Epigenomes最新文献_第9页

The Histone H3 K4me3, K27me3, and K27ac Genome-Wide Distributions Are Differently Influenced by Sex in Brain Cortexes and Gastrocnemius of the Alzheimer's Disease PSAPP Mouse Model. 阿尔茨海默病papp小鼠脑皮质和腓肠肌组蛋白H3、K4me3、K27me3和K27ac全基因组分布受性别影响

IF 2.5

Epigenomes Pub Date : 2021-11-25 DOI: 10.3390/epigenomes5040026

Francesca Casciaro, Giuseppe Persico, Martina Rusin, Stefano Amatori, Claire Montgomery, Jennifer R Rutkowsky, Jon J Ramsey, Gino Cortopassi, Mirco Fanelli, Marco Giorgio

{"title":"The Histone H3 K4me3, K27me3, and K27ac Genome-Wide Distributions Are Differently Influenced by Sex in Brain Cortexes and Gastrocnemius of the Alzheimer's Disease PSAPP Mouse Model.","authors":"Francesca Casciaro, Giuseppe Persico, Martina Rusin, Stefano Amatori, Claire Montgomery, Jennifer R Rutkowsky, Jon J Ramsey, Gino Cortopassi, Mirco Fanelli, Marco Giorgio","doi":"10.3390/epigenomes5040026","DOIUrl":"https://doi.org/10.3390/epigenomes5040026","url":null,"abstract":"Background: Women represent the majority of Alzheimer's disease patients and show typical symptoms. Genetic, hormonal, and behavioral mechanisms have been proposed to explain sex differences in dementia prevalence. However, whether sex differences exist in the epigenetic landscape of neuronal tissue during the progression of the disease is still unknown.Methods: To investigate the differences of histone H3 modifications involved in transcription, we determined the genome-wide profiles of H3K4me3, H3K27ac, and H3K27me3 in brain cortexes of an Alzheimer mouse model (PSAPP). Gastrocnemius muscles were also tested since they are known to be different in the two sexes and are affected during the disease progression.Results: Correlation analysis distinguished the samples based on sex for H3K4me3 and H3K27me3 but not for H3K27ac. The analysis of transcription starting sites (TSS) signal distribution, and analysis of bounding sites revealed that gastrocnemius is more influenced than brain by sex for the three histone modifications considered, exception made for H3K27me3 distribution on the X chromosome which showed sex-related differences in promoters belonging to behavior and cellular or neuronal spheres in mice cortexes.Conclusions: H3K4me3, H3K27ac, and H3K27me3 signals are slightly affected by sex in brain, with the exception of H3K27me3, while a higher number of differences can be found in gastrocnemius.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"5 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2021-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8715457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39772997","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: 3

Epigenetic Modifications in Plant Development and Reproduction. 植物发育和繁殖中的表观遗传修饰。

IF 2.5

Epigenomes Pub Date : 2021-11-19 DOI: 10.3390/epigenomes5040025

Vladimir Brukhin, Emidio Albertini

{"title":"Epigenetic Modifications in Plant Development and Reproduction.","authors":"Vladimir Brukhin, Emidio Albertini","doi":"10.3390/epigenomes5040025","DOIUrl":"https://doi.org/10.3390/epigenomes5040025","url":null,"abstract":"Plants are exposed to highly fluctuating effects of light, temperature, weather conditions, and many other environmental factors throughout their life. As sessile organisms, unlike animals, they are unable to escape, hide, or even change their position. Therefore, the growth and development of plants are largely determined by interaction with the external environment. The success of this interaction depends on the ability of the phenotype plasticity, which is largely determined by epigenetic regulation. In addition to how environmental factors can change the patterns of genes expression, epigenetic regulation determines how genetic expression changes during the differentiation of one cell type into another and how patterns of gene expression are passed from one cell to its descendants. Thus, one genome can generate many 'epigenomes'. Epigenetic modifications acquire special significance during the formation of gametes and plant reproduction when epigenetic marks are eliminated during meiosis and early embryogenesis and later reappear. However, during asexual plant reproduction, when meiosis is absent or suspended, epigenetic modifications that have arisen in the parental sporophyte can be transmitted to the next clonal generation practically unchanged. In plants that reproduce sexually and asexually, epigenetic variability has different adaptive significance. In asexuals, epigenetic regulation is of particular importance for imparting plasticity to the phenotype when, apart from mutations, the genotype remains unchanged for many generations of individuals. Of particular interest is the question of the possibility of transferring acquired epigenetic memory to future generations and its potential role for natural selection and evolution. All these issues will be discussed to some extent in this review.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"5 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2021-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8715465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39772996","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: 6

The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator. 植物营养相变和返老还童的调控:mirna，一个关键的调控因子。

IF 2.5

Epigenomes Pub Date : 2021-10-18 DOI: 10.3390/epigenomes5040024

Tajbir Raihan, Robert L Geneve, Sharyn E Perry, Carlos M Rodriguez Lopez

{"title":"The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator.","authors":"Tajbir Raihan, Robert L Geneve, Sharyn E Perry, Carlos M Rodriguez Lopez","doi":"10.3390/epigenomes5040024","DOIUrl":"https://doi.org/10.3390/epigenomes5040024","url":null,"abstract":"In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can reverse the otherwise unidirectional vector of plant development. Epigenetic factors regulating gene expression in response to internal cues and external (environmental) stimuli influencing the plant's phenotype and development have been shown to control phase transitions. How developmental and environmental cues interact to epigenetically alter gene expression and influence these transitions is not well understood, and understanding this interaction is important considering the current climate change scenarios, since epigenetic maladaptation could have catastrophic consequences for perennial plants in natural and agricultural ecosystems. Here, we review studies focusing on the epigenetic regulators of the vegetative phase change and highlight how these mechanisms might act in exogenously induced plant rejuvenation and regrowth following stress.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"5 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2021-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8715473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39772995","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: 6

One Omics Approach Does Not Rule Them All: The Metabolome and the Epigenome Join Forces in Haematological Malignancies. 一组学方法不能控制所有:代谢组学和表观基因组在血液恶性肿瘤中的联合作用。

IF 2.5

Epigenomes Pub Date : 2021-10-08 DOI: 10.3390/epigenomes5040022

Antonia Kalushkova, Patrick Nylund, Alba Atienza Párraga, Andreas Lennartsson, Helena Jernberg-Wiklund

{"title":"One Omics Approach Does Not Rule Them All: The Metabolome and the Epigenome Join Forces in Haematological Malignancies.","authors":"Antonia Kalushkova, Patrick Nylund, Alba Atienza Párraga, Andreas Lennartsson, Helena Jernberg-Wiklund","doi":"10.3390/epigenomes5040022","DOIUrl":"https://doi.org/10.3390/epigenomes5040022","url":null,"abstract":"Aberrant DNA methylation, dysregulation of chromatin-modifying enzymes, and microRNAs (miRNAs) play a crucial role in haematological malignancies. These epimutations, with an impact on chromatin accessibility and transcriptional output, are often associated with genomic instability and the emergence of drug resistance, disease progression, and poor survival. In order to exert their functions, epigenetic enzymes utilize cellular metabolites as co-factors and are highly dependent on their availability. By affecting the expression of metabolic enzymes, epigenetic modifiers may aid the generation of metabolite signatures that could be utilized as targets and biomarkers in cancer. This interdependency remains often neglected and poorly represented in studies, despite well-established methods to study the cellular metabolome. This review critically summarizes the current knowledge in the field to provide an integral picture of the interplay between epigenomic alterations and the cellular metabolome in haematological malignancies. Our recent findings defining a distinct metabolic signature upon response to enhancer of zeste homolog 2 (EZH2) inhibition in multiple myeloma (MM) highlight how a shift of preferred metabolic pathways may potentiate novel treatments. The suggested link between the epigenome and the metabolome in haematopoietic tumours holds promise for the use of metabolic signatures as possible biomarkers of response to treatment.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"5 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2021-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8715477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39772998","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: 1

Role of Enhancers in Development and Diseases. 增强剂在发育和疾病中的作用。

IF 2.5

Epigenomes Pub Date : 2021-10-04 DOI: 10.3390/epigenomes5040021

Shailendra S Maurya

{"title":"Role of Enhancers in Development and Diseases.","authors":"Shailendra S Maurya","doi":"10.3390/epigenomes5040021","DOIUrl":"https://doi.org/10.3390/epigenomes5040021","url":null,"abstract":"Enhancers are cis-regulatory elements containing short DNA sequences that serve as binding sites for pioneer/regulatory transcription factors, thus orchestrating the regulation of genes critical for lineage determination. The activity of enhancer elements is believed to be determined by transcription factor binding, thus determining the cell state identity during development. Precise spatio-temporal control of the transcriptome during lineage specification requires the coordinated binding of lineage-specific transcription factors to enhancers. Thus, enhancers are the primary determinants of cell identity. Numerous studies have explored the role and mechanism of enhancers during development and disease, and various basic questions related to the functions and mechanisms of enhancers have not yet been fully answered. In this review, we discuss the recently published literature regarding the roles of enhancers, which are critical for various biological processes governing development. Furthermore, we also highlight that altered enhancer landscapes provide an essential context to understand the etiologies and mechanisms behind numerous complex human diseases, providing new avenues for effective enhancer-based therapeutic interventions.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"5 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2021-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8715447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39772994","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: 5

Clinical Utility of Epigenetic Changes in Pancreatic Adenocarcinoma. 胰腺癌表观遗传学改变的临床应用。

IF 2.5

Epigenomes Pub Date : 2021-09-27 DOI: 10.3390/epigenomes5040020

Joyce K Thompson, Filip Bednar

引用次数: 3

Evolution of CG Methylation Maintenance Machinery in Plants. 植物CG甲基化维持机制的进化。

IF 2.5

Epigenomes Pub Date : 2021-09-14 DOI: 10.3390/epigenomes5030019

Louis Tirot, Pauline E Jullien, Mathieu Ingouff

引用次数: 10

Epigenetic Analyses of Alcohol Consumption in Combustible and Non-Combustible Nicotine Product Users. 可燃和非可燃尼古丁产品使用者酒精消费的表观遗传分析。

IF 2.5

Epigenomes Pub Date : 2021-09-01 DOI: 10.3390/epigenomes5030018

Kelsey Dawes, Luke Sampson, Rachel Reimer, Shelly Miller, Robert Philibert, Allan Andersen

{"title":"Epigenetic Analyses of Alcohol Consumption in Combustible and Non-Combustible Nicotine Product Users.","authors":"Kelsey Dawes, Luke Sampson, Rachel Reimer, Shelly Miller, Robert Philibert, Allan Andersen","doi":"10.3390/epigenomes5030018","DOIUrl":"https://doi.org/10.3390/epigenomes5030018","url":null,"abstract":"Alcohol and tobacco use are highly comorbid and exacerbate the associated morbidity and mortality of either substance alone. However, the relationship of alcohol consumption to the various forms of nicotine-containing products is not well understood. To improve this understanding, we examined the relationship of alcohol consumption to nicotine product use using self-report, cotinine, and two epigenetic biomarkers specific for smoking (cg05575921) and drinking (Alcohol T Scores (ATS)) in n = 424 subjects. Cigarette users had significantly higher ATS values than the other groups (p < 2.2 × 10-16). Using the objective biomarkers, the intensity of nicotine and alcohol consumption was correlated in both the cigarette and smokeless users (R = -0.66, p = 3.1 × 10-14; R2 = 0.61, p = 1.97 × 10-4). Building upon this idea, we used the objective nicotine biomarkers and age to build and test a Balanced Random Forest classification model for heavy alcohol consumption (ATS > 2.35). The model performed well with an AUC of 0.962, 89.3% sensitivity, and 85% specificity. We conclude that those who use non-combustible nicotine products drink significantly less than smokers, and cigarette and smokeless users drink more with heavier nicotine use. These findings further highlight the lack of informativeness of self-reported alcohol consumption and suggest given the public and private health burden of alcoholism, further research into whether using non-combustible nicotine products as a mode of treatment for dual users should be considered.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"5 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39650235","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: 4

Deciphering Plant Chromatin Regulation via CRISPR/dCas9-Based Epigenome Engineering. 基于CRISPR/ dcas9的表观基因组工程解读植物染色质调控

IF 2.5

Epigenomes Pub Date : 2021-08-24 DOI: 10.3390/epigenomes5030017

Annick Dubois, François Roudier

{"title":"Deciphering Plant Chromatin Regulation via CRISPR/dCas9-Based Epigenome Engineering.","authors":"Annick Dubois, François Roudier","doi":"10.3390/epigenomes5030017","DOIUrl":"https://doi.org/10.3390/epigenomes5030017","url":null,"abstract":"CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss how recent progress in plants and animals provides new routes to investigate the function of chromatin regulators and address the complexity of associated regulations that are often interconnected. While efficient transcriptional engineering methodologies have been developed and can be used as tools to alter the chromatin state of a locus, examples of direct manipulation of chromatin regulators remain scarce in plants. These reports also reveal pitfalls and limitations of epigenome engineering approaches that are nevertheless informative as they are often associated with locus- and context-dependent features, which include DNA accessibility, initial chromatin and transcriptional state or cellular dynamics. Strategies implemented in different organisms to overcome and even take advantage of these limitations are highlighted, which will further improve our ability to establish the causality and hierarchy of chromatin dynamics on genome regulation.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"5 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2021-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39650233","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: 4

Can Immune Suppression and Epigenome Regulation in Placenta Offer Novel Insights into Cancer Immune Evasion and Immunotherapy Resistance? 胎盘中的免疫抑制和表观基因组调控能否为癌症免疫逃避和免疫疗法抗性提供新的见解？

IF 2.5

Epigenomes Pub Date : 2021-07-25 DOI: 10.3390/epigenomes5030016

Sultana Mehbuba Hossain, Chiemi F Lynch-Sutherland, Aniruddha Chatterjee, Erin C Macaulay, Michael R Eccles

{"title":"Can Immune Suppression and Epigenome Regulation in Placenta Offer Novel Insights into Cancer Immune Evasion and Immunotherapy Resistance?","authors":"Sultana Mehbuba Hossain, Chiemi F Lynch-Sutherland, Aniruddha Chatterjee, Erin C Macaulay, Michael R Eccles","doi":"10.3390/epigenomes5030016","DOIUrl":"10.3390/epigenomes5030016","url":null,"abstract":"Cancer is the second leading cause of mortality and morbidity in the developed world. Cancer progression involves genetic and epigenetic alterations, accompanied by aggressive changes, such as increased immune evasion, onset of metastasis, and drug resistance. Similar to cancer, DNA hypomethylation, immune suppression, and invasive cell behaviours are also observed in the human placenta. Mechanisms that lead to the acquisition of invasive behaviour, immune evasion, and drug and immunotherapy resistance are presently under intense investigations to improve patient outcomes. Here, we review current knowledge regarding the similarities between immune suppression and epigenome regulation, including the expression of repetitive elements (REs), endogenous retroviruses (ERVs) and transposable elements (TEs) in cells of the placenta and in cancer, which are associated with changes in immune regulation and invasiveness. We explore whether immune suppression and epigenome regulation in placenta offers novel insights into immunotherapy resistance in cancer, and we also discuss the implications and the knowledge gaps relevant to these findings, which are rapidly being accrued in these quite disparate research fields. Finally, we discuss potential linkages between TE, ERV and RE activation and expression, regarding mechanisms of immune regulation in placenta and cancer. A greater understanding of the role of immune suppression and associated epigenome regulation in placenta could help to elucidate some comparable mechanisms operating in cancer, and identify potential new therapeutic targets for treating cancer.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"5 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2021-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39650234","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