Publication Date
5-10-2023
Journal
Cell Genomics
DOI
10.1016/j.xgen.2023.100303
PMID
37228754
PMCID
PMC10203258
PubMedCentral® Posted Date
4-20-2023
PubMedCentral® Full Text Version
Post-print
Published Open-Access
yes
Keywords
cell-free RNAs, RNA binding proteins, eCLIP, human biofluids, RNA footprint correlation, liquid biopsies, public resource, exRNA carriers, cell-free biomarkers, NIH ERCC
Abstract
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.
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Biochemistry, Biophysics, and Structural Biology Commons, Biology Commons, Genetic Phenomena Commons, Genetic Processes Commons, Medical Genetics Commons, Medical Specialties Commons
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