EpigenomicsPub Date : 2025-06-01Epub Date: 2025-04-18DOI: 10.1080/17501911.2025.2491294
Erin M O'Leary, Paul J Bonthuis
{"title":"Mom genes and dad genes: genomic imprinting in the regulation of social behaviors.","authors":"Erin M O'Leary, Paul J Bonthuis","doi":"10.1080/17501911.2025.2491294","DOIUrl":"10.1080/17501911.2025.2491294","url":null,"abstract":"<p><p>Genomic imprinting is an epigenetic phenomenon in mammals that affects brain development and behavior. Imprinting involves the regulation of allelic expression for some genes in offspring that depends on whether alleles are inherited from mothers compared to fathers, and is thought to provide parental control over offspring social behavior phenotypes. Imprinted gene expression is prevalent in the mammalian brain, and human imprinted gene mutations are associated with neurodevelopmental disorders and neurodivergent social behavior in Prader-Willi Syndrome, Angelman Syndrome, and autism. Here, we provide a review of the evidence that imprinted genes influence social behaviors across major neurodevelopmental stages in humans and mouse animal models that include parent-infant interactions, juvenile sociability, and adult aggression, dominance, and sexual behavior.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"555-573"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12140492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143985838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomicsPub Date : 2025-06-01Epub Date: 2025-05-06DOI: 10.1080/17501911.2025.2500914
Vaidotas Stankevičius, Liepa Gasiulė, Giedrius Vilkaitis, Saulius Klimašauskas
{"title":"Selective chemical tracking of DNA methylomes in live cells.","authors":"Vaidotas Stankevičius, Liepa Gasiulė, Giedrius Vilkaitis, Saulius Klimašauskas","doi":"10.1080/17501911.2025.2500914","DOIUrl":"10.1080/17501911.2025.2500914","url":null,"abstract":"","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"575-577"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomicsPub Date : 2025-06-01Epub Date: 2025-05-16DOI: 10.1080/17501911.2025.2504333
Michael S Bosmeny, Joao I Mamede, Keith T Gagnon
{"title":"Resolving sequencing-based HIV-1 epitranscriptomics.","authors":"Michael S Bosmeny, Joao I Mamede, Keith T Gagnon","doi":"10.1080/17501911.2025.2504333","DOIUrl":"10.1080/17501911.2025.2504333","url":null,"abstract":"<p><p>The collection of HIV-1 RNA chemical modifications and their functional consequences in viral gene expression, host interactions, and the viral life cycle, referred to as HIV-1 epitranscriptomics, remain incompletely understood. While the field is evolving, diverse modification discovery methods, cell lines, HIV-1 sequences, and bioinformatics methods make a consensus view of the HIV-1 epitranscriptome difficult to resolve. Here, we review methods for identifying and interpreting N<sup>6</sup>-methyladenosine (m<sup>6</sup>A), 5-methylcytosine (m<sup>5</sup>C), pseudouridine (Ψ), 2´-<i>O</i>-methylation (N<sub>m</sub>), and N<sup>4</sup>-acetylcytidine (ac<sup>4</sup>C) modifications in HIV-1, including antibody-based selection methods, chemical-treatment-based selection methods, and detection by nanopore direct RNA sequencing. We recommend the adoption of the latter as a standardized sequencing strategy to enable better benchmarking across diverse studies and help resolve HIV-1 epitranscriptomics.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"529-540"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12140454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144076852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomicsPub Date : 2025-06-01Epub Date: 2025-05-10DOI: 10.1080/17501911.2025.2500907
Paraskevi Christofidou, Christopher G Bell
{"title":"The predictive power of profiling the DNA methylome in human health and disease.","authors":"Paraskevi Christofidou, Christopher G Bell","doi":"10.1080/17501911.2025.2500907","DOIUrl":"10.1080/17501911.2025.2500907","url":null,"abstract":"<p><p>Early and accurate diagnosis significantly improves the chances of disease survival. DNA methylation (5mC), the major DNA modification in the human genome, is now recognized as a biomarker of immense clinical potential. This is due to its ability to delineate precisely cell-type, quantitate both internal and external exposures, as well as tracking chronological and biological components of the aging process. Here, we survey the current state of DNA methylation as a biomarker and predictor of traits and disease. This includes Epigenome-wide association study (EWAS) findings that inform Methylation Risk Scores (MRS), EpiScore long-term estimators of plasma protein levels, and machine learning (ML) derived DNA methylation clocks. These all highlight the significant benefits of accessible peripheral blood DNA methylation as a surrogate measure. However, detailed DNA methylation biopsy analysis in real-time is also empowering pathological diagnosis. Furthermore, moving forward, in this multi-omic and biobank scale era, novel insights will be enabled by the amplified power of increasing sample sizes and data integration.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"599-610"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomicsPub Date : 2025-06-01Epub Date: 2025-05-08DOI: 10.1080/17501911.2025.2501524
Srija Roy, Mrinal K Ghosh
{"title":"Ubiquitin proteasome system (UPS): a crucial determinant of the epigenetic landscape in cancer.","authors":"Srija Roy, Mrinal K Ghosh","doi":"10.1080/17501911.2025.2501524","DOIUrl":"10.1080/17501911.2025.2501524","url":null,"abstract":"<p><p>The ubiquitin proteasome system (UPS), comprising of ubiquitinases, deubiquitinases and 26S proteasome plays a significant role in directly or indirectly regulating epigenetic players. DNA-templated processes like replication, repair and transcription require chromatin decondensation to allow access to specific DNA sequence. A thorough survey of literary articles in PubMed database revealed that the UPS functions as a key regulator, determining the precise state of open and closed chromatin by influencing histones and histone modifiers through proteolytic or non-proteolytic means. However, a comprehensive understanding of how specific UPS components affect particular epigenetic pathways in response to environmental cues remains underexplored. This axis holds substantial potential for deciphering mechanisms of tumorigenesis. Although our current knowledge is limited, it can still guide the development of novel therapeutic strategies that can potentially bridge the gap between cancer chemotherapeutics in bench and bedside.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"625-644"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomicsPub Date : 2025-06-01Epub Date: 2025-05-30DOI: 10.1080/17501911.2025.2513215
Emese H C Kovács, Lucas G Casten, Niamh Mullins, Jenny Gringer Richards, Aislinn J Williams, John A Wemmie, Vincent A Magnotta, Jess G Fiedorowicz, Jacob Michaelson, Marie E Gaine
{"title":"SNP-associated differential methylation in <i>ARHGEF38</i>: insights into genetic-epigenetic interactions.","authors":"Emese H C Kovács, Lucas G Casten, Niamh Mullins, Jenny Gringer Richards, Aislinn J Williams, John A Wemmie, Vincent A Magnotta, Jess G Fiedorowicz, Jacob Michaelson, Marie E Gaine","doi":"10.1080/17501911.2025.2513215","DOIUrl":"10.1080/17501911.2025.2513215","url":null,"abstract":"<p><strong>Objective: </strong>Associations have been seen between suicide and differential DNA methylation, with one study showing significant hypomethylation of <i>ARHGEF38</i> in individuals with bipolar disorder who died by suicide. Our objective was to explore <i>ARHGEF38</i> methylation in individuals with bipolar disorder and a history of suicide attempt.</p><p><strong>Method: </strong>With pyrosequencing, we looked at the previously identified region of interest in <i>ARHGEF38</i>. We investigated the methylation levels of three CpG sites in 47 individuals with bipolar disorder and a history of suicide attempt, 47 individuals with bipolar disorder without a history of suicide attempt, and 47 non-bipolar disorder controls.</p><p><strong>Results: </strong>None of the CpG sites measured had an association between groups, although there were distinct clusters of differential methylation in each group. Applying genotypes of SNPs found in the region of interest, rs2121558 and rs1447093, these clusters showed stepwise methylation at each CpG site, regardless of phenotype.</p><p><strong>Conclusions: </strong>In this small sample size study, differential methylation in <i>ARHGEF38</i> was not associated with history of suicide attempt, failing to replicate findings from a related outcome, suicide death. However, we did provide evidence of SNP and DNA methylation interplay in this region. This highlights the relevance of considering genetics when interrogating epigenetic mechanisms.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"579-588"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomicsPub Date : 2025-06-01Epub Date: 2025-05-27DOI: 10.1080/17501911.2025.2510196
Wu Duan, Ziyi Peng, Kun Yang, Mengyuan Hu, Xuefeng Yu, Benping Zhang, Li Liu
{"title":"Transcriptome-wide N6-methyladenosine methylation dynamic profile in type 1 diabetes progression.","authors":"Wu Duan, Ziyi Peng, Kun Yang, Mengyuan Hu, Xuefeng Yu, Benping Zhang, Li Liu","doi":"10.1080/17501911.2025.2510196","DOIUrl":"10.1080/17501911.2025.2510196","url":null,"abstract":"<p><strong>Aims: </strong>To map transcriptome-wide N6-methyladenosine (m6A) profile at different stages of type 1 diabetes (T1D).</p><p><strong>Materials & methods: </strong>RNA extracted from islet tissues of non-obese diabetic mice at different ages (4-week-old control group, 8-week-old pre-diabetes group, and 14-week-old diabetes group) was analyzed by MeRIP-seq and mRNA-seq. Bioinformatics analyses, including m6A motif enrichment, differential methylation, gene ontology and pathway analysis.</p><p><strong>Results: </strong>Bioinformatic analysis revealed a progressive increase in m6A methylation sites and unique peaks throughout diabetes progression. The predominant m6A motif was \"GGACU\" in the control and pre-diabetes stages, shifting to \"GGACU/A\" in the diabetes stage. m6A modifications were primarily enriched at the start codon, coding region, and stop codon. Integrated analysis found pre-diabetes, diabetes groups showed distinct m6A and mRNA changes versus control. Pathway analysis indicated that differentially expressed mRNAs with m6A methylation were predominantly enriched in insulin/IGF-MAPKK/MAPK cascades, apoptosis, T-cell activation, interleukins, CCKR, and inflammation-related pathways in the pre-diabetes stage. As diabetes progressed, additional pathways, including Wnt, EGF receptor, PDGF, GnRH receptor, and angiogenesis, became involved in disease development. In vitro, cytokine stimulation of INS-1 cells increased m6A methylation, upregulated METTL3, downregulated ALKBH5.</p><p><strong>Conclusions: </strong>m6A methyl group dynamics in T1D disease progression, potentially influencing mRNA expression and signal transduction pathways.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"511-522"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12140450/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomicsPub Date : 2025-06-01Epub Date: 2025-05-25DOI: 10.1080/17501911.2025.2510190
Suvo Chatterjee, Jing Wu, Marion Ouidir, Katherine L Grantz, Fasil Tekola-Ayele
{"title":"Association of placental weight and placental-fetal weight ratio with DNA methylation in placenta.","authors":"Suvo Chatterjee, Jing Wu, Marion Ouidir, Katherine L Grantz, Fasil Tekola-Ayele","doi":"10.1080/17501911.2025.2510190","DOIUrl":"10.1080/17501911.2025.2510190","url":null,"abstract":"<p><strong>Aim: </strong>To investigate the association between placental methylation and placenta weight (PW) and placental-fetal weight ratio (PFR), which are markers of placental function linked to adverse pregnancy outcomes and risk for diseases in later life.</p><p><strong>Methods: </strong>We examined the association between placental epigenome-wide methylation and PW and PFR at birth (<i>n</i> = 301). Further tests assessed whether methylation levels of the cytosine-guanine sites (CpGs) linked to PW and PFR are associated with placental expression of nearby genes.</p><p><strong>Results: </strong>At a 5% false discovery rate (FDR), methylation at 27 CpGs was associated with PW, of which two CpGs were also associated with PFR. Methylation at four of the 27 CpGs was associated with placental expression of nearby genes including LEPR, RPS6KA1, and COX5A which have known roles in early development, cellular growth, and oxidative stress. The identified CpGs overlap with previously reported methylation sites associated with perinatal and adult health outcomes such as preeclampsia, preterm delivery, obesity, and type 2 diabetes.</p><p><strong>Conclusions: </strong>The findings reveal epigenetic underpinnings of placental development and functional efficiency, and suggest their potential roles in mediating fetal development and late-onset diseases.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"589-598"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomicsPub Date : 2025-06-01Epub Date: 2025-04-19DOI: 10.1080/17501911.2025.2494983
Zijun Wu, Changhong Miao, Hao Zhang
{"title":"METTL3-mediated m6A modification in sepsis: current evidence and future perspectives.","authors":"Zijun Wu, Changhong Miao, Hao Zhang","doi":"10.1080/17501911.2025.2494983","DOIUrl":"10.1080/17501911.2025.2494983","url":null,"abstract":"<p><p>Sepsis, a severe systemic inflammatory condition triggered by infection, is associated with high morbidity and mortality worldwide. While medical diagnosis and treatment have advanced in recent years, a specific therapy remains unavailable. Recently, significant progress has been made in studying the epigenetic RNA modification N6-methyladenosine (m6A) and its core methyltransferase METTL3. The role of m6A in sepsis has also been increasingly elucidated. This review aims to explore the pathological mechanisms of sepsis and its relationship with m6A, focusing on the role of the key m6A writer, METTL3, in sepsis.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"611-623"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143678/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}