Oxford Nanopore PromethION methylation sequencing of several species

DNA methylation is an important epigenetic mark playing a role in many biological processes. Historically, the methylation microarray has been the gold standard approach for initial methylation discovery work. While cost effective, the microarray is not without its downsides. For example, the microarray only queries a fraction of the CpG methylation sites in the human genome, exhibits considerable batch-to-batch variability, is limited to only human and mouse samples, and lacks the flexibility to interrogate multiple epigenetic marks simultaneously. Low pass Oxford Nanopore Technologies sequencing is poised to overcome these limitations. Here, we show the ability of Oxford Nanopore sequencing to cover more than 96% of CpG sites in the human genome at an average depth of 5x. We also show similar coverage of methylation sites in several other species without an out-of-the box microarray assay. Additionally, we show the limited batch effects of replicate samples run at multiple locations with this long-read sequencing technology. Finally, we demonstrate the ability of this technology to discriminate between two epigenetic marks with the same data.