UC San Diego

RNA can contain over 170 modified bases, adding another layer of information to transcripts and informing their functional outcomes in the cell. The function of many RNA modifications remains unknown, as well as how these modifications impact interactions between RNA and proteins. RNA binding proteins (RBPs) are a class of proteins that bind to RNA and are involved in all aspects of the RNA lifecycle. The ENCODE project has generated eCLIP data for 150 RBPs, revealing the binding locations of RBPs across the transcriptome. We leverage this dataset to compare where RBP binding overlaps with RNA modifications to infer interactions and identify functions of the modifications. We identified novel RBP interactions with the common mRNA modifications pseudouridine and m6A. m6A has been found to be dysregulated in cancer and is being investigated as a target for new therapeutics. To interrogate patterns of m6A deposition in cancer, m6A-eCLIP was performed on the NCI-60 cell lines. We identified common m6A peaks in oncogenes that could be targets for new treatments. This work will allow further studies of RNA modification-RBP interactions and their role in cancer progression.