Epigenomes最新文献

{"title":"Current Approaches to Epigenetic Therapy.","authors":"Ekaterina D Griazeva,&nbsp;Daria M Fedoseeva,&nbsp;Elizaveta I Radion,&nbsp;Pavel V Ershov,&nbsp;Ivan O Meshkov,&nbsp;Alexandra V Semyanihina,&nbsp;Anna S Makarova,&nbsp;Valentin V Makarov,&nbsp;Vladimir S Yudin,&nbsp;Anton A Keskinov,&nbsp;Sergey A Kraevoy","doi":"10.3390/epigenomes7040023","DOIUrl":"10.3390/epigenomes7040023","url":null,"abstract":"<p><p>Epigenetic therapy is a promising tool for the treatment of a wide range of diseases. Several fundamental epigenetic approaches have been proposed. Firstly, the use of small molecules as epigenetic effectors, as the most developed pharmacological method, has contributed to the introduction of a number of drugs into clinical practice. Secondly, various innovative epigenetic approaches based on dCas9 and the use of small non-coding RNAs as therapeutic agents are also under extensive research. In this review, we present the current state of research in the field of epigenetic therapy, considering the prospects for its application and possible limitations.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10594535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49694267","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}

{"title":"Linc2function: A Comprehensive Pipeline and Webserver for Long Non-Coding RNA (lncRNA) Identification and Functional Predictions Using Deep Learning Approaches.","authors":"Yashpal Ramakrishnaiah,&nbsp;Adam P Morris,&nbsp;Jasbir Dhaliwal,&nbsp;Melcy Philip,&nbsp;Levin Kuhlmann,&nbsp;Sonika Tyagi","doi":"10.3390/epigenomes7030022","DOIUrl":"https://doi.org/10.3390/epigenomes7030022","url":null,"abstract":"<p><p>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.</p>","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}

{"title":"Environmental Epigenomes.","authors":"Bambarendage P U Perera,&nbsp;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}

{"title":"Integrated Multimodal Omics and Dietary Approaches for the Management of Neurodegeneration.","authors":"Toshiyuki Murai,&nbsp;Satoru Matsuda","doi":"10.3390/epigenomes7030020","DOIUrl":"10.3390/epigenomes7030020","url":null,"abstract":"<p><p>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.</p>","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}

{"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":"<p><p>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 (<i>p</i> < 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 <i>CLCN6</i> gene. cg08639339 was hypermethylated in smokers and lowered the metabolic rate by increasing the expression of <i>RAB29</i>; furthermore, I noted <i>TMEM120A</i> mediated the impact of smoking-cg17325771 on LDL, and <i>LTBP3</i> 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.</p>","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}

{"title":"Excessive Gestational Weight Gain Alters DNA Methylation and Influences Foetal and Neonatal Body Composition.","authors":"Perla Pizzi Argentato,&nbsp;João Victor da Silva Guerra,&nbsp;Liania Alves Luzia,&nbsp;Ester Silveira Ramos,&nbsp;Mariana Maschietto,&nbsp;Patrícia Helen de Carvalho Rondó","doi":"10.3390/epigenomes7030018","DOIUrl":"https://doi.org/10.3390/epigenomes7030018","url":null,"abstract":"<p><strong>Background: </strong>Changes in body weight are associated with the regulation of DNA methylation (DNAm). In this study, we investigated the associations between maternal gestational weight gain-related DNAm and foetal and neonatal body composition.</p><p><strong>Methods: </strong>Brazilian pregnant women from the Araraquara Cohort Study were followed up during pregnancy, delivery, and after hospital discharge. Women with normal pre-pregnancy BMI were allocated into two groups: adequate gestational weight gain (AGWG, <i>n</i> = 45) and excessive gestational weight gain (EGWG, <i>n</i> = 30). Foetal and neonatal body composition was evaluated via ultrasound and plethysmography, respectively. DNAm was assessed in maternal blood using Illumina Infinium MethylationEPIC BeadChip arrays. Linear regression models were used to explore the associations between DNAm and foetal and neonatal body composition.</p><p><strong>Results: </strong>Maternal weight, GWG, neonatal weight, and fat mass were higher in the EGWG group. Analysis of DNAm identified 46 differentially methylated positions and 11 differentially methylated regions (DMRs) between the EGWG and AGWG groups. Nine human phenotypes were enriched for these 11 DMRs located in 13 genes (<i>EMILIN1</i>, <i>HOXA5</i>, <i>CPT1B</i>, <i>CLDN9</i>, <i>ZFP57</i>, <i>BRCA1</i>, <i>POU5F1</i>, <i>ANKRD33</i>, <i>HLA-B</i>, <i>RANBP17</i>, <i>ZMYND11</i>, <i>DIP2C</i>, <i>TMEM232</i>), highlighting the terms insulin resistance, and hyperglycaemia. Maternal DNAm was associated with foetal total thigh and arm tissues and subcutaneous thigh and arm fat, as well as with neonatal fat mass percentage and fat mass.</p><p><strong>Conclusion: </strong>The methylation pattern in the EGWG group indicated a risk for developing chronic diseases and involvement of maternal DNAm in foetal lean and fat mass and in neonatal fat mass.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10443290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10057995","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}

{"title":"Ribosomal Biogenesis and Heterogeneity in Development, Disease, and Aging.","authors":"Rowshan Ara Islam, Charalampos Rallis","doi":"10.3390/epigenomes7030017","DOIUrl":"10.3390/epigenomes7030017","url":null,"abstract":"<p><p>Although reported in the literature, ribosome heterogeneity is a phenomenon whose extent and implications in cell and organismal biology is not fully appreciated. This has been the case due to the lack of the appropriate techniques and approaches. Heterogeneity can arise from alternative use and differential content of protein and RNA constituents, as well as from post-transcriptional and post-translational modifications. In the few examples we have, it is apparent that ribosomal heterogeneity offers an additional level and potential for gene expression regulation and might be a way towards tuning metabolism, stress, and growth programs to external and internal stimuli and needs. Here, we introduce ribosome biogenesis and discuss ribosomal heterogeneity in various reported occasions. We conclude that a systematic approach in multiple organisms will be needed to delineate this biological phenomenon and its contributions to growth, aging, and disease. Finally, we discuss ribosome mutations and their roles in disease.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10443367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10057997","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}

{"title":"Evaluation of Exosomal miRNA as Potential Biomarkers in Cervical Cancer.","authors":"Jéssika Aline do Nascimento Medeiros,&nbsp;Ayane Cristine Alves Sarmento,&nbsp;Emanuelly Bernardes-Oliveira,&nbsp;Ronnier de Oliveira,&nbsp;Maysa Eunice Grigorio Bezerra Lima,&nbsp;Ana Katherine Gonçalves,&nbsp;Deyse de Souza Dantas,&nbsp;Janaina Cristiana de Oliveira Crispim","doi":"10.3390/epigenomes7030016","DOIUrl":"https://doi.org/10.3390/epigenomes7030016","url":null,"abstract":"<p><p>Different studies show that small non-coding RNAs, such as microRNAs (miRNAs) obtained from exosomes, are considered potential biomarkers in several types of cancer, including cervical cancer (CC). Therefore, the present study seeks to present an overview of the role of circulating exosomal miRNAs with the potential to act as biomarkers for the diagnosis and prognosis of CC and to analyze the presence of these miRNAs according to the stage of CC. For this purpose, a review was developed, with articles consulted from the electronic databases MEDLINE/PubMed, Scopus, and Web of Science published between 2015 and 2021. Seven articles were included after a selection of studies according to the eligibility criteria. In addition to the methods used for sample analysis, detection, and isolation of miRNAs in each article, clinical data were also extracted from the patients studied, such as the stage of cancer. After analyzing the network of the seven miRNAs, they were associated with the immune system, CC progression and staging, and cisplatin resistance. With the belief that studies on miRNAs in cervical cancer would have major clinical implications, in this review, we have attempted to summarize the current situation and potential development prospects.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10443249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10432889","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}

{"title":"Association of Toll-Like Receptor Gene Polymorphisms with Tuberculosis in HIV-Positive Participants.","authors":"Svetlana Salamaikina,&nbsp;Vitaly Korchagin,&nbsp;Ekaterina Kulabukhova,&nbsp;Konstantin Mironov,&nbsp;Vera Zimina,&nbsp;Alexey Kravtchenko,&nbsp;Vasily Akimkin","doi":"10.3390/epigenomes7030015","DOIUrl":"https://doi.org/10.3390/epigenomes7030015","url":null,"abstract":"<p><p>Genetic factors in the HIV-background may play a significant role in the susceptibility to secondary diseases, like tuberculosis, which is the leading cause in mortality of HIV-positive people. Toll-like receptors (TLRs) are considered to be receptors for adaptive immunity, and polymorphisms in TLR genes can influence the activity of the immune response to infection. We conducted a case-control study of the association of TLR gene polymorphisms with the risk of tuberculosis coinfection in a multi-country sample of HIV-positive participants. Our study revealed certain associations between <i>TLR4</i> and <i>TLR6</i> polymorphisms and HIV-tuberculosis coinfection. We also found that the analyzed <i>TLR1</i> and <i>TLR4</i> polymorphisms were linked with the decline in CD4+ cell count, which is a predictor of disease progression in HIV-infected individuals. Our findings confirm that TLR gene polymorphisms are factors that may contribute to development of HIV-tuberculosis coinfection. However, the essence of the observed associations remains unclear, since it can also include both environmental factors and epigenetic mechanisms of gene expression regulation.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10443360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10048146","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}

{"title":"Epigenetic Regulation in Heterosis and Environmental Stress: The Challenge of Producing Hybrid Epigenomes to Face Climate Change.","authors":"Fátima Duarte-Aké,&nbsp;Rosa Us-Camas,&nbsp;Clelia De-la-Peña","doi":"10.3390/epigenomes7030014","DOIUrl":"https://doi.org/10.3390/epigenomes7030014","url":null,"abstract":"<p><p>Epigenetic regulation has the potential to revolutionize plant breeding and improve crop yields by regulating gene expression in plants. DNA methylation and histone modifications are key epigenetic modifications that can impact plant development, stress responses, productivity, and yields. Higher-yielding crops not only generate greater profits for farmers and seed producers, but also require less land, water, fuel, and fertilizer than traditional crops for equivalent yields. The use of heterosis in crops can influence productivity and food quality, but producing hybrids with superior agronomic traits to their parents remains challenging. However, epigenetic markers, such as histone methylation and acetylation, may help select parental and hybrid combinations with better performances than the parental plants. This review assesses the potential applications of epigenetics in crop breeding and improvement, rendering agriculture more efficient, sustainable, and adaptable to changing environmental conditions.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"7 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10366763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10251564","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}