Development of long-read whole genome methylation sequencing method using the enzymatic base conversion and the nanopore sequencing

We developed nanoEM, a novel method for long-read whole genome methylation analysis from low DNA input, by combining enzymatic base conversion and nanopore sequencing. Firstly, to benchmark enzymatic base conversion, we performed whole genome bisulfite sequencing (WGBS) and enzymatic methyl sequencing in two breast cancer cell lines MDA-MB-231 and BT-474 using Illumina NovaSeq6000. We performed nanoEM using 1-50 ng of genomic DNA in the cell lines. We also performed whole genome sequencing from 1.5 microgram of DNA using nanopore sequencer and CpG methylation calling using nanopolish as comparison data.