2014
DNA methylation dynamics of the human preimplantation embryo
Smith ZD, Chan MM, Humm KC, Karnik R, Mekhoubad S, Regev A, Eggan K, Meissner A. DNA methylation dynamics of the human preimplantation embryo. Nature 2014, 511: 611-615. PMID: 25079558, PMCID: PMC4178976, DOI: 10.1038/nature13581.Peer-Reviewed Original ResearchConceptsGenome-scale DNA methylationMaternal-specific methylationDNA methylation dynamicsTransposable element activityEmbryonic stem cell derivationStem cell derivationEarly human embryogenesisHuman preimplantation embryosMethylation dynamicsDNA methylationHuman embryogenesisElement activityPreimplantation embryosCell derivationUnique modeMethylationEmbryogenesisMouse modelEmbryosRegulationExpression
2013
Proliferation-Dependent Alterations of the DNA Methylation Landscape Underlie Hematopoietic Stem Cell Aging
Beerman I, Bock C, Garrison BS, Smith ZD, Gu H, Meissner A, Rossi DJ. Proliferation-Dependent Alterations of the DNA Methylation Landscape Underlie Hematopoietic Stem Cell Aging. Cell Stem Cell 2013, 12: 413-425. PMID: 23415915, DOI: 10.1016/j.stem.2013.01.017.Peer-Reviewed Original ResearchConceptsDNA methylationHSC declineHematopoietic stem cell agingPolycomb repressive complex 2DNA methylation landscapeStem cell agingStem cell declineRepressive complex 2Global DNA methylationSite-specific alterationsHematopoietic lineage potentialMethylation landscapeDNA methylomeGenomic regionsLineage potentialEpigenomic alterationsDNA hypermethylationReplicative limitCell agingDownstream progenitorsFunctional analysisFunctional potentialMethylationProliferation of HSCsGenes
2012
Mouse ooplasm confers context-specific reprogramming capacity
Chan MM, Smith ZD, Egli D, Regev A, Meissner A. Mouse ooplasm confers context-specific reprogramming capacity. Nature Genetics 2012, 44: 978-980. PMID: 22902786, PMCID: PMC3432711, DOI: 10.1038/ng.2382.Peer-Reviewed Original Research
2009
Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses
Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A. Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses. Science 2009, 326: 257-263. PMID: 19729616, PMCID: PMC2879337, DOI: 10.1126/science.1179050.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBacteriaChromatin Assembly and DisassemblyDendritic CellsDNA, Single-StrandedFeedback, PhysiologicalGene Expression ProfilingGene Expression RegulationGene Regulatory NetworksInflammationLipopeptidesLipopolysaccharidesMiceMice, Inbred C57BLPoly I-CRNA-Binding ProteinsToll-Like ReceptorsTranscription FactorsTranscription, GeneticVirusesConceptsTranscriptional responseRegulatory networksMajor transcriptional responsePrimary mammalian cellsCellular transcriptional responsesPathogen-sensing pathwaysChromatin modifiersPathogen responseCandidate regulatorsCore regulatorsMammalian cellsTranscription factorsGenomic dataGene expressionRegulatory functionsUnbiased approachUnbiased strategyRegulatorUnbiased reconstructionPrimary dendritic cellsCellsRNAProteinPathwayPathogens