategy for ab initio prediction of alternative splice events.
Hiller
Michael
M
Institute of Computer Science, Friedrich-Schiller-University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany. hiller@inf.uni-jena.de
Huse
Klaus
K
Platzer
Matthias
M
Backofen
Rolf
R
D017398:Alternative Splicing; D005091:Exons; D020224:Expressed Sequence Tags; D015894:Genome, Human; D006031:Glycosylation; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010766:Phosphorylation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*
D008565:Membrane Proteins; D011506:Proteins