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Cell Rep. 2017 Aug 1;20(5):1229-1241. doi: 10.1016/j.celrep.2017.07.025.

Impact of Alternative Splicing on the Human Proteome.

Author information

1
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
2
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
3
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. Electronic address: aebersold@imsb.biol.ethz.ch.
4
The Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK. Electronic address: arv22@mrc-cu.cam.ac.uk.
5
The Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia. Electronic address: vi.wickramasinghe@petermac.org.

Abstract

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:

RNA; alternative splicing; proteomics

PMID:
28768205
PMCID:
PMC5554779
DOI:
10.1016/j.celrep.2017.07.025
[Indexed for MEDLINE]
Free PMC Article

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