The role of non-coding oligonucleotides in DNA repair regulation

<p dir="ltr">The integrity of DNA is constantly threatened by damaging effects from exoge- nous and endogenous sources. Genetic alterations can cause neurodegenerative disorders or premature aging, while genomic instability is a major contributor to cancer evolution. Human cells possess multiple pathways to repair damaged DNA and thereby preserve genomic integrity. Increasing evidence suggests a role for non-coding RNAs in the regulation of DNA repair pathway choice - either directly via binding to repair proteins or indirectly via transcriptional or splicing regulation.</p><p dir="ltr">In Paper I we studied the function of the small Cajal body-associated RNA scaRNA2 in DNA repair. We show that scaRNA2 binds the DNA repair kinase DNA- PKcs and thereby prevents formation of the catalytically active DNA-PK complex. Inhibition of DNA-PK reduces the activity of non-homologous end-joining and promotes repair of DNA double-strand breaks by homologous recombination. Our results suggest that the inhibitory activity of scaRNA2 on DNA-PK complex for- mation is at least partially regulated by the scaRNA-binding protein WRAP53B, which we show to sequester scaRNA2 away from DNA-PKcs.</p><p dir="ltr">Paper II is a study of DNA repair dysregulation by synthetic antisense oligonucle- otides. Antisense oligonucleotides containing a phosphorothioate-modified backbone have been shown to recruit various proteins which leads to the for- mation of liquid-liquid phase separated nuclear structures called PS bodies. We show that PS bodies sequester and activate DNA double-strand break repair pro- teins. This type of sequestration seems to be especially detrimental to the repair of bona fide DNA damage by homologous recombination and leads to the accu- mulation of unrepaired DNA damage over time.</p><p dir="ltr">Paper III is a continuation of the study in Paper I. We extended our observations to other scaRNA family members and revealed that various scaRNAs bind to DNA repair proteins. The interaction between scaRNAs and repair factors is promoted by their co-localization at specific nuclear sites. Loss of this interaction leads to the induction of DNA damage at telomeres. We propose that scaRNAs regulate the DNA damage response at telomeres via direct interactions with repair proteins and suggest a novel, non-canonical role for scaRNAs in DNA repair regulation.</p><p dir="ltr">Overall, the results described in Papers I to III highlight the regulation of DNA dam- age repair by non-coding nucleotide polymers - from endogenous or synthetic origin. In Papers I and III we suggest novel functions for scaRNAs and Cajal bodies in the regulation of DNA repair beyond their previously described canonical func- tions in RNA modification. The results in Paper II suggest dysregulation of DNA damage repair by PS-modified ASOs, highlighting the need for special considera- tion of this mechanism during drug development.</p><h3 dir="ltr">List of scientific papers</h3><p dir="ltr">I. Bergstrand, S *., O'Brien E. M .*, Coucoravas, C., Hrossova, D., Peirasmaki, D., <b>Schmidli, S.</b>, Dhanjal, S., Pederiva, C., Siggens, L., Mortusewicz, O., O'Rourke, J. J., Farnebo, M. Small Cajal body-associated RNA2 (scaRNA2) regulates DNA repair pathway choice by inhibiting DNA-PK. Nature Communications, 2022, 13(1), 1015. <a href="https://doi.org/10.1038/s41467-022-28646-5" rel="noreferrer" target="_blank">https://doi.org/10.1038/s41467-022-28646-5</a></p><p dir="ltr">II. Hjelmgren, L., Zhou, Q., <b>Schmidli, S.</b>, Gloudemans, M., Czapik, T., Roudi, S., Honcharenko, M., Hagey D. W., EL Andaloussi, S., Farnebo, M. Dysregulation of the DNA damage response by phosphorothioate antisense oligonucleotides. Nature Communications, 2026, 17(1), 2111. <a href="https://doi.org/10.1038/s41467-026-69980-2" rel="noreferrer" target="_blank">https://doi.org/10.1038/s41467-026-69980-2</a></p><p dir="ltr">III. <b>Schmidli, S.</b>, Zhou, Q., Hjelmgren, L., Pederiva, C., Islam, M. S., Gus- tafsson, O., Williams, R. L., EL Andaloussi, S., Farnebo, M. Small Cajal body-associated RNAs control the DNA damage response at telo- meres. [Manuscript]</p><p dir="ltr">* These authors contributed equally to this work</p>