scholarly journals The Role of DNA Methylation in Perennial Plants

2019 ◽  
Vol 11 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Lia BASDEKI ◽  
Marianna HAGIDIMITRIOU
Keyword(s):  
Dna Methylation ◽  
Developmental Stages ◽  
Epigenetic Modification ◽  
Fruit Trees ◽  
Bud Dormancy ◽  
Perennial Plants ◽  
Flavonoid Compounds ◽  
Epigenetic Diversity

DNA methylation is an important epigenetic modification of the genome in all organisms. This review presents the effect of DNA methylation in perennial fruit trees such as chestnut, apple, peach etc. In particular, DNA methylation has been shown to affect bud dormancy, the changes of developmental stages such as: flowering, the synthesis of anthocyanins, among other flavonoid compounds; it also affects the fertilization and perpetuation of many fruit trees. Finally, DNA methylation can be used as a tool for investigating the epigenetic diversity of a species.

scholarly journals DNA Methyltransferase 3A Is Involved in the Sustained Effects of Chronic Stress on Synaptic Functions and Behaviors

2020 ◽  
Author(s):  
Jing Wei ◽  
Jia Cheng ◽  
Nicholas J Waddell ◽  
Zi-Jun Wang ◽  
Xiaodong Pang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Epigenetic Modification ◽  
Substantial Reduction ◽  
Dna Methyltransferases ◽  
Male Rats ◽  
Neural Pathways ◽  
Dnmt Inhibitors ◽  
Synaptic Functions

Abstract Emerging evidence suggests that epigenetic mechanisms regulate aberrant gene transcription in stress-associated mental disorders. However, it remains to be elucidated about the role of DNA methylation and its catalyzing enzymes, DNA methyltransferases (DNMTs), in this process. Here, we found that male rats exposed to chronic (2-week) unpredictable stress exhibited a substantial reduction of Dnmt3a after stress cessation in the prefrontal cortex (PFC), a key target region of stress. Treatment of unstressed control rats with DNMT inhibitors recapitulated the effect of chronic unpredictable stress on decreased AMPAR expression and function in PFC. In contrast, overexpression of Dnmt3a in PFC of stressed animals prevented the loss of glutamatergic responses. Moreover, the stress-induced behavioral abnormalities, including the impaired recognition memory, heightened aggression, and hyperlocomotion, were partially attenuated by Dnmt3a expression in PFC of stressed animals. Finally, we found that there were genome-wide DNA methylation changes and transcriptome alterations in PFC of stressed rats, both of which were enriched at several neural pathways, including glutamatergic synapse and microtubule-associated protein kinase signaling. These results have therefore recognized the potential role of DNA epigenetic modification in stress-induced disturbance of synaptic functions and cognitive and emotional processes.

scholarly journals DNA Methylation: A Promising Approach in Management of Alzheimer’s Disease and Other Neurodegenerative Disorders

Biology ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 90
Author(s):  
Gagandeep Kaur ◽  
Suraj Singh S. Rathod ◽  
Mohammed M. Ghoneim ◽  
Sultan Alshehri ◽  
Javed Ahmad ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Dna Methylation ◽  
Neurodegenerative Diseases ◽  
Epigenetic Modification ◽  
Research Area ◽  
Potential Biomarker ◽  
Novel Biomarkers ◽  
Different Populations

DNA methylation, in the mammalian genome, is an epigenetic modification that involves the transfer of a methyl group on the C5 position of cytosine to derive 5-methylcytosine. The role of DNA methylation in the development of the nervous system and the progression of neurodegenerative diseases such as Alzheimer’s disease has been an interesting research area. Furthermore, mutations altering DNA methylation affect neurodevelopmental functions and may cause the progression of several neurodegenerative diseases. Epigenetic modifications in neurodegenerative diseases are widely studied in different populations to uncover the plausible mechanisms contributing to the development and progression of the disease and detect novel biomarkers for early prognosis and future pharmacotherapeutic targets. In this manuscript, we summarize the association of DNA methylation with the pathogenesis of the most common neurodegenerative diseases, such as, Alzheimer’s disease, Parkinson’s disease, Huntington diseases, and amyotrophic lateral sclerosis, and discuss the potential of DNA methylation as a potential biomarker and therapeutic tool for neurogenerative diseases.

scholarly journals The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development

2020 ◽  
Vol 10 (9) ◽  
pp. 3337-3346
Author(s):  
Yijia Zhou ◽  
Funan He ◽  
Weilin Pu ◽  
Xun Gu ◽  
Jiucun Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mutation Rate ◽  
Germline Mutation ◽  
Developmental Stages ◽  
Rare Variants ◽  
Epigenetic Modification ◽  
Genome Project ◽  
Germline Development ◽  
Cpg Sites ◽  
The Impact

Abstract DNA methylation is a dynamic epigenetic modification found in most eukaryotic genomes. It is known to lead to a high CpG to TpG mutation rate. However, the relationship between the methylation dynamics in germline development and the germline mutation rate remains unexplored. In this study, we used whole genome bisulfite sequencing (WGBS) data of cells at 13 stages of human germline development and rare variants from the 1000 Genome Project as proxies for germline mutations to investigate the correlation between dynamic methylation levels and germline mutation rates at different scales. At the single-site level, we found a significant correlation between methylation and the germline point mutation rate at CpG sites during germline developmental stages. Then we explored the mutability of methylation dynamics in all stages. Our results also showed a broad correlation between the regional methylation level and the rate of C > T mutation at CpG sites in all genomic regions, especially in intronic regions; a similar link was also seen at all chromosomal levels. Our findings indicate that the dynamic DNA methylome during human germline development has a broader mutational impact than is commonly assumed.

scholarly journals The Role of Host Cell DNA Methylation in the Immune Response to Bacterial Infection

2021 ◽  
Vol 12 ◽  
Author(s):  
Wanhai Qin ◽  
Brendon P. Scicluna ◽  
Tom van der Poll
Keyword(s):  
Dna Methylation ◽  
Immune Response ◽  
Bacterial Infection ◽  
Epigenetic Modification ◽  
Dna Methyltransferases ◽  
Host Cells ◽  
Regulate Gene Expression ◽  
Transcriptional Reprogramming ◽  
Methylation Patterns

Host cells undergo complex transcriptional reprogramming upon infection. Epigenetic changes play a key role in the immune response to bacteria, among which DNA modifications that include methylation have received much attention in recent years. The extent of DNA methylation is well known to regulate gene expression. Whilst historically DNA methylation was considered to be a stable epigenetic modification, accumulating evidence indicates that DNA methylation patterns can be altered rapidly upon exposure of cells to changing environments and pathogens. Furthermore, the action of proteins regulating DNA methylation, particularly DNA methyltransferases and ten-eleven translocation methylcytosine dioxygenases, may be modulated, at least in part, by bacteria. This review discusses the principles of DNA methylation, and recent insights about the regulation of host DNA methylation during bacterial infection.

scholarly journals Adiponectin Related Vascular and Cardiac Benefits in Obesity: Is There a Role for an Epigenetically Regulated Mechanism?

2021 ◽  
Vol 8 ◽  
Author(s):  
Rosaria Anna Fontanella ◽  
Lucia Scisciola ◽  
Maria Rosaria Rizzo ◽  
Surina Surina ◽  
Celestino Sardu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Blood Cells ◽  
Epigenetic Modification ◽  
Surrogate Marker ◽  
Left Ventricular ◽  
Epigenetic Modifications ◽  
Left Ventricular Ejection ◽  
Ventricular Ejection Fraction ◽  
Plasma Mirna

In obesity, several epigenetic modifications, including histones remodeling, DNA methylation, and microRNAs, could accumulate and determine increased expression of inflammatory molecules, the adipokines, that in turn might induce or accelerate the onset and development of cardiovascular and metabolic disorders. In order to better clarify the potential epigenetic mechanisms underlying the modulation of the inflammatory response by adipokines, the DNA methylation profile in peripheral leukocytes of the promoter region of IL-6 and NF-kB genes and plasma miRNA-21 levels were evaluated in 356 healthy subjects, using quantitative pyrosequencing-based analysis, and correlated with plasma adiponectin levels, body fat content and the primary pro-inflammatory markers. In addition, correlation analysis of DNA methylation profiles and miRNA-21 plasma levels with intima-media thickness (IMT), a surrogate marker for early atherosclerosis, left ventricular mass (LVM), left ventricular ejection fraction (LVEF), and cardiac performance index (MPI) was also performed to evaluate any potential clinical implication in terms of cardiovascular outcome. Results achieved confirmed the role of epigenetics in the obesity-related cardiovascular complications and firstly supported the potential role of plasma miRNA-21 and IL-6 and NF-kB DNA methylation changes in nucleated blood cells as potential biomarkers for predicting cardiovascular risk in obesity. Furthermore, our results, showing a role of adiponectin in preventing epigenetic modification induced by increased adipose tissue content in obese subjects, provide new evidence of an additional mechanism underlying the anti-inflammatory properties and the cardiovascular benefits of adiponectin. The exact mechanisms underlying the obesity-related epigenetic modifications found in the blood cells and whether similar epigenetic changes reflect adipose and myocardial tissue modifications need to be further investigated in future experiments.

scholarly journals Title: Hypermethylation of miRNA Genes During Nodule Development

2021 ◽  
Vol 8 ◽  
Author(s):  
Sarbottam Piya ◽  
Valeria S. Lopes-Caitar ◽  
Won‐Seok Kim ◽  
Vince Pantalone ◽  
Hari B. Krishnan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Developmental Stages ◽  
Nodule Development ◽  
Nodule Formation ◽  
Primary Transcript ◽  
Cellular Processes ◽  
Mirna Genes ◽  
Root Tissues ◽  
Methylation Patterns

DNA methylation has recently emerged as a powerful regulatory mechanism controlling the expression of key regulators of various developmental processes, including nodulation. However, the functional role of DNA methylation in regulating the expression of microRNA (miRNA) genes during the formation and development of nitrogen-fixing nodules remains largely unknown. In this study, we profiled DNA methylation patterns of miRNA genes during nodule formation, development, and early senescence stages in soybean (Glycine max) through the analysis of methylC—seq data. Absolute DNA methylation levels in the CG, CHH, and CHH sequence contexts over the promoter and primary transcript regions of miRNA genes were significantly higher in the nodules compared with the corresponding root tissues at these three distinct nodule developmental stages. We identified a total of 82 differentially methylated miRNAs in the nodules compared with roots. Differential DNA methylation of these 82 miRNAs was detected only in the promoter (69), primary transcript region (3), and both in the promoter and primary transcript regions (10). The large majority of these differentially methylated miRNAs were hypermethylated in nodules compared with the corresponding root tissues and were found mainly in the CHH context and showed stage-specific methylation patterns. Differentially methylated regions in the promoters of 25 miRNAs overlapped with transposable elements, a finding that may explain the vulnerability of miRNAs to DNA methylation changes during nodule development. Gene expression analysis of a set of promoter-differentially methylated miRNAs pointed to a negative association between DNA methylation and miRNA expression. Gene Ontology and pathways analyses indicate that changes in DNA methylation of miRNA genes are reprogrammed and contribute to nodule development through indirect regulation of genes involved in cellular processes and pathways with well-established roles in nodulation.

scholarly journals DNA methylation in germ cell tumour aetiology: current understanding and outstanding questions

Reproduction ◽  
2013 ◽  
Vol 146 (2) ◽  
pp. R49-R60 ◽  
Author(s):  
Martin Cusack ◽  
Paul Scotting
Keyword(s):  
Dna Methylation ◽  
Germ Cell ◽  
Epigenetic Modification ◽  
Germ Cell Tumour ◽  
Genome Wide ◽  
Recent Developments ◽  
Methylator Phenotype ◽  
Aberrant Dna Methylation ◽  
Promoter Region Hypermethylation

Germ cell tumours (GCTs) are a diverse group of neoplasms that can be histologically subclassified as either seminomatous or non-seminomatous. These two subtypes have distinct levels of differentiation and clinical characteristics, the non-seminomatous tumours being associated with poorer prognosis. In this article, we review how different patterns of aberrant DNA methylation relate to these subtypes. Aberrant DNA methylation is a hallmark of all human cancers, but particular subsets of cancers show unusually high frequencies of promoter region hypermethylation. Such a ‘methylator phenotype’ has been described in non-seminomatous tumours. We discuss the possible cause of distinct methylation profiles in GCTs and the potential of DNA methylation to provide new targets for therapy. We also consider how recent developments in our understanding of this epigenetic modification and the development of genome-wide technologies are shedding new light on the role of DNA methylation in cancer aetiology.

scholarly journals Multifaceted Roles of DNA Methylation in Neoplastic Transformation, from Tumor Suppressors to EMT and Metastasis

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 922 ◽  
Author(s):  
Laura Casalino ◽  
Pasquale Verde
Keyword(s):  
Dna Methylation ◽  
Cancer Cell ◽  
Tumor Suppressors ◽  
Epigenetic Modification ◽  
Dna Methyltransferases ◽  
Potential Contribution ◽  
Epigenetic Changes ◽  
Dna Hypomethylation ◽  
Mesenchymal Transition

Among the major mechanisms involved in tumorigenesis, DNA methylation is an important epigenetic modification impacting both genomic stability and gene expression. Methylation of promoter-proximal CpG islands (CGIs) and transcriptional silencing of tumor suppressors represent the best characterized epigenetic changes in neoplastic cells. The global cancer-associated effects of DNA hypomethylation influence chromatin architecture and reactivation of repetitive elements. Moreover, recent analyses of cancer cell methylomes highlight the role of the DNA hypomethylation of super-enhancer regions critically controlling the expression of key oncogenic players. We will first summarize some basic aspects of DNA methylation in tumorigenesis, along with the role of dysregulated DNA methyltransferases and TET (Ten-Eleven Translocation)-family methylcytosine dioxygenases. We will then examine the potential contribution of epimutations to causality and heritability of cancer. By reviewing some representative genes subjected to hypermethylation-mediated silencing, we will survey their oncosuppressor functions and roles as biomarkers in various types of cancer. Epithelial-to-mesenchymal transition (EMT) and the gain of stem-like properties are critically involved in cancer cell dissemination, metastasis, and therapeutic resistance. However, the driver vs passenger roles of epigenetic changes, such as DNA methylation in EMT, are still poorly understood. Therefore, we will focus our attention on several aspects of DNA methylation in control of EMT and metastasis suppressors, including both protein-coding and noncoding genes.

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