Decoding the epigenome with Oxford Nanopore real-time methylation detection

Oxford Nanopore sequencing enables accurate real-time detection of modifications in DNA and RNA without the need for chemical or enzymatic alterations. Nanopore methylation detection seamlessly integrates with native DNA or RNA sequencing, eliminating the necessity for additional library preparation. Our advanced basecaller, Dorado, accurately calls bases and modifications simultaneously, simplifying the workflow. For interpretation, we offer modkit — a tool for processing modification BAM files and generating summary statistics. This streamlined analysis workflow answers key questions in epigenetics and broader biological enquiries.

In this Knowledge Exchange, we focus on the relevance of modifications, particularly DNA methylation at the fifth position of cytosine (5mC), in studying disease mechanisms in humans. We present benchmarking results against other techniques and cover essential information for modification analysis, including modkit's new features. Lastly, we showcase the benefits of using native Oxford Nanopore sequencing for modification calling in real-world applications with high accuracy reads.

Authors: Rocio Esteban, Arthur Rand, and Sayonika Mohanta