Unbiased identification of TRAP1 RNA ligands in high grade serous ovarian cancer cells by eCLIP

The cancer-linked chaperone TRAP1 has been mainly characterized for its regulatory role on respiratory complex activity and mRNA translation rate, while its specific function as an RNA-binding protein (RBP) remains unclear. In this study, we confirmed the RNA-binding of TRAP1 in living cells using both protein- and RNA-centric approaches and demonstrated that multiple TRAP1 regions cooperate in such binding. Enhanced cross-linking and immunoprecipitation in high-grade serous ovarian cancer cells revealed that TRAP1 primarily binds cytosolic protein-coding genes, with the majority encoding for splicing-related factors. Notably, among TRAP1 most significantly bound transcripts, we identified the splicing factor LUC7L3, a U1 snRNP component involved in cell proliferation. We confirmed TRAP1 binding to LUC7L3 transcript by RIP-qPCR and showed that TRAP1 promotes LUC7L3 mRNA translation. Furthermore, we demonstrated that TRAP1 enhances ovarian cancer cell proliferation through LUC7L3 translational regulation. In summary, our findings provide the first comprehensive characterization of TRAP1 as an RNA-binding protein, offering new insights into its multifaceted roles in cancer biology.