Genome-wide Methylation Levels Research Articles

Genome-wide DNA methylomic differences between dorsolateral prefrontal and temporal pole cortices of bipolar disorder

Dorsolateral prefrontal cortex (DLPFC) and temporal pole (TP) are brain regions that display abnormalities in bipolar disorder (BD) patients. DNA methylation — an epigenetic mechanism both heritable and sensitive to the environment — may be involved in the pathophysiology of BD. To study BD-associated DNA methylomic differences in these brain regions, we extracted genomic DNA from the postmortem tissues of Brodmann Area (BA) 9 (DLPFC) and BA38 (TP) gray matter from 20 BD, ten major depression (MDD), and ten control age-and-sex-matched subjects. Genome-wide methylation levels were measured using the 850 K Illumina MethylationEPIC BeadChip. We detected striking differences between cortical regions, with greater numbers of between-brain-region differentially methylated positions (DMPs; i.e., CpG sites) in all groups, most pronounced in the BD group, and with substantial overlap across groups. The genes of DMPs common to both BD and MDD (hypothetically associated with their common features such as depression) and those distinct to BD (hypothetically associated with BD-specific features such as mania) were enriched in pathways involved in neurodevelopment including axon guidance. Pathways enriched only in the BD-MDD shared list pointed to GABAergic dysregulation, while those enriched in the BD-only list suggested glutamatergic dysregulation and greater impact on synaptogenesis and synaptic plasticity. We further detected group-specific between-brain-region gene expression differences in ODC1, CALY, GALNT2, and GABRD, which contained significant between-brain-region DMPs. In each brain region, no significant DMPs or differentially methylated regions (DMRs) were found between diagnostic groups. In summary, the methylation differences between DLPFC and TP may provide molecular targets for further investigations of genetic and environmental vulnerabilities associated with both unique and common features of various mood disorders and suggest directions of future development of individualized treatment strategies.

Analysis of genomic DNA methylation level in foxtail millet by Methylation Sensitive Amplified Polymorphism

DNA methylation is an important type of epigenetic modification in eukaryotes. In order to research genome-wide methylation levels and patterns in foxtail millet (Setaria italica), the Methylation Sensitive Amplified Polymorphism (MSAP) analysis (employing double digestion with EcoR I and Hpa II/Msp I) was established and applied in two foxtail millet cultivars (Chaogu 58 and Yugu 1). The results showed that 32 pairs of MSAP primers were selected from 100 MSAP primers, and 1 615 and 1 482 clearly distinguishable and reproducible bands were amplified from Chaogu 58 and Yugu 1 respectively, including 3 types of methylation patterns. Cytosine methylation levels of CCGG context in Chaogu 58 and Yugu 1 were characterized as 6.93% and 8.77% respectively. Such different genomic DNA methylation levels between two foxtail millet varieties may provide a preliminary reference for the cultivation of this crop from a novel epigenetic viewpoint.

Genome-wide DNA hypermethylation and homocysteine increase a risk for myopia.

To test for the association between genome-wide methylation and myopia in human and mice. Long interspersed nucleotide element 1 (LINE-1) methylation levels were used to surrogate genome-wide methylation level. We first tested for the association between high myopia (<-6 D) and LINE-1 methylation in leukocytes in 220 cases and 220 control subjects. Secondly, we validated the results of LINE-1 methylation in eyes from the form deprivation myopia (FDM) mice. Furthermore, we calculated the correlation of LINE-1 methylation levels between leukocyte DNA and ocular DNA in the mice. We also tested whether dopamine can alter LINE-1 methylation levels. The LINE-1 methylation level was significantly higher in the myopic human subjects than controls. The upper and middle tertiles of the methylation levels increased an approximately 2-fold (P≤0.002) risk for myopia than the lower tertile. Similarly, FDM mice had high LINE-1 methylation levels in the leukocyte, retina and sclera, and furthermore the methylation levels detected from these three tissues were significantly correlated. Immunohistochemical staining revealed higher levels of homocysteine and methionine in the rodent myopic eyes than normal eyes. Dopamine treatment to the cells reduced both LINE-1 methylation and DNA methyltransferase levels. LINE-1 hypermethylation may be associated with high myopia in human and mice. Homocysteine and methionine are accumulated in myopic eyes, which may provide excess methyl group for genome-wide methylation.

Intrauterine Programming of Diabetes Induced Cardiac Embryopathy

Background: Maternal hyperglycemia is a well-recognized risk factor for fetal congenital heart disease. However, the underlying cellular and molecular mechanisms are not well characterized. We hypothesize that maternal hyperglycemia leading to congenital heart are linked to abnormal DNA methylation and mRNA expression at cardiac specific loci. Methods: Hyperglycemia was induced in normal 8-week old CD-1 female mice with a one-time intraperitoneal injection of 150 mg/kg of streptozotocin (STZ) 2 weeks prior to mating. Histological analysis of fetal cardiac morphology was evaluated for malformations on embryonic day (E) 16.5 of control pups and pups exposed to maternal hyperglycemia. We used a massively-parallel sequencing-based methylation sensitive restriction based assay to examine genome-wide cytosine methylation levels at &gt;1.65 million loci in neonatal hearts on post-natal (P) day 0. Functional validation was performed with real time quantitative polymerase chain reaction (RT-qPCR). Results: Cardiac structural defects occurred in 28% of the pups (n=12/45) of hyperglycemic dams versus 7% (n=4/61) of controls. Notable phenotypes were hypoplastic left or right ventricle, double outlet right ventricle, ventricular septal defect, and left ventricular outflow tract obstruction. A 10-fold increase in DNA methylation of gene promoter regions was seen in many cardiac important genes in the experimental versus control P0 neonates and have corresponding decreases in gene expression in 21/32 genes functionally validated. Conclusion: Maternal hyperglycemia alters DNA methylation and mRNA expression of some cardiac genes during heart development. Quantitative, genome-wide assessment of cytosine methylation can be used as a discovery platform to gain insight into the mechanisms of hyperglycemia-induced cardiac anomalies.

Scots pine as a promising indicator organism for biomonitoring of the polluted environment: A case study on chronically irradiated populations

In this paper the main results of long-term (2003–2016) observations on Scots pine populations inhabiting sites affected by the Chernobyl accident are presented. Populations growing for many years under chronic radiation exposure are characterized by the enhanced mutation rates, increased genetic diversity, changes in the gene expression and in the level of genome-wide methylation, alterations in the temporal dynamics of cytogenetic abnormalities and genetic structure of populations. However, significant changes at the genetic level had no effects on enzymatic activity, morphological abnormalities, and reproductive ability of pine trees. The results presented increase our understanding of the long-term effects of chronic radiation exposure on plant populations in the wild nature and provide important information for the management and monitoring of radioactively contaminated territories.

909: Methylation profile of circulating cfDNA at term demonstrates relatively low placental contribution to hypomethylated cfDNA

The fetal fraction of circulating cell-free DNA (cfDNA) is placental in origin, and is a critical variable in noninvasive prenatal testing (NIPT). Although fetal cfDNA is known to be hypomethylated relative to maternal cfDNA, the methylation profile of circulating cfDNA in maternal plasma has not been well studied. We sought to determine whether hypomethylated cfDNA in maternal plasma: (i) could serve as a proxy for fetal fraction and (ii) was reduced in maternal obesity, as the fetal fraction of circulating cfDNA is known to be decreased in the setting of maternal obesity. In this prospective pilot study, maternal plasma was collected at admission and 24-48h postpartum (PP) from women admitted for delivery at term. Subjects were enrolled into 4 groups: lean (pre-pregnancy BMI <25 kg/m2) no labor (Lean-NL) (n=15); lean labor (Lean-L) (n=18); obese (pre-pregnancy BMI ≥30 kg/m2) no labor (OB- NL) (n=16); and obese labor (OB-L) (n=11). Total cfDNA was isolated and genome-wide methylation levels determined using 0.2x coverage whole-genome bisulfite sequencing (WGBS) in all 60 antepartum (AP) samples and in matching PP samples in ∼5 patients per study group. Calibration was performed using serial dilutions of fully methylated and unmethylated DNA. Hypomethylated cfDNA fraction was significantly lower in OB vs lean pregnant women (27.0 ±0.5% vs 28.5±0.3%, p=0.008). Hypomethylated fraction was significantly higher in AP vs PP samples overall, and when stratified by BMI (Fig 1A/B), demonstrating that the placenta contributes to hypomethylated cfDNA in maternal circulation. However, matched analyses of hypomethylation before and after delivery demonstrated a relatively small contribution of placental cfDNA to the overall hypomethylated fraction, ∼15%. The lower hypomethylated cfDNA fraction in OB patients is consistent with our prior observation of reduced placental cfDNA release in a mouse model of diet-induced obesity. Contrary to expectations, the placenta accounted for a relatively low proportion of all hypomethylated cfDNA in maternal plasma at term, suggesting that hypomethylation is not a good proxy for the fetal fraction. The finding of 20-25% hypomethylated cfDNA in non-pregnant healthy women is consistent with the oncology literature. Understanding the impact of pregnancy and maternal obesity on the methylation profile of cfDNA may have broader implications for NIPT, as well as for oncology researchers.

MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

BackgroundDNA methylation of CpG dinucleotides is an essential epigenetic modification that plays a key role in transcription. Widely used DNA enrichment-based methods offer high coverage for measuring methylated CpG dinucleotides, with the lowest cost per CpG covered genome-wide. However, these methods measure the DNA enrichment of methyl-CpG binding, and thus do not provide information on absolute methylation levels. Further, the enrichment is influenced by various confounding factors in addition to methylation status, for example, CpG density. Computational models that can accurately derive absolute methylation levels from DNA enrichment data are needed.ResultsWe developed “MeDEStrand,” a method that uses a sigmoid function to estimate and correct the CpG bias from enrichment results to infer absolute DNA methylation levels. Unlike previous methods, which estimate CpG bias based on reads mapped at the same genomic loci, MeDEStrand processes the reads for the positive and negative DNA strands separately. We compared the performance of MeDEStrand to that of three other state-of-the-art methods “MEDIPS,” “BayMeth,” and “QSEA” on four independent datasets generated using immortalized cell lines (GM12878 and K562) and human primary cells (foreskin fibroblasts and mammary epithelial cells). Based on the comparison of the inferred absolute methylation levels from MeDIP-seq data and the corresponding reduced-representation bisulfite sequencing data from each method, MeDEStrand showed the best performance at high resolution of 25, 50, and 100 base pairs.ConclusionsThe MeDEStrand tool can be used to infer whole-genome absolute DNA methylation levels at the same cost of enrichment-based methods with adequate accuracy and resolution. R package MeDEStrand and its tutorial is freely available for download at https://github.com/jxu1234/MeDEStrand.git.

Genome-wide methylation study of whole blood cellsDNA in men with congenital hypopituitarism disease.

Congenital hypopituitarism (CH) is a relatively rare disease that is characterized by the deficiency of one or more hormones secreted by the pituitary gland, which leads to metabolic disorders, amenorrhea and infertility. However, the underlying molecular mechanisms of CH have not yet been fully elucidated. The present study evaluated the genome-wide methylation level of whole blood DNA in 12 patients with CH and 12 age-matched controls using Illumina Human Methylation 450 array, in order to determine the roles of epigenetic regulation in the pathogenesis of CH. The results demonstrated that the methylation levels of 51 CpG sites were significantly different between the patients with CH and the controls. Functional enrichment analysis identified that the aberrant methylated genes were enriched in gene sets associated with metabolic or cellular process, immune system process and reproduction. In addition, two CpG sites on genes LIM domain kinase 2 (LIMK2) and piwi-like RNA-mediated gene silencing 2 (PIWIL2), which are involved in spermatogenesis and/or testicular development, were identified to be hypermethylated in male patients with CH. The hypermethylation of these sites was further validated in another 40 patients with CH and 40 matched controls with a quantitative bisulfite pyrosequencing method, and the methylation levels of these two loci demonstrated promising diagnostic capacities for CH. The present results suggested that aberrant methylation of genes may be involved in the pathogenesis of CH, and hypermethylation of LIMK2 and PIWIL2 may contribute to the infertility of male patients with CH. Further studies are required to elucidate the underlying mechanisms of the epigenetic regulation of these genes.

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR.

Studies in epigenetics have shown that DNA methylation is a key factor in regulating gene expression. Aberrant DNA methylation is often associated with DNA instability, which could lead to development of diseases such as cancer. DNA methylation typically occurs in CpG context. When located in a gene promoter, DNA methylation often acts to repress transcription and gene expression. The most commonly used technology of studying DNA methylation is bisulfite sequencing (BS-seq), which can be used to measure genomewide methylation levels on the single-nucleotide scale. Notably, BS-seq can also be combined with enrichment strategies, such as reduced representation bisulfite sequencing (RRBS), to target CpG-rich regions in order to save per-sample costs.A typical DNA methylation analysis involves identifying differentially methylated regions (DMRs) between different experimental conditions. Many statistical methods have been developed for finding DMRs in BS-seq data. In this workflow, we propose a novel approach of detecting DMRs using edgeR.By providing a complete analysis of RRBS profiles of epithelial populations in the mouse mammary gland, we will demonstrate that differential methylation analyses can be fit into the existing pipelines specifically designed for RNA-seq differential expression studies. In addition, the edgeRgeneralized linear model framework offers great flexibilities for complex experimental design, while still accounting for the biological variability. The analysis approach illustrated in this article can be applied to any BS-seq data that includes some replication, but it is especially appropriate for RRBS data with small numbers of biological replicates.

Bi-directional effects of vitamin B12 and methotrexate on Daphnia magna fitness and genomic methylation

Here we interrogated, using three separate but complementary experimental approaches, the impact of vitamin B12 availability and methotrexate exposure on Daphnia magna, which we hypothesised should have an opposite effect on One carbon metabolism (OCM). OCM is a vital biological process supporting a variety of physiological processes, including DNA methylation. Contrary to mammalian models, this process remains largely unexplored in invertebrates. The purpose of this study was to elucidate the impact of OCM short-term alteration on the fitness and epigenome of the keystone species, Daphnia. We used maternal age at reproduction, brood size and survival rates in combination with DNA methylation sensitive comet assay to determine the effects of vitamin B12 or MTX on fitness and the epigenome. Vitamin B12 had a positive influence on Daphnia fitness and we provide evidence demonstrating that this may be associated with an increased level of genome-wide DNA methylation. Conversely, exposing D. magna to MTX negatively influenced the fitness of the animals and was associated with loss of global DNA methylation, translating in decreased fitness. These results highlight the potential importance of OCM in invertebrates, providing novel evidence supporting a potential role for epigenetic modifications to the genome in D. magna environmental adaptability.

Exposure to Low Levels of Lead in Utero and Umbilical Cord Blood DNA Methylation in Project Viva: An Epigenome-Wide Association Study.

Background:Early-life exposure to lead is associated with deficits in neurodevelopment and with hematopoietic system toxicity. DNA methylation may be one of the underlying mechanisms for the adverse effects of prenatal lead on the offspring, but epigenome-wide methylation data for low levels of prenatal lead exposure are lacking.Objectives:We investigated the association between prenatal maternal lead exposure and epigenome-wide DNA methylation in umbilical cord blood nucleated cells in Project Viva, a prospective U.S.-based prebirth cohort with relatively low levels of lead exposure.Methods:Among 268 mother–infant pairs, we measured lead concentrations in red blood cells (RBC) from prenatal maternal blood samples, and using HumanMethylation450 Bead Chips, we measured genome-wide methylation levels at 482,397 CpG loci in umbilical cord blood and retained 394,460 loci after quality control. After adjustment for batch effects, cell types, and covariates, we used robust linear regression models to examine associations of prenatal lead exposure with DNA methylation in cord blood at epigenome-wide significance level [false discovery rate ].Results:The mean [standard deviation (SD)] maternal RBC lead level was 1.22 (0.63) . CpG cg10773601 showed an epigenome-wide significant negative association with prenatal lead exposure ( per doubling increase in lead exposure; ) and was annotated to C-Type Lectin Domain Family 11, Member A (CLEC11A), which functions as a growth factor for primitive hematopoietic progenitor cells. In sex-specific analyses, we identified more CpGs with among female infants () than among male infants (). One CpG (cg24637308), which showed a strong negative association with prenatal lead exposure among female infants ( per doubling increase in lead exposure; ), was annotated to Dynein Heavy Chain Domain 1 gene (DNHD1) which is highly expressed in human brain. Interestingly, there were strong correlations between blood and brain methylation for CpG (cg24637308) based on another independent set of samples with a high proportion of female participants.Conclusion:Prenatal low-level lead exposure was associated with newborn DNA methylation, particularly in female infants. https://doi.org/10.1289/EHP1246

DNA Methylome Profiling on the Infinium HumanMethylation450 Array from Limiting Quantities of Genomic DNA from a Single, Small Archived Bloodspot.

Aims: Archived newborn bloodspots are valuable sample collections for genetic and epigenetic disease research. However, they have often been stored for long periods of time, under less than ideal circumstances, and nucleic acid yields can be low, particularly when samples become limiting. We wished to determine whether the quantity and quality of genomic DNA (gDNA) isolated from a single, surgical bloodspot punch (2 mm dia.) was adequate for accurate and reliable DNA methylome profiling on the Illumina HumanMethylation450 array.Methods: A total of 25–750 ng of archived bloodspot or Jurkat cell gDNA were bisulfite converted and analyzed on the array without any additional DNA amplification steps. Methylation profiles were assessed for call rate, call confidence (detection p-value), and reproducibility.Results: Using 25 ng gDNA from either Jurkat cells or dried bloodspots, array-wide call rates (∼99.9%) and detection p-values (99.9% with p < 5 × 10−6) were excellent. There was good agreement between methylation profiles generated from 25 ng gDNA and those generated from 750 ng (ρ > 0.98), although a fraction of CpG sites (2–8% depending on experiment) exhibited quantitative differences. Genome-wide methylation levels were strikingly reproducible from 25 ng DNA in both replicate and interindividual samples (ρ > 0.98).Conclusions: Twenty-five nanograms of gDNA, isolated from a single, surgical punch (2 mm dia.) of an archived newborn bloodspot, generate a genome-wide methylation profile on the Illumina HumanMethylation450 array that is robust, reproducible, and suitable for differential methylation studies.

EXERCISE TRAINING-INDUCED CHANGES ON DNA METHYLATION IN MILD COGNITIVELY IMPAIRED OLDER AFRICAN AMERICANS: GEMS STUDY

DNA methylation at CpG sites is an important epigenetic modification of the human genome that can affect gene expression and potentially influence health outcomes. Notably, aging and physical exercise have been shown to influence epigenetic modification with during minimal exercise, inducing hypomethylation of the entire genome within muscle cells. However, there is paucity of data on exercise-induced training adaptation on DNA methylation in mild cognitively impaired (MCI) older African American (AA) undergoing well-characterized and supervised exercise intervention. Objective of Study: We explored the effects of a six-month aerobic and stretch exercise intervention on the epigenetic modifications and genome-wide DNA methylation of enrolled participants. Twenty-nine older AAs volunteers confirmed to be MCI, were randomly, assigned into a six-month program of either aerobic or stretch exercise. Participants underwent 40 minutes of supervised training 3 times/week. The maximal oxygen consumption (VO2Max) was determined at baseline and repeated after subjects completed the 6-month exercise program. Genome-wide methylation levels at CpG sites from 19 participants at baseline and a 6-month exercise training were profiled by using the Infinium HumanMethylation450 BeadChip assay. We examined the association between the change in CpG sites intensities and VO2 Max after 6 months of exercise adjusting for Age, APOE4 carrier status and randomization group. The participants averaged ∼71 years old in age, were 67.86% female and similar in mean relative VO2 Max (Stretch=24.72 (8.68) vs. Aerobic=22.74 (2.69); p = 0.715) at baseline. In total, we obtained DNA methylation data or 485,513 CpG sites from blood of 19 participants at baseline and after the exercise adaptation. Overall, six CpG sites demonstrated significant training-induced changes in methylation profile: p-values below 5 x 10-5 (cg06648780, cg06120404, cg08733824, cg14318197, cg26580761, cg24583624) with the first two CpG sites located on the ALCAM (leukocyte adhesion molecule) and C1orf88 (primary cilia formation) genes. We provide a genome-wide DNA methylation patterns associated with training-induced changes after a 6-month exercise adaptation. Whereas, efforts to understand the implications of these changes are ongoing, future studies should inform the relationships of changes in DNA methylation to mRNA expression in a predominantly AA sample, and correlate such changes with the MCI clinical phenotype.

MeDIPStrand: inferring genome-wide absolute methylation level from DNA enrichment experiment

MeDIPStrand: inferring genome-wide absolute methylation level from DNA enrichment experiment

Integrated transcriptome and methylome analysis in youth at high risk for bipolar disorder: a preliminary analysis

First-degree relatives of patients with bipolar disorder (BD), particularly their offspring, have a higher risk of developing BD and other mental illnesses than the general population. However, the biological mechanisms underlying this increased risk are still unknown, particularly because most of the studies so far have been conducted in chronically ill adults and not in unaffected youth at high risk. In this preliminary study we analyzed genome-wide expression and methylation levels in peripheral blood mononuclear cells from children and adolescents from three matched groups: BD patients, unaffected offspring of bipolar parents (high risk) and controls (low risk). By integrating gene expression and DNA methylation and comparing the lists of differentially expressed genes and differentially methylated probes between groups, we were able to identify 43 risk genes that discriminate patients and high-risk youth from controls. Pathway analysis showed an enrichment of the glucocorticoid receptor (GR) pathway with the genes MED1, HSPA1L, GTF2A1 and TAF15, which might underlie the previously reported role of stress response in the risk for BD in vulnerable populations. Cell-based assays indicate a GR hyporesponsiveness in cells from adult BD patients compared to controls and suggest that these GR-related genes can be modulated by DNA methylation, which poses the theoretical possibility of manipulating their expression as a means to counteract the familial risk presented by those subjects. Although preliminary, our results suggest the utility of peripheral measures in the identification of biomarkers of risk in high-risk populations and further emphasize the potential role of stress and DNA methylation in the risk for BD in youth.

Genome-wide DNA methylation analysis in renal ischemia reperfusion injury

Renal ischemia reperfusion injury (IRI) is frequently encountered after kidney transplantation and is a leading cause of acute renal failure. Aberrant gene expression and epigenetic regulation occur during the pathophysiology of IRI. In this study, we used reduced representation bisulfite sequencing to identify the DNA methylome of renal tissues during IRI and the sham-operated tissues in C57BL/6. The methylation status of approximately 1.29 million CpGs located in an average of 11554 CpG islands and 17113 promoters in genome was determined. Compared with sham-operated kidney, both acute and chronic IRI significantly decreased the genome-wide methylation level (1.1–1.8%) and the CpG methylation level in the promoter (0.4–0.5%), CpG island (0.5–1.3%), exon (1.3–1.9%), and intron (0.8–1.1%; all P<10−153). The promoters of 200, 191, and 79 genes were differentially methylated in the renal tissues at 24h, 7days, and at both the time points after IRI, respectively. Among the 79 genes, which were consistently epigenetically regulated at two time points, 18 genes (22.8%) showed differential expression after IRI in a previous study of renal expression. We validated the promoter methylation status and expression of five out of the 18 genes, including 2700049A03Rik, Ccr9, Fgd2, Pfkfb3, and Sdc4 in an independent renal tissue cohort. We found that all the five genes exhibited altered methylation of promoter (P=0.009–0.0001) following renal injury. The promoter methylation of 2700049A03Rik and Ccr9 was negatively correlated with their mRNA expression in renal tissues (P<0.001 and P<0.0001, respectively). Our study not only demonstrated a genome-wide DNA methylation pattern in the IR-injured renal tissue for the first time, but also indicated that the regulation of promoter methylation is an important mechanism underlying persistent alteration of gene expression.

Variation of global DNA methylation levels with age and in autistic children

BackgroundThe change in epigenetic signatures, in particular DNA methylation, has been proposed as risk markers for various age-related diseases. However, the course of variation in methylation levels with age, the difference in methylation between genders, and methylation-disease association at the whole genome level is unclear. In the present study, genome-wide methylation levels in DNA extracted from peripheral blood for 2116 healthy Chinese in the 2–97 age range and 280 autistic trios were examined using the fluorescence polarization-based genome-wide DNA methylation quantification method developed by us.ResultsGenome-wide or global DNA methylation levels proceeded through multiple phases of variation with age, consisting of a steady increase from age 2 to 25 (r = 0.382) and another rise from age 41 to 55 to reach a peak level of ~80 % (r = 0.265), followed by a sharp decrease to ~40 % in the mid-1970s (age 56 to 75; r = −0.395) and leveling off thereafter. Significant gender effect in methylation levels was observed only for the 41–55 age group in which methylation in females was significantly higher than in males (p = 0.010). In addition, global methylation level was significantly higher in autistic children than in age-matched healthy children (p < 0.001).ConclusionsThe multiphasic nature of changes in global methylation levels with age was delineated, and investigation into the factors underlying this profile will be essential to a proper understanding of the aging process. Furthermore, this first report of global hypermethylation in autistic children also illustrates the importance of age-matched controls in characterization of disease-associated variations in DNA methylation.Electronic supplementary materialThe online version of this article (doi:10.1186/s40246-016-0086-y) contains supplementary material, which is available to authorized users.

Methylation of the oxytocin receptor gene mediates the effect of adversity on negative schemas and depression.

Building upon various lines of research, we posited that methylation of the oxytocin receptor gene (OXTR) would mediate the effect of adult adversity on increased commitment to negative schemas and in turn the development of depression. We tested our model using structural equation modeling and longitudinal data from a sample of 100 middle-aged, African American women. The results provided strong support for the model. Analysis of the 12 CpG sites available for the promoter region of the OXTR gene identified four factors. One of these factors was related to the study variables, whereas the others were not. This factor mediated the effect of adult adversity on schemas relating to pessimism and distrust, and these schemas, in turn, mediated the impact of OXTR methylation on depression. All indirect effects were statistically significant, and they remained significant after controlling for childhood trauma, age, romantic relationship status, individual differences in cell types, and average level of genome-wide methylation. These finding suggest that epigenetic regulation of the oxytocin system may be a mechanism whereby the negative cognitions central to depression become biologically embedded.

Genome-wide methylation analysis of tubulocystic and papillary renal cell carcinomas.

Tubulocystic renal cell carcinoma (TRCC) represents arare tumor with incidence lower than 1% of all renal carcinomas. This study was undertaken to contribute to characterization of molecular signatures associated with TRCC and to compare them with the features of papillary renal cell carcinoma (PRCC) at the level of genome wide methylation analysis.We performed methylated DNA immunoprecipitation (MeDIP) coupled with microarray analysis (Roche NimbleGen). Using the CHARM package, we compared the levels of gene methylation between paired samples of tumors and control renal tissues of each examined individual. We found significant global demethylation in all tumor samples in comparison with adjacent kidney tissues of normal histological appearance but no significant differences in gene methylation between the both compared tumor entities. Therefore we focused on characterization of differentially methylated regions between both tumors and control tissues. We found 42 differentially methylated genes.Hypermethylated genes for protocadherins (PCDHG) and genes coding for products associated with functions of plasma membrane were evaluated as significantly overrepresented among hypermethylated genes detected in both types of renal cell carcinomas.In our pilot study, we provide the first evidence that identical features in the process of carcinogenesis leading to TRCC and/or to PRCC may be found at the gene methylation level.

Use of Blood as a Surrogate Model for the Assessment of Visceral Adipose Tissue Methylation Profiles Associated with the Metabolic Syndrome in Men

Epigenetic mechanisms are known to be involved in tissue-specific differentiation. DNA methylation patterns have been shown to be largely conserved across tissues but with variation for specific genes. However, it is unclear whether the variability observed in the methylation profile of a metabolically active tissue is reflected in other sources such as hematopoietic tissue. This study aimed to test blood genome-wide CpG site methylation levels as a surrogate model for visceral adipose tissue (VAT) methylation and to verify whether it appropriately reflects differences in methylation levels found in VAT between men discordant for the metabolic syndrome (MetS). Tissue specimens (VAT and blood samples) were obtained from 16 severely obese individuals discordant for the MetS. CpG sites methylation levels were measured with the Infinium HumanMethylation450 BeadChip and correlations of methylation levels between VAT and blood were computed. Differences in methylation levels between individuals with and without MetS were tested in both tissues. Pathway analysis was conducted for differentially methylated CpG sites common to both tissues. High cross-tissue correlations were observed for VAT and blood (0.952±0.014) while some CpG sites had significantly different methylation levels in VAT versus blood. Differential methylation analysis between individuals with and without MetS demonstrated a higher number of differentially methylated CpG sites in VAT than in blood (11,778 vs. 881, respectively) with nearly 4% of differentially methylated sites found in VAT being also represented in blood. Common differentially methylated sites were involved in inflammatory-, lipid- and diabetes-related pathways. These results suggest that blood methylation levels of specific CpG sites may adequately reflect VAT methylation levels for some of the MetS-related genes, specifically for inflammatory, lipid and glucose metabolism genes.