we used @nanopore sequencing to profile #DNAmethylation in human mitochondria in different conditions: differentiation, cancer, and oxidative stress

some details in this thread...
@goldsmith_chloe @GabrielIchim1 @harry_brennan
first, mtDNA methylation has been studied earlier by many labs, but there are some advantages of using nanopore:
long reads are aligned more specifically, use of native DNA to avoid bisulfite DNA damage, confusion with other base modifications and PCR biases...
so far we have only checked CpG context (5mCpG), while others have reported abundant non-CpG methylation...
we checked first how nanopore works to detect 5mCpG in general
nanopore correlates nicely with bead array methylation (nuclear DNA)
and two algorithms to call methylation (guppy+medaka, thanks @nanopore) and nanopolish (thanks @jaredtsimpson) give similar results
fully methylated and fully unmethylated mtDNA are properly detected
[thanks @wouter_decoster for this nice tool: methplotlib]
we did not detect 5mCpG in a liver progenitor cell line before or after differentiation...
or in a different cell line after oxidative stress
although we did not see a difference in cancer (matched normal/tumor pairs), some CpG sites are clearly methylated in both tissue types (in particular in the heavy strand)
we think that some changes are sample-specific or related to placing cells in culture,
but we welcome comments and suggestions

and stay tuned for other base modifications!

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