1. RNA Biogenesis and Genome Integrity

The process of RNA biogenesis is tightly coupled with transcription and DNA replication. However, disruptions during transcription can form R-loops—structures composed of an RNA–DNA hybrid and a displaced single-stranded DNA—which, if unresolved, can threaten genome integrity by obstructing replication fork progression and repair mechanisms [1,2]. Studies have shown that components such as DDX5, RNase H1, and senataxin (SETX) play a vital role in resolving R-loops [3,4].

Table 1. Key RNA Biogenesis Factors Involved in R-Loop Suppression

Failure of these regulators can lead to replication stress and double-strand breaks, hallmarks of genome instability in diseases such as cancer and neurodegeneration [6,7].

2. m6A Modification in circRNA Biogenesis and Function

The m6A modification is the most prevalent internal RNA modification in eukaryotic cells, significantly impacting mRNA splicing, transport, degradation, and translation [8,9]. It also influences the biogenesis of circRNAs—covalently closed, stable RNAs that arise from back-splicing events. m6A modifications promote efficient circRNA production and alter their cellular functions, including immune response regulation and inflammation [10,11].

Table 2. Key Components in m6A Modification

In inflammatory diseases, circRNAs such as circZNF609 and circHIPK2 have shown altered expression linked to m6A regulation, suggesting therapeutic potential [12,13]. Furthermore, m6A-modified circRNAs serve as sponges for miRNAs or protein scaffolds, modulating inflammation and immune cell signaling [14].

3. Extracellular Vesicles as RNA Carriers in Inflammation

Extracellular vesicles (EVs), including exosomes, microvesicles, and apoptotic bodies, facilitate intercellular communication by delivering nucleic acids and proteins [15,16]. EV-associated RNAs (EV-RNAs) include mRNAs, miRNAs, and circRNAs, all implicated in immune modulation and disease biomarkers. However, variability in isolation protocols and data processing has hindered reproducibility across EV studies [17].

Emerging sequencing tools and computational platforms are essential to map EV-RNA landscapes and establish their diagnostic value in inflammation and cancer [18].

Table 3. Bioinformatic Tools for circRNA and m6A Detection

 Proper computational analysis, including normalization and quality control, is critical to interpreting the biological significance of EV-RNA cargo [19,20].

 4. Challenges and Future Directions

Despite growing interest, significant hurdles remain in linking RNA regulatory mechanisms to disease. These include the need for:

·                     Standardized protocols for EV-RNA isolation

·                     Cross-platform reproducibility of m6A-circRNA sequencing

·                     Comprehensive bioinformatic pipelines for R-loop prediction

Combining molecular biology with machine learning–based analytics could yield new insights into RNA-based regulation of inflammation and genome maintenance [23,24].

5. Conclusion

The intersection of RNA biogenesis, epitranscriptomic modification, and extracellular transport provides a complex yet promising framework to understand genomic integrity and inflammatory disorders. A deeper understanding of R-loop resolution mechanisms, m6A-modified circRNAs, and extracellular RNA profiling—supported by robust bioinformatic tools—can pave the way for novel biomarkers and therapeutic strategies. Addressing current gaps in methodology and data interpretation will be key to translating these discoveries into clinical applications.

6. Conflict of Interest

The authors declare no conflict of interest.

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