Differentially Methylated Regions Research Articles

EpigenPlot: An interactive web platform for DNA methylation-based biomarker and drug target discovery in colorectal cancer.

Genome-wide methylation studies have significantly advanced our understanding of colorectal adenocarcinoma progression and biomarker discovery. Aberrant DNA methylation plays a crucial role in gene expression regulation during cancer transformation, highlighting the need to identify differentially methylated regions (DMRs) as potential diagnostic and therapeutic markers. However, an integrated resource to explore and validate methylation alterations across colorectal cancer stages has been lacking. We aimed to develop a platform that integrates existing methylation data, systematically identifies DMRs and provides a tool for further investigation. We created a database combining Illumina HumanMethylation450K and EPIC data from normal colon, adenoma and adenocarcinoma tissues, comprising 2346 samples from 19 datasets. Methylation levels were analysed in six gene regions, and comparisons between tissue types were made using Mann-Whitney, Kruskal-Wallis and ROC tests. Both adenoma and adenocarcinoma samples exhibited a general decrease in methylation compared to healthy tissue. Differential methylation in genes such as ITGA4, NPY, IGFL1 and LRRC4 was validated. The strongest DMRs were observed in the C1orf70 gene's 5'UTR and TSS200 regions, with AUC values of 0.98 in both of the HM450K and EPIC datasets. We established an interactive web-based platform accessible at https://epigenplot.com/ enabling future analysis of individual gene regions. Our study provides an integrated database of DNA methylation profiles across normal, adenoma and adenocarcinoma tissues, offering a valuable resource for biomarker discovery. The integrated web platform can serve as a tool for the development of methylation-based therapies in the future.

Non-invasive diagnosis for urothelial carcinoma using a dual-target DNA methylation biomarker panel.

Urothelial carcinoma (UC) is a common malignancy worldwide. Aberrant DNA methylation is implicated in UC carcinogenesis. This study sought to delineate the DNA methylation landscape in UC and identify DNA methylation-based biomarkers for early detection of UC. Whole genome bisulfite sequencing (WGBS) was conducted on bladder cancer tissues and paired normal tissues. By integrating WGBS data with The Cancer Genome Atlas (TCGA) UBC data, a DNA methylation-based biomarker was identified. When combined with a known UC biomarker AL021918.2, the performance of the dual-target test was evaluated in voided urine samples from 224 UC patients and 419 controls. Notable hypomethylation was observed in UC samples compared to normal samples. Through differential methylation analysis, differential methylation CpG sites, regions, and genes were identified. Of these, Transmembrane protein 106A gene (TMEM106A) was screened as a new UC biomarker. In a dual-target test, using triplex quantitative methylation-specific PCR (qMSP) to examine TMEM106A and AL021918.2 methylation levels, the training set showed a sensitivity of 89.0%, a specificity of 92.9%, and an area under the curve (AUC) value of 0.941 (95% confidence interval [CI]: 0.913-0.969). Similarly, the validation set showed a sensitivity of 90.0%, a specificity of 91.1%, and an AUC value of 0.922 (95% CI: 0.881-0.962). Thus, our dual-target test demonstrated outstanding detection rates for low-grade or early-stage tumors. We provide a comprehensive analysis of DNA methylation profiles in UC, and highlight the promising clinical potential of dual-target urine tests for UC detection.

Effects of subclinical hypothyroidism during pregnancy on mtDNA methylation in the brain of rat offspring

ObjectiveThis study aims to investigate the impact of subclinical hypothyroidism (SCH) during pregnancy on mitochondrial DNA (mtDNA) methylation in the brain tissues of rat offspring.Materials and methodsSixteen SD rats were randomly divided into two groups: control group (CON) and SCH group. BS-seq sequencing was used to analyze mtDNA methylation levels in the offspring’s brain tissues; the 2,7-dichlorofluorescin diacetate (DCFH-DA) probe method was employed to detect reactive oxygen species (ROS) levels in brain tissues; electron microscopy was utilized to observe the mitochondrial structure in the hippocampal tissues of the offspring.ResultsIn the analysis of differentially methylated regions (DMRs), the mitochondrial chromosome in the SCH group exhibited 23 DMRs compared to the control group. ROS levels in the brain tissues of the SCH group were significantly higher than those in the control group (P < 0.05). The mitochondrial structure in the hippocampus of the SCH group was less intact compared to the CON group.ConclusionSubclinical hypothyroidism in pregnant rats may alter the mtDNA methylation pattern in the brains of their offspring, potentially affecting mitochondrial function and structure.

Epigenome-wide association study of Chinese monozygotic twins identifies DNA methylation loci associated with estimated glomerular filtration rate

BackgroundDNA methylation (DNAm) has been shown in multiple studies to be associated with the estimated glomerular filtration rate (eGFR). However, studies focusing on Chinese populations are lacking. We conducted an epigenome-wide association study to investigate the association between DNAm and eGFR in Chinese monozygotic twins.MethodsGenome-wide DNAm level was detected using Reduced Representation Bisulfite Sequencing test. Generalized estimation equation (GEE) was used to examine the association between Cytosine-phosphate-Guanines (CpGs) DNAm and eGFR. Inference about Causation from Examination of FAmiliaL CONfounding was employed to infer the causal relationship. The comb-p was used to identify differentially methylated regions (DMRs). GeneMANIA was used to analyze the gene interaction network. The Genomic Regions Enrichment of Annotations Tool enriched biological functions and pathways. Gene expression profiling sequencing was employed to measure mRNA expression levels, and the GEE model was used to investigate the association between gene expression and eGFR. The candidate gene was validated in a community population by calculating the methylation risk score (MRS).ResultsA total of 80 CpGs and 28 DMRs, located at genes such as OLIG2, SYNGR3, LONP1, CDCP1, and SHANK1, achieved genome-wide significance level (FDR < 0.05). The causal effect of DNAm on eGFR was supported by 12 CpGs located at genes such as SYNGR3 and C9orf3. In contrast, the causal effect of eGFR on DNAm is proved by 13 CpGs located at genes such as EPHB3 and MLLT1. Enrichment analysis revealed several important biological functions and pathways related to eGFR, including alpha-2A adrenergic receptor binding pathway and corticotropin-releasing hormone receptor activity pathway. GeneMANIA results showed that SYNGR3 was co-expressed with MLLT1 and had genetic interactions with AFF4 and EDIL3. Gene expression analysis found that SYNGR3 expression was negatively associated with eGFR. Validation analysis showed that the MRS of SYNGR3 was positively associated with low eGFR levels.ConclusionsWe identified a set of CpGs, DMRs, and pathways potentially associated with eGFR, particularly in the SYNGR3 gene. These findings provided new insights into the epigenetic modifications related to the decline in eGFR and chronic kidney disease.

Generation of live mice from haploid ESCs with germline-DMR deletions or switch

Genomic imprinting is required for sexual reproduction and embryonic development of mammals, in which, differentially methylated regions (DMRs) regulate the parent-specific monoallelic expression of imprinted genes. Numerous studies on imprinted genes have highlighted their critical roles in development. However, what imprinting network is essential for development is still unclear. Here, we establish a stepwise system to reconstruct a development-related imprinting network, in which diploid embryonic stem cells (ESCs) are derived by fusing between parthenogenetic (PG)- and androgenetic (AG)-haploid embryonic stem cells (haESCs) with different DMR deletions (termed Ha-Ha-fusion system), followed by tetraploid complementation to produce all-haESC fetuses. Diploid ESCs fused between PG-haESCs carrying 8 maternally-derived DMR deletions and AG-haESCs with 2 paternally-derived DMR deletions give rise to live pups efficiently, among which, one lives to weaning. Strikingly, diploid ESCs derived from the fusion of PG-haESCs with 7 maternal DMR deletions and AG-haESCs with 2 paternal DMR deletions and maternal Snrpn-DMR deletion also support full-term embryonic development. Moreover, embryos reconstructed by injection of AG-haESCs with hypomethylated H19-DMR into oocytes with H19-DMR deletion develop into live mice sustaining inverted allelic gene expression. Together, our findings indicate that restoration of monoallelic expression of 10 imprinted regions is adequate for the full-term development of all-haESC pups, and it works irrespective of their parental origins. Meanwhile, Ha-Ha-fusion system provides a useful tool for deciphering imprinting regulation networks during embryonic development.

Genome-wide DNA methylation analysis of sorghum leaves following foreign GA3 exposure under salt stress.

Sorghum is an increasingly popular topic of research in elucidating survival and adaptation approaches to augmented salinity. Nonetheless, little is known about the outcome and modulatory networks involved in the gibberellic acid (GA3)-induced salt stress alleviation in sorghum. Here, we identified 50 mg/L GA3 as the optimal concentration for sorghum ('Jitian 3') development under salt stress. Based on genome-wide DNA methylation analysis, CpG sites displayed the most abundant methylation statuses among all stages, with a mean value of 68.2 %, then CHG (57.9 %), and CHH (21.2 %). We identified 18,032 differentially methylated regions (DMRs) in the GA3-exposed groups. In particular, we recognized 5943 DMR genes and 269 DMR-promoter genes. Using conjoint transcriptome and DNA methylation analyses, we identified 337 important methylated-genes, which were involved in "phenylpropanoid biosynthesis", "arginine and proline metabolism" and "tyrosine metabolism". Together, the aforementioned data provides an in-depth understanding of the epigenetic modulation of gene expression during GA3 treatment.

Epigenome-wide association study meta-analysis of BMI in African Americans.

Despite considerable advances in identifying risk factors for obesity development, there remains substantial gaps in our knowledge about its etiology. Variation in obesity (defined by BMI) is thought to be due in part to heritable factors; however, obesity-associated genetic variants only account for a small portion of heritability. Epigenetic regulation, defined by genetic and/or environmental factors with changes in gene expression, may account for some of this "missing heritability". Epigenetic studies of obesity have largely been conducted in populations of European ancestry, despite the disproportionate burden of obesity in African Americans (AAs). To address race/ethnic (RE)-differences in obesity, we conducted a BMI epigenome-wide association study (EWAS) meta-analysis using AA participants from the Jackson Heart Study (JHS, n=1604) and the Multi-Ethnic Study of Atherosclerosis (MESA, n=179). Analyses using a linear regression model with methylation as the outcome and continuous BMI as the predictor were stratified by study and sex, then meta-analyzed. There were 208 methylation sites (CpGs) that reached epigenome-wide significance (p< 8.72×10 -8 ); 151 of these were novel. Of the novel CpGs, 29 CpGs were available for replication testing in a separate sample of AA and 20 replicated. Differentially methylated region (DMR) analysis resulted in 54 DMRs significantly associated with BMI. Several regions are proximal to, or include, genes previously associated with obesity traits (e.g., SOCS3, ABCG1 , and TGFB1 ) in GWAS. Gene and trait enrichment and pathway analysis showed enrichment for genes in immune system and inflammation related pathways (e.g., the IL-6/JAK/STAT pathway). In conclusion, EWAS of BMI in AAs replicated previously known associations identified in European ancestry and multi-ethnic EWAS and identified novel obesity-associated CpGs.

Fade into you: genetic control of pigmentation patterns in red-flesh apple (Malus domestica).

The genetic basis of type 1 red-flesh color development in apple (Malus domestica) depends upon a particular allele of the MdMYB10 gene. Interestingly, type 1 red-flesh apples are fully red after fruit set, but anthocyanin pigmentation in apple fruit cortex may decrease during fruit growth and maturation, leading to variable red patterning and intensities in the mature cortical flesh. We developed a histogram-based color analysis method to quantitatively estimate pigmentation patterns. This methodology was applied to investigate the phenotypic diversity in four hybrid F1 families segregating for red-flesh color. Pigmentation patterns were found to be heritable allowing the identification of a new locus by QTL analysis. To further investigate the mechanisms involved in the spatial deposition of anthocyanin, metabolome, transcriptome and methylome comparisons between white and red flesh areas within the red-flesh genotype cv. 'R201' exhibiting flesh pigmentation patterns, was performed. Wide-targeted analysis showed that white-flesh areas accumulate more dihydrochalcones and hydroxycinnamic acids than red-flesh areas while red-flesh areas accumulate more flavonoids. Anthocyanin biosynthesis genes and anthocyanin positive regulators (MBW complex) were up-regulated in red-flesh areas, while a reduction in anthocyanin storage, transport and stability (increase of pH, down-regulation of MdGSTU22) and an increase in phenolic catabolism were concomitant with color fading process in white-flesh areas. Expression of MdGSTU22 was linked to a differentially methylated region (DMR) suggesting a potential environmental effect on the epigenetic control of gene expression involved in color fading. Altogether, these results provide the first characterization and functional identification of color fading in apple fruit flesh.

Hypermethylation of PM20D1 Is Associated With Carotid Bifurcation Intima-Media Thickness in Dominican Republic Families.

Carotid intima-media thickness (IMT) is a measure of atherosclerosis and a predictor of vascular diseases. Traditional vascular risk factors and genetic variants do not completely explain the variation in carotid IMT. We sought to identify epigenetic factors that may contribute to the remaining carotid IMT variability. An epigenome-wide association study was performed in 61 Dominican families with 769 individuals. A cytosine nucleotide that precedes a guanine nucleotide methylation in blood-derived DNA was measured using the Human MethylationEPIC BeadChip. Linear mixed model analyses were performed regressing bifurcation carotid IMT (bIMT) on beta values for cytosine nucleotide that precedes a guanine nucleotide sites, adjusting for covariates, followed by differentially methylated region (DMR) analysis. One-sample Mendelian randomization analysis was conducted to investigate causal associations between DMRs and bIMT. Twenty-five DMRs were associated with bIMT (Sidak P <0.05), with the strongest DMR (Sidak P =2.45×10-17) overlapping with the promoter of PM20D1. All 11 cytosine nucleotides that precede a guanine nucleotide within the PM20D1 DMR were positively associated with bIMT (P=0.0007-0.00006). Methylation of the PM20D1 DMR was associated with cis variants, including rs823154 (β=0.26; P=1.1×10-121). As reported in GTEx (Genotype-Tissue Expression project), rs823154 is an expression quantitative trait locus for PM20D1 in multiple tissues, including the aorta (P=2.3×10-60) and blood (P=4.0×10-73), suggesting that hypermethylation of the PM20D1 DMR directs lower expression of the gene. Mendelian randomization analysis supported a causal role for PM20D1 DMR in bIMT (P=0.049). Our study and previous expression quantitative trait locus studies provide converging evidence that reduced PM20D1 expression via hypermethylation of the promoter is associated with increased atherosclerosis.

Peripheral Blood DNA Methylation Changes in Response to Centella asiatica Treatment in Aged Mice.

Alterations in epigenetic modifications, like DNA methylation, in peripheral blood could serve as a useful, minimally invasive biomarker of the effects of anti-aging interventions. This study explores this potential with a water extract of the botanical Centella asiatica (CAW). Eighteen-month-old mice were treated with CAW in their drinking water for 5 weeks alongside vehicle-treated eighteen-month-old C57BL6 mice. Reduced representation bisulfite sequencing (RRBS) was used to identify genome-wide differential methylation in the blood of CAW-treated aged mice compared to vehicle-treated aged mice. Our results showed a distinct enrichment of differentially methylated regions (DMRs) nearby genes involved in biological processes relevant to aging (i.e., antioxidant response, metabolic regulation, cellular metabolism). A distinct difference was observed between males and females in both the number of methylation sites and the state of methylation. Moreover, genes nearby or overlapping DMRs were found to be enriched for biological processes related to previously described cellular effects of CAW in the mouse brain (i.e., antioxidant response, metabolic regulation, calcium regulation, and circadian rhythm). Together, our data suggest that the peripheral blood methylation signature of CAW in the blood could be a useful, and readily accessible, biomarker of CAW's effects in aging.

Analysis of differentially methylated sites and regions associated with intrauterine transmission of hepatitis B virus in infants.

The goal is to identify methylation sites linked to transmission and their impact on host gene expression and HBV spread, aiming to uncover new molecular targets for preventing and treating intrauterine HBV infection. This study recruited 1205 infants born to HBsAg-positive mothers in Liuzhou City, China, between July 2023 and January 2024. Infants were followed up at 7-12months of age and classified as HBsAg-positive (case, n=5) or HBsAg-negative (control, n=14) based on serological testing. Peripheral blood samples were collected for DNA extraction. DNA methylation profiling was performed using the Illumina Infinium MethylationEPIC BeadChip (850K). Data were processed using the ChAMP package in R, including quality control, normalization, and identification of Differentially Methylated Positions (DMPs) and differentially methylated regions (DMRs). DMPs and DMRs were annotated using ANNOVAR 2018Apr16, and GO enrichment analysis was conducted using DAVID. The study was approved by the Guangxi University of Chinese Medicine Ethics Committee, and informed consent was obtained. We identified 734,978 DMPs and 660 DMRs, with 1813 DMPs and 221 DMRs showing significant differences between groups. HBV-infected infants exhibited lower overall genomic methylation levels, with significant concentrations in gene body regions and CpG islands. GO enrichment analysis indicated that differentially methylated genes were enriched in processes related to cell adhesion and calcium ion binding. Prenatal HBV exposure was associated with significant infant hypomethylation, particularly in regulatory regions like TSS1500, TSS200, and CpG islands, potentially impacting gene expression. Enrichment of immune-related pathways among differentially methylated genes suggests that HBV may alter infant immune development through epigenetic modifications.

Association between dietary fructose and human colon DNA methylation: implication for racial disparities in colorectal cancer risk using a cross-sectional study.

An increasing body of evidence has linked fructose intake to colorectal cancer (CRC). African American (AA) adults consume greater quantities of fructose and are more likely to develop right-side colon cancer than European American (EA) adults. We examined the hypothesis that fructose consumption leads to epigenomic and transcriptomic differences associated with CRC tumor biology. Deoxyribonucleic acid (DNA) methylation data from this cross-sectional study was obtained using the Illumina Infinium MethylationEPIC kit (GSE151732). Right and left colon differentially methylated regions (DMRs) were identified using DMRcate through analysis of food frequency questionnaire data on fructose consumption in normal colon biopsies (n=79) of AA adults undergoing screening colonoscopy. Secondary analysis of CRC tumors was carried out using data derived from TCGA-COAD, GSE101764 and GSE193535. Right colon organoids derived from AA (n=5) and EA (n=5) adults were exposed to 4.4mM of fructose for 72 hours. Differentially expressed genes (DEGs) were identified using DESeq2. We identified 4,263 right colon fructose-associated DMRs (FDR<0.05). In contrast, only 24 DMRs survived multiple testing corrections (FDR<0.05) in matched, left colon. Almost 50% of right colon fructose-associated DMRs overlapped regions implicated in CRC in at least one of three datasets. A highly significant enrichment was also observed between genes corresponding to right colon fructose-associated DMRs and DEGs associated with fructose exposure in right colon organoids of AA individuals (P=3.28E-30). Overlapping and significant enrichments for fatty acid metabolism, glycolysis and cell proliferation pathways were also found. Cross-referencing genes within these pathways to DEGs in CRC tumors reveals potential roles for ankyrin repeat domain-containing protein 23 (ANKRD23) and phosphofructokinase, platelet (PFKP) in fructose-mediated CRC risk for AA individuals. Our data support that dietary fructose exerts a greater CRC risk-related effect in right than left colon among AA adults, alluding to its potential role in contributing to racial disparities in CRC.

Acupuncture Increased the Number of Retrieved Oocytes in a Mouse Model of POR: The Involvement of DNA Methylation in the Oocytes

Background: 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. Objective: 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. Methods:: 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. Results: A dissecting microscope revealed that the Ac therapy improved the number of retrieved oocytes compared with the POR group (p &lt; 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. Conclusion: 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.

Association between epigenome-wide DNA methylation changes and early neurodevelopment in preschool children: Evidence from a former impoverished county in Central China.

Existing epigenome-wide association study (EWAS) investigating the association between DNA methylation (DNAm) and child neurodevelopment have been predominantly conducted within Western populations, and yielded inconsistent results, leading to a significant gap within non-Western setting, particularly in resource-limited rural areas of Central China. To investigate the association between altered epigenome-wide DNAm and neurodevelopment in preschool children from resource-limited rural areas of Central China. This case-control study involved 64 preschoolers. We assessed children's neurodevelopment using the Gesell Developmental Diagnostic Scale. The neurodevelopmental potential was expressed as a global developmental quotient (DQ) score. We conducted an EWAS with an Illumina Infinium MethylationEPIC v1.0 BeadChip array, using blood samples from 32 suspected developmental delay children (DQ scores < 85) and 32 controls (DQ scores ≥ 85). Differentially methylated probes (DMPs) and differentially methylated regions (DMRs) between the suspected developmental delay and control groups were analyzed. Multivariate linear regression models were used to evaluate the association between global DQ scores and DNAm. Functional enrichment analyses were conducted using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The BECon tool was utilized to estimate the concordance of CpGs between blood and the human brain. A total of 66 DMRs (PFDR < 0.05) were identified between the two groups, but no DMPs were found. After FDR correction, 844 methylated CpG sites exhibited significant associations with the global DQ scores in children. Genes annotated by methylated CpGs were enriched in the "oxytocin signaling pathway", "mTOR signaling pathway", and "thyroid hormone signaling pathway". They were also involved in the "regulation of cell development", "cell-cell junction", and "ATPase activity". Among the top 20 CpGs, nine global DQ scores related-CpGs had blood-brain DNA methylation correlations, and six CpGs among them had an absolute Spearman correlation coefficient bigger than 0.2. Preschoolers from a former impoverished county exhibited epigenome-wide DNAm changes strongly linked to early neurodevelopment. This study enhances our understanding of the epigenetic landscape associated with early neurodevelopment, and suggests the potential for developmenting epigenetic biomarkers that could facilitate the early identification of children at a higher risk of compromised neurodevelopment, as well as holding implication to inform novel interventions, especially in underprivileged regions.

DNA methylation landscapes before and after Pacific Oyster Mortality Syndrome are different within and between resistant and susceptible Magallana gigas.

Pacific oysters face recurring outbreaks of Pacific Oyster Mortality Syndrome (POMS), a polymicrobial multifactorial disease. Although this interaction is increasingly understood, the role of epigenetics (e.g., DNA methylation) appears to be of fundamental importance because of its ability to shape oyster resistance/susceptibility and respond to environmental triggers, including infections. In this context, we comprehensively characterized basal (no infection) and POMS-induced changes in the methylome of resistant and susceptible oysters, focusing on the gills and mantle. Our analysis identified differentially methylated regions (DMRs) that revealed distinct methylation patterns uniquely associated with the susceptible or resistant phenotypes in each tissue. Enrichment analysis of genes bearing DMRs highlighted that these epigenetic changes were specifically linked to immunity, signaling, metabolism, and transport. Notably, 31 genes with well-known immune functions were differentially methylated after POMS, with contrasting methylation patterns between the phenotypes. Based on the methylome differences between phenotypes, we identified a set of candidate epibiomarkers that could characterize whether an oyster is resistant or susceptible (1998 candidates) and whether a site has been exposed to POMS (164 candidates). Overall, the findings provide a deeper understanding of the molecular interactions between oysters and POMS infection, opening new questions about the broader implications of epigenetic mechanisms in host-pathogen dynamics and offering promising strategies for mitigating the impacts of this devastating disease. Beyond its biological aspects, this study provides insights into potential epigenetic biomarkers for POMS disease management and targets for enhancing oyster health and productivity.

Whole-Genome Methylation Sequencing Analysis and Functional Verification of LIM-Homeobox Family Genes in Cervical Cancer.

Gene methylation in cells is an important factor in tumorigenesis, and radiotherapy can change DNA methylation in cells. In this study, complete genome methylation sequencing (BS-Seq) technology was used to analyze the genome-wide methylation of patients with cervical cancer before and after radiotherapy. Three pairs of cervical squamous cell carcinoma samples were collected from patients before and after radiotherapy in July 2020. Genome-wide DNA methylation profiles were generated using WGBS. Bioinformatics analysis was conducted to identify differential methylation regions (DMRs) and their associated genes and pathways. The study focused on the methylation changes of LHX2, LHX5, and LHX9 genes, assessing their expression levels using qRT-PCR and correlating these changes with cervical cancer stages. MCG was the main way of genomic DNA methylation in the three patients. The DNA methylation level and methylation density on each chromosome varied greatly. As revealed by comparison of methylation before and after radiation in the three patients, 1287, 1261 and 789 differential methylation genes were identified, respectively.3) Combined with clinical treatment, methylation level difference and correlation enrichment analysis, it was found that LHX2, LHX5 and LHX9 were closely related to the occurrence and development of cervical cancer. After 5-Aza-DC and radiotherapy, the methylation of the CpG islands in LHX2, LHX5 and LHX9 genes in these patients was decreased (p < 0.01), and the mRNA and protein expression levels were relatively increased (p < 0.01). In our present work, genome-wide DNA methylation maps of cervical cancer tissues before and after radiotherapy were successfully constructed. We found that LHX5 and LHX9 genes are closely related to cervical cancer. LHX5 and LHX9have a negative effect on cervical cancer. The migration ability of LHX9 silenced cells was significantly enhanced after irradiation.

Decoding epigenetic markers: implications of traits and genes through DNA methylation in resilience and susceptibility to mastitis in dairy cows

ABSTRACT Cattle farming faces challenges linked to intensive exploitation and climate change, requiring the reinforcement of animal resilience in response to these dynamic environments. Currently, genetic selection is used to enhance resilience by identifying animals resistant to specific diseases; however, certain diseases, such as mastitis, pose difficulties in genetic prediction. This study introduced the utilization of enzymatic methyl sequencing (EM-seq) of the blood genomic DNA from twelve dairy cows to identify DNA methylation biomarkers, with the aim of predicting resilience and susceptibility to mastitis. The analysis uncovered significant differences between cows resilient and susceptible to mastitis, with 196,275 differentially methylated cytosines (DMCs) and 1,227 Differentially Methylated Regions (DMRs). Key genes associated with the immune response and morphological traits, including ENOPH1, MYL10 and KIR2DL5A, were identified by our analysis. Quantitative trait loci (QTL) were also highlighted and the body weight trait was the most targeted by DMCs and DMRs. Based on our results, the risk of developing mastitis can potentially be estimated with as few as fifty methylation biomarkers, paving the way for early animal selection. This research sets the stage for improved animal health management and economic yields within the framework of agricultural sustainability through early selection based on the epigenetic status of animals.

Profiling Genome-Wide Methylation Patterns in Cattle Infected with Ostertagia ostertagi.

DNA methylation (DNAm) regulates gene expression and genomic imprinting. This study aimed to investigate the effect of gastrointestinal (GI) nematode infection on host DNAm. Helminth-free Holstein steers were either infected with Ostertagia ostertagi (the brown stomach worm) or given tap water only as a control. Animals were euthanized 30 days post-infection, and tissues were collected at necropsy. We conducted epigenome-wide profiling using a mammalian methylation array to explore the impact of infection on methylation patterns in the mucosa from abomasal fundus (FUN), pylorus (PYL), draining lymph nodes (dLNs), and the duodenum (DUO). The analysis covered 31,107 cattle CpGs of 5082 genes and revealed infection-driven, tissue-specific, differential methylation patterns. A total of 389 shared and 2770 tissue-specific, differentially methylated positions (DMPs) were identified in dLN and FUN, particularly in genes associated with immune responses. The shared DMPs were found in 263 genes, many of which are involved in immune responses. Furthermore, 282, 244, 52, and 24 differentially methylated regions (DMRs) were observed in dLN, FUN, PYL, and DUO, respectively. More hypomethylated DMRs were detected in dLN and FUN, while more hypermethylated DMRs were found in PYL and DUO. Genes carrying DMPs and DMRs and enriched pathways relating to immune functions/responses were detected in infected animals, indicating a link between DNA methylation and the infection. The data may implicate a crucial role of DNAm in regulating the nature/strength of host immunity to infection and contribute to a deeper understanding of the epigenetic regulatory landscape in cattle infected by GI nematodes.

DEMETER DNA demethylase reshapes the global DNA methylation landscape and controls cell identity transition during plant regeneration

Abstract Background Plants possess a high potential for somatic cell reprogramming, enabling the transition from differentiated tissue to pluripotent callus, followed by the formation of de novo shoots during plant regeneration. Despite extensive studies on the molecular network and key genetic factors involved in this process, the underlying epigenetic landscape remains incompletely understood. Results Here, we explored the dynamics of the methylome and transcriptome during the two-step plant regeneration process. During the leaf-to-callus transition in Arabidopsis Ler, CG methylation shifted across genic regions, exhibiting a similar number of differentially methylated regions (DMRs) for both hypo- and hypermethylation. Pericentromeric regions underwent substantial CG and extensive CHH hypomethylation, alongside some CHG hypermethylation. Upon shoot regeneration from callus, genic regions displayed extensive reconfiguration of CG methylation, while pericentromeric methylation levels highly increased across all cytosine contexts, coinciding with the activation of the RNA-directed DNA methylation (RdDM) pathway. However, mutation in DEMETER (DME) DNA demethylase gene resulted in significant genic CG redistribution and global non-CG hypomethylation in pericentromeric regions, particularly during shoot regeneration. This non-CG hypomethylation observed in dme-2 mutants was, at least partly, due to RdDM downregulation. The dme-2 mutants affected gene expression involved in pluripotency and shoot meristem development, resulting in enhanced shoot regeneration through a reprogrammed state established by pericentromeric hypomethylation compared to wild type. Conclusion Our study demonstrates epigenetic changes, accompanied by transcriptome alterations, during pluripotency acquisition (leaf-to-callus) and regeneration (callus-to-de novo shoot). Additionally, it highlights the functions of the DME demethylase, particularly its close association with the RdDM pathway, which underlies pericentromeric non-CG methylation maintenance. These results provide important insights into the epigenetic reconfiguration associated with cell identity transition during somatic cell reprogramming.

Recurrent Small Variants in NESP55/NESPAS Associated with Broad GNAS Methylation Defects and Pseudohypoparathyroidism Type 1b.

Pseudohypoparathyroidism type 1B (PHP1B) is associated with epigenetic changes on the maternal allele of the imprinted GNAS gene that inhibit expression of the alpha subunit of Gs (Gsα), thereby leading to parathyroid hormone resistance in renal proximal tubule cells where expression of Gs from the paternal GNAS allele is normally silent. Although all patients with PHP1B show loss of methylation for the exon A/B differentially methylated region (DMR), some patients with autosomal dominant PHP1B (AD-PHP1B) and most patients with sporadic PHP1B have additional methylation defects that affect the DMRs corresponding to exons XL, AS1, and NESP. Because the genetic defect is unknown in most of these patients, we sought to identify the underlying genetic basis for AD-PHP1B in two multigenerational families with broad GNAS methylation defects and negative clinical exomes. Genome sequencing identified small GNAS variants in each family that were also present in unrelated PHP1B subjects in a replication cohort. Maternal transmission of one GNAS microdeletion showed reduced penetrance in some unaffected patients. Expression of AS transcripts was increased, and NESP was decreased, in cells from affected patients. These results suggest that the small deletion activate AS transcription leading to methylation of the NESP DMR with consequent inhibition of NESP transcription, and thereby provide a potential mechanism for PHP1B.