AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsInformation ScienceHealth Care
ChromatinMethylationCytosineDNA Methylation5-MethylcytosineDNA-Cytosine MethylasesSulfitesGenomeDNA (Cytosine-5-)-MethyltransferaseBase SequenceMolecular Sequence DataGenome, BacterialChromatin Assembly and DisassemblyCpG IslandsDNAGenome, HumanGenome, ViralUracilHistonesSequence Analysis, DNAPromoter Regions, GeneticGenome, PlantEpigenesis, GeneticDinucleoside PhosphatesAmino Acid SequenceCytosine DeaminaseChromatin ImmunoprecipitationPentoxylMutationTranscription, GeneticDeoxyribonuclease HpaIIAzacitidineBinding SitesGenomicsEscherichia coliNucleic Acid ConformationPhylogenyAdenineGuaninePolymerase Chain ReactionEvolution, MolecularDNA-Binding ProteinsGene SilencingNucleosomesCell LineSubstrate SpecificityChromosome MappingGenome, FungalKineticsBase CompositionDNA, BacterialSequence AlignmentNucleic Acid DenaturationProtein BindingOligodeoxyribonucleotidesDNA, ViralCloning, MolecularGenome, MitochondrialGene Expression ProfilingOligonucleotide Array Sequence AnalysisAcetylationLysineHydroxylaminesModels, GeneticModels, MolecularMethyltransferasesTranscription FactorsProtein Structure, TertiaryDNA Restriction EnzymesGene Expression RegulationHistone-Lysine N-MethyltransferaseChromosomal Proteins, Non-HistoneDNA Modification MethylasesGenome, InsectGenome, ProtozoanHigh-Throughput Nucleotide SequencingSequence Homology, Amino AcidConserved SequenceSyntenyCell NucleusGenetic VariationComputational BiologyGenome SizeNuclear ProteinsDNA PrimersGene DuplicationGenomic ImprintingMutagenesis, Site-DirectedHeterochromatinGenome, ArchaealSoftwareSpecies SpecificityChromosomes, Artificial, BacterialPolymorphism, Single NucleotideDeaminationMicrococcal NucleaseSaccharomyces cerevisiaeDNA, PlantProtein MethyltransferasesRepressor Proteins
EpigeneticsWhole genome bisulfiteProteinsHuman genomeCarbon of a cytosine residDinucleotidesEukaryotesGlobal DNA methylationAnalyzed genome-widePatternsAddition of a methyl groupModificationsAcetylationPattern of DNA methylationMethyl groupModificationGenesHistonesTranscriptionalMechanismsAssaysImmunoprecipitationForm of methylationAberrant DNA methylationAssociated with unmethylatedGenomicBisulfite treatmentDNMTsRegions of the genomeGuanineTransposable elementsLysineNucleosomesRegulatoryDevelopmentalDnmt1HeritableDemethylationReplicationMethyltransferaseTranscriptionMicroRNADynamicsHypomethylationMethylated regionsBiologyDifferentialHeterochromatinAlterations2023SequencesMethyltransferasesUracilEpigenetic markPromoter regions
Epigenetics7
  • Recent achievements highlight the accelerated development of epigenetics, such as the definition of a human DNA methylome at single-nucleotide resolution, the various discoveries of histone variants and modifications, the study of the CpG island in the genome, and the progress of genome-wide nucleosome positioning maps ( Baldi, 2019 ). (frontiersin.org)
  • The overarching aim of the Epigenetics common cause of gastric cancer, Pan-cancer genoMe and Group (EGE) is to advance the which is the third most common cause tranScriPtoMe analySiS and understanding of the role of epigenetic of cancer-related deaths worldwide. (who.int)
  • This review briefly summarizes the major aspects of epigenetics and presents a comprehensive overview about the fundamental principles of DNA methylation analysis. (pediatricendoreviews.com)
  • Epigenetics is the study of how the environment, behavior, and other mechanisms cause changes to the genome that can contribute to the regulation of gene expression and other biological processes without changing to the underlying primary DNA sequences. (activemotif.com.cn)
  • Explore in detail new epigenetic research techniques and tips for topics like next-generation sequencing (NGS) in epigenetics, m6A RNA methylation , CRISPR/Cas9 system epigenetic editing, chromatin immunoprecipitation (ChIP) protocol optimization, and single-cell epigenomics methods . (whatisepigenetics.com)
  • To unravel the complexities surrounding the genome, advanced technologies in genomics and epigenetics are typically necessary. (whatisepigenetics.com)
  • Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers. (shengsci.com)
Whole genome bisulfite4
  • Several methyl-seq strategies have been developed including whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS), which enriches for CpG islands. (roche.com)
  • Here we report genome-wide composition, patterning, and stage-specific dynamics of DNA methylation in pre-implantation rhesus monkey embryos as well as male and female gametes studied using an optimized tagmentation-based whole-genome bisulfite sequencing method. (nature.com)
  • In mouse, a unidirectional demethylation process from the zygote stage to blastocyst stage is observed using either reduced representation bisulfite sequencing (RRBS) or single-base resolution whole-genome bisulfite sequencing (WGBS) method. (nature.com)
  • Summary: Whole genome bisulfite sequencing (WGBS) has emerged as the primary technique for DNA methylation studies, because of its great potential in terms of speed, specificity, and the capability of addressing new biological implications as non-CpG context methylation or hemimethylation. (zbmath.org)
Proteins14
  • ChIP-seq combines chromatin immunoprecipitation (ChIP) with NGS to identify binding sites of DNA-associated proteins throughout the genome, and is routinely used to map histone modifications and transcription factors. (roche.com)
  • ATAC-seq , an assay for transposase-accessible chromatin sequencing, determines regions of chromatin accessibility and maps DNA binding proteins to identify active promoters, enhancers, and other cis -regulatory elements. (roche.com)
  • Adding chemical groups to the DNA backbone and modifying histone proteins impart distinct characteristics on chromatin architecture. (frontiersin.org)
  • Methylation also refers to the addition of methyl group to lysine residues in the histone proteins around which DNA is wrapped. (basicmedicalkey.com)
  • Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. (researchgate.net)
  • To do so, they coupled findings from 238 DNA-protein-binding experiments performed by the ENCODE project - a massive, multiyear international effort to identify the functional elements of the human genome - with a laboratory-based technique to identify binding patterns among the proteins themselves. (pharmaceuticalintelligence.com)
  • They studied 128 proteins, called trans-acting factors , which are known to regulate gene expression by binding to regulatory regions within the genome. (pharmaceuticalintelligence.com)
  • His fields of research comprise RNA-mediated gene silencing processes with a focus on epigenetic phenomena, including studies on RNA-directed DNA methylation, the characterization of virus silencing suppressor proteins, the development of plant bioreactor platforms and viroid research. (degruyter.com)
  • DNA meth-ylation represses transcription by interfering with transcription factor binding and indirectly by recruiting methyl-CpG-binding proteins and reducing chromatin remodeling activities ( 12 ). (spandidos-publications.com)
  • Because MMP-13 and its regulatory networks are suitable targets for the development of effective early treatment strategies for OA, we discuss the specific targets of MMP-13, including upstream regulatory proteins, DNA methylation, non-coding RNAs, and autophagy-related proteins of MMP-13, and their therapeutic potential to inhibit the development of OA. (biomedcentral.com)
  • The effects of DNA methylation and the histone code are due, at least in part, to modification-specific recruitment of factors, such as heterochromatin-associated proteins (HP1) and methyl-binding domain proteins, which establish and maintain higher order of chromatin structure. (aacrjournals.org)
  • As the primary protein constituent of chromatin, forming complexes with DNA to compact our large genome for efficient nuclear organization, histones support critical cellular processes such as transcription, DNA replication, and DNA repair through diverse post-translational modifications that regulate their interactions with DNA and other nuclear proteins. (whatisepigenetics.com)
  • Consistent with a chromatin-associated role, the MORCs display fusions to several DNA- and peptide-binding domains, which are commonly found other eukaryotic chromatin proteins [ 5 ]. (beds.ac.uk)
  • Methyl marks are recognized by plant homeodomain (PHD) fingers and the Royal-superfamily of chromatin-binding proteins, including chromodomain, tudor, and MBT domains. (musculoskeletalkey.com)
Human genome6
  • Indeed, the initial enthusiasm in decoding this manual through the Human Genome Project has inadvertently fueled the perception, especially among nongeneticists, that deciphering the DNA sequence is the ultimate answer to biologic diversity. (basicmedicalkey.com)
  • However, the remarkable progress made in this regard left many questions unanswered and only emphasized that DNA sequence represents only the most basic level of analysis of the human genome and that higher-order organization is key to its proper function, much like how the amino acid sequence of a protein is only meaningful in the context of its tertiary structure. (basicmedicalkey.com)
  • Interestingly, this is usually restricted to cytosine that exists in the context of CpG dinucleotides which are widely spread in the human genome. (basicmedicalkey.com)
  • Methylating these dinucleotides is thought to represent an important defense mechanism that protects the genome from the harmful expression of sequences that have parasitized the human genome in ancient times such as retroviral DNA-derived sequences. (basicmedicalkey.com)
  • After sequencing the human genome, it has become clear that genetic information alone is not sufficient to understand phenotypic manifestations. (pediatricendoreviews.com)
  • Because of the Human Genome and the HapMap projects, developments in genotyping technology have brought the possibility of identifying associations between specific genetic alterations and common diseases closer to reality. (hindawi.com)
Carbon of a cytosine resid1
Dinucleotides5
  • In eukaryotes, methylation is most commonly found on the carbon 5 position of cytosine residues (5mC) adjacent to guanine, termed CpG dinucleotides. (wikipedia.org)
  • Methylation of cytosine (5 mC) residues in CpG dinucleotides across the genome is an epigenetic modification that plays a pivotal role in the establishment of cellular identity by influencing gene expression during development [ 1 ]. (biomedcentral.com)
  • In many plants and animals, it is characterized by the biochemical addition of a methyl group (CH3) to the cytosine 5-carbon in cytosine-phosphate-guanosine (CpG) dinucleotides via a methyltransferase enzyme (Adams et. (thermofisher.com)
  • Although CpG dinucleotides occur rather infrequently in mammalian genomes (approximately one-fourth the expected frequency), DNA segments abundant with CpG dinucleotides do exist. (thermofisher.com)
  • The most common sites of DNA methylation are CpG dinucleotides. (troscriptions.com)
Eukaryotes4
Global DNA methylation1
  • By the 8-cell stage, remethylation becomes more pronounced than demethylation, resulting in an increase in global DNA methylation. (nature.com)
Analyzed genome-wide1
  • We analyzed genome-wide changes in DNA methylation and their relationship to gene regulation in the brain of Xenopus tadpoles during metamorphosis, a thyroid hormone-dependent developmental process. (nih.gov)
Patterns15
  • DNA methylation patterns vary greatly between species and even within the same organism. (wikipedia.org)
  • Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. (biomedcentral.com)
  • Disruption of DNA methylation patterns is associated with diseases, and particularly with cancer [ 3 ]. (biomedcentral.com)
  • However, the genome-wide DNA methylation patterns have not yet been comprehensively described for all subtypes of ALL and the synergy between DNA methylation, leukemogenesis, drug resistance, and relapse in ALL is poorly understood. (biomedcentral.com)
  • Patterns of methylation over multiple CpG sites in a region are often complex and cell type specific, with the region showing multiple allelic patterns in a sample. (biomedcentral.com)
  • True representation of methylation patterns can only be fully characterised by clonal analysis. (biomedcentral.com)
  • Deep sequencing provides the ability to investigate clonal DNA methylation patterns in unprecedented detail and scale, enabling the proper characterisation of the heterogeneity of methylation patterns. (biomedcentral.com)
  • We have developed a new analysis and visualisation software tool "Methpat", that extracts and displays clonal DNA methylation patterns from massively parallel sequencing data aligned using Bismark. (biomedcentral.com)
  • Unlike currently available tools, Methpat can visualise the diversity of epiallelic DNA methylation patterns in a sample. (biomedcentral.com)
  • 1986. "DNA methylation patterns of the calcitonin gene in human lung cancers and lymphomas. (esmed.org)
  • It has been almost an established dogma that DNA methylation patterns form during embryogenesis by innate organized developmental programs and that DNA methylation is mainly involved in cellular differentiation. (biomedcentral.com)
  • It was therefore believed that DNA methylation patterns once formed remained fixed since cellular differentiation was believed to be terminal. (biomedcentral.com)
  • Because Dnmt1 shows preferential activity against hemimethylated DNA, it has been proposed to be involved primarily in maintaining methylation patterns through rounds of DNA replication, rather than establishing them de novo . (biomedcentral.com)
  • this might involve the replication, propagation or interpretation of early methylation patterns at selected loci (in particular imprinted genes) that are then subsequently able to escape the global genomic demethylation that occurs in later preimplantation development [ 8 ]. (biomedcentral.com)
  • Promoter CpG methylation patterns of three imprinting genes, small nuclear ribonucleoprotein polypeptide N (SNRPN), paternally expressed 3 (Peg3), and potassium voltage-gated channel 1 overlapping transcript 1 (Kcnq1ot1), were examined from genomic DNA of a single mouse blastocyst. (ndltd.org)
Addition of a methyl group2
Modifications16
  • Two of the most characterized epigenetic modifications are DNA methylation and histone modification. (wikipedia.org)
  • With the finding that DNA methylation and histone modifications are stable, heritable, and also reversible processes that influence gene expression without altering DNA primary structure, a mechanism for the observed variability in cell gene expression was provided. (wikipedia.org)
  • Epigenetic changes, such as DNA methylation and histone modifications, represent a heritable layer of information that regulates DNA transcription. (roche.com)
  • Epigenetic dysregulation, such as the methylation of DNA (CpG), modifications of histones, binding of microRNAs to block translation, post-transcriptional silencing by short interfering RNA (siRNA), and modification of chromatin structure by noncoding RNA (ncRNA), are associated with several diseases, including cancer. (roche.com)
  • Here, we summarize the different types of epigenetic enzymes which target corresponding protein domains, emphasize DNA methylation , histone modifications, and microRNA-mediated cooperation with epigenetic modification, and highlight recent achievements in developing targets for epigenetic inhibitor therapy. (frontiersin.org)
  • Key regulators that are essential for establishing and maintaining the epigenomic landscape are frequently mutated and can drive cancer development via alterations of DNA methylation and histone modifications [ 4 ]. (biomedcentral.com)
  • DNA accessibility for the transcriptional machinery is regulated in part by chemical modifications to histones that can alter chromatin structure or nucleosome positioning, and by direct DNA modifications that can alter transcription factor-binding sites [ 5 ]. (biomedcentral.com)
  • Epigenetic mechanisms like DNA methylation and histone modifications are essential for multiple physiological processes like development, establishment of tissue identity, imprinting, X-chromosome inactivation, chromosomal stability and gene transcription regulation. (pediatricendoreviews.com)
  • Although epigenetic information is heritable, it is not stored in the sequence of the DNA but mainly in the modification pattern of the chromatin, i.e. the methylation of cytosine residues in the DNA or covalent modifications of the histones. (pediatricendoreviews.com)
  • The code is an array of post-translational modifications (acetylation, phosphorylation, methylation, ubiquitination, and sumoylation) of NH 2 -terminal tails of core histone and to a lesser degree their globular domains. (aacrjournals.org)
  • Cross-talk between different histone modifications, as well as DNA methylation, seems complex. (aacrjournals.org)
  • A large number of covalent modifications on histone, such as different types, residues, and amount, will affect the inhibition or activation of gene expression. (gjkqyxzz.cn)
  • The term epigenetic describes a number of chromatin modifications that stably alter gene expression without changing the sequence of the DNA. (musculoskeletalkey.com)
  • In the last few years, the study of epigenetic mechanisms strongly progressed, yielding insight into the mechanisms by which epigenetic chromatin modifications regulate gene expression. (musculoskeletalkey.com)
  • 2 In addition to the well-established epigenetic role of DNA methylation, this definition includes a variety of more transient histone modifications such as acetylation, methylation, or phosphorylation that underlie epigenetic effects, and that will be discussed in this chapter along with the influence of SUMOylation, ubiquitination, adenosine diphosphate (ADP) ribosylation, and microRNA. (musculoskeletalkey.com)
  • DNA methylation is one of the key epigenetic modifications that play a role in regulating genes. (troscriptions.com)
Acetylation1
Pattern of DNA methylation3
Methyl group2
Modification9
Genes14
  • In contrast, Hp1 and Dim5 mutants that are impacted in chromatin-associated processes upstream of DNA methylation are severely affected in development and virulence and display transcriptional reprogramming in specific hypervariable genomic regions (so-called adaptive genomic regions) that contain genes associated with host colonization. (biomedcentral.com)
  • Setting aside sporadic mutations, every somatic cell in the body contains an identical genome with an identical complement of genes, each of which encodes a specific protein. (ernolaszlo.com)
  • Cytosine methylation has been studied in wheat rRNA genes at nucleolar organizers displaying different activities. (ncsu.edu)
  • The methylation pattern within a specific multigene locus is influenced by the number and type of rRNA genes in other rDNA loci in the cell. (ncsu.edu)
  • Dominant, very active loci have a higher proportion of rRNA genes with unmethylated cytosine residues in comparison with recessive and inactive loci. (ncsu.edu)
  • Chromatin structure and expression of plant ribosomal RNA genes. (ncsu.edu)
  • DNase I sensitivity of ribosomal RNA Genes in chromatin and nucleolar dominance in wheat. (ncsu.edu)
  • Here, we show that rRNA genes at dominant loci are organized in a chromatin conformation that renders them more sensitive to DNase I digestion than other rRNA genes. (ncsu.edu)
  • Differential methylation of the two alleles is a hallmark of imprinted genes. (biomedcentral.com)
  • Thus H3K9 methylation at the promoter region silences transcription, but within the coding region, H3K9 methylation was found to be associated with actively transcribed genes. (musculoskeletalkey.com)
  • During preimplantation embryonic development, imprinting genes are susceptible to methylation changes by artificial manipulation, which may lead to developmental abnormalities. (ndltd.org)
  • While embryo supply is scarce and conventional epigenetic studies require embryos in vast amount, an assay was developed in this study to examine the methylation statuses of imprinting genes using DNA from single mouse blastocysts cultured in-vitro or exposed to EDs. (ndltd.org)
  • Despite that there was no significant difference in overall methylation rates between in-vivo or in-vitro developed blastocysts, certain CpG residues appeared to displayed significant loss of methylation (LOM) or gain of methylation (GOM) induced by in-vitro culture in all three genes being studied. (ndltd.org)
  • We lose methylation capacity as we age, leading to more genes turned on errantly. (troscriptions.com)
Histones1
Transcriptional4
  • This lack of methylation confers a permissive environment of transcription and represents an important transcriptional regulatory mechanism. (basicmedicalkey.com)
  • The present study investigated the methylation of CpG sites in the cyclooxygenase (COX)‑2 promoter via nuclear factor (NF)‑κB transcriptional regulation and elucidated its effect on the COX‑2 transcriptional expression in a ketamine‑induced ulcerative cystitis (KIC) animal model. (spandidos-publications.com)
  • DNA methylation typically causes gene transcriptional silencing, whereas demethylation leads to transcription activation. (gjkqyxzz.cn)
  • It is generally believed that the histone code can influence transcriptional activity directly by affecting chromatin structure, thereby making it more or less accessible for transcription factors and indirectly leading to the attraction of effector molecules that in turn recruit and stabilize the transcription machinery. (musculoskeletalkey.com)
Mechanisms3
  • Epigenomic maintenance is a continuous process and plays an important role in stability of eukaryotic genomes by taking part in crucial biological mechanisms like DNA repair. (wikipedia.org)
  • We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. (elifesciences.org)
  • DNA CpG methylation on the cytosine is among the most stable forms of epigenetic mechanisms in the life cycle of mammals. (nature.com)
Assays4
  • DNA methylation readouts at single sites employing bisulfite conversion become analogous to genotyping assays by detecting either a cytosine or thymidine at the C position of a CpG site and are interpreted as methylated or unmethylated cytosines respectively. (biomedcentral.com)
  • This project focuses on developing computational tools for better analysis of the wealth of data from chromosome conformation capture assays with the ultimate goal of inferring functional chromatin contacts such as those between enhancers and promoters. (ucsd.edu)
  • From early techniques that measured overall DNA methylation levels to enzyme-associated techniques that interrogated methylation at a single CpG dinucleotide to present day assays that catalogue the methylation of every cytosine in the genome, technical advancement progressively has brought increasing clarity to our understanding of the complex epigenomes of normal and neoplastic cells. (esmed.org)
  • However, despite the improvement that has meant the appearance of WGBS, processing and analyzing the resulting datasets is not as straightforward as in other methylation assays, and special care should be taken to obtain reliable results. (zbmath.org)
Immunoprecipitation1
  • Ketamine treatment increased the binding of NF‑κB and permissive histone H3 lysine‑4 (H3K4)m3, but caused a decrease in the repressive histone H3K27m3 and H3K36m3 on the COX‑2 promoter ranging from ‑1,522 to ‑1,331 bp as determined by a chromatin immunoprecipitation assay. (spandidos-publications.com)
Form of methylation1
Aberrant DNA methylation1
Associated with unmethylated1
Genomic11
  • The CpG sites that constituted these two signatures differed in their functional genomic enrichment to regions with marks of active or repressed chromatin. (biomedcentral.com)
  • On the molecular level, it is well known that CpG methylation leads to X-chromosome inactivation, genomic imprinting, and suppression of transposable elements. (biomedcentral.com)
  • DNA methylation is an important epigenetic control mechanism that in many fungi is restricted to genomic regions containing transposable elements (TEs). (biomedcentral.com)
  • As these adaptive genomic regions are largely devoid of DNA methylation and of Hp1- and Dim5-associated heterochromatin, the differential transcription is likely caused by pleiotropic effects rather than by differential DNA methylation. (biomedcentral.com)
  • Cytosine methylation can occur in symmetric CG or CHG genomic contexts, or in the asymmetric CHH genomic context, where H stands for either A, C or T. In general, 5mC occurs more commonly at symmetric sites because maintenance methylation can cause methylation of daughter strands during DNA-replication, whereas asymmetric sites require de novo methylation [ 7 ]. (biomedcentral.com)
  • In mammals, DNA methylation is largely restricted to CG sites, while plants and fungi show methylation in each of the genomic contexts [ 8 ]. (biomedcentral.com)
  • Dim2 operates in a complex with Heterochromatin Protein-1 (Hp1) that recognizes and directs DNA methylation to genomic regions marked by tri-methylation of histone 3 lysine 9 (H3K9me3) that is deposited by the histone methyltransferase Deficient In Methylation-5 (Dim5) [ 11 , 12 ]. (biomedcentral.com)
  • Along with co-ordinate (location) details of S/MARs, the dataset also revealed details of S/MAR features, namely, length, inter-SMAR length (the chromatin loop size), nucleotide repeats, motif abundance, chromosomal distribution and genomic context. (researchgate.net)
  • DNMT1 preserves the methyltransferase by binding to hemi-methylated CpG sites and methylates the cytosine on the newly synthesized strand after DNA replication, whereas DNMT3a/DNMT3b are required for the de novo genomic methylation of DNA ( 15 ). (spandidos-publications.com)
  • The vast majority of methods that investigate DNA methylation utilise bisulfite treatment of genomic DNA followed by PCR amplification to distinguish methylated from unmethylated CpG sites [ 2 - 5 ]. (biomedcentral.com)
  • In some cases, genomic features may be deleted or new features inserted (in comparison to reference genomes). (xcode.in)
Bisulfite treatment2
  • This method employs bisulfite treatment, which converts cytosine residues into uracil, while methylated residues are left unmodified. (roche.com)
  • Bisulfite treatment discriminates methylated from unmethylated cytosines by selectively reacting with unmethylated cytosines to generate uracil. (biomedcentral.com)
DNMTs2
Regions of the genome2
  • For many regions of the genome, we have detected multiple overlapping transcripts including both small, gene-sized RNAs and large transcripts covering entire gene clusters. (ncsu.edu)
  • Imprinted regions of the genome such as IGF2/H19 and MEST typically display two epialleles, where one is completely methylated and the other is unmethylated. (biomedcentral.com)
Guanine1
Transposable elements1
  • In N. crassa , DNA methylation is restricted to transposable elements (TEs) and is dependent on a single DNMT, Deficient In Methylation-2 (Dim2), an ortholog of Human Dnmt1 that performs de novo as well as maintenance methylation [ 10 ]. (biomedcentral.com)
Lysine3
  • We demonstrate the presence of telomeric silencing in Neurospora and show a dependence on histone deacetylases and methylation of histone H3 lysine 9. (biomedcentral.com)
  • The fission yeast S. pombe lacks Sir3p and Sir4p but employs methylation of histone H3 lysine 9 (K9) plus a Sir2p homologue (Sir2) for silencing [ 15 ]. (biomedcentral.com)
  • This S5 domain usually provides a conserved basic residue, which might function similar to the arginine or lysine finger observed in various phosphohydrolase reactions [ 6 ]. (beds.ac.uk)
Nucleosomes1
Regulatory4
  • DNA methylation studies have come into prominence, in part, because of expectations that CpG islands occurring in promoter regions are likely to play a regulatory role. (thermofisher.com)
  • In this review, we highlight the main MMP-13-related changes in OA chondrocytes, including alterations in the activity and expression level of MMP-13 by upstream regulatory factors, DNA methylation, various non-coding RNAs (ncRNAs), and autophagy. (biomedcentral.com)
  • Percentage methylation described in most DNA methylation studies hides important pattern and positional information of DNA methylation with potential functional and regulatory relevance [ 7 ]. (biomedcentral.com)
  • We have ongoing interests in the systems level analysis and reconstruction of regulatory networks, inference of enhancer-promoter contacts, predictive models of gene expression and integration of three-dimensional chromatin structure with one-dimensional epigenetic measurements in the context of cancer, malaria, asthma and several autoimmune diseases. (ucsd.edu)
Developmental2
  • Our findings show that the genome of tadpole neural cells undergoes significant changes in DNA methylation during metamorphosis, and these changes likely influence chromatin architecture, and gene regulation programs occurring during this developmental period. (nih.gov)
  • However, robust and large-scale genome-wide reprogramming of DNA methylome occurs during two critical developmental processes: (1) development of primordial germ cells and (2) pre-implantation embryogenesis. (nature.com)
Dnmt12
  • In animals, 5mC is maintained during DNA replication by DNMT1 together with UHRF1, which directly recognizes hemimethylated cytosine via the SRA domain and stimulates activity of DNMT1 in a manner dependent on its ubiquitin-ligase activity ( Nishiyama and Nakanishi, 2021 ). (elifesciences.org)
  • Although the genome-wide DNA demethylation is believed to be a hallmark of mammalian embryogenesis, previous study also indicated that the somatic form of dnmt1 ( dnmt1s ) is actually expressed at each stage of pre-implantation embryos and plays a role in the maintenance of DNA imprinting 8 . (nature.com)
Heritable2
  • While DNA methylation is stable and heritable, it can be reversed by an antagonistic group of enzymes known as DNA de-methylases. (wikipedia.org)
  • We suggest that the parent seed nitrogen content decreased induced DNA methylation changes at the epigenetic level and significantly decreased the expression of OsNAR2.1 , resulting in a heritable phenotype of N deficiency over two generations of the overexpression line. (biomedcentral.com)
Demethylation4
  • The largest changes in DNA methylation were seen from metamorphic climax to the completion of metamorphosis (2960 DMRs), with 80% of the DMRs representing demethylation. (nih.gov)
  • Moreover, in the ketamine group, the level of Ten‑Eleven‑Translocation methylcytosine dioxygenase for demethylation as determined by reverse transcription‑quantitative PCR assay was increased in comparison with the control group, but that was not the case for the level of DNA methyltransferases for methylation. (spandidos-publications.com)
  • In contrast, the Ten-Eleven-Translocation (TET) dioxygenase family, including TET1, TET2 and TET3, mediates active DNA demethylation and hydroxylate-methylated DNA by converting 5-methylcyto-sine to 5-hydroxymethylcytosine to regulate DNA methylation status. (spandidos-publications.com)
  • We show that upon fertilization, both paternal and maternal genomes undergo active DNA demethylation, and genome-wide de novo DNA methylation is also initiated in the same period. (nature.com)
Replication2
  • The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules designated as components A and B. The A component contains the only virally-encoded function required for autonomous replication in infected plant cells. (ncsu.edu)
  • Shortening of the 5'-terminus of the daughter strand, caused by the removal of the terminal RNA-primer and the subsequent incomplete replication of linear DNA molecules, is observed during the genome replication occurring upon cell fission. (actanaturae.ru)
Methyltransferase4
  • Our results show that Dim2, but not Dnmt5 or the putative sexual-cycle-related DNA methyltransferase Rid, is responsible for the majority of DNA methylation under the tested conditions. (biomedcentral.com)
  • Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. (elifesciences.org)
  • Most importantly, our DNA methyltransferase loss-of-function analysis indicates that DNA methylation influences early monkey embryogenesis. (nature.com)
  • DNA cytosine methylation is facilitated by DNA methyltransferase (DNMT). (troscriptions.com)
Transcription5
  • Methylation of cytosine residues in DNA influences chromatin structure and gene transcription, and its regulation is crucial for brain development. (nih.gov)
  • It is concluded that cytosine methylation in rDNA is regulated and that the methylation pattern correlates with the transcription potential of an rRNA gene. (ncsu.edu)
  • A transcription map of the pea chloroplast genome. (ncsu.edu)
  • A set of 53 cloned pea chloroplast DNA fragments representing approximately 90% of the chloroplast genome was used to probe Northern blots of total pea RNA, resulting in a nearly complete chloroplast transcription map. (ncsu.edu)
  • DNA methylation at a gene promoter region has the potential to regulate gene transcription. (biomedcentral.com)
MicroRNA1
  • Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. (nature.com)
Dynamics4
  • Our study provides the first comprehensive illustration of the 'wax and wane' phases of DNA methylation dynamics. (nature.com)
  • We therefore decided to investigate comprehensively the global and high-resolution DNA methylation dynamics during early development of a non-human primate (rhesus monkey, Macaca mulatta ). (nature.com)
  • Monkeys have served as one of the most valuable models for understanding DNA methylation dynamics during early embryogenesis in human due to their similarities in genetics and early embryonic development 17 , 18 . (nature.com)
  • However, their exact functions in chromatin dynamics are poorly understood. (beds.ac.uk)
Hypomethylation2
  • Over the past 10 years we have been witness to an explosion of investigation into the epigenetic basis of cancer, and application of the powerful genome-wide DNA methylation profiling techniques to be reviewed have yielded critical insights into the organization of the cancer methylome with its broad regions of hypomethylation and foci of hypermethylation resulting in critical differences in gene expression and chromosomal stability compared to normal cells. (esmed.org)
  • When compared to blastocysts cultured with KSOM+AA medium as controls, CdCl2-treated blastocysts displayed the most methylation aberrations in both alleles and within particular CpG residues, possibly due to its dual effect in both hypermethylation and hypomethylation across the methylome. (ndltd.org)
Methylated regions1
  • Using Methylated DNA Capture sequencing (MethylCap-seq) we discovered a diverse landscape of DNA methylation across the tadpole neural cell genome, and pairwise stage comparisons identified several thousand differentially methylated regions (DMRs). (nih.gov)
Biology1
Differential2
Heterochromatin1
Alterations2
  • It has been increasingly recognized that other types of alterations in the genome, known as epigenetic changes, can modulate its structure and function without affecting the underlying DNA sequence. (ernolaszlo.com)
  • 1998. "Alterations in DNA methylation: a fundamental aspect of neoplasia. (esmed.org)
20231
  • 2023. EpiCRISPR targeted methylation of Arx gene initiates transient switch of mouse pancreatic alpha to insulin-producing cells . (cardiff.ac.uk)
Sequences3
  • The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. (degruyter.com)
  • In mammals, the predominant and most widely studied DNA methylation mark occurs at CpG dinucleotide (CpG) palindromic sequences [ 1 ]. (biomedcentral.com)
  • A variety of simple repeat sequences that are distributed throughout the GENOME. (lookformedical.com)
Methyltransferases2
Uracil1
  • For methyl-seq studies, the KAPA HiFi Uracil+ HotStart DNA Polymerase is essential for the amplification of bisulfite-converted libraries due to its tolerance to uracil residues. (roche.com)
Epigenetic mark2
Promoter regions1