Nanopore Sequencing for Epigenetic Decoding: Applications, Analytical Constraints, and Translational Prospects

Epigenetic regulation involves multiple molecular layers, including DNA and RNA modifications, histone post-translational modifications (PTMs), and chromatin accessibility. These processes contribute to cell identity, development, and disease, but their measurement remains technically challenging because sequence context, molecular modification, chromatin state, and transcript structure are often assayed separately. As a representative third-generation sequencing technology, nanopore sequencing is profoundly reshaping the interpretation of the epigenetic code through its distinctive capabilities, including long-read sequencing, direct single-molecule signal detection, and the identification of nucleic acid modifications without bisulfite conversion or PCR in appropriate workflows. This review summarizes applications of nanopore sequencing in epigenomics and epitranscriptomics and evaluates emerging nanopore-based approaches for protein and histone sensing. We focus on what can currently be measured, the experimental and computational requirements for reliable decoding, and the limitations that must be addressed before broader multi-omic and clinical use.