2024
DNA methylation in mammalian development and disease
Smith Z, Hetzel S, Meissner A. DNA methylation in mammalian development and disease. Nature Reviews Genetics 2024, 1-24. PMID: 39134824, DOI: 10.1038/s41576-024-00760-8.Peer-Reviewed Original ResearchLong-read sequencing technologiesDNA methylation fieldDNA methylation landscapeGenome functionMethylation landscapeSequencing technologiesEpigenetic codeGenomic characterizationRegulatory layerDNA methylationCell physiologyMammalian developmentMammalian lifespanGenetic featuresFunctional understandingSingle-cellDNAMechanistic discoveriesSomatic transitionsPhases of discoveryDevelopmental potentialDiscoveryPhenotypeSenescencePhysiology
2018
Global delay in nascent strand DNA methylation
Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A. Global delay in nascent strand DNA methylation. Nature Structural & Molecular Biology 2018, 25: 327-332. PMID: 29531288, PMCID: PMC5889353, DOI: 10.1038/s41594-018-0046-4.Peer-Reviewed Original ResearchMeSH KeywordsCell CycleCell ProliferationCpG IslandsCytosineDNADNA (Cytosine-5-)-MethyltransferasesDNA MethylationDNA Methyltransferase 3ADNA ReplicationEmbryonic Stem CellsEpigenesis, GeneticGene Expression RegulationGenome, HumanHCT116 CellsHumansMaleMethylationMitosisMotor NeuronsNeoplasmsSequence Analysis, RNATranscription FactorsConceptsCytosine methylationCpG methylationGenome-wide bisulfite sequencingCis-regulatory elementsEmbryonic stem cellsCancer cell line HCT116Cell cycle arrestEpigenetic informationMammalian developmentGene regulationMitotic transmissionEpigenetic heterogeneityEpigenetic roleBisulfite sequencingCell line HCT116DNA methylationHuman cellsMethylationHeterogeneous methylationStem cellsCellsBrdU labelingPronounced lagGlobal reductionImmunoprecipitation
2013
DNA methylation: roles in mammalian development
Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nature Reviews Genetics 2013, 14: 204-220. PMID: 23400093, DOI: 10.1038/nrg3354.Peer-Reviewed Original ResearchConceptsEmbryonic stem cellsDNA methylationMammalian developmentPaternal genomeEmbryonic lineagesEpigenetic mechanismsPrimordial germ cell specificationDNA methylation erasureDNA methylation functionsKey PointsDNA methylationGerm cell specificationGermline-specific genesGlobal nuclear organizationSimilar epigenetic mechanismsTranscription factor bindingStem cellsPre-implantation stagesAdult stem cellsCpG island methylationMethylation erasureHeritable memoryMethylation functionsCell specificationCpG densityLineage specification
2009
High-throughput bisulfite sequencing in mammalian genomes
Smith ZD, Gu H, Bock C, Gnirke A, Meissner A. High-throughput bisulfite sequencing in mammalian genomes. Methods 2009, 48: 226-232. PMID: 19442738, PMCID: PMC2864123, DOI: 10.1016/j.ymeth.2009.05.003.Peer-Reviewed Original ResearchConceptsDNA methylationHigh-throughput bisulfite sequencingCritical epigenetic markCpG-dense regionsGenome-wide distributionArray-based technologiesMammalian genomesEpigenetic marksMammalian developmentGenomic regionsRRBS librariesBisulfite sequencingMethylome profilingSequencing librariesRRBS librarySequence analysisMethylationRestriction digestionSequencingGenomeLibraryRelative coverageMspIProfilingSample throughput