Nucleic acid modifications are widely distributed among biological macromolecules, including DNA and RNA. They provide a complex layer of gene expression regulation by modulating transcription, RNA stability, or translation processes within the cell. To date, more than 160 chemically distinct internal, 5’- and 3’-end covalent modifications have been identified in various RNA species in prokaryotic and eukaryotic cells. However, the landscape of signals and biological roles of many of these modifications still remains unclear. Therefore, there is a need for new tools to analyse nucleic acid modifications and advance epitranscriptomic or epigenomic studies.