A systematic analysis of the effects of splicing on the diversity of post-translational modifications in protein isoforms

Abstract

Post-translational modifications (PTMs) and splicing are known to be important regulatory processes for controlling protein function and activity. However, there have been limitations in analyzing the interplay of alternative splicing and PTMs, both from the standpoint of PTM presence and in the possible diversification of the regulatory windows of PTMs, which define the connection to regulatory enzymes and possible binding partners. Limitations stem from the deep differences in genomic and proteomic databases, where PTMs are predominantly identified by mass spectrometry and subsequently assigned to the canonical isoform of the protein in databases. In this work, we bridge the protein- and genome-centric world views to map PTMs to genomic locations for subsequent projection of PTMs onto alternative isoforms. We then perform a systematic analysis of the diversification of PTMs within all defined protein isoforms, focusing on the PTM-specific profiles that may differ across the various major modifications found in humans, including exploration of how often alternative splicing leads to diversification of the regulatory sequences directly flanking a PTM. We found the interplay between splicing and PTMs is PTM-specific across a range of behaviors, such as PTM inclusion rates across isoforms and tissues. Additionally we found that ~2% of prospective PTM sites exhibited altered regulatory sequences surrounding the modification site, suggesting that regulatory or binding interactions might be diversified in these proteoforms. In addition to exploring isoforms as defined by Ensembl, we applied this PTM-to-isoform mapping approach to explore the impacts of disease-related splicing in prostate cancer, identifying possible new hypotheses as to the variable mechanisms of ESRP1 expression in different cancers.