exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers

Although the role of RNA binding proteins (RBPs) in extracellular RNA (exRNA) biology is well established, their exRNA cargo and distribution across biofluids are largely unknown. To address this gap, we extend the exRNA Atlas resource by mapping exRNAs carried by extracellular RBPs (exRBPs). This map was developed through an integrative analysis of ENCODE enhanced crosslinking and immunoprecipitation (eCLIP) data (150 RBPs) and human exRNA profiles (6,930 samples). Computational analysis and experimental validation identified exRBPs in plasma, serum, saliva, urine, cerebrospinal fluid, and cell-culture-conditioned medium. exRBPs carry exRNA transcripts from small non-coding RNA biotypes, including microRNA (miRNA), piRNA, tRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), Y RNA, and lncRNA, as well as protein-coding mRNA fragments. Computational deconvolution of exRBP RNA cargo reveals associations of exRBPs with extracellular vesicles, lipoproteins, and ribonucleoproteins across human biofluids. Overall, we mapped the distribution of exRBPs across human biofluids, presenting a resource for the community. [Display omitted] •Intersecting eCLIP and exRNA dataset predicts extracellular RBPs in human biofluids•Deconvolution of RNA bound by RBPs associates RBPs with exRNA carrier classes•Generated RNA-RBP coverage map of more than 6,900 biofluid samples across whole human genome•Differential release of extracellular RBPs and their isoforms across different cell types By intersecting and deconvoluting extracellular RNAs (exRNAs) and eCLIP datasets, LaPlante and Stürchler et al. predict and validate novel extracellular RNA-binding proteins (exRBPs) associated with exRNA carriers in human biofluids and cell-conditioned medium. This work dramatically expands our current view on the role of exRBPs in cell-free RNA profiles.