Maintaining genome integrity is vital for cellular homeostasis, yet transcriptional processes inherently risk introducing mutations and recombination. A growing body of evidence highlights a critical but underappreciated interplay between RNA metabolism and DNA stability, largely mediated through the formation and resolution of R-loops—DNA–RNA hybrid structures that, when improperly regulated, can obstruct replication and repair mechanisms, leading to genomic instability. Central to this regulation are RNA biogenesis and processing factors, which act as suppressors of R-loops and modulators of transcription–replication conflicts.

Simultaneously, the post-transcriptional modification N6-methyladenosine (m6A) has emerged as a key epigenetic mark influencing RNA fate, including the biogenesis and function of circular RNAs (circRNAs). CircRNAs, characterized by their covalently closed loop structure, exhibit exceptional stability and have been implicated in gene regulation, immune responses, and disease pathogenesis. Recent findings suggest that m6A modifications not only influence the processing of linear mRNAs into circRNAs but also modulate circRNA function during inflammatory responses.

Moreover, extracellular vesicles (EVs)—including exosomes and other nanoparticle subtypes—serve as vehicles for the systemic transport of RNA species, including circRNAs and small RNAs. However, comprehensive transcriptomic profiling of EV-RNAs remains limited due to technical variability and a lack of standardized bioinformatic pipelines. Advances in high-throughput sequencing and integrative bioinformatics are crucial for decoding EV RNA cargo and harnessing its potential in diagnostics and therapeutics.

This review integrates emerging insights into RNA biogenesis, m6A-modified circRNA regulation, and extracellular RNA transcriptomics, underscoring their collective impact on genome stability and inflammation. We also highlight the methodological challenges and provide recommendations for improving the reproducibility and accuracy of bioinformatic analyses in this evolving field.