2015
Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency
Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Sui S, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell 2015, 162: 412-424. PMID: 26186193, PMCID: PMC4511597, DOI: 10.1016/j.cell.2015.06.016.Peer-Reviewed Original ResearchMeSH KeywordsCellular ReprogrammingChromatinChromatin Assembly and DisassemblyEpigenesis, GeneticGene Expression ProfilingHistone DemethylasesHumansInduced Pluripotent Stem CellsConceptsInduced pluripotencyHuman cellsEmbryonic patterning genesComplementary functional analysesPre-implantation stagesPatterning genesDevelopmental regulatorsEpigenomic analysisMolecular principlesNovel regulatorFunctional analysisIntegrative analysisIntercellular heterogeneityMolecular underpinningsPluripotencyDisease modelingCell platformRegulatorCellsDistinct wavesDonor variabilityGenes
2011
Lung Stem Cell Self-Renewal Relies on BMI1-Dependent Control of Expression at Imprinted Loci
Zacharek SJ, Fillmore CM, Lau AN, Gludish DW, Chou A, Ho JW, Zamponi R, Gazit R, Bock C, Jäger N, Smith ZD, Kim TM, Saunders AH, Wong J, Lee JH, Roach RR, Rossi DJ, Meissner A, Gimelbrant AA, Park PJ, Kim CF. Lung Stem Cell Self-Renewal Relies on BMI1-Dependent Control of Expression at Imprinted Loci. Cell Stem Cell 2011, 9: 272-281. PMID: 21885022, PMCID: PMC3167236, DOI: 10.1016/j.stem.2011.07.007.Peer-Reviewed Original ResearchMeSH KeywordsAdult Stem CellsAnimalsCell SurvivalCells, CulturedCyclin-Dependent Kinase Inhibitor p16Gene Expression ProfilingGene Expression Regulation, DevelopmentalGenes, p16Genetic LociGenomic ImprintingLungMiceMice, Mutant StrainsNuclear ProteinsPolycomb Repressive Complex 1Proto-Oncogene ProteinsRegenerationRepressor ProteinsRNA, Small InterferingS-Phase Kinase-Associated ProteinsConceptsImprinted lociBronchioalveolar stem cellsStem cellsAdult tissue-specific stem cellsTissue-specific stem cellsLung epithelial stem cellsSelf-renewal defectLung epithelial cell injuryLung stem cellsDevelopmental processesEpithelial stem cellsExpression of p57Bmi1 knockout miceLung cellsGenesAdult cellsLociExpressionCellsAllelesRegulationKnockout miceEpithelial cell injuryFundamental questionsCDKN1CReference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, Gnirke A, Eggan K, Meissner A. Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines. Cell 2011, 144: 439-452. PMID: 21295703, PMCID: PMC3063454, DOI: 10.1016/j.cell.2010.12.032.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCell LineDNA MethylationEmbryonic Stem CellsGene Expression ProfilingHumansInduced Pluripotent Stem CellsConceptsPluripotent cell linesEmbryonic stemPluripotent stem cellsCell linesDisease-relevant cell typesHuman iPS cell linesStem cellsReference mapHuman pluripotent stem cellsHuman embryonic stemIPS cell linesDifferentiation propensityDNA methylationIndividual cell linesHigh-throughput characterizationTranscriptional similarityGene expressionIPS cellsCell typesDifferentiation efficiencyDevelopmental potentialBiomedical researchComprehensive characterizationSpecific differencesCells
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