Genome-wide characterization of mitochondrial DNA methylation in human brain

Here, we present a novel approach to interrogate the mitochondrial DNA (mtDNA) methylome at single base resolution using targeted bisulfite sequencing. We applied this method to investigate mitochondrial DNA methylation patterns in post-mortem superior temporal gyrus and cerebellum brain tissue from seven human donors. We show that mitochondrial DNA methylation patterns are relatively low but conserved, with peaks in DNA methylation >5% at a number of sites and higher levels of methylation at non-CpG compared to CpG sites. We identify a number of loci that show differential DNA methylation patterns associated with age, sex and brain region. Finally we validate differences between cortical and cerebellar mitochondrial DNA methylation patterns using data previously generated using methylated DNA immunoprecipitation sequencing. We used a customized, targeted bisulfite sequencing method to assess mitochondrial DNA methylation at single nucleotide resolution in isolated mitochondrial DNA from matched cortex (superior temporal gyrus [STG]) and cerebellum [CER] brain tissue from seven donors free of neurodegenerative disease, including three males and four females.