R-loops, RNA:DNA hybrids formed during transcription, play critical roles in regulating gene expression and maintaining genome stability. Dysregulation of R-loop formation and resolution has been linked to genomic instability, a hallmark of cancer. Recent advances have highlighted the pivotal role of non-coding RNAs (ncRNAs), particularly long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), in modulating R-loop dynamics, influencing tumorigenesis, and contributing to therapeutic resistance. These ncRNAs participate in the formation, stabilization, and resolution of R-loops, which in turn regulate critical processes such as transcriptional regulation, DNA repair, and chromatin architecture. For example, circRNAs such as circSMARCA5 and circDMD have been shown to induce R-loop formation, influencing gene expression and sensitizing cancer cells to chemotherapy. Conversely, lncRNAs such as TUG1 and NEAT1 regulate R-loop resolution, maintaining genome stability and enhancing tumor cell survival. The interaction between ncRNAs and R-loops offers promising avenues for targeted therapeutic strategies aimed at restoring R-loop balance to improve cancer treatment outcomes. This review provides an in-depth exploration of the molecular mechanisms by which ncRNAs modulate R-loop dynamics and discusses their potential as biomarkers and therapeutic targets in oncology. Furthermore, we highlight the challenges and future directions in translating these findings into clinical applications.

R-loop  /  ncRNA  /  Cancer  /  Gene regulation  /  Molecular mechanism  /  Genome instability  /  DNA damage response  /  Therapeutic resistance