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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 -
Neuroscience and Biobehavioral Reviews Apr 2020Neuromodulation techniques have shown promising efficacy on memory function and understanding the epigenetic mechanisms contributing to these processes would shed light... (Review)
Review
Neuromodulation techniques have shown promising efficacy on memory function and understanding the epigenetic mechanisms contributing to these processes would shed light on the molecular outcomes essential for cognition. In this review, we highlight some epigenetic mechanisms underlying neuromodulation and regulatory effects of neuronal activity-induced DNA methylation on genes that are highly involved in memory formation. Next, we examine the evidence to support DNA methyltransferase 3a, methyl-CpG binding protein 2, and DNA demethylase as possible memory modulation targets. Finally, we report the recent developments in the field of neuromodulation and explore the potential of these techniques for future neuroepigenetic research.
Topics: Animals; DNA Methylation; DNA Methyltransferase 3A; Electric Stimulation Therapy; Epigenesis, Genetic; Hippocampus; Humans; Memory
PubMed: 31846654
DOI: 10.1016/j.neubiorev.2019.12.022 -
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 -
Cells Oct 2019DNA methylation controls several cellular processes, from early development to old age, including biological responses to endogenous or exogenous stimuli contributing to... (Review)
Review
DNA methylation controls several cellular processes, from early development to old age, including biological responses to endogenous or exogenous stimuli contributing to disease transition. As a result, minimal DNA methylation changes during developmental stages drive severe phenotypes, as observed in germ-line imprinting disorders, while genome-wide alterations occurring in somatic cells are linked to cancer onset and progression. By summarizing the molecular events governing DNA methylation, we focus on the methods that have facilitated mapping and understanding of this epigenetic mark in healthy conditions and diseases. Overall, we review the bright (health-related) and dark (disease-related) side of DNA methylation changes, outlining how bulk and single-cell genomic analyses are moving toward the identification of new molecular targets and driving the development of more specific and less toxic demethylating agents.
Topics: Animals; DNA Methylation; Epigenesis, Genetic; Epigenomics; Genome; Genomic Imprinting; Humans; Neoplasms
PubMed: 31614870
DOI: 10.3390/cells8101243 -
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 -
The New Phytologist Jul 2020DNA methylation is an epigenetic mark that regulates multiple processes, such as gene expression and genome stability. Mutants and pharmacological treatments have been... (Review)
Review
DNA methylation is an epigenetic mark that regulates multiple processes, such as gene expression and genome stability. Mutants and pharmacological treatments have been instrumental in the study of this mark in plants, although their genome-wide effect complicates the direct association between changes in methylation and a particular phenotype. A variety of tools that allow locus-specific manipulation of DNA methylation can be used to assess its direct role in specific processes, as well as to create novel epialleles. Recently, new tools that recruit the methylation machinery directly to target loci through programmable DNA-binding proteins have expanded the tool kit available to researchers. This review provides an overview of DNA methylation in plants and discusses the tools that have recently been developed for its manipulation.
Topics: DNA Methylation; Plants
PubMed: 32159848
DOI: 10.1111/nph.16529 -
Nucleic Acids Research Aug 2023Integrative analysis of multi-omic datasets has proven to be extremely valuable in cancer research and precision medicine. However, obtaining multimodal data from the...
Integrative analysis of multi-omic datasets has proven to be extremely valuable in cancer research and precision medicine. However, obtaining multimodal data from the same samples is often difficult. Integrating multiple datasets of different omics remains a challenge, with only a few available algorithms developed to solve it. Here, we present INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples. To enable integration, INTEND learns a predictive model between the two omics by training on multi-omic data measured on the same set of samples. In comprehensive testing on 11 TCGA (The Cancer Genome Atlas) cancer datasets spanning 4329 patients, INTEND achieves significantly superior results compared with four state-of-the-art integration algorithms. We also demonstrate INTEND's ability to uncover connections between DNA methylation and the regulation of gene expression in the joint analysis of two lung adenocarcinoma single-omic datasets from different sources. INTEND's data-driven approach makes it a valuable multi-omic data integration tool. The code for INTEND is available at https://github.com/Shamir-Lab/INTEND.
Topics: Humans; DNA Methylation; Neoplasms; Algorithms; Gene Expression Profiling; Transcriptome
PubMed: 37395437
DOI: 10.1093/nar/gkad566 -
Discovery Medicine 2021Cardiovascular disease (CVD) is a top public health problem especially for the elderly. Atherosclerosis is the pathological basis of CVD. Many studies have shown that...
Cardiovascular disease (CVD) is a top public health problem especially for the elderly. Atherosclerosis is the pathological basis of CVD. Many studies have shown that epigenetics plays a key role in regulating the development of atherosclerotic disease. Epigenetics includes DNA methylation, histone modification, RNA methylation, and non-coding RNA. More and more epigenetic regulations are confirmed to take part in heart development, response to stress, and endothelial injury, it is even suggested that atherosclerosis is the result of abnormal epigenetic regulation. Researchers have performed studies on novel drugs through epigenetic modification, yielding varied results. It is necessary to explore a range of epigenetic mechanisms to explain the causes and progression of atherosclerosis and uncover new targets for treatment. This article summarizes the latest development of epigenetic modification and its effect on the occurrence and progression of atherosclerosis and the possible prevention and treatment modalities of atherosclerosis that these research findings would engender.
Topics: Aged; Atherosclerosis; Cardiovascular Diseases; DNA Methylation; Epigenesis, Genetic; Humans
PubMed: 34965371
DOI: No ID Found -
Plant Cell Reports Aug 2020RNA Directed DNA Methylation (RdDM) is a pathway that mediates de novo DNA methylation, an evolutionary conserved chemical modification of cytosine bases, which exists... (Review)
Review
RNA Directed DNA Methylation (RdDM) is a pathway that mediates de novo DNA methylation, an evolutionary conserved chemical modification of cytosine bases, which exists in living organisms and utilizes small interfering RNA. Plants utilize DNA methylation for transposable element (TE) repression, regulation of gene expression and developmental regulation. TE activity strongly influences genome size and evolution, therefore making DNA methylation a key component in understanding divergence in genome evolution among seed plants. Multiple proteins that have extensively been studied in model plant Arabidopsis thaliana catalyze RNA dependent DNA Methylation pathway along with small interfering RNA. Several developmental functions have also been attributed to DNA methylation. This review will highlight aspects of RdDM pathway dynamics, evolution and functions in seed plants with focus on recent findings on conserved and non-conserved attributes between angiosperms and gymnosperms to potentially explain how methylation has impacted variations in evolutionary and developmental complexity among them and advance current understanding of this crucial epigenetic pathway.
Topics: DNA Methylation; Evolution, Molecular; Gene Expression Regulation, Plant; Genome, Plant; RNA, Plant; Seeds
PubMed: 32594202
DOI: 10.1007/s00299-020-02558-4