Advancing DNA and RNA Modification Detection via Nanopore Sequencing

DNA/RNA modifications are crucial for biological processes. To understand their regulatory mechanisms, precise mapping and quantification of these modifications are essential. Although next-generation sequencing can detect the location and stoichiometry of modifications, complex treatments are required, hindering efficiency and long-range analysis. In contrast, nanopore sequencing eliminates the need for additional treatment and PCR amplification, thus preserving DNA/RNA modification information. It enables modifications to be identified and quantified directly at the single-molecule level. Therefore, nanopore sequencing facilitates long-read, real-time modification detection, and has gained widespread applications. This perspective introduces the principles of nanopore sequencing, evaluates its strengths/weaknesses, and critically examines its broader real-world applications. To expand the utility of nanopore sequencing further, we discuss the current challenges and suggest future directions.