Epigenomes最新文献_第2页

Decoding the Epigenetics of Infertility: Mechanisms, Environmental Influences, and Therapeutic Strategies. 解码不孕症的表观遗传学：机制、环境影响和治疗策略。

IF 2.5

Epigenomes Pub Date : 2024-09-05 DOI: 10.3390/epigenomes8030034

Lara Saftić Martinović, Tea Mladenić, Dora Lovrić, Saša Ostojić, Sanja Dević Pavlić

{"title":"Decoding the Epigenetics of Infertility: Mechanisms, Environmental Influences, and Therapeutic Strategies.","authors":"Lara Saftić Martinović, Tea Mladenić, Dora Lovrić, Saša Ostojić, Sanja Dević Pavlić","doi":"10.3390/epigenomes8030034","DOIUrl":"10.3390/epigenomes8030034","url":null,"abstract":"Infertility is a complex condition caused by a combination of genetic, environmental, and lifestyle factors. Recent advances in epigenetics have highlighted the importance of epigenetic changes in fertility regulation. This review aims to provide a comprehensive overview of the epigenetic mechanisms involved in infertility, with a focus on DNA methylation, histone modification, and non-coding RNAs. We investigate the specific epigenetic events that occur during gametogenesis, with a focus on spermatogenesis and oogenesis as distinct processes. Furthermore, we investigate how environmental factors such as diet, stress, and toxin exposure can influence these epigenetic changes, potentially leading to infertility. The second part of the review explores epigenetic changes as therapeutic targets for infertility. Emerging therapies that modulate epigenetic marks present promising opportunities for fertility restoration, particularly in spermatogenesis. By summarizing current research findings, this review emphasizes the importance of understanding epigenetic contributions to infertility. Our discussion aims to lay the groundwork for future research directions and clinical applications in reproductive health.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301724","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

α-Crystalline Domains and Intrinsically Disordered Regions Can Work in Parallel to Induce Accumulation of MBD6 at Chromocenters in Arabidopsis thaliana. 拟南芥中的α-结晶结构域和内在无序区可同时发挥作用，诱导 MBD6 在染色体中心聚集。

IF 2.5

Epigenomes Pub Date : 2024-08-28 DOI: 10.3390/epigenomes8030033

Brandon A Boone, Cristy P Mendoza, Noah J Behrendt, Steven E Jacobsen

{"title":"α-Crystalline Domains and Intrinsically Disordered Regions Can Work in Parallel to Induce Accumulation of MBD6 at Chromocenters in Arabidopsis thaliana.","authors":"Brandon A Boone, Cristy P Mendoza, Noah J Behrendt, Steven E Jacobsen","doi":"10.3390/epigenomes8030033","DOIUrl":"10.3390/epigenomes8030033","url":null,"abstract":"Proteins are localized and concentrated at cellular and genomic locations for specific and efficient functions. Efforts to understand protein accumulation in eukaryotic organisms have primarily focused on multivalent interactions between intrinsically disordered regions (IDRs) as mediators of protein condensation. We previously showed that α-crystalline domain (ACD) proteins 15 (ACD15) and 21 (ACD21) were required for multimerization and the accumulation of gene-silencing methyl-CpG-binding domain protein 6 (MBD6) at chromocenters in Arabidopsis thaliana. Here, we demonstrate that ACDs and IDRs can act as parallel mechanisms, facilitating higher-order MBD6 assemblies. Using human IDRs known to be important for protein accumulation, we replicated and enhanced the accumulation of MBD6 at chromocenters. In addition, IDRs fused to MBD6 could substitute for ACD function and partially reconstitute the MBD6 gene-silencing function. However, the accumulation of MBD6 by IDRs still required ACD15 and ACD21 for full effect. These results establish that ACD-mediated protein accumulation is a mechanism that can function similarly to and together with IDR-mediated mechanisms.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301727","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

Genome-Wide Methylation Profiling of Peripheral T-Cell Lymphomas Identifies TRIP13 as a Critical Driver of Tumor Proliferation and Survival. 外周T细胞淋巴瘤的全基因组甲基化分析发现TRIP13是肿瘤增殖和存活的关键驱动因素

IF 2.5

Epigenomes Pub Date : 2024-08-21 DOI: 10.3390/epigenomes8030032

Pawel Nowialis, Julian Tobon, Katarina Lopusna, Jana Opavska, Arshee Badar, Duo Chen, Reem Abdelghany, Gene Pozas, Jacob Fingeret, Emma Noel, Alberto Riva, Hiroshi Fujiwara, Alexander Ishov, Rene Opavsky

{"title":"Genome-Wide Methylation Profiling of Peripheral T-Cell Lymphomas Identifies TRIP13 as a Critical Driver of Tumor Proliferation and Survival.","authors":"Pawel Nowialis, Julian Tobon, Katarina Lopusna, Jana Opavska, Arshee Badar, Duo Chen, Reem Abdelghany, Gene Pozas, Jacob Fingeret, Emma Noel, Alberto Riva, Hiroshi Fujiwara, Alexander Ishov, Rene Opavsky","doi":"10.3390/epigenomes8030032","DOIUrl":"10.3390/epigenomes8030032","url":null,"abstract":"Cytosine methylation contributes to the regulation of gene expression and normal hematopoiesis in mammals. It is catalyzed by the family of DNA methyltransferases that include DNMT1, DNMT3A, and DNMT3B. Peripheral T-cell lymphomas (PTCLs) represent aggressive mature T-cell malignancies exhibiting a broad spectrum of clinical features with poor prognosis and inadequately understood molecular pathobiology. To better understand the molecular landscape and identify candidate genes involved in disease maintenance, we profiled DNA methylation and gene expression of PTCLs. We found that the methylation patterns in PTCLs are deregulated and heterogeneous but share 767 hypo- and 567 hypermethylated differentially methylated regions (DMRs) along with 231 genes up- and 91 genes downregulated in all samples, suggesting a potential association with tumor development. We further identified 39 hypomethylated promoters associated with increased gene expression in the majority of PTCLs. This putative oncogenic signature included the TRIP13 (thyroid hormone receptor interactor 13) gene whose genetic and pharmacologic inactivation inhibited the proliferation of T-cell lines by inducing G2-M arrest and apoptosis. Our data thus show that human PTCLs have a significant number of recurrent methylation alterations that may affect the expression of genes critical for proliferation whose targeting might be beneficial in anti-lymphoma treatments.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074586","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

Sex-Specific Associations between Prenatal Exposure to Bisphenols and Phthalates and Infant Epigenetic Age Acceleration. 产前暴露于双酚和邻苯二甲酸盐与婴儿表观遗传年龄加速之间的性别特异性关联。

IF 2.5

Epigenomes Pub Date : 2024-08-10 DOI: 10.3390/epigenomes8030031

Gillian England-Mason, Sarah M Merrill, Jiaying Liu, Jonathan W Martin, Amy M MacDonald, David W Kinniburgh, Nicole Gladish, Julia L MacIsaac, Gerald F Giesbrecht, Nicole Letourneau, Michael S Kobor, Deborah Dewey

{"title":"Sex-Specific Associations between Prenatal Exposure to Bisphenols and Phthalates and Infant Epigenetic Age Acceleration.","authors":"Gillian England-Mason, Sarah M Merrill, Jiaying Liu, Jonathan W Martin, Amy M MacDonald, David W Kinniburgh, Nicole Gladish, Julia L MacIsaac, Gerald F Giesbrecht, Nicole Letourneau, Michael S Kobor, Deborah Dewey","doi":"10.3390/epigenomes8030031","DOIUrl":"10.3390/epigenomes8030031","url":null,"abstract":"We examined whether prenatal exposure to two classes of endocrine-disrupting chemicals (EDCs) was associated with infant epigenetic age acceleration (EAA), a DNA methylation biomarker of aging. Participants included 224 maternal-infant pairs from a Canadian pregnancy cohort study. Two bisphenols and 12 phthalate metabolites were measured in maternal second trimester urines. Buccal epithelial cell cheek swabs were collected from 3 month old infants and DNA methylation was profiled using the Infinium MethylationEPIC BeadChip. The Pediatric-Buccal-Epigenetic tool was used to estimate EAA. Sex-stratified robust regressions examined individual chemical associations with EAA, and Bayesian kernel machine regression (BKMR) examined chemical mixture effects. Adjusted robust models showed that in female infants, prenatal exposure to total bisphenol A (BPA) was positively associated with EAA (B = 0.72, 95% CI: 0.21, 1.24), and multiple phthalate metabolites were inversely associated with EAA (Bs from -0.36 to -0.66, 95% CIs from -1.28 to -0.02). BKMR showed that prenatal BPA was the most important chemical in the mixture and was positively associated with EAA in both sexes. No overall chemical mixture effects or male-specific associations were noted. These findings indicate that prenatal EDC exposures are associated with sex-specific deviations in biological aging, which may have lasting implications for child health and development.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074631","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

Multiomics Screening Identified CpG Sites and Genes That Mediate the Impact of Exposure to Environmental Chemicals on Cardiometabolic Traits. 多组学筛选确定了介导暴露于环境化学品对心脏代谢特征影响的 CpG 位点和基因。

IF 2.5

Epigenomes Pub Date : 2024-07-29 DOI: 10.3390/epigenomes8030029

Majid Nikpay

{"title":"Multiomics Screening Identified CpG Sites and Genes That Mediate the Impact of Exposure to Environmental Chemicals on Cardiometabolic Traits.","authors":"Majid Nikpay","doi":"10.3390/epigenomes8030029","DOIUrl":"10.3390/epigenomes8030029","url":null,"abstract":"An understanding of the molecular mechanism whereby an environmental chemical causes a disease is important for the purposes of future applications. In this study, a multiomics workflow was designed to combine several publicly available datasets in order to identify CpG sites and genes that mediate the impact of exposure to environmental chemicals on cardiometabolic traits. Organophosphate and prenatal lead exposure were previously reported to change methylation level at the cg23627948 site. The outcome of the analyses conducted in this study revealed that, as the cg23627948 site becomes methylated, the expression of the GNA12 gene decreases, which leads to a higher body fat percentage. Prenatal perfluorooctane sulfonate exposure was reported to increase the methylation level at the cg21153102 site. Findings of this study revealed that higher methylation at this site contributes to higher diastolic blood pressure by changing the expression of CHP1 and GCHFR genes. Moreover, HKR1 mediates the impact of B12 supplementation → cg05280698 hypermethylation on higher kidney function, while CTDNEP1 mediates the impact of air pollution → cg03186999 hypomethylation on higher systolic blood pressure. This study investigates CpG sites and genes that mediate the impact of environmental chemicals on cardiometabolic traits. Furthermore, the multiomics approach described in this study provides a convenient workflow with which to investigate the impact of an environmental factor on the body's biomarkers, and, consequently, on health conditions, using publicly available data.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074587","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

Epigenetic Regulation of Mammalian Cardiomyocyte Development. 哺乳动物心肌细胞发育的表观遗传调控

IF 2.5

Epigenomes Pub Date : 2024-06-29 DOI: 10.3390/epigenomes8030025

Isaiah K Mensah, Humaira Gowher

引用次数: 0

DNA Hypomethylation Underlies Epigenetic Swapping between AGO1 and AGO1-V2 Isoforms in Tumors. DNA低甲基化是肿瘤中AGO1和AGO1-V2异构体表观遗传交换的基础

IF 2.5

Epigenomes Pub Date : 2024-06-22 DOI: 10.3390/epigenomes8030024

Jean S Fain, Camille Wangermez, Axelle Loriot, Claudia Denoue, Charles De Smet

{"title":"DNA Hypomethylation Underlies Epigenetic Swapping between AGO1 and AGO1-V2 Isoforms in Tumors.","authors":"Jean S Fain, Camille Wangermez, Axelle Loriot, Claudia Denoue, Charles De Smet","doi":"10.3390/epigenomes8030024","DOIUrl":"10.3390/epigenomes8030024","url":null,"abstract":"Human tumors progress in part by accumulating epigenetic alterations, which include gains and losses of DNA methylation in different parts of the cancer cell genome. Recent work has revealed a link between these two opposite alterations by showing that DNA hypomethylation in tumors can induce the expression of transcripts that overlap downstream gene promoters and thereby induce their hypermethylation. Preliminary in silico evidence prompted us to investigate if this mechanism applies to the locus harboring AGO1, a gene that plays a central role in miRNA biogenesis and RNA interference. Inspection of public RNA-Seq datasets and RT-qPCR experiments show that an alternative transcript starting 13.4 kb upstream of AGO1 (AGO1-V2) is expressed specifically in testicular germ cells, and becomes aberrantly activated in different types of tumors, particularly in tumors of the esophagus, stomach, and lung. This expression pattern classifies AGO1-V2 into the group of \"Cancer-Germline\" (CG) genes. Analysis of transcriptomic and methylomic datasets provided evidence that transcriptional activation of AGO1-V2 depends on DNA demethylation of its promoter region. Western blot experiments revealed that AGO1-V2 encodes a shortened isoform of AGO1, corresponding to a truncation of 75 aa in the N-terminal domain, and which we therefore referred to as \"∆NAGO1\". Interestingly, significant correlations between hypomethylation/activation of AGO1-V2 and hypermethylation/repression of AGO1 were observed upon examination of tumor cell lines and tissue datasets. Overall, our study reveals the existence of a process of interdependent epigenetic alterations in the AGO1 locus, which promotes swapping between two AGO1 protein-coding mRNA isoforms in tumors.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11270204/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762942","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

Keep Fingers on the CpG Islands. 把手指放在 CpG 岛上

IF 2.5

Epigenomes Pub Date : 2024-06-19 DOI: 10.3390/epigenomes8020023

Xing Zhang, Robert M Blumenthal, Xiaodong Cheng

引用次数: 0

Structural and Biochemical Characterization of the Nucleosome Containing Variants H3.3 and H2A.Z. 含变体 H3.3 和 H2A.Z 的核小体的结构和生化特征

IF 2.5

Epigenomes Pub Date : 2024-05-27 DOI: 10.3390/epigenomes8020021

Harry Jung, Vladyslava Sokolova, Gahyun Lee, Victoria Rose Stevens, Dongyan Tan

引用次数: 0

Blood Vitamin C Levels of Patients Receiving Immunotherapy and Relationship to Monocyte Subtype and Epigenetic Modification. 接受免疫治疗的患者血液中的维生素 C 水平及其与单核细胞亚型和表观遗传修饰的关系。

IF 2.5

Epigenomes Pub Date : 2024-04-30 DOI: 10.3390/epigenomes8020017

Ben Topham, Millie de Vries, Maria Nonis, Rebecca van Berkel, Juliet M Pullar, Nicholas J Magon, Margreet C M Vissers, Margaret J Currie, Bridget A Robinson, David Gibbs, Abel Ang, Gabi U Dachs

{"title":"Blood Vitamin C Levels of Patients Receiving Immunotherapy and Relationship to Monocyte Subtype and Epigenetic Modification.","authors":"Ben Topham, Millie de Vries, Maria Nonis, Rebecca van Berkel, Juliet M Pullar, Nicholas J Magon, Margreet C M Vissers, Margaret J Currie, Bridget A Robinson, David Gibbs, Abel Ang, Gabi U Dachs","doi":"10.3390/epigenomes8020017","DOIUrl":"10.3390/epigenomes8020017","url":null,"abstract":"The treatment of metastatic melanoma has been revolutionised by immunotherapy, yet a significant number of patients do not respond, and many experience autoimmune adverse events. Associations have been reported between patient outcome and monocyte subsets, whereas vitamin C (ascorbate) has been shown to mediate changes in cancer-stimulated monocytes in vitro. We therefore investigated the relationship of ascorbate with monocyte subsets and epigenetic modifications in patients with metastatic melanoma receiving immunotherapy. Patients receiving immunotherapy were compared to other cancer cohorts and age-matched healthy controls. Ascorbate levels in plasma and peripheral blood-derived mononuclear cells (PBMCs), monocyte subtype and epigenetic markers were measured, and adverse events, tumour response and survival were recorded. A quarter of the immunotherapy cohort had hypovitaminosis C, with plasma and PBMC ascorbate levels significantly lower than those from other cancer patients or healthy controls. PBMCs from the immunotherapy cohort contained similar frequencies of non-classical and classical monocytes. DNA methylation markers and intracellular ascorbate concentration were correlated with monocyte subset frequency in healthy controls, but correlation was lost in immunotherapy patients. No associations between ascorbate status and immune-related adverse events or tumour response or overall survival were apparent.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"8 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11130941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158953","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