Epigenomes最新文献_第4页

IndiSPENsable for X Chromosome Inactivation and Gene Silencing 对X染色体失活和基因沉默不可或缺

Epigenomes Pub Date : 2023-11-02 DOI: 10.3390/epigenomes7040028

Corinne Kaufmann, Anton Wutz

{"title":"IndiSPENsable for X Chromosome Inactivation and Gene Silencing","authors":"Corinne Kaufmann, Anton Wutz","doi":"10.3390/epigenomes7040028","DOIUrl":"https://doi.org/10.3390/epigenomes7040028","url":null,"abstract":"For about 30 years, SPEN has been the subject of research in many different fields due to its variety of functions and its conservation throughout a wide spectrum of species, like worms, arthropods, and vertebrates. To date, 216 orthologues have been documented. SPEN had been studied for its role in gene regulation in the context of cell signaling, including the NOTCH or nuclear hormone receptor signaling pathways. More recently, SPEN has been identified as a major regulator of initiation of chromosome-wide gene silencing during X chromosome inactivation (XCI) in mammals, where its function remains to be fully understood. Dependent on the biological context, SPEN functions via mechanisms which include different domains. While some domains of SPEN are highly conserved in sequence and secondary structure, species-to-species differences exist that might lead to mechanistic differences. Initiation of XCI appears to be different between humans and mice, which raises additional questions about the extent of generalization of SPEN’s function in XCI. In this review, we dissect the mechanism of SPEN in XCI. We discuss its subregions and domains, focusing on its role as a major regulator. We further highlight species-related research, specifically of mouse and human SPEN, with the aim to reveal and clarify potential species-to-species differences in SPEN’s function.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"3 10","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135973460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Stress and DNA Methylation of Blood Leukocytes among Pregnant Latina Women 应激与拉丁裔孕妇血液白细胞DNA甲基化

Epigenomes Pub Date : 2023-11-01 DOI: 10.3390/epigenomes7040027

Veronica Barcelona, Sameera Abuaish, Seonjoo Lee, Sarah Harkins, Ashlie Butler, Benjamin Tycko, Andrea A. Baccarelli, Kate Walsh, Catherine E. Monk

{"title":"Stress and DNA Methylation of Blood Leukocytes among Pregnant Latina Women","authors":"Veronica Barcelona, Sameera Abuaish, Seonjoo Lee, Sarah Harkins, Ashlie Butler, Benjamin Tycko, Andrea A. Baccarelli, Kate Walsh, Catherine E. Monk","doi":"10.3390/epigenomes7040027","DOIUrl":"https://doi.org/10.3390/epigenomes7040027","url":null,"abstract":"Latinas experience physical and psychological stressors in pregnancy leading to increased morbidity and higher risk for adverse birth outcomes. Epigenetic changes, including DNA methylation (DNAm), have been proposed as markers to create more refined risk stratification, yet few of these studies have examined these changes in Latinas. We conducted a secondary analysis of stored blood leukocytes of Latina women (n = 58) enrolled in a larger National Institutes of Health funded R01 project (2011–2016). We examined DNAm on eight candidate stress genes to compare physically and psychologically stressed participants to healthy (low stress) participants. We found unique CpGs that were differentially methylated in stressed women early- and mid-pregnancy compared to the healthy group, though none remained significant after FDR correction. Both physical and psychological stress were associated with hypomethylation at two consecutive CpG sites on NR3C1 in early pregnancy and one CpG site on NR3C1 in mid-pregnancy before adjustment. Stress was also associated with hypomethylation at two CpG sites on FKBP5 in early and mid-pregnancy but were no longer significant after FDR adjustment. Though we did not find statistically significant differences in DNAm during pregnancy between stressed and healthy women in this sample, signals were consistent with previous findings. Future work in larger samples should further examine the associations between stress and DNAm in pregnancy as this mechanism may explain underlying perinatal health inequities.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"77 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135373260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction: Islam, R.A.; Rallis, C. Ribosomal Biogenesis and Heterogeneity in Development, Disease, and Aging. Epigenomes 2023, 7, 17 更正:伊斯兰教，R.A.;核糖体在发育、疾病和衰老中的生物发生和异质性。表观基因组学，2017,7,17

Epigenomes Pub Date : 2023-10-26 DOI: 10.3390/epigenomes7040026

Rowshan Ara Islam, Charalampos Rallis

引用次数: 0

Maternal MicroRNA Profile Changes When LH Is Added to the Ovarian Stimulation Protocol: A Pilot Study. 当LH被添加到卵巢刺激方案中时，母体微小RNA图谱的变化：一项初步研究。

IF 2.5

Epigenomes Pub Date : 2023-10-06 DOI: 10.3390/epigenomes7040025

Fani Konstantinidou, Martina Placidi, Giovanna Di Emidio, Liborio Stuppia, Carla Tatone, Valentina Gatta, Paolo Giovanni Artini

{"title":"Maternal MicroRNA Profile Changes When LH Is Added to the Ovarian Stimulation Protocol: A Pilot Study.","authors":"Fani Konstantinidou, Martina Placidi, Giovanna Di Emidio, Liborio Stuppia, Carla Tatone, Valentina Gatta, Paolo Giovanni Artini","doi":"10.3390/epigenomes7040025","DOIUrl":"10.3390/epigenomes7040025","url":null,"abstract":"While the use of follicle-stimulating hormone (FSH) in ovarian stimulation for in vitro fertilization (IVF) is an established practice, the use of luteinizing hormone (LH) remains debatable. MicroRNAs (miRNAs) are short, endogenous, non-coding transcripts that control a variety of cellular functions, such as gonadotrophin production and follicular development. The goal of this pilot study was to investigate whether the employment of recombinant LH (rLH) in ovarian stimulation protocols results in changes in the miRNA profiles in human oocytes. Patients were divided into two groups: seven received recombinant FSH (rFSH, 225 IU), and six received rFSH (150 IU) plus rLH (75 IU). MiRNA predesigned panels and real-time PCR technology were used to analyze the oocytes retrieved from the follicular ovarian retrieval. Among the miRNAs evaluated, a series of them evidenced upregulation or downregulation in their expression in the FSH plus LH group compared to the FSH group. Considering the results obtained from the functional and network analysis, the different maternal miRNA profiles in the two groups revealed a differential modulation of pathways involved in numerous biological functions. Overall, based on the pathways associated with most of these maternal miRNAs, the presence of LH may result in a different modulation of pathways regulating survival under the control of a Tp53-related mechanism. Interestingly, among the miRNAs differentially expressed in oocytes of the two groups, we have found miRNAs already investigated at ovarian, follicular, oocyte, and embryonic levels: hsa-miR-484, hsa-miR-222, hsa-miR-520d-5p, hsa-miRNA-17, hsa-miR-548, and hsa-miR-140. Thus, investigation into the role of these miRNAs in oocyte molecular pathways may help determine how LH affects oocyte competence and eventually leads to the clinical improvement of IVF.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10594432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49694268","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

The ErbB Signaling Network and Its Potential Role in Endometrial Cancer. ErbB信号网络及其在子宫内膜癌症中的潜在作用。

IF 2.5

Epigenomes Pub Date : 2023-10-01 DOI: 10.3390/epigenomes7040024

Georgios Androutsopoulos, Ioanna Styliara, Evgenia Zarogianni, Nadia Lazurko, George Valasoulis, Georgios Michail, Georgios Adonakis

{"title":"The ErbB Signaling Network and Its Potential Role in Endometrial Cancer.","authors":"Georgios Androutsopoulos, Ioanna Styliara, Evgenia Zarogianni, Nadia Lazurko, George Valasoulis, Georgios Michail, Georgios Adonakis","doi":"10.3390/epigenomes7040024","DOIUrl":"10.3390/epigenomes7040024","url":null,"abstract":"Endometrial cancer (EC) is the second most common malignancy of the female reproductive system worldwide. The updated EC classification emphasizes the significant role of various signaling pathways such as PIK3CA-PIK3R1-PTEN and RTK/RAS/β-catenin in EC pathogenesis. Some of these pathways are part of the EGF system signaling network, which becomes hyperactivated by various mechanisms and participates in cancer pathogenesis. In EC, the expression of ErbB receptors is significantly different, compared with the premenopausal and postmenopausal endometrium, mainly because of the increased transcriptional activity of ErbB encoding genes in EC cells. Moreover, there are some differences in ErbB-2 receptor profile among EC subgroups that could be explained by the alterations in pathophysiology and clinical behavior of various EC histologic subtypes. The fact that ErbB-2 receptor expression is more common in aggressive EC histologic subtypes (papillary serous and clear cell) could indicate a future role of ErbB-targeted therapies in well-defined EC subgroups with overexpression of ErbB receptors.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10594534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49694269","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: 2

Current Approaches to Epigenetic Therapy. 表观遗传学治疗的最新方法。

IF 2.5

Epigenomes Pub Date : 2023-09-30 DOI: 10.3390/epigenomes7040023

Ekaterina D Griazeva, Daria M Fedoseeva, Elizaveta I Radion, Pavel V Ershov, Ivan O Meshkov, Alexandra V Semyanihina, Anna S Makarova, Valentin V Makarov, Vladimir S Yudin, Anton A Keskinov, Sergey A Kraevoy

引用次数: 0

Linc2function: A Comprehensive Pipeline and Webserver for Long Non-Coding RNA (lncRNA) Identification and Functional Predictions Using Deep Learning Approaches. Linc2function：使用深度学习方法进行长非编码RNA（lncRNA）识别和功能预测的综合管道和Web服务器。

IF 2.5

Epigenomes Pub Date : 2023-09-15 DOI: 10.3390/epigenomes7030022

Yashpal Ramakrishnaiah, Adam P Morris, Jasbir Dhaliwal, Melcy Philip, Levin Kuhlmann, Sonika Tyagi

{"title":"Linc2function: A Comprehensive Pipeline and Webserver for Long Non-Coding RNA (lncRNA) Identification and Functional Predictions Using Deep Learning Approaches.","authors":"Yashpal Ramakrishnaiah, Adam P Morris, Jasbir Dhaliwal, Melcy Philip, Levin Kuhlmann, Sonika Tyagi","doi":"10.3390/epigenomes7030022","DOIUrl":"https://doi.org/10.3390/epigenomes7030022","url":null,"abstract":"Long non-coding RNAs (lncRNAs), comprising a significant portion of the human transcriptome, serve as vital regulators of cellular processes and potential disease biomarkers. However, the function of most lncRNAs remains unknown, and furthermore, existing approaches have focused on gene-level investigation. Our work emphasizes the importance of transcript-level annotation to uncover the roles of specific transcript isoforms. We propose that understanding the mechanisms of lncRNA in pathological processes requires solving their structural motifs and interactomes. A complete lncRNA annotation first involves discriminating them from their coding counterparts and then predicting their functional motifs and target bio-molecules. Current in silico methods mainly perform primary-sequence-based discrimination using a reference model, limiting their comprehensiveness and generalizability. We demonstrate that integrating secondary structure and interactome information, in addition to using transcript sequence, enables a comprehensive functional annotation. Annotating lncRNA for newly sequenced species is challenging due to inconsistencies in functional annotations, specialized computational techniques, limited accessibility to source code, and the shortcomings of reference-based methods for cross-species predictions. To address these challenges, we developed a pipeline for identifying and annotating transcript sequences at the isoform level. We demonstrate the effectiveness of the pipeline by comprehensively annotating the lncRNA associated with two specific disease groups. The source code of our pipeline is available under the MIT licensefor local use by researchers to make new predictions using the pre-trained models or to re-train models on new sequence datasets. Non-technical users can access the pipeline through a web server setup.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10528440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41122414","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

Environmental Epigenomes. 环境表观基因组。

IF 2.5

Epigenomes Pub Date : 2023-09-07 DOI: 10.3390/epigenomes7030021

Bambarendage P U Perera, Frédéric Silvestre

{"title":"Environmental Epigenomes.","authors":"Bambarendage P U Perera, Frédéric Silvestre","doi":"10.3390/epigenomes7030021","DOIUrl":"10.3390/epigenomes7030021","url":null,"abstract":"Research in epigenetics has dramatically risen during the last decade to include aspects of environmental biology. However, many questions remain regarding the effects of environmental stressors on the epigenome, incorporating the particular role of epigenetic mechanisms in the adaptation and evolution of organisms in changing environments. Epigenetics is commonly defined as mitotically and/or meiotically heritable changes in gene function that occur without altering the underlying DNA sequence. It encompasses DNA (hydroxy)methylation, histone modifications, chromatin structure, and non-coding RNAs that may be inherited across generations under certain circumstances. Epigenetic mechanisms are perfect candidates to extend our understanding of the impact of environmental stressors on organisms and to explain the rapid phenomenon of adaptive evolution. Existing evidence shows that environmental cues can affect the epigenome and modify gene expression accordingly. These changes can then induce phenotypic modifications that are morphological, physiological, or behavioral at the organismal level. In this Special Issue focusing on environmental epigenetics, we provide an overview of influences to the epigenome that are driven by various environmental and evolutionary factors, with a particular focus on DNA methylation (DNAm). Five research groups have contributed insightful studies or reviews on (1) DNAm and demethylation events affected by the exposome; (2) DNAm as a potential biomarker to determine cardiometabolic risk early in life; (3) consequences of DNAm across multiple generations; (4) DNAm variation within natural animal populations; and (5) epigenetic mechanisms in genetically uniform organisms. Collectively, the articles from this Special Issue consistently support that environmental changes can induce long-lasting epigenetic effects within a given organism pertaining to individual risk for disease, or multi-generational impacts that ultimately impact evolution.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10527617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41141748","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

Integrated Multimodal Omics and Dietary Approaches for the Management of Neurodegeneration. 管理神经变性的综合多模式奥密克戎和饮食方法。

IF 2.5

Epigenomes Pub Date : 2023-09-01 DOI: 10.3390/epigenomes7030020

Toshiyuki Murai, Satoru Matsuda

{"title":"Integrated Multimodal Omics and Dietary Approaches for the Management of Neurodegeneration.","authors":"Toshiyuki Murai, Satoru Matsuda","doi":"10.3390/epigenomes7030020","DOIUrl":"10.3390/epigenomes7030020","url":null,"abstract":"Neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease, are caused by a combination of multiple events that damage neuronal function. A well-characterized biomarker of neurodegeneration is the accumulation of proteinaceous aggregates in the brain. However, the gradually worsening symptoms of neurodegenerative diseases are unlikely to be solely due to the result of a mutation in a single gene, but rather a multi-step process involving epigenetic changes. Recently, it has been suggested that a fraction of epigenetic alternations may be correlated to neurodegeneration in the brain. Unlike DNA mutations, epigenetic alterations are reversible, and therefore raise the possibilities for therapeutic intervention, including dietary modifications. Additionally, reactive oxygen species may contribute to the pathogenesis of Alzheimer's disease and Parkinson's disease through epigenetic alternation. Given that the antioxidant properties of plant-derived phytochemicals are likely to exhibit pleiotropic effects against ROS-mediated epigenetic alternation, dietary intervention may be promising for the management of neurodegeneration in these diseases. In this review, the state-of-the-art applications using single-cell multimodal omics approaches, including epigenetics, and dietary approaches for the identification of novel biomarkers and therapeutic approaches for the treatment of neurodegenerative diseases are discussed.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10529483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41174669","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 Data Analysis Identified CpG Sites That Mediate the Impact of Smoking on Cardiometabolic Traits. 多组学数据分析确定了介导吸烟对心脏代谢特征影响的CpG位点。

IF 2.5

Epigenomes Pub Date : 2023-08-22 DOI: 10.3390/epigenomes7030019

Majid Nikpay

{"title":"Multiomics Data Analysis Identified CpG Sites That Mediate the Impact of Smoking on Cardiometabolic Traits.","authors":"Majid Nikpay","doi":"10.3390/epigenomes7030019","DOIUrl":"https://doi.org/10.3390/epigenomes7030019","url":null,"abstract":"Understanding the epigenome paths through which smoking contributes to cardiometabolic traits is important for downstream applications. In this study, an SNP-based analytical pipeline was used to integrate several publicly available datasets in order to identify CpG sites that mediate the impact of smoking on cardiometabolic traits and to investigate the underlying molecular mechanisms. After applying stringent statistical criteria, 11 CpG sites were detected that showed significant association (p < 5 × 10-8) with cardiometabolic traits at both the discovery and replication stages. By integrating eQTL data, I found genes behind a number of these associations. cg05228408 was hypomethylated in smokers and contributed to higher blood pressure by lowering the expression of the CLCN6 gene. cg08639339 was hypermethylated in smokers and lowered the metabolic rate by increasing the expression of RAB29; furthermore, I noted TMEM120A mediated the impact of smoking-cg17325771 on LDL, and LTBP3 mediated the smoking-cg07029024 effect on heart rate. The pathway analysis identified processes through which the identified genes impact their traits. This study provides a list of CpG sites that mediates the impact of smoking on cardiometabolic traits and a framework to investigate the underlying molecular paths using publicly available data.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10528714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41175125","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