Meta-analysis of cellular phosphoproteome datasets exploring phospho-signaling associated with the RNA-binding protein RAVER1

RAVER1 is a conserved PTBP1-associated regulator of alternative splicing with emerging roles in cytoskeletal organisation and proliferative signaling. Despite the central role of phosphorylation in intracellular signaling, phospho-dependent regulation of RAVER1 remains poorly defined. To address this gap, we performed a comprehensive meta-analysis of global human cellular phosphoproteome datasets to characterise RAVER1 phosphorylation and its associated signaling networks. Class I phosphosites were systematically compiled, and phosphosite-centric analyses were conducted to evaluate site predominance, co-occurrence patterns, phosphoproteome-wide co-regulation, and predicted upstream kinase associations. Thirteen Class I phosphosites were identified, of which S14, S17, and T463 emerged as predominant based on consistent detection across profiling and differential datasets. Significant phosphosite co-occurrence among S6, T8, and S14 within the N-terminal region suggests coordinated, context-dependent regulation and functional association of these sites. Phosphoproteome-wide co-regulation analysis linked RAVER1 phosphorylation states to proteins involved in RNA processing, cell-cycle regulation, and DNA repair. Kinase-oriented analyses identified CDK family members (CDK9, CDK12, and CDK13) as high-confidence predicted upstream kinases for RAVER1 S14. Notably, phosphosites in several epithelial–mesenchymal transition (EMT)-associated regulators, including KDM1A, VIM, and PTK2, showed positive co-regulation with RAVER1 phosphosites, consistent with multi-omics perturbation datasets reporting EMT-associated changes upon RAVER1 depletion. To our knowledge, this study provides the first phospho-signaling map of RAVER1 and establishes a phosphosite-centric analytical framework for functional investigation of RAVER1 phosphorylation, with potential implications for targeted therapeutic strategies.