AquIRE reveals the mechanisms of clinically induced RNA damage and the conservation and dynamics of glycoRNAs.

RNA is subject to many modifications, from small chemical changes like methylation to conjugation of biomolecules such as glycans. As well as endogenously written modifications, RNA is also exposed to damage induced by its environment. Certain clinical compounds are known to covalently modify RNA with a growing appreciation of how these impact clinical efficacy. To understand the regulation of these modifications, we need a reliable, sensitive, and rapid methodology for their quantification. Thus, we developed Aqueous Identification of RNA Elements (AquIRE) and applied it to the analysis of drug-induced RNA damage by 5FU, oxaliplatin, and temozolomide in clinically relevant cell models. We demonstrate that RNA damage is widespread and follows previously unappreciated temporal dynamics. AquIRE also provides a highly sensitive method to detect RNAs modified by glycans. We leverage this to expand the horizons of the glycoRNA world across the kingdoms of life as well as identifying cell-free glycoRNAs in multiple species. We demonstrate that glycoRNA expression is dynamic during embryo development, modulated during senescence, and elevated by RNA-damaging agents. Finally, we use RNA digestion to demonstrate that cell surface or cell-free RNA promotes the cytotoxicity of RNA-damaging chemotherapy. Together, the AquIRE platform provides an intrinsically flexible method to study diverse RNA modifications from any sample.