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Journal of Genetics and Genomics = Yi... Jan 2021Decades of investigation on DNA methylation have led to deeper insights into its metabolic mechanisms and biological functions. This understanding was fueled by the... (Review)
Review
Decades of investigation on DNA methylation have led to deeper insights into its metabolic mechanisms and biological functions. This understanding was fueled by the recent development of genome editing tools and our improved capacity for analyzing the global DNA methylome in mammalian cells. This review focuses on the maintenance of DNA methylation patterns during mitotic cell division. We discuss the latest discoveries of the mechanisms for the inheritance of DNA methylation as a stable epigenetic memory. We also highlight recent evidence showing the rapid turnover of DNA methylation as a dynamic gene regulatory mechanism. A body of work has shown that altered DNA methylomes are common features in aging and disease. We discuss the potential links between methylation maintenance mechanisms and disease-associated methylation changes.
Topics: Animals; DNA Methylation; Databases, Genetic; Epigenome; Epigenomics; Gene Expression Regulation
PubMed: 33771455
DOI: 10.1016/j.jgg.2021.01.006 -
Nature Chemical Biology Aug 2023
Topics: DNA Methylation; Demethylation
PubMed: 37500897
DOI: 10.1038/s41589-023-01398-z -
Stem Cell Reviews and Reports Dec 2022Epigenetic regulation, mainly involving DNA methylation, histone modification, and noncoding RNAs (ncRNAs), is essential for the regulation of multiple cellular... (Review)
Review
Epigenetic regulation, mainly involving DNA methylation, histone modification, and noncoding RNAs (ncRNAs), is essential for the regulation of multiple cellular processes. Dental-derived mesenchymal stem cells (DMSCs), a kind of multipotent cells derived from dental tissues, are impactful in regenerative medicine. Recent studies have shown that epigenetic regulation plays a major role in DMSCs. Therefore, exploring how epigenetic regulation is involved in DMSCs may be of guiding significance for tissue repair and regeneration or for exploring more effective treatments. A number of research of ncRNAs in DMSCs have been reported. However, little is known about the roles of DNA methylation and histone modifications in DMSCs. In this review, we summarize the important roles of DNA methylation and histone modifications of the fate of DMSCs.
Topics: DNA Methylation; Epigenesis, Genetic; Histone Code; Mesenchymal Stem Cells; Multipotent Stem Cells; RNA, Untranslated
PubMed: 35896859
DOI: 10.1007/s12015-022-10413-0 -
ELife Mar 2024A technique called mSTARR-seq sheds light on how DNA methylation may shape responses to external stimuli by altering the activity of sequences that control gene...
A technique called mSTARR-seq sheds light on how DNA methylation may shape responses to external stimuli by altering the activity of sequences that control gene expression.
Topics: Epigenesis, Genetic; DNA Methylation; Gene Expression Regulation
PubMed: 38497535
DOI: 10.7554/eLife.96710 -
Chemical Communications (Cambridge,... Nov 2022Since DNA methylation alters the chromatin state and regulates gene expression, elucidating the regulatory mechanisms of DNA methylation in response to environmental...
Since DNA methylation alters the chromatin state and regulates gene expression, elucidating the regulatory mechanisms of DNA methylation in response to environmental changes in the cell is crucial and urgent in understanding and regulating DNA methylation. G-quadruplex (G4) regulates transcription, translation and replication. Although it has recently been suggested that G4 regulates methylation, the detailed regulatory mechanism remains unclear. Here, we systematically analysed the effect of G4 formation on DNA methylation using G4s with various stabilities and topologies. The methylation efficiency decreased as the stability of G4 increased. Moreover, the degree of methylation suppression can be also controlled by G4 topology. Furthermore, our results showed the possibility of regulating methylation by modulating G4 stability and topology.
Topics: DNA Methylation; G-Quadruplexes
PubMed: 36263745
DOI: 10.1039/d2cc04383a -
Genes May 2022Nutrient stress as abiotic stress has become one of the important factors restricting crop yield and quality. DNA methylation is an essential epigenetic modification... (Review)
Review
Nutrient stress as abiotic stress has become one of the important factors restricting crop yield and quality. DNA methylation is an essential epigenetic modification that can effectively regulate genome stability. Exploring DNA methylation responses to nutrient stress could lay the foundation for improving plant tolerance to nutrient stress. This article summarizes the plant DNA methylation patterns, the effects of nutrient stress, such as nitrogen, phosphorus, iron, zinc and sulfur stress, on plant DNA methylation and research techniques for plant DNA methylation, etc. Our discussion provides insight for further research on epigenetics response to nutrient stress in the future.
Topics: DNA Methylation; DNA, Plant; Gene Expression Regulation, Plant; Nutrients; Plants
PubMed: 35741754
DOI: 10.3390/genes13060992 -
Experimental Eye Research Oct 2021DNA methylation is important in developing and post-mitotic cells in various tissues. Recent studies have shown that DNA methylation is highly dynamic, and plays... (Review)
Review
DNA methylation is important in developing and post-mitotic cells in various tissues. Recent studies have shown that DNA methylation is highly dynamic, and plays important roles during retinal development and aging. In addition, the dynamic regulation of DNA methylation is involved in the occurrence and development of age-related macular degeneration and diabetic retinopathy and shows potential in disease diagnoses and prognoses. This review introduces the epigenetic concepts of DNA methylation and demethylation with an emphasis on their regulatory roles in retinal development and related diseases. Moreover, we propose exciting ideas such as its crosstalk with other epigenetic modifications and retinal regeneration, to provide a potential direction for understanding retinal diseases from the epigenetic perspective.
Topics: Animals; DNA Methylation; Diabetic Retinopathy; Epigenesis, Genetic; Humans; Macular Degeneration; Retina
PubMed: 34418429
DOI: 10.1016/j.exer.2021.108733 -
Journal of Translational Medicine Mar 2023Fibrosis, a process caused by excessive deposition of extracellular matrix (ECM), is a common cause and outcome of organ failure and even death. Researchers have made... (Review)
Review
Fibrosis, a process caused by excessive deposition of extracellular matrix (ECM), is a common cause and outcome of organ failure and even death. Researchers have made many efforts to understand the mechanism of fibrogenesis and to develop therapeutic strategies; yet, the outcome remains unsatisfactory. In recent years, advances in epigenetics, including chromatin remodeling, histone modification, DNA methylation, and noncoding RNA (ncRNA), have provided more insights into the fibrotic process and have suggested the possibility of novel therapy for organ fibrosis. In this review, we summarize the current research on the epigenetic mechanisms involved in organ fibrosis and their possible clinical applications.
Topics: Humans; Epigenesis, Genetic; DNA Methylation; Extracellular Matrix; Protein Processing, Post-Translational; Research Personnel
PubMed: 36864460
DOI: 10.1186/s12967-023-04018-5 -
Molecular Biology Reports Sep 2023DNA methylation and demethylation are widely acknowledged epigenetic phenomena which can cause heritable and phenotypic changes in functional genes without changing the... (Review)
Review
DNA methylation and demethylation are widely acknowledged epigenetic phenomena which can cause heritable and phenotypic changes in functional genes without changing the DNA sequence. They can thus affect phenotype formation in medicinal plants. However, a comprehensive review of the literature summarizing current research trends in this field is lacking. Thus, this review aims to provide an up-to-date summary of current methods for the detection of 5-mC DNA methylation, identification and analysis of DNA methyltransferases and demethyltransferases, and regulation of DNA methylation in medicinal plants. The data showed that polyploidy and environmental changes can affect DNA methylation levels in medicinal plants. Changes in DNA methylation can thus regulate plant morphogenesis, growth and development, and formation of secondary metabolites. Future research is required to explore the mechanisms by which DNA methylation regulates the accumulation of secondary metabolites in medicinal plants.
Topics: Plants, Medicinal; DNA Methylation; DNA Modification Methylases; Epigenomics; Demethylation
PubMed: 37480509
DOI: 10.1007/s11033-023-08618-8 -
Plant Cell Reports Oct 2022DNA methylation is a dynamic epigenetic mechanism that plays a significant role in gene expression and also maintains chromatin stability. The process is conserved in... (Review)
Review
DNA methylation is a dynamic epigenetic mechanism that plays a significant role in gene expression and also maintains chromatin stability. The process is conserved in both plants and animals, and crucial for development and stress responses. Differential DNA methylation during adverse environmental conditions or pathogen attack facilitates the selective expression of defense-related genes. Both stress-induced DNA hypomethylation and hypermethylation play beneficial roles in activating the defense response. These DNA marks may be carried to the next generation making the progenies 'primed' for abiotic and biotic stress responses. Over the recent years, rapid advancements in the area of high throughput sequencing have enabled the detection of methylation status at genome levels in several plant species. Epigenotyping offers an alternative tool to plant breeders in addition to conventional markers for the selection of the desired offspring. In this review, we briefly discuss the mechanism of DNA methylation, recent understanding of DNA methylation-mediated gene regulation during abiotic and biotic stress responses, and stress memory in plants.
Topics: Animals; Chromatin; DNA Methylation; Epigenesis, Genetic; Gene Expression Regulation, Plant; Plants; Stress, Physiological
PubMed: 35833989
DOI: 10.1007/s00299-022-02901-x