Epigenomes最新文献

{"title":"Methylation of the Glucocorticoid Receptor Gene in Children with Somatic Symptom Disorder: A Case-Control Study.","authors":"Kyoko Hatta, Masato Kantake, Kyoko Tanaka, Hirofumi Nakaoka, Toshiaki Shimizu, Hiromichi Shoji","doi":"10.3390/epigenomes9020022","DOIUrl":"10.3390/epigenomes9020022","url":null,"abstract":"<p><p><b>Background:</b> Somatic symptom disorder (SSD) in children may be influenced by stress reactivity and psychosocial factors. The glucocorticoid receptor (GR), encoded by NR3C1, is a key mediator of stress responses. However, the relationship between NR3C1 methylation and SSD remains unclear. <b>Methods:</b> We analyzed NR3C1 exon 1F methylation in cell-free DNA from saliva in 34 children with SSD and 29 age- and sex-matched controls using bisulfite amplicon sequencing. Psychological assessments included the Beck Depression Inventory-II (BDI-II) and KINDL questionnaires to evaluate associations with methylation patterns. <b>Results:</b> Methylation levels showed age-related differences. In children under 13, CpG sites displayed mixed methylation, and specific sites correlated with KINDL and BDI-II scores. KINDL physical and total well-being scores negatively correlated with CpG30 and positively with CpG35; BDI-II scores negatively correlated with CpG32 and CpG35. In children aged 13 or older, CpG sites showed uniformly high methylation with no correlation to psychological measures. The SSD group showed significantly higher average methylation across the exon 1F region than controls in the older age group. These children also had more cases of orthostatic dysregulation and longer illness duration. <b>Conclusions:</b> This study suggests age-dependent epigenetic regulation of NR3C1 in SSD. While younger children showed CpG-specific correlations with psychological symptoms, older children demonstrated uniformly high methylation and potentially reduced gene expression, potentially reflecting cumulative stress, autonomic dysfunction, and internalizing disorders such as anxiety and depression.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12192148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Dynamic Interactions of m6A Modification and R-Loops: Implications for Genome Stability.","authors":"Nicholas Kim, Hong Sun","doi":"10.3390/epigenomes9020021","DOIUrl":"10.3390/epigenomes9020021","url":null,"abstract":"<p><p>R-loops, three-stranded RNA-DNA hybrid nucleic acid structures, are recognized for their roles in both physiological and pathological processes. Regulation of R-loops is critical for genome stability as disruption of R-loop homeostasis can lead to aberrant gene expression, replication stress, and DNA damage. Recent studies suggest that the RNA modification, N6-methyladenosine (m6A), can modify R-loops and the writers, erasers, and readers of m6A are involved in the dynamic regulation of R-loops. Here, we discuss the reported functions of various m6A regulatory proteins in relation to R-loops, highlighting their distinct roles in recognizing and modulating the formation, stability, and resolution of these structures. We further examine the functional implications of m6A and R-loop interaction in human diseases, with a particular emphasis on their roles in cancer.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12192009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenetic Insights into Tuberous Sclerosis Complex, Von Hippel-Lindau Syndrome, and Ataxia-Telangiectasia.","authors":"Gavriel Hadjigavriel, Christina Stylianides, Evangelos Axarloglou, Maria Eleni Manthou, Efstratios Vakirlis, Paschalis Theotokis, Soultana Meditskou, Iasonas Dermitzakis","doi":"10.3390/epigenomes9020020","DOIUrl":"10.3390/epigenomes9020020","url":null,"abstract":"<p><p>Neurocutaneous syndromes represent a clinically and genetically heterogeneous group of disorders, with tuberous sclerosis complex (TSC), von Hippel-Lindau syndrome (VHL), and ataxia-telangiectasia (A-T) exemplifying some of the most complex entities within this category. These syndromes have traditionally been considered monogenic disorders, caused by germline mutations in tumor suppressor or regulatory genes. However, they exhibit a striking degree of phenotypic variability and divergent clinical trajectories that cannot be fully explained by their underlying genetic alterations alone. Increasingly, epigenetic regulatory mechanisms, such as DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA (ncRNA) activity, are recognized as key modulators of gene expression, cellular differentiation, and tissue-specific function. Disruption of these mechanisms has been implicated in disease pathogenesis, tumorigenesis, and neurodegeneration associated with TSC, VHL, and A-T. Aberrant epigenetic profiles may underlie the observed variability in clinical outcomes, even among individuals with identical mutations. This review consolidates current evidence on the epigenetic landscape of these syndromes, elucidating how these modifications may influence disease behavior and contribute to incomplete genotype-phenotype correlations. By integrating epigenetic insights with known molecular pathways, a more nuanced understanding of disease biology emerges, with potential implications for diagnostic stratification, prognostic assessment, and therapeutic innovation.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12191455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association of Model-Predicted Epigenetic Age and Female Infertility.","authors":"Elena Pozdysheva, Vitaly Korchagin, Tatiana Rumyantseva, Daria Ogneva, Vera Zhivotova, Irina Gaponova, Konstantin Mironov, Vasily Akimkin","doi":"10.3390/epigenomes9020019","DOIUrl":"10.3390/epigenomes9020019","url":null,"abstract":"<p><strong>Background: </strong>To date, there are no precise clinical and laboratory methods to accurately predict the onset of fertility decline in women, with chronological age being the ultimate predictor. This has led to increased interest in developing methods to determine biological age, as it provides a more accurate understanding of individual age-related physiological changes.</p><p><strong>Methods: </strong>In this study, we developed a model for estimating biological age based on DNA methylation levels in the <i>ELOVL2</i>, <i>TRIM59</i>, <i>C1orf132</i>, <i>FHL2</i>, and <i>KLF14</i> genes using pyrosequencing. The model was tested in 64 Russian women, aged 25-39 years, to find an association between epigenetic age, infertility, low anti-Müllerian hormone (AMH) levels, and assisted reproductive technology (ART) failure.</p><p><strong>Results: </strong>The predictive performance of the model was evaluated. The mean absolute deviation of the model was 2.8 years; the mean absolute error was 2.6 years (R² = 0.95). In the studied cohort, 33% of women exhibited epigenetic age acceleration (EAA), while 45% showed epigenetic age deceleration (EAD). All women with an EAA of ≥3 years (n = 6) had a history of infertility.</p><p><strong>Conclusions: </strong>In this study, no statistically significant associations were observed between EAA/EAD and AMH, body mass index, infertility, or ART failure in women.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12192080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA Methylation, Aging, and Cancer.","authors":"Himani Vaidya, Jaroslav Jelinek, Jean-Pierre J Issa","doi":"10.3390/epigenomes9020018","DOIUrl":"10.3390/epigenomes9020018","url":null,"abstract":"<p><p>Aging and cancer, though distinct biological processes, share overlapping molecular pathways, particularly in epigenetic regulation. Among these, DNA methylation is central to mediating gene expression, maintaining cellular identity, and regulating genome stability. This review explores how age-associated changes in DNA methylation, characterized by both global hypomethylation and focal hypermethylation, contribute to the emergence of cancer. We discuss mechanisms of DNA methylation drift, the development of epigenetic clocks, and the role of entropy and epigenetic mosaicism, in aging and tumorigenesis. Emphasis is placed on how stochastic methylation errors accumulate in aging cells and lead to epiallelic shifts and gene silencing, predisposing tissues to malignant transformation, even despite recently increased cancer incidences at younger ages. We also highlight the translational potential of DNA methylation-based biomarkers, and therapeutic targets, in age-related diseases. By framing cancer as a disease of accelerated epigenetic aging, this review offers a unifying perspective and calls for age-aware approaches to both basic research and clinical oncology.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12192155/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenetic DNA Methylation Under the Influence of Low-Dose Ionizing Radiation, and Supplementation with Vitamin B12 and Folic Acid: Harmful or Beneficial for Professionals?","authors":"Borivoje Savic, Bozidar Savic, Svetlana Stanojlovic","doi":"10.3390/epigenomes9020017","DOIUrl":"10.3390/epigenomes9020017","url":null,"abstract":"<p><p>This review paper highlights the importance of educating current and future professionals about epigenetic mechanisms and recognizing epigenetics as a crucial model for protection against ionizing radiation. Two basic models for radiation-induced DNA damage are currently in use. The association between mutations and chromosomal aberrations provides a framework for analyzing risks at low radiation doses and exposure to small doses. However, there is no monitoring of epigenetic changes in professionals exposed to low doses of ionizing radiation. Epigenetic events regulate gene activity and expression not only during cell development and differentiation but also in response to environmental stimuli, such as ionizing radiation. Furthermore, the potential occurrence of malignant and hereditary diseases at low doses of ionizing radiation is linearly correlated and is considered a scientifically accepted assumption, despite recognized scientific limitations associated with this assessment. The aim of this review is to integrate novel and intriguing radiobiological paradigms regarding the effects of ionizing radiation on DNA methylation and epigenetic regulation of the DNA molecule. Several hypothesized biological responses to ionizing radiation are examined, linking them to epigenetic mechanisms involved in health risk assessment for professionals. The second part of the review includes published research related to epigenetics, supplementation, and virus reactivation in the context of epigenetic modifications of the DNA molecule. We hypothesize that different cycles lead to changes in the epigenome, which may be associated with the reactivation of certain viruses and the deficiency of specific dietary elements. These findings are linked to minimal deficiencies in vitamin B12 and folic acid, which may contribute to epigenomic changes. This aspect is crucial for the immune status of individuals working in high-risk environments.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12191453/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetics and Epigenetics of Chemoinduced Oral Mucositis in Paediatric Patients with Haematological Malignancies-A Review.","authors":"Juliana Ramalho Guimarães, José Maria Chagas Viana Filho, Naila Francis Paulo de Oliveira","doi":"10.3390/epigenomes9020016","DOIUrl":"10.3390/epigenomes9020016","url":null,"abstract":"<p><strong>Background: </strong>Oral mucositis (OM) is a painful inflammation resulting from chemotherapy. It is dependent on factors such as age, gender, chemotherapy regimen, oral health, immunological and nutritional status, and genetics.</p><p><strong>Objectives: </strong>The aim of the study was to conduct a narrative review to compile studies on the contribution of genetic and epigenetic aspects to the pathogenesis of OM in children with haematological malignancies undergoing chemotherapy treatment.</p><p><strong>Methods: </strong>The literature search was performed in Pubmed, Scopus, Web of Science, Cochrane, Lilacs, and grey literature databases covering articles published since 2010.</p><p><strong>Results: </strong>Twenty-two studies investigating polymorphisms and four studies investigating DNA methylation were included. Polymorphisms in the <i>MTHFR</i>, <i>ABCB1</i>, <i>ABCC2</i>, <i>ABCG2</i>, <i>SLCO1B</i>, <i>miR-1206</i>, <i>miR-3683</i>, <i>CAT</i>, and <i>VDR</i> genes were associated as risk factors for OM and polymorphisms in the <i>TYMS</i> and <i>miR-4268</i> genes were associated as protective factors. With regard to DNA methylation, associations such as protection or susceptibility to OM have not yet been proven. However, studies have shown that <i>DNMT1</i> methylation and hypomethylation in total DNA and in the <i>TNF-α</i> gene are associated with recovery of the oral mucosa.</p><p><strong>Conclusions: </strong>Genetic variants are associated with OM in various biological pathways, such as folate metabolism, transport proteins, epigenetic machinery, oxidative stress, and vitamin D metabolism. The DNA methylation profile, which is still poorly understood in the pathogenesis of OM, is associated with mucosal recovery (inflammation and epigenetic machinery). Genetic and epigenetic markers may be tools to indicate a patient's susceptibility to developing OM, and epigenetic markers may be a target for therapies.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12191452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Histone H3 Lysine 9 Acetylation Plays a Role in Adipogenesis of Periodontal Ligament-Derived Stem Cells.","authors":"Julio A Montero-Del-Toro, Angelica A Serralta-Interian, Geovanny I Nic-Can, Mónica Lamas, Rodrigo A Rivera-Solís, Beatriz A Rodas-Junco","doi":"10.3390/epigenomes9020015","DOIUrl":"10.3390/epigenomes9020015","url":null,"abstract":"<p><strong>Background: </strong>The epigenetic regulation of adipogenic differentiation in dental stem cells (DSCs) remains poorly understood, as research has prioritized osteogenic differentiation for dental applications. However, elucidating these mechanisms could enable novel regenerative strategies for soft tissue engineering. Periodontal ligament stem cells (PDLSCs) exhibit notable adipogenic potential, possibly linked to histone 3 acetylation at lysine 9 (H3K9ac); however, the mechanistic role of this modification remains unclear.</p><p><strong>Methods: </strong>To address this gap, we investigated how histone deacetylase inhibitors (HDACis)-valproic acid (VPA, 8 mM) and trichostatin A (TSA, 100 nM)-modulate H3K9ac dynamics, adipogenic gene expression (<i>C/EBPβ</i> and <i>PPARγ-2</i>), and chromatin remodeling during PDLSCs differentiation. Techniques used included quantitative PCR (qPCR), lipid droplet analysis, and chromatin immunoprecipitation followed by qPCR (ChIP-qPCR).</p><p><strong>Results: </strong>TSA-treated cells exhibited increased lipid deposition with smaller lipid droplets compared to VPA-treated cells. Global H3K9ac levels correlated positively with adipogenic progression. VPA induced early upregulation of <i>C/EBPβ</i> and <i>PPARγ-2</i> (day 7), whereas TSA triggered a delayed but stronger <i>PPARγ-2</i> expression. ChIP-qPCR analysis revealed significant H3K9ac enrichment at the <i>PPARγ-2</i> promoter in TSA-treated cells, indicating enhanced chromatin accessibility.</p><p><strong>Conclusions: </strong>These findings demonstrate that H3K9ac-mediated epigenetic remodeling plays a critical role in the adipogenic differentiation of PDLSCs and identifies TSA as a potential tool for modulating this process.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12192146/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discrimination, Coping, and DNAm Accelerated Aging Among African American Mothers of the InterGEN Study.","authors":"Alexandria Nyembwe, Yihong Zhao, Billy A Caceres, Daniel W Belsky, Calen Patrick Ryan, Brittany Taylor, Morgan T Morrison, Laura Prescott, Stephanie Potts-Thompson, Arezo Aziz, Fisola Aruleba, Erica Matute-Arcos, Olajide Williams, Cindy Crusto, Jacquelyn Y Taylor","doi":"10.3390/epigenomes9020014","DOIUrl":"10.3390/epigenomes9020014","url":null,"abstract":"<p><p><b>Background:</b> Racial discrimination experiences are associated with the activation of stress biology pathways and signs of accelerated biological aging, including alterations in DNA methylation (DNAm). Coping strategies may mitigate stress from racial discrimination and protect against long-term adverse health outcomes. <b>Methods:</b> We conducted a secondary analysis of data from the Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure cohort, an all-African-American sample, to test the hypothesis that social support can protect against accelerated biological aging associated with experiences of racial discrimination. We measured biological aging from saliva DNAm using six epigenetic clocks. Clock values were residualized on participant age and the estimated proportion of epithelial cells contributing to the DNA sample and standardized to M = 0, SD = 1 within the analysis sample. The primary analysis was focused on the second-generation PhenoAge and GrimAge clocks and the third-generation DunedinPACE \"speedometer,\" which previous studies have linked with racial discrimination. <b>Results:</b> In our sample (<i>n</i> = 234; mean age = 31.9 years; SD = 5.80), we found evidence consistent with our hypothesis in the case of the PhenoAge clock, but not the other clocks. Among mothers who did not seek social support, experiences of racial discrimination were associated with an older PhenoAge (b = 0.26, 95% CI = 0.02-0.50, <i>p</i> = 0.03). However, social-support seeking mitigated this risk; at the highest levels of social support, no adverse consequences of discrimination were observed (interaction b = -0.01, 95% CI = -0.02--0.00, <i>p</i> = 0.03). <b>Conclusions:</b> The replication of results is needed. Future research should also investigate additional adaptive and maladaptive coping strategies utilized by African American women and mothers to identify protective measures that influence health outcomes.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Arabidopsis thaliana</i> Roots Exposed to Extracellular Self-DNA: Evidence of Epigenetic Effects.","authors":"Alessia Ronchi, Guido Incerti, Emanuele De Paoli, Speranza Claudia Panico, Giovanni Luca Sciabbarrasi, Pasquale Termolino, Fabrizio Cartenì, Mariachiara Langella, Maria Luisa Chiusano, Stefano Mazzoleni","doi":"10.3390/epigenomes9020013","DOIUrl":"10.3390/epigenomes9020013","url":null,"abstract":"<p><strong>Background: </strong>Previous evidence demonstrated DNA methylation changes in response to stress in plants, showing rapid changes within a limited time frame. Exposure to self-DNA inhibits seedling root elongation, and it was shown that it causes changes in CG DNA methylation in <i>Lactuca sativa</i>. We assessed cytosine methylation changes and associated gene expression patterns in roots of <i>Arabidopsis thaliana</i> Col-0 seedlings exposed to self-DNA for 6 and 24 h.</p><p><strong>Methods: </strong>We used whole genome bisulfite sequencing (WGBS) and RNA-seq analyses to assess genomic cytosine methylation and corresponding gene expression, respectively, on DNA and RNA extracted with commercial kits from roots exposed to self-DNA by an original setup. Fifteen hundred roots replicates, including the control in distilled water, were collected after exposure. Sequencing was performed on a NovaSeq 6000 platform and Ultralow Methyl-Seq System for RNA and DNA WGBS, respectively.</p><p><strong>Results: </strong>Gene expression in roots exposed to self-DNA differed from that of untreated controls, with a total of 305 genes differentially expressed and 87 ontologies enriched in at least one treatment vs. control comparison, and particularly after 24 h of exposure. DNA methylation, particularly in CHG and CHH contexts, was also different, with hyper- and hypomethylation prevailing in treatments vs. controls at 6 h and 24 h, respectively. Differentially expressed genes (DEGs) analysis, Gene Ontology (GO) enrichment analysis, and differentially methylated regions (DMRs) analysis, provided an integrated understanding of the changes associated with self-DNA exposure. Our results suggest differential gene expression associated with DNA methylation in response to self-DNA exposure in <i>A. thaliana</i> roots, enhanced after prolonged exposure.</p><p><strong>Conclusions: </strong>Main functional indications of association between DNA methylation and gene expression involved hypomethylation and downregulation of genes related to nucleotide/nucleoside metabolism (ATP synthase subunit) and cell wall structure (XyG synthase), consistent with previous observations from metabolomics and physiological studies. Further confirmation of these findings will contribute to improving our understanding of the plant molecular response to self-DNA and its implications in stress responses.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}