Advances in nanopore direct RNA sequencing and its impact on biological research

Abstract

Nanopore direct RNA sequencing (DRS) is a transformative technology that enables full-length, single-molecule sequencing of native RNA, capturing transcript isoforms and preserving epitranscriptomic modifications without cDNA conversion. This review outlines key advances in DRS, including optimized protocols for mRNA, rRNA, tRNA, circRNA, and viral RNA, as well as analytical tools for isoform quantification, poly(A) tail measurement, fusion transcript identification, and base modification profiling. We highlight how DRS has redefined transcriptomic studies across diverse systems—from uncovering novel transcripts and alternative splicing events in cancer, plants, and parasites to enabling the direct detection of m6A, m5C, pseudouridine, and RNA editing events. Emerging applications such as co-transcriptional splicing analysis, lncRNA and circRNA discovery, and real-time RNA structural mapping are also discussed. Beyond basic research, DRS offers powerful capabilities in mRNA vaccine quality control and RNA-based data storage. Despite current limitations in sequencing accuracy, input requirements, and cost, ongoing improvements in nanopore chemistry, basecalling algorithms, and machine learning integration are rapidly expanding DRS utility. As it matures, DRS is poised to become a core platform for high-resolution transcriptome profiling, RNA regulatory analysis, and integrative multi-omics applications, offering novel insights into gene expression, regulation, and evolution.