Pseudouridine is one of the most abundant and evolutionarily conserved RNA modifications, playing a critical role in enhancing RNA stability, proper folding, and function. It is implicated in various cellular processes including translation regulation and stress responses [1].
Urban particulate matter (PM) exposure is known to induce cellular stress, and emerging studies suggest that environmental factors may influence RNA modifications. Evaluating how PM exposure affects pseudouridine patterns can shed light on adaptive stress responses at the RNA level.
Different sequencing platforms can detect Ψ modifications with varying sensitivity and specificity. For instance, nanopore direct RNA sequencing offers isoform-specific and transcriptome-wide data, whereas BID‑Seq (a next-generation sequencing method) provides genome-based modification information [2,3].
This technology directly sequences native RNA molecules by passing them through nanopores and detecting changes in electrical current. It offers the advantage of capturing isoform-specific information in real time and can detect RNA modifications by their signature on the current, providing a high-resolution view of the RNA landscape [2].
In BID‑Seq, RNA is treated with sodium bisulfite to convert unmodified uridines (U) into cytidines (C), while pseudouridines (Ψ) resist conversion. Although it operates at the genome level (reporting genomic coordinates), it provides highly specific signals for the presence of modifications. However, it may not capture isoform-specific details as clearly as Nanopore [3].