CpG methylation patterns of human mitochondrial DNA

Osteoarthritis year in review 2017: genetics and epigenetics

OBJECTIVE

The purpose of this review is to describe highlights from original research publications related to osteoarthritis (OA), epigenetics and genomics with the intention of recognising significant advances.

DESIGN

To identify relevant papers a Pubmed literature search was conducted for articles published between April 2016 and April 2017 using the search terms 'osteoarthritis' together with 'genetics', 'genomics', 'epigenetics', 'microRNA', 'lncRNA', 'DNA methylation' and 'histone modification'.

RESULTS

The search term OA generated almost 4000 references. Publications using the combination of descriptors OA and genetics provided the most references (82 references). However this was reduced compared to the same period in the previous year; 8.1-2.1% (expressed as a percentage of the total publications combining the terms OA and genetics). Publications combining the terms OA with genomics (29 references), epigenetics (16 references), long non-coding RNA (lncRNA) (11 references; including the identification of novel lncRNAs in OA), DNA methylation (21 references), histone modification (3 references) and microRNA (miR) (79 references) were reviewed. Potential OA therapeutics such as histone deacetylase (HDAC) inhibitors have been identified. A number of non-coding RNAs may also provide targets for future treatments.

CONCLUSION

There continues to be a year on year increase in publications researching miRs in OA (expressed as a percentage of the total publications), with a doubling over the last 4 years. An overview on the last year's progress within the fields of epigenetics and genomics with respect to OA will be given.

Immunothrombotic Activity of Damage-Associated Molecular Patterns and Extracellular Vesicles in Secondary Organ Failure Induced by Trauma and Sterile Insults

Despite significant improvements in injury prevention and emergency response, injury-related death and morbidity continues to increase in the US and worldwide. Patients with trauma, invasive operations, anti-cancer treatment, and organ transplantation produce a host of danger signals and high levels of pro-inflammatory and pro-thrombotic mediators, such as damage-associated molecular patterns (DAMPs) and extracellular vesicles (EVs). DAMPs (e.g., nucleic acids, histone, high-mobility group box 1 protein, and S100) are molecules released from injured, stressed, or activated cells that act as endogenous ligands of innate immune receptors, whereas EVs (e.g., microparticle and exosome) are membranous vesicles budding off from plasma membranes and act as messengers between cells. DAMPs and EVs can stimulate multiple innate immune signaling pathways and coagulation cascades, and uncontrolled DAMP and EV production causes systemic inflammatory and thrombotic complications and secondary organ failure (SOF). Thus, DAMPs and EVs represent potential therapeutic targets and diagnostic biomarkers for SOF. High plasma levels of DAMPs and EVs have been positively correlated with mortality and morbidity of patients or animals with trauma or surgical insults. Blocking or neutralizing DAMPs using antibodies or small molecules has been demonstrated to ameliorate sepsis and SOF in animal models. Furthermore, a membrane immobilized with nucleic acid-binding polymers captured and removed multiple DAMPs and EVs from extracellular fluids, thereby preventing the onset of DAMP- and EV-induced inflammatory and thrombotic complications in vitro and in vivo. In this review, we will summarize the current state of knowledge of DAMPs, EVs, and SOF and discuss potential therapeutics and preventive intervention for organ failure secondary to trauma, surgery, anti-cancer therapy, and allogeneic transplantation.

Technical adequacy of bisulfite sequencing and pyrosequencing for detection of mitochondrial DNA methylation: Sources and avoidance of false-positive detection

The existence of cytosine methylation in mammalian mitochondrial DNA (mtDNA) is a controversial subject. Because detection of DNA methylation depends on resistance of 5'-modified cytosines to bisulfite-catalyzed conversion to uracil, examined parameters that affect technical adequacy of mtDNA methylation analysis. Negative control amplicons (NCAs) devoid of cytosine methylation were amplified to cover the entire human or mouse mtDNA by long-range PCR. When the pyrosequencing template amplicons were gel-purified after bisulfite conversion, bisulfite pyrosequencing of NCAs did not detect significant levels of bisulfite-resistant cytosines (brCs) at ND1 (7 CpG sites) or CYTB (8 CpG sites) genes (CI95 = 0%-0.94%); without gel-purification, significant false-positive brCs were detected from NCAs (CI95 = 4.2%-6.8%). Bisulfite pyrosequencing of highly purified, linearized mtDNA isolated from human iPS cells or mouse liver detected significant brCs (~30%) in human ND1 gene when the sequencing primer was not selective in bisulfite-converted and unconverted templates. However, repeated experiments using a sequencing primer selective in bisulfite-converted templates almost completely (< 0.8%) suppressed brC detection, supporting the false-positive nature of brCs detected using the non-selective primer. Bisulfite-seq deep sequencing of linearized, gel-purified human mtDNA detected 9.4%-14.8% brCs for 9 CpG sites in ND1 gene. However, because all these brCs were associated with adjacent non-CpG brCs showing the same degrees of bisulfite resistance, DNA methylation in this mtDNA-encoded gene was not confirmed. Without linearization, data generated by bisulfite pyrosequencing or deep sequencing of purified mtDNA templates did not pass the quality control criteria. Shotgun bisulfite sequencing of human mtDNA detected extremely low levels of CpG methylation (<0.65%) over non-CpG methylation (<0.55%). Taken together, our study demonstrates that adequacy of mtDNA methylation analysis using methods dependent on bisulfite conversion needs to be established for each experiment, taking effects of incomplete bisulfite conversion and template impurity or topology into consideration.

An Epigenetic Spin to ALS and FTD

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two devastating and lethal neurodegenerative diseases seen comorbidly in up to 15% of patients. Despite several decades of research, no effective treatment or disease-modifying strategies have been developed. We now understand more than before about the genetics and biology behind ALS and FTD, but the genetic etiology for the majority of patients is still unknown and the phenotypic variability observed across patients, even those carrying the same mutation, is enigmatic. Additionally, susceptibility factors leading to neuronal vulnerability in specific central nervous system regions involved in disease are yet to be identified. As the inherited but dynamic epigenome acts as a cell-specific interface between the inherited fixed genome and both cell-intrinsic mechanisms and environmental input, adaptive epigenetic changes might contribute to the ALS/FTD aspects we still struggle to comprehend. This chapter summarizes our current understanding of basic epigenetic mechanisms, how they relate to ALS and FTD, and their potential as therapeutic targets. A clear understanding of the biological mechanisms driving these two currently incurable diseases is urgent-well-needed therapeutic strategies need to be developed soon. Disease-specific epigenetic changes have already been observed in patients and these might be central to this endeavor.

Background sequence characteristics influence the occurrence and severity of disease-causing mtDNA mutations

Inherited mitochondrial DNA (mtDNA) mutations have emerged as a common cause of human disease, with mutations occurring multiple times in the world population. The clinical presentation of three pathogenic mtDNA mutations is strongly associated with a background mtDNA haplogroup, but it is not clear whether this is limited to a handful of examples or is a more general phenomenon. To address this, we determined the characteristics of 30,506 mtDNA sequences sampled globally. After performing several quality control steps, we ascribed an established pathogenicity score to the major alleles for each sequence. The mean pathogenicity score for known disease-causing mutations was significantly different between mtDNA macro-haplogroups. Several mutations were observed across all haplogroup backgrounds, whereas others were only observed on specific clades. In some instances this reflected a founder effect, but in others, the mutation recurred but only within the same phylogenetic cluster. Sequence diversity estimates showed that disease-causing mutations were more frequent on young sequences, and genomes with two or more disease-causing mutations were more common than expected by chance. These findings implicate the mtDNA background more generally in recurrent mutation events that have been purified through natural selection in older populations. This provides an explanation for the low frequency of mtDNA disease reported in specific ethnic groups.

MtDNA mutations are a major cause of genetic disease. Many of these variants have recurred several times in different populations and on diverse haplogroup backgrounds, but the clinical presentation of mutations causing Leber Hereditary Optic Neuropathy (LHON: m.14484T>C, m.3460G>A, m.11778G>A) are strongly associated with a specific mtDNA haplogroup. This raises the possibility that many pathogenic mtDNA mutations are subject to the same effects. Here, our analysis of 30,506 human mtDNA sequences shows that the association between disease-causing mtDNA mutations and background mtDNA haplogroups is not only restricted to three disease-causing mtDNA mutations known to cause LHON. The frequent recurrence of the same mutations on a population clade, and the reduced frequency of European mtDNAs harboring two or more diseases-causing mutations, suggest that the population mtDNA background influences the risk of developing mtDNA mutations. Our analysis also shows that disease-causing mtDNA mutations also occur more frequently on younger mtDNAs. This implies that, once formed, the mutations are selected against. These findings indicate that the clinical interpretation of mtDNA variants should be performed within an ethnogeographic context.

More than a powerplant: the influence of mitochondrial transfer on the epigenome

Each cell in the human body, with the exception of red blood cells, contains multiple copies of mitochondria that house their own genetic material, the maternally inherited mitochondrial DNA. Mitochondria are the cell's powerplant due to their massive ATP generation. However, the mitochondrion is also a hub for metabolite production from the TCA cycle, fatty acid beta-oxidation, and ketogenesis. In addition to producing macromolecules for biosynthetic reactions and cell replication, several mitochondrial intermediate metabolites serve as cofactors or substrates for epigenome modifying enzymes that regulate chromatin structure and impact gene expression. Here, we discuss connections between mitochondrial metabolites and enzymatic writers and erasers of chromatin modifications. We do this from the unique perspective of cell-to-cell mitochondrial transfer and its potential impact on mitochondrial replacement therapies.

'Omics' and endocrine-disrupting chemicals - new paths forward

The emerging field of omics - large-scale data-rich biological measurements of the genome - provides new opportunities to advance and strengthen research into endocrine-disrupting chemicals (EDCs). Although some EDCs have been associated with adverse health effects in humans, our understanding of their impact remains incomplete. Progress in the field has been primarily limited by our inability to adequately estimate and characterize exposure and identify sensitive and measurable outcomes during windows of vulnerability. Evolving omics technologies in genomics, epigenomics and mitochondriomics have the potential to generate data that enhance exposure assessment to include the exposome - the totality of the lifetime exposure burden - and provide biology-based estimates of individual risks. Applying omics technologies to expand our knowledge of individual risk and susceptibility will augment biological data in the prediction of variability and response to disease, thereby further advancing EDC research. Together, refined exposure characterization and enhanced disease-risk prediction will help to bridge crucial gaps in EDC research and create opportunities to move the field towards a new vision - precision public health.

Epigenetic Biomarkers for Parkinson's Disease: From Diagnostics to Therapeutics

Parkinson’s disease (PD) is a prevalent neurodegenerative illness that is often diagnosed after significant pathology and neuronal cell loss has occurred. Biomarkers of PD are greatly needed for early diagnosis, as well as for the prediction of disease progression and treatment outcome. In this regard, the epigenome, which is partially dynamic, holds considerable promise for the development of molecular biomarkers for PD. Epigenetic marks are modified by both DNA sequence and environmental factors associated with PD, and such marks could serve as a unifying predictor of at-risk individuals. Epigenetic abnormalities have been detected in PD and other age-dependent neurodegenerative diseases, some of which were reported to occur early on and were reversible by PD medications. Emerging reports indicate that certain epigenetic differences observed in the PD brain are detectable in more easily accessible tissues. In this review, we examine epigenetic-based strategies for the development of PD biomarkers. Despite the complexities and challenges faced, the epigenome offers a new source of biomarkers with potential etiological relevance to PD, and may expand opportunities for personalized therapies.

Evidence Suggesting Absence of Mitochondrial DNA Methylation

Methylation of nuclear genes encoding mitochondrial proteins participates in the regulation of mitochondria function. The existence of cytosine methylation in the mitochondrial genome is debated. To investigate whether mitochondrial DNA (mtDNA) is methylated, we used both targeted- and whole mitochondrial genome bisulfite sequencing in cell lines and muscle tissue from mouse and human origin. While unconverted cytosines were detected in some portion of the mitochondrial genome, their abundance was inversely associated to the sequencing depth, indicating that sequencing analysis can bias the estimation of mtDNA methylation levels. In intact mtDNA, few cytosines remained 100% unconverted. However, removal of supercoiled structures of mtDNA with the restriction enzyme BamHI prior to bisulfite sequencing decreased cytosine unconversion rate to <1.5% at all the investigated regions: D-loop, tRNA-F+12S, 16S, ND5 and CYTB, suggesting that mtDNA supercoiled structure blocks the access to bisulfite conversion. Here, we identified an artifact of mtDNA bisulfite sequencing that can lead to an overestimation of mtDNA methylation levels. Our study supports that cytosine methylation is virtually absent in mtDNA.

Hypo-hydroxymethylation of rRNA genes in the precocious Eriocheir sinensis testes revealed using hMeDIP-seq

Precocious puberty is a common phenomenon in crab breeding that seriously reduces the economic benefits for crab farmers. To address this problem, this study aimed to explore the potential functions of both methylation and hydroxymethylation of testis rRNA genes with respect to precocious puberty in Eriocheir sinensis. The results showed that the rRNA genes in normally developing testes of E. sinensis had low levels of methylation and high levels of hydroxymethylation; however, although methylation levels were similar, the level of hydroxymethylation in precocious testes was lower than normal. Highly significant differences (P < 0.01) in the hydroxymethylation of the 18S and 28S rRNA genes were found between precocious and normal testes. Our results suggested that both the 18S and 28S rRNA genes, which are normally downregulated by hypo-hydroxymethylation, might be involved in the process of precocious puberty. Our results also implied that hydroxymethylation of the 18S and 28S rRNA genes might be used as an important epigenetic molecular marker to evaluate economically significant potential for growth and breeding in this species.

Maternal trans-general analysis of the human mitochondrial DNA pattern

There is an intimate connection between mitochondrial DNA (mtDNA) methylation and some diseases, such as cancer. MtDNA is almost strictly maternally inherited. However, whether the aberrant mtDNA methylation involved in breast cancer progression and whether mtDNA methylation can be transmitted through maternal line are poorly understood. Here we applied bisulfite sequencing to global mitochondrial DNA and whole genomic DNA methylation array from fifteen members of five three-female-generation families with one breast cancer patient in each family. We found that mtDNA methylation was maternally inherited in D-loop region and eight aberrant mtDNA methylation sites were correlated with breast cancer. Furthermore, conjoint analysis showed that mtDNA methylation sites could be potential biomarkers combined with nuclear DNA methylation sites for breast cancer risk prediction.

Diabetic retinopathy, metabolic memory and epigenetic modifications

Retinopathy, a sight-threatening disease, remains one of the most feared complications of diabetes. Although hyperglycemia is the main initiator, progression of diabetic retinopathy continues even after re-institution of normal glycemic control in diabetic patients, and the deleterious effects of prior hyperglycemic insult depend on the duration and the severity of this insult, suggesting a 'metabolic memory' phenomenon. Metabolic memory phenomenon is successfully duplicated in the experimental models of diabetic retinopathy. Hyperglycemia, in addition to initiating many other biochemical and functional abnormalities and altering expression of genes associated with them, also increases oxidative stress. Increased production of cytosolic reactive oxygen species dysfunctions the mitochondria, and a compromised antioxidant defense system becomes overwhelmed to neutralize free radicals. With the duration of diabetes extending, mitochondrial DNA (mtDNA) is also damaged, and transcription of mtDNA-encoded genes, important for function of the electron transport chain, is compromised. This fuels into a 'self-propagating' vicious cycle of free radicals, and retinopathy continues to progress. Hyperglycemic insult also affects the enzymatic machinery responsible for epigenetic modifications; these modifications alter gene expression without affecting the DNA sequence. Histones and/or DNA modifications of many enzymes, important in mitochondrial homeostasis, affect their activities and disturb mitochondrial homeostasis. Experimental models have shown that these epigenetic modifications have potential to halt only if normal glycemia is maintained from the day of induction of diabetes (streptozotocin) in rats, but if hyperglycemia is allowed to proceed even for couple months before initiation of normal glycemia, these epigenetic modification resist reversal. Supplementation of a therapy targeted to prevent increased oxidative stress or epigenetic modifications, during the normal glucose phase, which has followed high glucose insult, however, helps ameliorate these abnormalities and prevents the progression of diabetic retinopathy. Thus, without undermining the importance of tight glycemic control for a diabetic patient, supplementation of their 'best possible' glycemic control with such targeted therapies has potential to retard further progression of this blinding disease.

Regulating role of fetal thyroid hormones on placental mitochondrial DNA methylation: epidemiological evidence from the ENVIRONAGE birth cohort study

BACKGROUND

Fetal development largely depends on thyroid hormone availability and proper placental function with an important role played by placental mitochondria. The biological mechanisms by which thyroid hormones exert their effects on mitochondrial function are not well understood. We investigated the role of fetal thyroid hormones on placental mitochondrial DNA (mtDNA) content and mtDNA methylation. We collected placental tissue and cord blood from 305 mother-child pairs that were enrolled between February 2010 and June 2014 in the ENVIRONAGE (ENVIRonmental influence ON early AGEing) birth cohort (province of Limburg, Belgium). Placental mtDNA content was determined by qPCR and placental mtDNA methylation by bisulfite-pyrosequencing in two regions, i.e., the D-loop control region and 12S ribosomal RNA (MT-RNR1). The levels of free thyroid hormones (FT₃, FT₄) and thyroid-stimulating hormone (TSH) were measured in cord blood.

RESULTS

Cord blood FT₃ and FT₄ were inversely associated with placental mtDNA methylation at the MT-RNR1 (p ≤ 0.01) and D-loop (p ≤ 0.05) regions, whereas a positive association was observed for both hormones with placental mtDNA content (p ≤ 0.04). Assuming causality, we estimated that MT-RNR1 and D-loop methylation mediated, respectively, 77% [indirect effect +14.61% (95% CI 2.64 to 27.98%, p = 0.01)] and 47% [indirect effect +8.60% (95% CI 1.23 to 16.50%, p = 0.02] of the positive association between FT₃ and placental mtDNA content. Mediation models with FT₄ gave similar results but the estimated effect proportions were smaller compared with those of FT₃ (54% and 24%, respectively).

CONCLUSIONS

We showed that epigenetic modification at specific loci of the mitochondrial genome could intervene with the thyroid-dependent regulation of mitochondrial DNA copy numbers.

MicroRNA-34a Encapsulated in Hyaluronic Acid Nanoparticles Induces Epigenetic Changes with Altered Mitochondrial Bioenergetics and Apoptosis in Non-Small-Cell Lung Cancer Cells

Therapies targeting epigenetic changes for cancer treatment are in Phase I/II trials; however, all of these target only nuclear DNA. Emerging evidence suggests presence of methylation marks on mitochondrial DNA (mtDNA); but their contribution in cancer is unidentified. Expression of genes encoded on mtDNA are altered in cancer cells, along with increased glycolytic flux. Such glycolytic flux and elevated reactive oxygen species is supported by increased antioxidant; glutathione. MicroRNA-34a can translocate to mitochondria, mediate downstream apoptotic effects of tumor suppressor P53, and inhibit the antioxidant response element Nrf-2, resulting in depleted glutathione levels. Based on such strong rationale, we encapsulated microRNA-34a in our well-established Hyaluronic-Acid nanoparticles and delivered to cisplatin-sensitive and cisplatin-resistant A549-lung adenocarcinoma cells. Successful delivery and uptake in cells resulted in altered ATP levels, decreased glycolytic flux, Nrf-2 and glutathione levels, ultimately resulting in caspase-3 activation and apoptosis. Most important were the concurrent underlying molecular changes in epigenetic status of D-loop on the mtDNA and transcription of mtDNA-encoded genes. Although preliminary, we provide a novel therapeutic approach in form of altered mitochondrial bioenergetics and redox status of cancer cells with underlying changes in epigenetic status of mtDNA that can subsequently results in induction of cancer cell apoptosis.

CpG and Non-CpG Methylation in Epigenetic Gene Regulation and Brain Function

DNA methylation is a major epigenetic mark with important roles in genetic regulation. Methylated cytosines are found primarily at CpG dinucleotides, but are also found at non-CpG sites (CpA, CpT, and CpC). The general functions of CpG and non-CpG methylation include gene silencing or activation depending on the methylated regions. CpG and non-CpG methylation are found throughout the whole genome, including repetitive sequences, enhancers, promoters, and gene bodies. Interestingly, however, non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells. Thus, accumulation of methylation at non-CpG sites and CpG sites in neurons seems to be involved in development and disease etiology. Here, we provide an overview of CpG and non-CpG methylation and their roles in neurological diseases.

Mitochondrial DNA Hypomethylation Is a Biomarker Associated with Induced Senescence in Human Fetal Heart Mesenchymal Stem Cells

Background. Fetal heart can regenerate to restore its normal anatomy and function in response to injury, but this regenerative capacity is lost within the first week of postnatal life. Although the specific molecular mechanisms remain to be defined, it is presumed that aging of cardiac stem or progenitor cells may contribute to the loss of regenerative potential. Methods. To study this aging-related dysfunction, we cultured mesenchymal stem cells (MSCs) from human fetal heart tissues. Senescence was induced by exposing cells to chronic oxidative stress/low serum. Mitochondrial DNA methylation was examined during the period of senescence. Results. Senescent MSCs exhibited flattened and enlarged morphology and were positive for the senescence-associated beta-galactosidase (SA-β-Gal). By scanning the entire mitochondrial genome, we found that four CpG islands were hypomethylated in close association with senescence in MSCs. The mitochondrial COX1 gene, which encodes the main subunit of the cytochrome c oxidase complex and contains the differentially methylated CpG island 4, was upregulated in MSCs in parallel with the onset of senescence. Knockdown of DNA methyltransferases (DNMT1, DNMT3a, and DNMT3B) also upregulated COX1 expression and induced cellular senescence in MSCs. Conclusions. This study demonstrates that mitochondrial CpG hypomethylation may serve as a critical biomarker associated with cellular senescence induced by chronic oxidative stress.

Experimental mitochondria-targeted DNA methylation identifies GpC methylation, not CpG methylation, as potential regulator of mitochondrial gene expression

Like the nucleus, mitochondria contain their own DNA and recent reports provide accumulating evidence that also the mitochondrial DNA (mtDNA) is subjective to DNA methylation. This evidence includes the demonstration of mitochondria-localised DNA methyltransferases and demethylases, and the detection of mtDNA methylation as well as hydroxymethylation. Importantly, differential mtDNA methylation has been linked to aging and diseases, including cancer and diabetes. However, functionality of mtDNA methylation has not been demonstrated. Therefore, we targeted DNA methylating enzymes (modifying cytosine in the CpG or GpC context) to the mtDNA. Unexpectedly, mtDNA gene expression remained unchanged upon induction of CpG mtDNA methylation, whereas induction of C-methylation in the GpC context decreased mtDNA gene expression. Intriguingly, in the latter case, the three mtDNA promoters were differentially affected in each cell line, while cellular function seemed undisturbed. In conclusion, this is the first study which directly addresses the potential functionality of mtDNA methylation. Giving the important role of mitochondria in health and disease, unravelling the impact of mtDNA methylation adds to our understanding of the role of mitochondria in physiological and pathophysiological processes.

Occupational exposure to particles and mitochondrial DNA - relevance for blood pressure

BACKGROUND

Particle exposure is a risk factor for cardiovascular diseases. Mitochondrial DNA (mtDNA) is a primary target for oxidative stress generated by particle exposure. We aimed to elucidate the effects of occupational exposure to particle-containing welding fumes on different biomarkers of mtDNA function, and in turn, explore if they modify the association between particle exposure and cardiovascular response, measured as blood pressure.

METHODS

We investigated 101 welders and 127 controls (all non-smoking males) from southern Sweden. Personal sampling of the welders' exposure to respirable dust was performed during work hours (average sampling time: 6.8 h; range: 2.4-8.6 h) and blood pressure was measured once for each subject. We measured relative mtDNA copy number by quantitative PCR and methylation of the mitochondrial regulatory region D-loop and the tRNA encoding gene MT-TF by bisulfite-pyrosequencing. We calculated the relative number of unmethylated D-loop and MT-TF as markers of mtDNA function to explore the modification of mtDNA on the association between particle exposure and blood pressure. General linear models were used for statistical analyses.

RESULTS

Welders had higher mtDNA copy number (β = 0.11, p = 0.003) and lower DNA methylation of D-loop (β = -1.4, p = 0.002) and MT-TF (β = -1.5, p = 0.004) than controls. Higher mtDNA copy number was weakly associated with higher personal respirable dust exposure among welders with exposure level above 0.7 mg/m3 (β = 0.037, p = 0.054). MtDNA function modified the effect of welding fumes on blood pressure: welders with low mtDNA function had higher blood pressure than controls, while no such difference was found in the group with high mtDNA function.

CONCLUSION

Increased mtDNA copy number and decreased D-loop and MT-TF methylation were associated with particle-containing welding fumes exposure, indicating exposure-related oxidative stress. The modification of mtDNA function on exposure-associated increase in blood pressure may represent a mitochondria-environment interaction.

MeDIP-seq reveals the features of mitochondrial genomic methylation in immature testis of Chinese mitten crab Eriocheir sinensis

In this study, the methylation of mitochondrial genome in the immature testis of Chinese mitten crab Eriocheir sinensis of the Yangtze River system was determined for the first time using MeDIP-seq. Our methylated DNA fragments covered more than 99% of the mitochondrial genome in E. sinensis loaded from GenBank. There were 8 mutated bases and 42 SNPs in the crab mitochondrial genome. The methylation presented in all genes as well as in an A + T region, but less in intergenic regions in the mitochondrial genome. However, the level of methylation of most genes coding proteins and the A + T region were high. But, the majority of genes encoding tRNAs were hypomethylated, and both the rRNA genes also showed methylation of low or median frequency. Especially, the level of methylation of the intergenic regions is the lowest. Those features indicated that the methylation of DNA may play an important role in gene expressing regulation in the mitochondrial genome of immature testis in E. sinensis.

The methylation of nuclear and mitochondrial DNA in ageing phenotypes and longevity

An increasing body of data is progressively indicating that the comprehension of the epigenetic landscape, actively integrated with the genetic elements, is crucial to delineate the molecular basis of the inter-individual complexity of ageing process. Indeed, it has emerged that DNA methylation changes occur during ageing, consisting mainly in a progressive process of genome demethylation, in a hypermethylation of gene-specific CpG dinucleotides, as well as in an inter-individual divergence of the epigenome due to stochastic events and environmental exposures throughout life, namely as epigenetic drift. Additionally, it has also come to light an implication of the mitochondrial genome in the regulation of the intracellular epigenetic landscape, as demonstrated by the being itself object of epigenetic modifications. An overview of DNA methylation changes occurring during ageing process at both nuclear and mitochondrial level will be described in this review, also taking into account the recent and promising data available on the 5-hydroxymethylcytosine.

Near-complete elimination of mutant mtDNA by iterative or dynamic dose-controlled treatment with mtZFNs

Mitochondrial diseases are frequently associated with mutations in mitochondrial DNA (mtDNA). In most cases, mutant and wild-type mtDNAs coexist, resulting in heteroplasmy. The selective elimination of mutant mtDNA, and consequent enrichment of wild-type mtDNA, can rescue pathological phenotypes in heteroplasmic cells. Use of the mitochondrially targeted zinc finger-nuclease (mtZFN) results in degradation of mutant mtDNA through site-specific DNA cleavage. Here, we describe a substantial enhancement of our previous mtZFN-based approaches to targeting mtDNA, allowing near-complete directional shifts of mtDNA heteroplasmy, either by iterative treatment or through finely controlled expression of mtZFN, which limits off-target catalysis and undesired mtDNA copy number depletion. To demonstrate the utility of this improved approach, we generated an isogenic distribution of heteroplasmic cells with variable mtDNA mutant level from the same parental source without clonal selection. Analysis of these populations demonstrated an altered metabolic signature in cells harbouring decreased levels of mutant m.8993T>G mtDNA, associated with neuropathy, ataxia, and retinitis pigmentosa (NARP). We conclude that mtZFN-based approaches offer means for mtDNA heteroplasmy manipulation in basic research, and may provide a strategy for therapeutic intervention in selected mitochondrial diseases.