Emerging gene therapy approaches that aim to eliminate pathogenic mutations of mitochondrial DNA (mtDNA) rely on efficient degradation of linearized mtDNA, but the enzymatic machinery performing this task is presently unknown. Here, we show that, in cellular models of restriction endonuclease-induced mtDNA double-strand breaks, linear mtDNA is eliminated within hours by exonucleolytic activities. Inactivation of the mitochondrial 5′-3′exonuclease MGME1, elimination of the 3′-5′exonuclease activity of the mitochondrial DNA polymerase POLG by introducing the p.D274A mutation, or knockdown of the mitochondrial DNA helicase TWNK leads to severe impediment of mtDNA degradation. We do not observe similar effects when inactivating other known mitochondrial nucleases (EXOG, APEX2, ENDOG, FEN1, DNA2, MRE11, or RBBP8). Our data suggest that rapid degradation of linearized mtDNA is performed by the same machinery that is responsible for mtDNA replication, thus proposing novel roles for the participating enzymes POLG, TWNK, and MGME1.

Scope Alterations in DNA methylation patterns are correlated with aging, environmental exposures, and disease pathophysiology; the possibility of reverting or preventing these processes through dietary intervention is gaining momentum. In particular, methyl donors that provide S‐adenosyl‐methionine for one‐carbon metabolism and polyphenols such as flavanols that inhibit the activity of DNA methyltransferases (DNMTs) can be key modifiers of epigenetic patterns. Methods and results DNA methylation patterns are assessed in publicly available Illumina Infinium 450K methylation datasets from intervention studies with either folic acid + vitamin B12 (GSE74548) or monomeric and oligomeric flavanols (MOF) (GSE54690) in 44 and 13 participants, respectively. Global DNA methylation levels are increased in unmethylated regions such as CpG islands and shores following folic acid + vitamin B12 supplementation and decreased in highly methylated regions, including shelves and open‐seas, following intervention with MOF. After supplementation with folic acid + vitamin B12, epigenetic age, estimated by the Horvath “epigenetic clock” model, is reduced in women with the MTHFR 677CC genotype. Conclusions The effects of supplementation with folic acid + vitamin B12 and MOF on DNA methylation age are dependent upon gender and MTHFR genotype. Additionally, the findings demonstrate the potential for these dietary factors to modulate global DNA methylation profiles.

Epigenetic clocks are mathematically derived age estimators that are based on combinations of methylation values that change with age at specific CpGs in the genome. These clocks are widely used to measure the age of tissues and cells1,2. The discrepancy between epigenetic age (EpiAge), as estimated by these clocks, and chronological age is referred to as EpiAge acceleration. Epidemiological studies have linked EpiAge acceleration to a wide variety of pathologies, health states, lifestyle, mental state and environmental factors2, indicating that epigenetic clocks tap into critical biological processes that are involved in aging. Despite the importance of this inference, the mechanisms underpinning these clocks remained largely uncharacterized and unelucidated. Here, using primary human cells, we set out to investigate whether epigenetic aging is the manifestation of one or more of the aging hallmarks previously identified3. We show that although epigenetic aging is distinct from cellular senescence, telomere attrition and genomic instability, it is associated with nutrient sensing, mitochondrial activity and stem cell composition.

Background: The association between obesity and cardiovascular disease (CVD) is proven, but why some adults with obesity develop CVD while others remain disease-free is poorly understood. Here, we investigated whether mitochondrial DNA (mtDNA) methylation in platelets is altered prior to CVD development in a population of adults with overweight and obesity. Methods: We devised a nested case-control study of 200 adults with overweight or obesity who were CVD-free at baseline, of whom 84 developed CVD within 5 years, while 116 remained CVD-free. Platelet mtDNA was isolated from plasma samples at baseline, and mtDNA methylation was quantified in mitochondrially encoded cytochrome-C-oxidase I (MT-CO1; nt6797 and nt6807), II (MT-CO2; nt8113 and nt8117), and III (MT-CO3; nt9444 and nt9449); tRNA leucine 1 (MT-TL1; nt3247 and nt3254); D-loop (nt16383); tRNA phenylalanine (MT-TF; nt624); and light-strand-originof-replication (MT-OLR; nt5737, nt5740, and nt5743) by bisulfite-pyrosequencing. Logistic regression was used to estimate the contribution of mtDNA methylation to future CVD risk. ROC curve analysis was used to identify the optimal mtDNA methylation threshold for future CVD risk prediction. A model was generated incorporating methylation at three loci (score 0, 1, or 2 according to 0, 1, or 2-3 hypermethylated loci, respectively), adjusted for potential confounders, such as diastolic and systolic blood pressure, fasting blood glucose, and cholesterol ratio. mtDNA methylation at MT-CO1 nt6807 (OR = 1.08, 95% CI 1.02-1.16; P = 0.014), MT-CO3 nt9444 (OR = 1.22, 95% CI 1.02-1.46, P = 0.042), and MT-TL1 nt3254 (OR = 1.30, 95% CI 1.05-1.61, P = 0.008) was higher at baseline in those who developed CVD by follow-up, compared with those who remained CVD-free. Combined use of the three loci significantly enhanced risk prediction, with hazard ratios of 1.38 (95% CI 0.68-2.78) and 2.68 (95% CI 1.41-5.08) for individuals with score 1 or 2, respectively (P = 0.003). Methylation at these sites was independent of conventional CVD risk factors, including inflammation markers, fasting blood glucose concentration, and blood pressure. Conclusions: Methylations of MT-CO1, MT-CO3, and MT-TL1 are, together, strong predictors of future CVD incidence. Since methylation of these mtDNA domains was independent of conventional CVD risk factors, these markers may represent a novel intrinsic predictor of CVD risk in adults with overweight and obesity.

AbstractIntroductionAdherence to the Mediterranean dietary pattern (MeDiet) and adiposity, respectively, decreases and increases the risk of multiple common age-related diseases through several mechanisms including inflammation, reactive oxygen species (ROS) production in the mitochondria, and DNA methylation. For example, adverse changes in platelets from obese and overweight adults include hyperaggregability and increased ROS. Since platelets are anuclear, their prothrombotic function is fully orchestrated by the mitochondria and the only DNA present is the mitochondrial DNA (mtDNA). In this study, we tested the hypothesis that MeDiet influences patterns of mtDNA methylation in platelets from older adults with greater adiposity.Material and methodsWe selected 134 participants with overweight or obesity (mean BMI = 35.5 ± 5.1 and age = 62 ± 10 years) from the “Susceptibility to particle health effects, miRNA and exosomes”(SPEHRE) Study. Dietary intake was assessed using a food frequency questionnaire and MeDiet adherence was calculated using the MeDiet Score described by Martínez-González et al.(2012). MtDNA was extracted from platelets, linearized, bisulfite converted and DNA methylation was quantified by pyrosequencing at 13 CpG in seven genes that encode for tRNAs (MT-TF and MT-TL1), regulatory regions (D-Loop and MT-OLR), and subunits of the electron-transport-chain (MT-CO1, MT-CO2, and MT-CO3).ResultsIn these participants, MeDiet score ranged from 3 to 12 (mean = 6.5), with higher scores reflecting greater MeDiet adherence. Regression analysis showed that higher MeDiet score was associated with lower D-loop (β = -0.031, P = 0.019) and higher MT-CO2 CpG1 (β = 0.040, P = 0.023) methylation. No associations were found between MeDiet Score and methylation level at MT-CO1(2 CpGs), MT-CO2(CpG2), MT-CO3(2 CpGs), MT-TL1(2 CpGs), MT-TF(CpG1), MT-OLR(3 CpGs).In addition, there was no association between mtDNA methylation and BMI.DiscussionThe D-loop is critical for mitochondrial function since it initiates mtDNA replication and transcription. Increased D-loop methylation has been associated with reduced mitochondrial functionality, and insulin resistance. Our results suggest that higher adherence to MeDiet lowers D-loop methylation which may protect against obesity-related comorbidities (e.g. insulin resistance).Higher MeDiet scores are associated with MT-CO2 CpG1 hypermethylation. MT-CO2 encodes for a subunit of the Cytochrome-C-oxidase, a highly regulated enzyme involved in the oxidative metabolism. MT-CO2 demethylation, induced by Valproic-Acid administration, has been reported to be associated with increased ROS production. Our results suggest a possible role of MeDiet in mitochondrial ROS regulation via methylation of MT-CO2.For the first time, we observed associations between MeDiet adherence and mtDNA methylation. Validation of these findings in independent cohorts is required.