Alternative splicing fine-tunes modular protein interfaces to control protein localisation

Alternative splicing provides a pervasive means to expand proteome complexity, yet how it reorganises protein interactions and constrains where proteins act within cell remains unclear. By constructing an interface-resolved interaction network composed of 17,660 experimentally defined contact sites, we reveal that tissue-specific alternative splicing remodels protein connectivity by reshaping modular protein architecture. Longer exons reshape local interaction patterns whereas microexons fine-tune key interfaces linking distinct cellular processes. Integration of subcellular localisation data further indicates that such rewiring can redistribute proteins within cells. To test this, we developed a high-content imaging approach to systematically evaluate the influence of individual exons on protein localisation and screened a targeted library of protein isoforms differing in individual exons. 38% of the tested isoform pairs altered localisation, with microexons, although typically shorter than five amino acids, accounting for a substantial proportion of these effects. Bioinformatic and structural analyses identified that microexons can extend secondary structural regions and reposition charged residues, suggesting a potential to modulate local electrostatic environments. Consistent with this, biochemical analysis of a four–amino acid microexon in sorting nexin 2 - identified through our screen - confirmed that residue insertion, rather than side chain chemistry, was driving differences in protein localisation through repositioning of a flanking, charged residue. Together, these findings describe a principle by which alternative splicing fine-tunes interface architecture to coordinate protein assembly, localisation, and proteome organisation.