The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A

Abstract

How individual genes are regulated from a mitochondrial polycistronic transcript to have variable expression remains an enigma. Here, through bisulfite sequencing and strand-specific mapping, we show mitochondrial genomes in humans and other animals are strongly biased to light (L)-strand non-CpG methylation with conserved peak loci preferentially located at gene-gene boundaries, which was also independently validated by MeDIP and FspEI digestion. Such mtDNA methylation patterns are conserved across different species and developmental stages but display dynamic local or global changes during development and aging. Knockout of DNMT3A alone perturbed mtDNA regional methylation patterns, but not global levels, and altered mitochondrial gene expression, copy number, and oxygen respiration. Overexpression of DNMT3A strongly increased mtDNA methylation and strand bias. Overall, methylation at gene bodies and boundaries was negatively associated with mitochondrial transcript abundance and also polycistronic transcript processing. Furthermore, HPLC-MS confirmed the methylation signals on mitochondria DNA. Together, these data provide highresolution mtDNA methylation maps that revealed a strand-specific non-CpG methylation, its dynamic regulation, and its impact on the polycistronic mitochondrial transcript processing.

Mitoepigenetics: Methylation of mitochondrial DNA is strand‐biased in bovine oocytes and embryos

“…In both groups, the L-strand presents higher and more variable methylation patterns. The strand-biased nature of mtDNA methylation has been previously described in mouse embryos and in cancer cells (Dou et al, 2019;Patil et al, 2019), and is consistent with reports examining different mtDNA loci (Bellizzi et al, 2013). However, as far as we know, it is the first time that this phenomenon is demonstrated in bovine.…”

“…However, the existence of an autonomous epigenetic control of mtDNA was controversial (Hong, Okitsu, Smith, & Hsieh, 2013;Patil et al, 2019). Finally, with improvements in detection techniques, recent studies proposed that similarly to nuclear DNA, mtDNA is also subjected to cytosine methylation (Dou et al, 2019;Patil et al, 2019). These studies have successfully demonstrated, in different models, the non-random patterns of cytosine methylation in mtDNA, predominantly observed in a non-CpG context (Dou et al, 2019).…”

Widespread Mitochondrial DNA Methylation Drift Contributes to Postoperative Delirium in Young and Old Mice

“…Theoretically, for speci c coding genes, mtDNA methylation levels negatively correlate with mitochondrial gene transcript abundance. However, mtDNA methylation drift with decreased methylation levels at most coding gene loci was observed in brains from older humans, and mitochondrial gene expression decreased with age [13]. Our data suggested that anesthesia and surgery induced mtDNA methylation drift at coding gene loci, thereby in uencing the transcriptional levels of COX1, ND2, and ND5, which encode the subunits of cytochrome c oxidase (complex IV) and NADH dehydrogenase (complex I)…”

“…In particular mtDNA is susceptible to reactive oxygen species (ROS), which are established determinants of DNA methylation modi cation on cytosine residues [11,12]. Although not completely characterized, emerging ndings have indicated that 5-methylcytosine (5-mC) in mtDNA can be detected in approximately 2-18% of CpG and non-CpG sites using bisul te conversion and pyrosequencing, and mitochondrially targeted DNA methyltransferase 1 (DNMT1) and DNMT3A are suggested to be responsible [13,14].…”

“…In prefrontal cortex (PFC) samples, mtDNA methylation at most elements decreases signi cantly with age. Thus, mtDNA copy numbers and mitochondrial gene expression increase and decrease with age, respectively [13]. However, no data have reported mitochondrial 5-mC levels in speci c brain regions associated with cognition, consciousness, attention, and emotion, such as the PFC, hippocampus, amygdala, and anterior cingulate cortex (ACC), in postoperative delirium.…”