Nanopore DNA sequencing of a human liver progenitor-like cell line

Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mCpG has a regulatory role in this context. The main aim of this work was to develop and validate a novel tool for determining methylation of mtDNA and to corroborate its existence across different biological contexts. Here, we profiled the human hepatocyte-like progenitor cell line HepaRG, before and after in vitro differentiation, using long-read nanopore sequencing. Overall design: HepaRG cell were differentiated in vitro in three independent wells. mtDNA was enriched by sequential gradient centrifugation and, after linearization with BamH1, samples were barcoded and sequenced with a MinION device (ONT).