Epigenetic remodeling of sheep oocytes and embryos induced by maternal methionine supplementation

BackgroundIn vitro follicle culture (IFC), as applied in the mouse system, allows the growth and maturation of a large number of immature preantral follicles to become mature and competent oocytes. In the human oncofertility clinic, there is increasing interest in developing this technique as an alternative to ovarian cortical tissue transplantation and to preserve the fertility of prepubertal cancer patients. However, the effect of IFC and hormonal stimulation on DNA methylation in the oocyte is not fully known, and there is legitimate concern over epigenetic abnormalities that could be induced by procedures applied during assisted reproductive technology (ART).ResultsIn this study, we present the first genome-wide analysis of DNA methylation in MII oocytes obtained after natural ovulation, after IFC and after superovulation. We also performed a comparison between prepubertal and adult hormonally stimulated oocytes. Globally, the distinctive methylation landscape of oocytes, comprising alternating hyper- and hypomethylated domains, is preserved irrespective of the procedure. The conservation of methylation extends to the germline differential methylated regions (DMRs) of imprinted genes, necessary for their monoallelic expression in the embryo. However, we do detect specific, consistent, and coherent differences in DNA methylation in IFC oocytes, and between oocytes obtained after superovulation from prepubertal compared with sexually mature females. Several methylation differences span entire transcription units. Among these, we found alterations in Tcf4, Sox5, Zfp521, and other genes related to nervous system development.ConclusionsOur observations show that IFC is associated with altered methylation at specific set of loci. DNA methylation of superovulated prepubertal oocytes differs from that of superovulated adult oocytes, whereas oocytes from superovulated adult females differ very little from naturally ovulated oocytes. Importantly, we show that regions other than imprinted gDMRs are susceptible to methylation changes associated with superovulation, IFC, and/or sexual immaturity in mouse oocytes. Our results provide an important reference for the use of in vitro growth and maturation of oocytes, particularly from prepubertal females, in assisted reproductive treatments or fertility preservation.

Establishment of a proper DNA methylation landscape in mammalian oocytes is important for maternal imprinting and embryonic development. De novo DNA methylation in oocytes is mediated by the DNA methyltransferase DNMT3A, which has an ATRX-DNMT3-DNMT3L (ADD) domain that interacts with histone H3 tail unmethylated at lysine-4 (H3K4me0). The domain normally blocks the methyltransferase domain via intramolecular interaction and binding to histone H3K4me0 releases the autoinhibition. However, H3K4me0 is widespread in chromatin and the role of the ADD-histone interaction has not been studied in vivo. We herein show that amino-acid substitutions in the ADD domain of mouse DNMT3A cause dwarfism. Oocytes derived from homozygous females show mosaic loss of CG methylation and almost complete loss of non-CG methylation. Embryos derived from such oocytes die in mid-to-late gestation, with stochastic and often all-or-none-type CG-methylation loss at imprinting control regions and misexpression of the linked genes. The stochastic loss is a two-step process, with loss occurring in cleavage-stage embryos and regaining occurring after implantation. These results highlight an important role for the ADD domain in efficient, and likely processive, de novo CG methylation and pose a model for stochastic inheritance of epigenetic perturbations in germ cells to the next generation.

BackgroundThe evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental perturbations. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to assess potential changes in splicing events in the longissimus dorsi muscle of beef calves gestated under control or methionine-rich diets. RNA sequencing and whole-genome bisulfite sequencing were used to evaluate muscle transcriptome and methylome, respectively.ResultsAlternative splicing patterns were significantly altered by maternal methionine supplementation. Most of the altered genes were directly implicated in muscle development, muscle physiology, ATP activities, RNA splicing and DNA methylation, among other functions. Interestingly, there was a significant association between DNA methylation and differential exon usage. Indeed, among the set of genes that showed differential exon usage, significant differences in methylation level were detected between significant and non-significant exons, and between contiguous and non-contiguous introns to significant exons.ConclusionsOverall, our findings provide evidence that a prenatal diet rich in methyl donors can significantly alter the offspring transcriptome, including changes in isoform expression and exon usage, and some of these changes are mediated by changes in DNA methylation.

The tumor microenvironment (TME) comprises diverse cell types whose interactions are crucial for cancer progression. Traditional bulk tissue analyses mask cell-type-specific epigenetic changes that may drive disease progression. We used DNA methylation data and a reference- based cell-type deconvolution algorithm — hierarchical tumor immune microenvironment epigenetic deconvolution (HiTIMED) — to quantify cell types in the TME. Then, we employed CellDMC, a statistical interaction testing framework that can use cell type proportions in conjunction with differential methylation analysis to identify cell-specific differential methylation. Genome-scale DNA methylation profiles from breast cancer tissue (n=609) and normal breast tissue (n=230) samples were accessed in GEO and GTEx. Our novel approach leverages bulk DNA methylation data to infer cell-type-specific epigenetic landscapes, circumventing challenges and limitations associated with direct single-cell methylation profiling, such as high costs and technical variability. Reference-based computational tools allow us to dissect complex tissue compositions and reveal distinct methylation patterns and pathways that may be unique to individual cell types, providing insights that are not discernible from traditional bulk tumor analysis approaches. Compared with nontumor normal samples, we identified significant DNA methylation alterations (FDR≤0.05) across tumor, stromal, endothelial, epithelial, lymphocytes, and myeloid cells in breast tumors. Tumor cells exhibited the highest number, 8,510, differentially methylated cytosines (DMCs) with 1,966 of these unique to tumor cells. Stromal, endothelial, and epithelial cells also showed considerable methylation alterations, with a total of 530, 440, 339 DMCs, respectively, with 5 DMCs unique to epithelial cells. Despite lower immune cell proportions in our samples, we identified 104 lymphocyte specific DMCs and 185 myeloid specific DMCs, with 14 and 20 DMCs unique to these cell types respectively. The unique DMCs identified in each cell type suggest distinct epigenetic landscapes that may drive specific cellular functions and interactions within the TME. Importantly, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the annotated cell-type-specific DMCs revealed distinct pathways that were not apparent in the pathway analysis of bulk tumor versus normal tissue, underscoring the value of examining epigenetic alterations at the cell-type level. Our findings highlight the opportunity to leverage DNA-based cell typing with DNA methylation data to discern cell-specific molecular alterations. By focusing on cell-type-specific alterations, we can better understand the epigenetic mechanisms driving TME crosstalk, such as the activation of stromal cells and the modulation of immune responses by tumor cells. Our findings underscore the need for targeted therapeutic strategies that consider the unique epigenetic landscapes of individual cell types within the TME, offering new avenues for improving cancer treatment outcomes. Citation Format: Barbara Karakyriakou, Brock C. Christensen, Lucas A. Salas. Identification of cell-specific DNA methylation alterations in the breast tumor microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B033.

Poor ovarian response (POR) reduces the success rate of in vitro fertilization mainly because of fewer oocytes retrieved. Acupuncture (Ac) therapy can improve the number of retrieved oocytes in the controlled ovarian stimulation program. The role of Ac in the corresponding epigenetic mechanism of POR has not been studied. This study was conducted to determine the effect of Ac on the number of retrieved oocytes and its role in DNA methylation in a mouse model of POR. Forty C57BL/6N female mice with normal estrous cycles were randomly classified into 4 groups of 10 each: control (Con) group, Ac-Con group, POR group, and Ac-POR group. Mice in POR and Ac-POR groups received a gastric gavage of Tripterygium wilfordii polyglycoside suspension of 50 mg/kg-1 once a day for 14 consecutive days. Ac was applied at "Shenting" (DU 24), "Guanyuan" (CV 4), "Zusanli" (ST 36), and "Shenshu" (BL 23) in the Ac-POR group for 10 min per session, once a day for 14 consecutive days. All four groups were stimulated with pregnant mare serum gonadotropin and human chorionic gonadotropin, and the number of retrieved oocytes and proportion of mature oocytes were recorded. The DNA methylation level in a single mouse oocyte in each group was analyzed using single-cell genome-wide bisulfite sequencing (scBSseq), and key pathways were identified using GO and KEGG enrichment analyses. A dissecting microscope revealed that the Ac therapy improved the number of retrieved oocytes compared with the POR group (p < 0.05). ScBS-seq showed that there was no significant change in global DNA methylation levels between the POR model and control group mice. However, differences were primarily observed in the differentially methylated regions (DMRs) of each chromosome, and Ac decreased global DNA methylation. DMR analysis identified 13 genes that may be associated with Ac treatment. Cdk5rap2 and Igf1r, which mediate germ cell apoptosis, growth, and development, maybe most closely related to the Ac treatment of POR. KEGG analysis revealed that differentially expressed genes were mainly enriched in Wnt, GnRH, and calcium signaling pathways. The genes were closely related to the regulation of POR via Ac. The results suggest that DNA methylation in oocytes is related to the development of POR and that the role of Ac in affecting DNA methylation in oocytes is associated with the Wnt, GnRH, and calcium signaling pathways as well as Cdk5rap2 and Igf1r in POR mice.

Differential methylation of mitochondrial and nuclear DNA in cultured mouse, hamster and virus-transformed hamster cells In vivo and in vitro methylation

Comparison of mitochondrial DNA (mtDNA) methylation patterns in oocytes, blastocysts and ovarian granulosa cells indicates hitherto unsuspected dynamics. Oocytes and blastocysts recovered from cows subjected to ovarian stimulation and from non-stimulated abattoir ovaries were analyzed using bisulphite transformation of DNA followed by whole genome sequencing. The cow is a recognized as a good model for human oocyte and pre-implantation development. The number of mtDNA copies is high in oocytes (200,000–400,000) and early embryos, resulting in very high coverage (>3000x) and very low p values for each of 716 cytosine-based nucleosides. Methylation ratio was lowest in oocytes, following by blastocysts then granulosa cells and was not restricted to CG sites but was found also at CHG and CHH sites. The initial methylation pattern is conserved during the first week of life but not in somatic cells. RNA analysis of mitochondria encoded genes showed a significant inverse correlation between methylation and expression for almost all sequences. Methylation was more extensive in somatic tissues from mature animals than in immature pre-pubertal animals. Our findings suggest that mtDNA methylation might play a programming role during gametogenesis and would be subject to epigenetic regulation according to environment and/or maternal maturity.

DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. Bulls from the Pacific Northwest region of the United States and other northern areas are exposed to extreme cold temperatures during winter. However, the effects of cold exposure on the methylation patterns of bovine sperm remain unclear. To address, DNA methylation profiles of sperm collected during late spring and winter from the same bulls were analyzed using whole genome bisulfite sequencing (WGBS). Bismark (0.22.3) were used for mapping the WGBS reads and R Bioconductor package DSS was used for differential methylation analysis. Cold exposure induced 3,163 differentially methylated cytosines (DMCs) with methylation difference ≥10% and a q-value < 0.05. We identified 438 differentially methylated regions (DMRs) with q-value < 0.05, which overlapped with 186 unique genes. We also identified eight unique differentially methylated genes (DMGs) (Pax6, Macf1, Mest, Ubqln1, Smg9, Ctnnb1, Lsm4, and Peg10) involved in embryonic development, and nine unique DMGs (Prmt6, Nipal1, C21h15orf40, Slc37a3, Fam210a, Raly, Rgs3, Lmbr1, and Gan) involved in osteogenesis. Peg10 and Mest, two paternally expressed imprinted genes, exhibited >50% higher methylation. The differential methylation patterns of six distinct DMRs: Peg10, Smg9 and Mest related to embryonic development and Lmbr1, C21h15orf40 and Prtm6 related to osteogenesis, were assessed by methylation-specific PCR (MS-PCR), which confirmed the existence of variable methylation patterns in those locations across the two seasons. In summary, cold exposure induces differential DNA methylation patterns in genes that appear to affect embryonic development and osteogenesis in the offspring. Our findings suggest the importance of replicating the results of the current study with a larger sample size and exploring the potential of these changes in affecting offspring development.

DNA methylation in the oocyte has a particular significance: it may contribute to gene regulation in the oocyte and marks specific genes for activity in the embryo, as in the case of imprinted genes. Despite the fundamental importance of DNA methylation established in the oocyte, knowledge of the mechanisms by which it is conferred and how much is stably maintained in the embryo has remained very limited. Next generation sequencing approaches have dramatically altered our views on DNA methylation in oocytes. They have revealed that most methylation occurs in gene bodies in the oocyte. This observation ties in with genetic evidence showing that transcription is essential for methylation of imprinted genes, and is consistent with a model in which DNA methyltransferases are recruited by the histone modification patterns laid down by transcription events. These findings lead to a new perspective that transcription events dictate the placing and timing of methylation in specific genes and suggest a mechanism by which methylation could be coordinated by the events and factors regulating oocyte growth. With these new insights into the de novo methylation mechanism and new methods that allow high resolution profiling of DNA methylation in oocytes, we should be in a position to investigate whether and how DNA methylation errors could arise in association with assisted reproduction technologies or in response to exposure to environmental toxins.

The normal progression of acquisition of global DNA methylation in oocytes of adult female mice is not known. Assisted reproductive technologies (ART) are commonly used for the treatment of infertility problems. Several studies have shown that ART procedures alter the expression of genes, causing delayed embryonic development, increased abnormal blastocyst formation, pronounced fetal growth retardation and is associated with increased incidence of loss-of-imprinting syndromes. A previous study from our laboratory showed that the maternal pronuclei of one-cell mouse embryos formed after superovulation (SO) had 50% less methylation when compared to those formed after natural ovulation (NO). We hypothesize that oocytes in ovaries of females undergoing a SO scheme will have different levels of global DNA methylation than oocytes from naturally cycling animals. First, we determined the progression of global DNA methylation during oocyte growth in naturally cycling animals and then compared this to the levels of DNA methylation in oocytes from females undergoing a SO scheme. A group of 14 cyclic females were selected at diestrus and divided into seven groups. Two females were sacrificed and collected ovaries at diestrus (0h). Six females underwent a SO scheme while the remaining six did not. In brief, SO females were injected with 5 IU of eCG followed 44 h later by 5 IU of hCG. Ovaries were collected at 24- and 44 h post-eCG and 10 h post-hCG (data not discussed). Ovaries from their NO counterparts were collected at the same time as the SO females. Ovarian sections were stained with an antibody that recognizes methylated cytosines (5MeC). All oocytes in a section were photographed and the largest cross section was used for analysis. Measurements related to oocyte growth were; 1) oocyte size in micrometers, 2) area of germinal vesicle, 3) size and type of enclosing follicle. Global DNA methylation was determined using the background corrected density macro of ImageJ. The 5MeC staining intensity level of the GV was normalized to the staining of the surrounding granulosa cells. For analyses, correlations were made between oocyte size and level of methylation and GV size and level of methylation. These numbers were then compared between similar size oocytes from SO and NO females. Results show that at diestrus the level of methylation increases in a linear manner form 10 to 80 µm diameter. The curve becomes exponential at 24 and 44 h in the NO group but is sigmoid in both SO groups. Analysis of full-grown oocytes (>70 µm) show that global methylation increases from diestrus (0 h) to 24 h and again to 44 h in the NO group but not in the SO groups. Interestingly, the levels of methylation remain low until ~ 40 µm diameter and start increasing exponentially in oocytes > 41 µm. This is coincident with the initiation of the formation of the second layer of granulosa cells. At 44 h, levels of DNA methylation were different in full-grown oocytes of NO vs. SO groups (P < 0.02). These full-grown oocytes are expected to ovulate upon the LH surge. Our results show that acquisition of DNA methylation continues in full grown oocytes until the presumed LH surge and we speculated that this is necessary to attain full developmental competence. On the other hand, SO full-grown oocytes do not attained full methylation before ovulation and this may in part be responsible for the lower developmental competence observed in embryos produced from SO oocytes. (poster)

Background: Maternal obesity has adverse effects on oocyte quality, embryo development, and the health of the offspring.Objectives: To understand the underlying mechanisms responsible for the negative effects of maternal obesity, we investigated the DNA methylation status of several imprinted genes and metabolism-related genes.Methods: Using a high-fat-diet (HFD)-induced mouse model of obesity, we analyzed the DNA methylation of several imprinted genes and metabolism-related genes in oocytes from control and obese dams and in oocytes and liver from their offspring. Analysis was performed using combined bisulfite restriction analysis (COBRA) and bisulfite sequencing.Results: DNA methylation of imprinted genes in oocytes was not altered in either obese dams or their offspring; however, DNA methylation of metabolism-related genes was changed. In oocytes of obese mice, the DNA methylation level of the leptin (Lep) promoter was significantly increased and that of the Ppar-α promoter was reduced. Increased methylation of Lep and decreased methylation of Ppar-α was also observed in the liver of female offspring from dams fed the high-fat diet (OHFD). mRNA expression of Lep and Ppar-α was also significantly altered in the liver of these OHFD. In OHFD oocytes, the DNA methylation level of Ppar-α promoter was increased.Conclusions: Our results indicate that DNA methylation patterns of several metabolism-related genes are changed not only in oocytes of obese mice but also in oocytes and liver of their offspring. These data may contribute to the understanding of adverse effects of maternal obesity on reproduction and health of the offspring.Citation: Ge ZJ, Luo SM, Lin F, Liang QX, Huang L, Wei YC, Hou Y, Han ZM, Schatten H, Sun QY. 2014. DNA methylation in oocytes and liver of female mice and their offspring: effects of high-fat-diet–induced obesity. Environ Health Perspect 122:159–164; http://dx.doi.org/10.1289/ehp.1307047

DNA methylation (DNAme) erasure and reacquisition occur during prenatal male germ cell development; some further remodeling takes place after birth during spermatogenesis. Environmental insults during germline epigenetic reprogramming may affect DNAme, presenting a potential mechanism for transmission of environmental exposures across multiple generations. We investigated how germ cell DNAme is impacted by lifetime exposures to diets containing either low or high, clinically relevant, levels of the methyl donor folic acid and whether resulting DNAme alterations were inherited in germ cells of male offspring of subsequent generations. Female mice were placed on a control (FCD), 7-fold folic acid deficient (7FD) or10-to20-fold supplemented (10FS and 20FS) diet before and during pregnancy. Resulting F1 litters were weaned on the respective diets. F2 and F3 males received control diets. Genome-wide DNAme at cytosines (within CpG sites) was assessed in F1 spermatogonia, and in F1, F2 and F3 sperm. In F1 germ cells, a greater number of differentially methylated cytosines (DMCs) were observed in spermatogonia as compared with F1 sperm for all folic acid diets. DMCs were lower in number in F2 versus F1 sperm, while an unexpected increase was found in F3 sperm. DMCs were predominantly hypomethylated, with genes in neurodevelopmental pathways commonly affected in F1, F2 and F3 male germ cells. While no DMCs were found to be significantly inherited inter- or transgenerationally, we observed over-representation of repetitive elements, particularly young longinterspersednuclearelements(LINEs). These results suggest that the prenatal window is the time most susceptible to folate-induced alterations in sperm DNAme in male germ cells. Altered methylation of specific sites in F1 germ cells was not present in later generations. However, the presence of DNAme perturbations in the sperm of males of the F2 and F3 generations suggests that epigenetic inheritance mechanisms other than DNAme may have been impacted by the folate diet exposure of F1 germ cells.

Meniere disease (MD) is a cochleo-vestibular syndrome defined by episodes of vertigo associated with tinnitus and sensorineural hearing loss. While MD immune response has been linked to autoinflammation and type 2 cytokines, other molecular mechanisms such as DNA methylation have an emerging yet underexplored role in MD pathophysiology.To understand the role of DNA methylation in MD, we performed whole-genome bisulphite sequencing in MD patients (n = 40) and controls (n = 13) and used differentially methylated cytosines (DMCs) to define clusters, cell types, and biochemical pathways in MD. We found three MD subclusters: Cluster 1 (40% of patients) and Cluster 3 (25%) showed DMC profiles against controls, while Cluster 2 (35%) did not. Significant DMCs from Cluster 1 and Cluster 3 versus Control analysis were annotated to 3033 and 59 unique genes, respectively. Each cluster showed a different gene enrichment; however, the KDMB4 gene had significant upregulated DNA accessibility in a complementary ATAC-seq dataset and showed significant DMCs in both Cluster 1 and Cluster 3. DNA methylation patterns in MD reveal three clusters which are reflective of an underlying difference in pathways related to cytokine stimulus, immunity T-cell, and NK-cell pathways. KDMB4 emerges as a critical MD gene which deserves further research.Key messagesWe asked if DNA methylation can help understand Meniere’s Disease (MD) pathophysiology.DNA methylomes group MD patients into three distinct sub-clusters.DNA methylation in MD reflect difference in pathways related to neurons and cytokine stimulus.The data shows KDMB4 emerging as a key gene that requires further multi-modal investigation.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00109-025-02581-6.

BackgroundOvarian stimulation (OS) during assisted reproductive technology (ART) appears to be an independent factor influencing the risk of low birth weight (LBW). Previous studies identified the association between LBW and placenta deterioration, potentially resulting from disturbed genomic DNA methylation in oocytes caused by OS. However, the mechanisms by which OS leads to aberrant DNA methylation patterns in oocytes remains unclear.MethodsMouse oocytes and mouse parthenogenetic embryonic stem cells (pESCs) were used to investigate the roles of OS in oocyte DNA methylation. Global 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) levels were evaluated using immunofluorescence or colorimetry. Genome-wide DNA methylation was quantified using an Agilent SureSelectXT mouse Methyl-Seq. The DNA methylation status of mesoderm-specific transcript homologue (Mest) promoter region was analyzed using bisulfite sequencing polymerase chain reaction (BSP). The regulatory network between estrogen receptor alpha (ERα, ESR1) and DNA methylation status of Mest promoter region was further detected following the knockdown of ERα or ten-eleven translocation 2 (Tet2).ResultsOS resulted in a significant decrease in global 5mC levels and an increase in global 5hmC levels in oocytes. Further investigation revealed that supraphysiological β-estradiol (E2) during OS induced a notable decrease in DNA 5mC and an increase in 5hmC in both oocytes and pESCs of mice, whereas inhibition of estrogen signaling abolished such induction. Moreover, Tet2 may be a direct transcriptional target gene of ERα, and through the ERα-TET2 axis, supraphysiological E2 resulted in the reduced global levels of DNA 5mC. Furthermore, we identified that MEST, a maternal imprinted gene essential for placental development, lost its imprinted methylation in parthenogenetic placentas originating from OS, and ERα and TET2 combined together to form a protein complex that may promote Mest demethylation.ConclusionsIn this study, a possible mechanism of loss of DNA methylation in oocyte caused by OS was revealed, which may help increase safety and reduce epigenetic abnormalities in ART procedures.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12964-024-01516-x.

BackgroundDNA methylation is an important epigenetic mechanism involved in gene regulation, with alterations in DNA methylation in the nuclear genome being linked to numerous complex diseases. Mitochondrial DNA methylation is a phenomenon that is receiving ever-increasing interest, particularly in diseases characterized by mitochondrial dysfunction; however, most studies have been limited to the investigation of specific target regions. Analyses spanning the entire mitochondrial genome have been limited, potentially due to the amount of input DNA required. Further, mitochondrial genetic studies have been previously confounded by nuclear-mitochondrial pseudogenes. Methylated DNA Immunoprecipitation Sequencing is a technique widely used to profile DNA methylation across the nuclear genome; however, reads mapped to mitochondrial DNA are often discarded. Here, we have developed an approach to control for nuclear-mitochondrial pseudogenes within Methylated DNA Immunoprecipitation Sequencing data. We highlight the utility of this approach in identifying differences in mitochondrial DNA methylation across regions of the human brain and pre-mortem blood.ResultsWe were able to correlate mitochondrial DNA methylation patterns between the cortex, cerebellum and blood. We identified 74 nominally significant differentially methylated regions (p < 0.05) in the mitochondrial genome, between anatomically separate cortical regions and the cerebellum in matched samples (N = 3 matched donors). Further analysis identified eight significant differentially methylated regions between the total cortex and cerebellum after correcting for multiple testing. Using unsupervised hierarchical clustering analysis of the mitochondrial DNA methylome, we were able to identify tissue-specific patterns of mitochondrial DNA methylation between blood, cerebellum and cortex.ConclusionsOur study represents a comprehensive analysis of the mitochondrial methylome using pre-existing Methylated DNA Immunoprecipitation Sequencing data to identify brain region-specific patterns of mitochondrial DNA methylation.