Cell Reports
Volume 20, Issue 5, 1 August 2017, Pages 1229-1241
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Impact of Alternative Splicing on the Human Proteome

https://doi.org/10.1016/j.celrep.2017.07.025Get rights and content
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Highlights

  • Integrative approach to study contribution of alternative splicing to proteome

  • Changes in isoform usage alter protein abundance proportionate to transcript levels

  • Intron retention is accompanied by decreased protein abundance

  • Differential gene expression functionally tunes the human proteome

Summary

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 perturbations in mRNA splicing patterns alter the composition of the proteome. We integrate RNA sequencing (RNA-seq) (to comprehensively report intron retention, differential transcript usage, and gene expression) with a data-independent acquisition (DIA) method, SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry), to capture an unbiased, quantitative snapshot of the impact of constitutive and alternative splicing events on the proteome. Whereas intron retention is accompanied by decreased protein abundance, alterations in differential transcript usage and gene expression alter protein abundance proportionate to transcript levels. Our findings illustrate how RNA splicing links isoform expression in the human transcriptome with proteomic diversity and provides a foundation for studying perturbations associated with human diseases.

Keywords

alternative splicing
proteomics
RNA

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