Impact of alternative splicing on the human proteome

Alternative splicing is a critical determinant of genome complexity and by implication, is assumed to engender proteomic diversity. This notion has not been experimentally tested in a targeted, quantitative manner. Here, we have developed an integrative approach to ask whether dynamic perturbations in mRNA splicing patterns that follow depletion of the core spliceosome factor PRPF8 alter the composition of the proteome. We integrate RNA-sequencing (to comprehensively report intron retention, differential transcript usage and gene expression) with a newly developed data-independent acquisition (DIA) method, SWATH-MS (Sequential Window Acquisition of all THeoretical spectra – mass spectrometry), to capture an unbiased and quantitative snapshot of constitutive and alternative splicing events at the protein level. Whereas intron retention is accompanied by decreased protein abundance, dynamic alterations in differential transcript usage and gene expression alter protein abundance proportionally to transcript levels. Our findings exemplify how RNA splicing exerts a pervasive effect linking isoform expression in the human transcriptome with proteomic diversity, and provide a toolkit for studying its perturbation in human diseases.