Epigenetics最新文献_第8页

Implementation of the Methyl-Seq platform to identify tissue- and sex-specific DNA methylation differences in the rat epigenome. 利用 Methyl-Seq 平台鉴定大鼠表观基因组中组织和性别特异性 DNA 甲基化差异。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-09-22 DOI: 10.1080/15592294.2024.2393945

Olivia H Cox, Fayaz Seifuddin, Jeffrey Guo, Mehdi Pirooznia, Gretha J Boersma, Josh Wang, Kellie L K Tamashiro, Richard S Lee

{"title":"Implementation of the Methyl-Seq platform to identify tissue- and sex-specific DNA methylation differences in the rat epigenome.","authors":"Olivia H Cox, Fayaz Seifuddin, Jeffrey Guo, Mehdi Pirooznia, Gretha J Boersma, Josh Wang, Kellie L K Tamashiro, Richard S Lee","doi":"10.1080/15592294.2024.2393945","DOIUrl":"10.1080/15592294.2024.2393945","url":null,"abstract":"Epigenomic annotations for the rat lag far behind those of human and mouse, despite the rat's immense utility in pharmacological and behavioral studies and the need to understand their epigenetic mechanisms. We have designed a targeted-enrichment method followed by next-generation sequencing (Methyl-Seq) to identify DNA methylation (DNAm) signatures across the rat genome. The design reflected an attempt to create a more comprehensive investigation of the rat epigenome, as it included promoters, CpG islands, and island shores of all RefSeq genes. In this study, we implemented the rat Methyl-Seq platform and tested its ability to distinguish differentially methylated regions (DMRs) among three different tissue types, three distinct brain regions, and, in the hippocampus, between males and females. These comparisons yielded DNAm differences of differing magnitudes, many of which were independently validated by bisulfite pyrosequencing, including autosomal regions that were predicted to show the least degree of difference in DNAm between males and females. Quantitative reverse transcription PCR revealed that most genes associated with the DMRs showed tissue-, brain region-, and sex-specific differences in expression. In particular, we found evidence for sex-specific DNAm and expression differences at Tubb6, Lrrn2, Tex26, and Sox5l1, all of which play important roles in neurodevelopment and have been implicated in studies examining sex differences. Our results demonstrate the utility of the rat Methyl-Seq platform and suggest the presence of DNAm differences between the male and female hippocampus. The rat Methyl-Seq has the potential to provide epigenomic insights into pharmacological and behavioral studies performed in the rat.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2393945"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Widespread genomic de novo DNA methylation occurs following CD8⁺ T cell activation and proliferation. CD8+ T 细胞活化和增殖后，基因组会发生广泛的新 DNA 甲基化。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-06-20 DOI: 10.1080/15592294.2024.2367385

Annika R Seddon, Olivia M Damiano, Mark B Hampton, Aaron J Stevens

{"title":"Widespread genomic de novo DNA methylation occurs following CD8+ T cell activation and proliferation.","authors":"Annika R Seddon, Olivia M Damiano, Mark B Hampton, Aaron J Stevens","doi":"10.1080/15592294.2024.2367385","DOIUrl":"10.1080/15592294.2024.2367385","url":null,"abstract":"This research investigates the intricate dynamics of DNA methylation in the hours following CD8+ T cell activation, during a critical yet understudied temporal window. DNA methylation is an epigenetic modification central to regulation of gene expression and directing immune responses. Our investigation spanned 96-h post-activation and unveils a nuanced tapestry of global and site-specific methylation changes. We identified 15,626 significant differentially methylated CpGs spread across the genome, with the most significant changes occurring within the genes ADAM10, ICA1, and LAPTM5. While many changes had modest effect sizes, approximately 120 CpGs exhibited a log2FC above 1.5, with cell activation and proliferation pathways the most affected. Relatively few of the differentially methylated CpGs occurred along adjacent gene regions. The exceptions were seven differentially methylated gene regions, with the Human T cell Receptor Alpha Joining Genes demonstrating consistent methylation change over a 3kb window. We also investigated whether an inflammatory environment could alter DNA methylation during activation, with proliferating cells exposed to the oxidant glycine chloramine. No substantial differential methylation was observed in this context. The temporal perspective of early activation adds depth to the evolving field of epigenetic immunology, offering insights with implications for therapeutic innovation and expanding our understanding of epigenetic modulation in immune function.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2367385"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11195465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction. 更正。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-08-04 DOI: 10.1080/15592294.2024.2388007

引用次数: 0

Biogenesis of circRBM33 mediated by N6-methyladenosine and its function in abdominal aortic aneurysm. 由 N6-甲基腺苷介导的 circRBM33 的生物生成及其在腹主动脉瘤中的功能。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-09-09 DOI: 10.1080/15592294.2024.2392401

Yingqi Xu, Xiang Weng, Jiacong Qiu, Shizhi Wang

{"title":"Biogenesis of circRBM33 mediated by N6-methyladenosine and its function in abdominal aortic aneurysm.","authors":"Yingqi Xu, Xiang Weng, Jiacong Qiu, Shizhi Wang","doi":"10.1080/15592294.2024.2392401","DOIUrl":"10.1080/15592294.2024.2392401","url":null,"abstract":"This study aimed to explore whether m6A modification affects the biogenesis of circRBM33, which is involved in the progression of abdominal aortic aneurysm (AAA). For in vitro experiments, vascular smooth muscle cells (VSMCs) were treated with Ang II. MeRIP‒PCR was used to assess m6A modification of circRBM33. Gene expression was measured using RT‒qPCR and Western blotting. For in vivo experiments, a mouse model of AAA was established via Ang II infusion. HE, Sirius Red and TUNEL staining was performed to evaluate pathological changes and cell apoptosis in aortic vessels. The results showed that the m6A level of circRBM33 was abnormally increased in Ang II-induced VSMCs. In addition, METTL3 positively regulated circRBM33 expression. YTHDC1 deficiency decreased circRBM33 expression but had no effect on RBM33 mRNA expression. Notably, neither METTL3 nor YTHDC1 influenced the stability of circRBM33 or RBM33 mRNA. The interaction between circRBM33 and METTL3/YTHDC1 was verified by RIP analysis. Moreover, the Ang II-induced increase in circRBM33 expression was reversed by cycloleucine (an inhibitor of m6A methylation). Importantly, the m6A modification and expression of circRBM33 in the circRBM33-m6A-mut2-expressing VSMCs were not altered by METTL3 silencing. Mechanistically, METTL3/YTHDC1 modulates the biogenesis of circRBM33 in an m6A-dependent manner. In addition, circRBM33 knockdown alleviated AAA by reducing ECM degradation in the Ang II-infused mice. In conclusion, this study demonstrated that METTL3/YTHDC1-mediated m6A modification modulates the biogenesis of circRBM33 from exons of the RBM33 gene. Moreover, knockdown of circRBM33 alleviated AAA by reducing ECM degradation, which may provide a novel therapeutic strategy for treating AAA.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2392401"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11385162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142153399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Heavy alcohol consumption but not smoking predicts mortality in patients with acute coronary syndrome. 大量饮酒而非吸烟可预测急性冠状动脉综合征患者的死亡率。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-11-27 DOI: 10.1080/15592294.2024.2433833

Allan Andersen, Steven R H Beach, Willem Philibert, James A Mills, Emily Milefchik, Emma Papworth, Kelsey Dawes, Joanna Moody, Gracie Weeks, Ellyse Froehlich, Kaitlyn deBlois, Jeffrey D Long, Ferhaan Ahmad, Robert Philibert

{"title":"Heavy alcohol consumption but not smoking predicts mortality in patients with acute coronary syndrome.","authors":"Allan Andersen, Steven R H Beach, Willem Philibert, James A Mills, Emily Milefchik, Emma Papworth, Kelsey Dawes, Joanna Moody, Gracie Weeks, Ellyse Froehlich, Kaitlyn deBlois, Jeffrey D Long, Ferhaan Ahmad, Robert Philibert","doi":"10.1080/15592294.2024.2433833","DOIUrl":"10.1080/15592294.2024.2433833","url":null,"abstract":"The relationship of heavy alcohol consumption (HAC) and smoking to mortality in those with CHD, and mechanisms through which these effects are elicited are not clear. In order to improve our understanding, we examined the relationship of Alcohol T-Scores (ATS), an epigenetic biomarker of chronic HAC, and cg05575921 methylation, a biomarker of smoking intensity, with all-cause mortality and degree of coronary artery obstruction in a cohort of 217 subjects admitted for CHD-related acute coronary syndrome (ACS). We found that 65% of the subjects had ATS values indicative of chronic HAC. ATS values, but not cg05575921 values, were significantly associated (p < 0.02) with subsequent proband death (total of 28 deaths) with a Cox Proportional Hazards model showing a slightly larger effect of ATS levels than age on all-cause mortality survival (overall model, p < 0.003). Subjects in the highest decile of ATS scores had a 2.4-fold increase in the risk for mortality as compared to those in the lowest decile. In contrast, cg05575921 methylation (p < 0.003) but not ATS scores, were significantly inversely associated with degree of obstruction. Only 2 of the 217 subjects were referred for treatment for either smoking or drinking. We conclude that HAC is an underappreciated driver of CHD-related mortality, that those with ACS who smoke are much less likely to have significant obstruction upon cardiac imaging and that substance use treatment may be underutilized in those with CHD.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2433833"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142738808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Maternal glucose levels and late pregnancy circulating extracellular vesicle and particle miRNAs in the MADRES pregnancy cohort. MADRES 妊娠队列中的母体血糖水平与妊娠晚期循环细胞外囊泡和颗粒 miRNAs。

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-09-18 DOI: 10.1080/15592294.2024.2404198

Elizabeth C Anderson,Helen B Foley,Joshua J Levy,Megan E Romano,Jiang Gui,Jessica L Bentz,Luis E Maldonado,Shohreh F Farzan,Theresa M Bastain,Carmen J Marsit,Carrie V Breton,Caitlin G Howe

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Exploring fatty acids from royal jelly as a source of histone deacetylase inhibitors: from the hive to applications in human well-being and health. 探索从蜂王浆中提取脂肪酸作为组蛋白去乙酰化酶抑制剂的来源：从蜂巢到在人类福祉和健康中的应用。

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-09-10 DOI: 10.1080/15592294.2024.2400423

Fernanda Aparecida Dos Santos France,Debora Kazumi Maeda,Ana Beatriz Rodrigues,Mai Ono,Franciele Lopes Nogueira Marchetti,Marcos Martins Marchetti,Allana Cristina Faustino Martins,Roberto da Silva Gomes,Cláudia Aparecida Rainho

{"title":"Exploring fatty acids from royal jelly as a source of histone deacetylase inhibitors: from the hive to applications in human well-being and health.","authors":"Fernanda Aparecida Dos Santos France,Debora Kazumi Maeda,Ana Beatriz Rodrigues,Mai Ono,Franciele Lopes Nogueira Marchetti,Marcos Martins Marchetti,Allana Cristina Faustino Martins,Roberto da Silva Gomes,Cláudia Aparecida Rainho","doi":"10.1080/15592294.2024.2400423","DOIUrl":"https://doi.org/10.1080/15592294.2024.2400423","url":null,"abstract":"A differential diet with royal jelly (RJ) during early larval development in honeybees shapes the phenotype, which is probably mediated by epigenetic regulation of gene expression. Evidence indicates that small molecules in RJ can modulate gene expression in mammalian cells, such as the fatty acid 10-hydroxy-2-decenoic acid (10-HDA), previously associated with the inhibition of histone deacetylase enzymes (HDACs). Therefore, we combined computational (molecular docking simulations) and experimental approaches for the screening of potential HDAC inhibitors (HDACi) among 32 RJ-derived fatty acids. Biochemical assays and gene expression analyses (Reverse Transcriptase - quantitative Polymerase Chain Reaction) were performed to evaluate the functional effects of the major RJ fatty acids, 10-HDA and 10-HDAA (10-hydroxy-decanoic acid), in two human cancer cell lines (HCT116 and MDA-MB-231). The molecular docking simulations indicate that these fatty acids might interact with class I HDACs, specifically with the catalytic domain of human HDAC2, likewise well-known HDAC inhibitors (HDACi) such as SAHA (suberoylanilide hydroxamic acid) and TSA (Trichostatin A). In addition, the combined treatment with 10-HDA and 10-HDAA inhibits the activity of human nuclear HDACs and leads to a slight increase in the expression of HDAC-coding genes in cancer cells. Our findings indicate that royal jelly fatty acids collectively contribute to HDAC inhibition and that 10-HDA and 10-HDAA are weak HDACi that facilitate the acetylation of lysine residues of chromatin, triggering an increase in gene expression levels in cancer cells.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"2 1","pages":"2400423"},"PeriodicalIF":3.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142222205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Folate-mediated transgenerational inheritance of sperm DNA methylation patterns correlate with spinal axon regeneration 叶酸介导的精子DNA甲基化模式转代遗传与脊髓轴突再生相关

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-07-27 DOI: 10.1080/15592294.2024.2380930

Andy Madrid, Joyce Koueik, Ligia A. Papale, Roy Chebel, Isabelle Renteria, Emily Cannon, Kirk J. Hogan, Reid S. Alisch, Bermans J. Iskandar

引用次数: 0

H4K20me3, H3K4me2 and H3K9me2 mediate the effect of ER on prognosis in breast cancer H4K20me3、H3K4me2 和 H3K9me2 介导 ER 对乳腺癌预后的影响

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-04-21 DOI: 10.1080/15592294.2024.2343593

Cheng-Kun Xiao, Yuexiang Ren, Qianxin Chen, Yuanzhong Yang, Luying Tang, Lin Xu, Zefang Ren

引用次数: 0

SOX6 AU controls myogenesis by cis-modulation of SOX6 in cattle SOX6 AU 通过顺式调节控制牛的肌肉发生