Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

Abstract

SUMMARY While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative ‘isoforms’ are functionally divergent (i.e., ‘functional alloforms’).

Alternative splicing and the evolution of phenotypic novelty

“…These regions may also experience stronger selection for functions related to binding-flexible sensors are more adaptable than rigid ones [74,75]-supporting an association of alternative splicing with the evolution of regulatory networks [76] (see [77] for a review of the regulatory circuits through which alternative splicing may act to regulate expression). Indeed, a comparison of the proteinprotein interaction profiles of hundreds of protein isoform pairs suggests that the majority share less than half of their interactions-the principal and alternative isoforms belong to separate functional modules, suggesting functional differences between the set of splicing isoforms produced by the same gene [65]. Taken together, these observations are consistent with a role of alternative splicing in the diversification of the proteome and the modulation of protein-protein interactions.…”

“…It is clear that alternative splicing makes a large contribution to the number of distinct transcripts produced in many speciesbut the contribution of alternative splicing to the proteome is less clear [65]. Alternative splicing can modify the properties of encoded proteins, including the set of domains it contains, its binding properties, stability, intracellular localization and enzymatic activity [66][67][68].…”

Whippet: an efficient method for the detection and quantification of alternative splicing reveals extensive transcriptomic complexity

“…Given that previous studies have illustrated the importance of AS in rewiring protein-protein interaction networks, as well as controlling additional aspects of protein function 22,23 , we hypothesized that increasing levels of AS event entropy may be associated with specific protein structural features. We observe a significant monotonic increase in the frequency of overlap with intrinsically disordered regions as a function of increasing entropy of AS events ( Fig.…”

Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale

“…Interestingly, half of the interactions in this network involved splicing variants, thereby emphasizing the importance of protein isoforms in interactome networks. An expanded study by Yang et al was the first to examine isoforms across large numbers of genes ($1500 human genes), including those involved in Mendelian diseases [66 ]. Isoforms for these genes were cloned from five different tissues and screened by Y2H against $15 000 human ORF clones to determine protein interaction profiles.…”