Mapping of HOCl-oxidized RNA identifies abasic sites as major damage and oxidation product of oxo8G

Marlies Weber, Kasturi Raorane, Clara Johanna Grampp, Valérie Bourguignon, Lea-Marie Kilz, David Glänzer, Virginie Marchand, Christoph Kreutz, Yuri Motorin () and Mark Helm ()
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Marlies Weber: Johannes Gutenberg-University Mainz, Institute of Pharmacy and Biomedical Sciences, Staudingerweg
Kasturi Raorane: IMoPA UMR7365, Université de Lorraine CNRS
Clara Johanna Grampp: Johannes Gutenberg-University Mainz, Institute of Pharmacy and Biomedical Sciences, Staudingerweg
Valérie Bourguignon: IMoPA UMR7365, Université de Lorraine CNRS
Lea-Marie Kilz: Johannes Gutenberg-University Mainz, Institute of Pharmacy and Biomedical Sciences, Staudingerweg
David Glänzer: Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82 6020
Virginie Marchand: UAR2008 IBSLor Epitranscriptomics and RNA Sequencing Core Facility, Université de Lorraine CNRS, INSERM
Christoph Kreutz: Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82 6020
Yuri Motorin: IMoPA UMR7365, Université de Lorraine CNRS
Mark Helm: Johannes Gutenberg-University Mainz, Institute of Pharmacy and Biomedical Sciences, Staudingerweg

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract RNA oxidation is an important yet understudied process, partly because methods to localize oxidized residues in RNA are lacking. We introduce OAbSeq, a deep-sequencing approach that maps oxidized sites with high sensitivity by exploiting aniline-induced strand scission at noncanonical nucleosides to generate unique ligation-competent fragments utilized for library preparation. Applied to yeast RNA, OAbSeq detects widespread signals predominating at purines, especially at guanosines. Exogenous oxidation increased signal intensity but preserved the guanosine-dominated pattern. Parallel quantification of 8-oxoguanosine (oxo8G) and abasic sites revealed that abasic sites are more abundant than oxo8G following oxidative treatment in vitro and under physiological conditions. These data support a model in which guanosine oxidation proceeds via transient oxo8G yielding abasic sites that can be mapped at nucleotide resolution by OAbSeq. Our findings also suggest abasic sites may be a more informative marker of RNA oxidative damage than oxo8G, facilitating studies of RNA oxidation dynamics in cells.

Date: 2025
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DOI: 10.1038/s41467-025-65108-0

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