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Current Opinion in Plant Biology Aug 2022Cytosine is methylated in both CpG and non-CpG contexts (mCG and mCH, respectively) in plant genomes. Although mCG and mCH are almost independent in regard to their... (Review)
Review
Cytosine is methylated in both CpG and non-CpG contexts (mCG and mCH, respectively) in plant genomes. Although mCG and mCH are almost independent in regard to their "maintenance," recent studies uncovered crosstalk between them during their "establishment," which unexpectedly functions in both RNAi-dependent and -independent pathways. In addition, the importance of linker histone H1 and variants of histone H2A to DNA methylation dynamics is starting to be understood. We summarize these new aspects of mechanisms to generate DNA methylomes and discuss future prospects.
Topics: DNA Methylation; Epigenome
PubMed: 35724481
DOI: 10.1016/j.pbi.2022.102248 -
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 -
Critical Reviews in Biochemistry and... 2016Over the past decade, since epigenetic mechanisms were first implicated in memory formation and synaptic plasticity, dynamic DNA methylation reactions have been... (Review)
Review
Over the past decade, since epigenetic mechanisms were first implicated in memory formation and synaptic plasticity, dynamic DNA methylation reactions have been identified as integral to long-term memory formation, maintenance, and recall. This review incorporates various new findings that DNA methylation mechanisms are important regulators of non-Hebbian plasticity mechanisms, suggesting that these epigenetic mechanisms are a fundamental link between synaptic plasticity and metaplasticity. Because the field of neuroepigenetics is so young and the biochemical tools necessary to probe gene-specific questions are just now being developed and used, this review also speculates about the direction and potential of therapeutics that target epigenetic mechanisms in the central nervous system and the unique pharmacokinetic and pharmacodynamic properties that epigenetic therapies may possess. Mapping the dynamics of the epigenome in response to experiential learning, even a single epigenetic mark in isolation, remains a significant technical and bioinformatic hurdle facing the field, but will be necessary to identify changes to the methylome that govern memory-associated gene expression and effectively drug the epigenome.
Topics: Animals; DNA Methylation; Drug Discovery; Epigenesis, Genetic; Genomics; Humans; Memory; Neuronal Plasticity
PubMed: 26915423
DOI: 10.3109/10409238.2016.1150958 -
Acta Physiologica (Oxford, England) Jan 2015The response to exercise training (trainability) has been shown to have a strong heritable component. There is growing evidence suggesting that traits such as... (Review)
Review
The response to exercise training (trainability) has been shown to have a strong heritable component. There is growing evidence suggesting that traits such as trainability do not only depend on the genetic code, but also on epigenetic signals. Epigenetic signals play an important role in the modulation of gene expression, through mechanisms such as DNA methylation and histone modifications. There is an emerging evidence to show that physical activity influences DNA methylation in humans. The present review aims to summarize current knowledge on the link between DNA methylation and physical activity in humans. We have critically reviewed the literature and only papers focused on physical activity and its influence on DNA methylation status were included; a total of 25 papers were selected. We concluded that both acute and chronic exercises significantly impact DNA methylation, in a highly tissue- and gene-specific manner. This review also provides insights into the molecular mechanisms of exercise-induced DNA methylation changes, and recommendations for future research.
Topics: Animals; DNA Methylation; Exercise; Exercise Therapy; Gene Expression; Gene Expression Regulation; Humans; Phenotype
PubMed: 25345837
DOI: 10.1111/apha.12414 -
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 -
Molecular Genetics and Genomics : MGG Nov 2022Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly... (Review)
Review
Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly influence sex-specific differences. The evolution of sex chromosomes with epigenetics as the driving force may have led to one sex being more adaptable than the other when exposed to various factors over time. Identifying and understanding sex-specific differences, particularly in DNA methylation, will help determine how each gender responds to factors, such as disease susceptibility, environmental exposure, brain development and neurodegeneration. From a medicine and health standpoint, sex-specific methylation studies have shed light on human disease severity, progression, and response to therapeutic intervention. Interesting findings in gender incongruent individuals highlight the role of genetic makeup in influencing DNA methylation differences. Sex-specific DNA methylation studies will empower the biotechnology and pharmaceutical industry with more knowledge to identify biomarkers, design and develop sex bias drugs leading to better treatment in men and women based on their response to different diseases.
Topics: Male; Humans; Female; DNA Methylation; Sex Characteristics; Epigenesis, Genetic; Sex Factors
PubMed: 35969270
DOI: 10.1007/s00438-022-01935-w -
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 -
Progress in Molecular Biology and... 2023Epigenetic modifications such as DNA methylation, post-translational chromatin modifications and non-coding RNA-mediated mechanisms are responsible for epigenetic...
Epigenetic modifications such as DNA methylation, post-translational chromatin modifications and non-coding RNA-mediated mechanisms are responsible for epigenetic inheritance. Change in gene expression due to these epigenetic modifications are responsible for new traits in different organisms leading to various diseases including cancer, diabetic kidney disease (DKD), diabetic nephropathy (DN) and renal fibrosis. Bioinformatics is an effective approach for epigenomic profiling. These epigenomic data can be analyzed by a large number of bioinformatics tools and software. Many databases are available online, which comprises huge amount of information regarding these modifications. Recent methodologies include many sequencing and analytical techniques to extrapolate different types of epigenetic data. This data can be used to design drugs against diseases linked to epigenetic modifications. This chapter briefly highlights different epigenetics databases (MethDB, REBASE, Pubmeth, MethPrimerDB, Histone Database, ChromDB, MeInfoText database, EpimiR, Methylome DB, and dbHiMo), and tools (compEpiTools, CpGProD, MethBlAST, EpiExplorer, and BiQ analyzer), which are being utilized to retrieve the data and mechanistically analysis of epigenetics modifications.
Topics: Humans; Epigenomics; Epigenesis, Genetic; Histones; DNA Methylation; Computational Biology
PubMed: 37225316
DOI: 10.1016/bs.pmbts.2023.03.023 -
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 -
Nature Genetics Sep 2022
Topics: DNA Methylation; Histones; RNA; RNA, Plant
PubMed: 36071174
DOI: 10.1038/s41588-022-01166-0