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Trends in Genetics : TIG Jan 2015Some of our fate is predetermined, by genetics and by the environment in the womb. Gestational environments are reflected in the DNA methylomes of newborns, in a manner... (Review)
Review
Some of our fate is predetermined, by genetics and by the environment in the womb. Gestational environments are reflected in the DNA methylomes of newborns, in a manner that is often influenced by genotype. Therefore, DNA methylation serves as molecular mechanism linking the interplay of early life environments and genetics to later life health. As such, methylation marks are potential biomarkers of suboptimal developmental trajectories. Can DNA methylation also be used to construct an escape route from biological fate?
Topics: Biomarkers; DNA Methylation; Epigenesis, Genetic; Genetic Determinism; Humans; Models, Genetic
PubMed: 25547197
DOI: 10.1016/j.tig.2014.09.007 -
Trends in Genetics : TIG Jan 2024First identified in isogenic mice, metastable epialleles (MEs) are loci where the extent of DNA methylation (DNAm) is variable between individuals but correlates across... (Review)
Review
First identified in isogenic mice, metastable epialleles (MEs) are loci where the extent of DNA methylation (DNAm) is variable between individuals but correlates across tissues derived from different germ layers within a given individual. This property, termed systemic interindividual variation (SIV), is attributed to stochastic methylation establishment before germ layer differentiation. Evidence suggests that some putative human MEs are sensitive to environmental exposures in early development. In this review we introduce key concepts pertaining to human MEs, describe methods used to identify MEs in humans, and review their genomic features. We also highlight studies linking DNAm at putative human MEs to early environmental exposures and postnatal (including disease) phenotypes.
Topics: Humans; Animals; Mice; Epigenesis, Genetic; DNA Methylation; Phenotype; Genomics; Alleles
PubMed: 38000919
DOI: 10.1016/j.tig.2023.09.007 -
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 -
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 -
Cells Dec 2022DNA methylation, histone posttranslational modifications, higher-order chromatin organization and regulation by noncoding RNAs are considered as the basic mechanisms...
DNA methylation, histone posttranslational modifications, higher-order chromatin organization and regulation by noncoding RNAs are considered as the basic mechanisms underlying the epigenetic memory [...].
Topics: Histones; Epigenesis, Genetic; DNA Methylation; Histone Code; Protein Processing, Post-Translational
PubMed: 36611903
DOI: 10.3390/cells12010109 -
Molecular Aspects of Medicine Feb 2018Epigenetic regulation plays crucial roles in the development and disease processes. Since different cell types with distinct epigenetic characteristics are always... (Review)
Review
Epigenetic regulation plays crucial roles in the development and disease processes. Since different cell types with distinct epigenetic characteristics are always intermingled together in the tissues or organs, the single cell analysis provides a universal resolution for dissecting their intrinsic complexities. In this review, we discuss recent advances of developing single cell epigenome sequencing techniques for profiling DNA modifications (5mC, 5hmC, 5fC and 5caC), chromatin accessibility, histone modifications, protein-DNA interactions and three-dimensional genome architecture (Hi-C) in an individual mammalian cell. Recent progresses of single cell multi-omics sequencing techniques are also reviewed. These techniques are emerging as powerful tools for unravelling the unique epigenomic features of rare cell types and epigenetic heterogeneity within a seemingly homogenous cell population. We also discussed the current limitations and future development trend of single cell epigenome sequencing techniques.
Topics: Animals; DNA Methylation; Epigenesis, Genetic; Epigenomics; Humans; Protein Binding
PubMed: 28923782
DOI: 10.1016/j.mam.2017.09.002 -
Progress in Molecular Biology and... 2023Epigenetics is the field of science that deals with the study of changes in gene function that do not involve changes in DNA sequence and are heritable while epigenetics...
Epigenetics is the field of science that deals with the study of changes in gene function that do not involve changes in DNA sequence and are heritable while epigenetics inheritance is the process of transmission of epigenetic modifications to the next generation. It can be transient, intergenerational, or transgenerational. There are various epigenetic modifications involving mechanisms such as DNA methylation, histone modification, and noncoding RNA expression, all of which are inheritable. In this chapter, we summarize the information on epigenetic inheritance, its mechanism, inheritance studies on various organisms, factors affecting epigenetic modifications and their inheritance, and the role of epigenetic inheritance in the heritability of diseases.
Topics: Humans; Heredity; DNA Methylation; Epigenesis, Genetic; Epigenomics; Inheritance Patterns
PubMed: 37225323
DOI: 10.1016/bs.pmbts.2023.03.006 -
Genes Jan 2022Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for... (Review)
Review
Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to infer epigenetic changes in the past. Investigating genome-wide methylation patterns of ancient humans may ultimately yield in a more comprehensive understanding of how our ancestors have adapted to the changing environment, and modified their lifestyles accordingly. We discuss the difficulties of working with ancient DNA in particular utilizing paleoepigenomic approaches, and assess new paleoepigenomic data, which might be helpful in future studies.
Topics: Animals; DNA Methylation; DNA, Ancient; Epigenesis, Genetic; Epigenomics; Genome
PubMed: 35205223
DOI: 10.3390/genes13020178 -
Archives of Pharmacal Research Feb 2019Cancer can be identified as a chaotic cell state, which breaks the rules that govern growth and reproduction, with main characteristics such as uncontrolled division,... (Review)
Review
Cancer can be identified as a chaotic cell state, which breaks the rules that govern growth and reproduction, with main characteristics such as uncontrolled division, invading other tissues, usurping resources, and eventually killing its host. It was once believed that cancer is caused by a progressive series of genetic aberrations, and certain mutations of genes, including oncogenes and tumor suppressor genes, have been identified as the cause of cancer. However, piling evidence suggests that epigenetic modifications working in concert with genetic mechanisms to regulate transcriptional activity are dysregulated in many diseases, including cancer. Cancer epigenetics explain a wide range of heritable changes in gene expression, which do not come from any alteration in DNA sequences. Aberrant DNA methylation, histone modifications, and expression of long non-coding RNAs (lncRNAs) are key epigenetic mechanisms associated with tumor initiation, cancer progression, and metastasis. Within the past decade, cancer epigenetics have enabled us to develop novel biomarkers and therapeutic target for many types of cancers. In this review, we will summarize the major epigenetic changes involved in cancer biology along with clinical and preclinical results developed as novel cancer therapeutics.
Topics: Animals; DNA Methylation; Epigenesis, Genetic; Genetic Therapy; Histones; Humans; Neoplasms
PubMed: 30806885
DOI: 10.1007/s12272-019-01126-z -
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