Conclusions

In summary, nanopore DRS has developed from a specialized tool for isoform discovery into a versatile, integrative platform capable of jointly profiling transcript structure, APA, RNA modifications, and haplotype context at the level of native RNA molecules. Across diverse biological systems, this unified molecular readout has enabled mechanistic insights that extend beyond descriptive transcript catalogues, revealing how multiple layers of RNA regulation are coordinated on individual transcripts. We present DRS not as a standalone solution to RNA biology, but as a molecule-level integrative scaffold for interrogating native RNA features across transcript structure, tailing states, and chemical signals. Within this conceptual framework, we organize the field around three key questions: (i) which biological problems are best addressed by DRS, (ii) what levels of confidence can be assigned to different classes of conclusions, and (iii) which benchmarking and validation strategies are required to ensure robustness and reproducibility. Under this trajectory, DRS is likely to become an important layer for evolutionary transcriptomics and for the development of data-driven models of RNA regulation across biological domains.