Epigenetics reports最新文献

Chromatin Meets Condensates: Emerging Interplays Linking Nuclear Paraspeckles to Gene Activation. 染色质与凝聚物：核副斑与基因激活之间的相互作用。

Epigenetics reports Pub Date : 2026-01-01 Epub Date: 2026-01-18 DOI: 10.1080/28361512.2026.2617266

Chih-Han Tu, Chen-I Hsu, Jia-Ray Yu

引用次数: 0

Implication of the Mediator kinase module in CIZ1 recruitment and gene silencing by Xist during the initiation of X inactivation. 中介激酶模块在CIZ1募集和X失活起始过程中Xist基因沉默中的意义。

Epigenetics reports Pub Date : 2025-12-31 Epub Date: 2025-02-12 DOI: 10.1080/28361512.2025.2456806

Jingyi Chen, Kevin Halter, Timothe Weitzel, Anton Wutz

{"title":"Implication of the Mediator kinase module in CIZ1 recruitment and gene silencing by Xist during the initiation of X inactivation.","authors":"Jingyi Chen, Kevin Halter, Timothe Weitzel, Anton Wutz","doi":"10.1080/28361512.2025.2456806","DOIUrl":"10.1080/28361512.2025.2456806","url":null,"abstract":"In mammals, dosage compensation between the sexes is mediated by X chromosome inactivation. The long non-coding Xist RNA initiates this process. The molecular mechanism of X-linked gene silencing is beginning to be understood. We have previously reported that the cyclin-dependent kinase CDK8 is required for gene silencing and histone H3 trimethyl-lysine 27 recruitment by Xist. CDK8 functions in cell signalling and transcriptional regulation, in particular, it associates with MED12, MED13, and cyclin C to form a kinase submodule of the Mediator complex. It remains unknown if CDK8 acts as a Mediator kinase in X chromosome inactivation. Here, we analyse a Med12 mutation in an embryonic stem cell model for the initiation of X chromosome inactivation. Loss of Med12 is compatible with self-renewal and survival of mouse embryonic stem cells, but impairs X-linked gene silencing by Xist. In addition, recruitment of CIZ1 and histone H3 trimethyl-lysine 27 by Xist are significantly reduced in the absence of Med12. We further show that CIZ1 recruitment is also modulated by Cdk8. Our study shows that mutations of Med12 and Cdk8 have similar effects on Xist function and provide a cell system for studying the role of the Mediator kinase module in X chromosome inactivation.","PeriodicalId":520309,"journal":{"name":"Epigenetics reports","volume":"3 1","pages":"1-13"},"PeriodicalIF":0.0,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7618334/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145461120","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}

引用次数: 0

Vafidemstat: a lysine-specific demethylase 1A inhibitor that shows promise for treating neuropsychiatric disorders. Vafidemstat：一种赖氨酸特异性去甲基酶1A抑制剂，有望用于治疗神经精神疾病。

Epigenetics reports Pub Date : 2025-01-01 Epub Date: 2025-09-04 DOI: 10.1080/28361512.2025.2552947

Jacob Peedicayil, Dennis R Grayson

引用次数: 0

Maternal Diet Quality in Pregnancy and Human Milk Extracellular Vesicle and Particle microRNA. 孕妇饮食质量与母乳细胞外囊泡和微粒microRNA。

Epigenetics reports Pub Date : 2025-01-01 Epub Date: 2025-05-30 DOI: 10.1080/28361512.2025.2508883

Meghan E Muse, Yuting Wang, Diane Gilbert-Diamond, David A Armstrong, Anne G Hoen, Megan E Romano, Jiang Gui, Thomas J Palys, Frederick W Kolling, Brock C Christensen, Margaret R Karagas, Caitlin G Howe

{"title":"Maternal Diet Quality in Pregnancy and Human Milk Extracellular Vesicle and Particle microRNA.","authors":"Meghan E Muse, Yuting Wang, Diane Gilbert-Diamond, David A Armstrong, Anne G Hoen, Megan E Romano, Jiang Gui, Thomas J Palys, Frederick W Kolling, Brock C Christensen, Margaret R Karagas, Caitlin G Howe","doi":"10.1080/28361512.2025.2508883","DOIUrl":"10.1080/28361512.2025.2508883","url":null,"abstract":"Extracellular vesicle and particle microRNAs (EVP miRNA) in milk have the capacity to facilitate maternal-infant communication in the postpartum period and are hypothesized to play important roles in child development. Maternal diet quality has been linked to milk macronutrient composition, microbiota profiles, as well as various child health outcomes. The aim of this study was to assess the association between maternal diet quality and milk EVP miRNA. In a pilot study of 54 participants from a larger birth cohort study, diet quality was measure by the Alternative Healthy Eating Index 2010 (AHEI-2010) during the second trimester of pregnancy and 798 EVP miRNA were profiled in mature milk samples (collected approximately six weeks postpartum) using the NanoString nCounter platform. In covariate-adjusted models, AHEI-2010 was positively associated (Q < 0.05) with levels of miR-1283, miR-520h, and mir-570-3p in milk EVPs. Predicted target genes of these diet-associated miRNA are enriched in pathways related to lactation and mammary development (PI3 kinase signaling and Wnt signaling pathways) and milk protein and fat synthesis (PI3 kinase signaling). Further research is needed to investigate whether these diet-associated miRNA influence lactation, human milk quality, and child growth and development.","PeriodicalId":520309,"journal":{"name":"Epigenetics reports","volume":"3 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12234000/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144593739","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}

引用次数: 0

DNA methylation clocks and cognitive status among older adults in the US, NHANES 1999-2002. 美国老年人的DNA甲基化时钟和认知状态，NHANES 1999-2002。

Epigenetics reports Pub Date : 2025-01-01 Epub Date: 2025-12-12 DOI: 10.1080/28361512.2025.2599769

Erika Walker, Scarlet Cockell, Belinda L Needham, Andres Cardenas, Sung Kyun Park, Kelly M Bakulski

{"title":"DNA methylation clocks and cognitive status among older adults in the US, NHANES 1999-2002.","authors":"Erika Walker, Scarlet Cockell, Belinda L Needham, Andres Cardenas, Sung Kyun Park, Kelly M Bakulski","doi":"10.1080/28361512.2025.2599769","DOIUrl":"10.1080/28361512.2025.2599769","url":null,"abstract":"Biological aging, measured using DNA methylation, is a potential biomarker for cognitive health outcomes. We evaluated associations between DNA methylation clocks and cognition in a nationally representative sample of adults aged 60+ in the National Health and Nutrition Examination Survey (NHANES), 1999-2002. Genome-wide DNA methylation data were used to create 13 measures of biological aging trained on different aging phenotypes. Cognition was assessed with the Digit Symbol Substitution Test (DSST). To evaluate associations between each DNA methylation clock and DSST score, survey-weighted linear regression models adjusted for calendar age, sex, race/ethnicity, education, smoking, serum cotinine, and BMI were run. We assessed effect modification by sex, education, and race and ethnicity. Included participants (N=1,463) were an average of 70.5 years old and 82.7% non-Hispanic White. The average DSST score was 46.9 (SD 17.6). Ten of 13 DNA methylation clocks were associated with DSST (adjusted p<0.05). One year of GrimAge2 accelerated aging was associated with -0.41 points lower DSST score (95% CI: -0.61, -0.21; adjusted p=5×10-4). In stratified analyses, higher magnitudes of association were observed among male and non-Hispanic White participants across multiple clocks. DNA methylation clocks may be a useful biomarker of cognitive status among older adults.","PeriodicalId":520309,"journal":{"name":"Epigenetics reports","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13309178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148348497","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}

引用次数: 0

Normal gastric tissue Helicobacter pylori infection is associated with tissue cell composition, and cell type-specific epigenetic age acceleration, mitotic tick rate, and repetitive element methylation alterations. 正常胃组织幽门螺杆菌感染与组织细胞组成、细胞类型特异性表观遗传年龄加速、有丝分裂滴答率和重复元件甲基化改变有关。

Epigenetics reports Pub Date : 2025-01-01 Epub Date: 2025-09-06 DOI: 10.1080/28361512.2025.2554836

Irma Vlasac, Brock C Christensen, Lucas A Salas

{"title":"Normal gastric tissue Helicobacter pylori infection is associated with tissue cell composition, and cell type-specific epigenetic age acceleration, mitotic tick rate, and repetitive element methylation alterations.","authors":"Irma Vlasac, Brock C Christensen, Lucas A Salas","doi":"10.1080/28361512.2025.2554836","DOIUrl":"10.1080/28361512.2025.2554836","url":null,"abstract":"Helicobacter pylori (H. pylori) infection is a well-established risk factor for gastric adenocarcinoma, one of the leading causes of cancer-related death worldwide. While H. pylori infection induces significant DNA methylation changes, the cell type-specific epigenetic mechanisms contributing to carcinogenesis are not understood. To investigate these mechanisms, we analysed publicly available DNA methylation data from normal gastric mucosa of gastric cancer cases and controls stratified by H. pylori infection status, as well as tumour tissue from stomach adenocarcinoma. Using cell-type deconvolution and statistical modelling, we assessed epigenetic age acceleration, mitotic tick rate, cell-type composition, repetitive element methylation, and differentially methylated cell types. We reveal that (1) H. pylori infection is associated with increased epigenetic age acceleration and mitotic tick rate after adjustment for cell-type, independent of cancer status; (2) H. pylori infection corresponds to reduced epithelial and fibroblast proportions and increased infiltration of immune cell types, independent of cancer status; and (3) H. pylori infection influences LINE-1 and ERV repetitive element methylation in a cell type-specific fashion, particularly in epithelial and monocyte lineages. Our findings suggest that H. pylori infection induces lasting, cell-specific epigenetic alterations that may promote a pro-inflammatory and carcinogenic gastric microenvironment through altered cell pathways, genomic instability, and sustained inflammation.","PeriodicalId":520309,"journal":{"name":"Epigenetics reports","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12782233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145954851","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}

引用次数: 0

Characterizing DNA Methylation and Hydroxymethylation in Cord Blood and Identifying Sex-Specific Differences using the Illumina EPIC Array. 使用Illumina EPIC阵列表征脐带血DNA甲基化和羟甲基化并鉴定性别特异性差异。

Epigenetics reports Pub Date : 2024-01-01 Epub Date: 2024-11-14 DOI: 10.1080/28361512.2024.2427955

Rebekah L Petroff, Dana C Dolinoy, Vasantha Padmanabhan, Jaclyn M Goodrich

{"title":"Characterizing DNA Methylation and Hydroxymethylation in Cord Blood and Identifying Sex-Specific Differences using the Illumina EPIC Array.","authors":"Rebekah L Petroff, Dana C Dolinoy, Vasantha Padmanabhan, Jaclyn M Goodrich","doi":"10.1080/28361512.2024.2427955","DOIUrl":"10.1080/28361512.2024.2427955","url":null,"abstract":"DNA methylation, an epigenetic mark, has become a common outcome in epidemiological studies with the aid of affordable and reliable technologies. Yet the most widespread technique used to assess methylation, bisulfite conversion, does not allow for the differentiation of regular DNA methylation (5-mC) and other cytosine modifications, like that of hydroxymethylation (5-hmC). As both 5-mC and 5-hmC have distinct biological roles, sometimes with opposing effects, it is crucial to understand the difference between these marks. To characterize 5-mC and 5-hmC in cord blood and expand on previously published results in smaller cohorts, 73 samples from infants in the Michigan Mother Infant Pairs cohort were paired bisulfite and oxidative bisulfite converted. 5-mC and 5-hmC were assessed on the Illumina Infinium EPIC array, using maximum likelihood methods, and sex-specific differences of these marks were analyzed. 5-mC and 5-hmC were both broadly distributed across the genome, and 5-hmC was prevalent, with proportions of 0.01-0.55. Sex-specific analysis revealed total methylation was different on 17,000 sites (q<0.05), but only different at 1,866 and 5 sites of 5-mC and 5-hmC specifically. These results add additional support to the literature and demonstrate the importance of differentiating between 5-mC and 5-hmC in epidemiological studies going forward.","PeriodicalId":520309,"journal":{"name":"Epigenetics reports","volume":"2 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11600988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142752778","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}

引用次数: 0