2019
In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation
Andergassen D, Smith ZD, Lewandowski JP, Gerhardinger C, Meissner A, Rinn JL. In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation. ELife 2019, 8: e47214. PMID: 31738164, PMCID: PMC6860989, DOI: 10.7554/elife.47214.Peer-Reviewed Original ResearchConceptsX-chromosome inactivationAutosomal gene regulationGene regulationDouble deletionOrgan-specific mannerChromosome inactivationGene setsX chromosomeTranscriptional effectsExpression signaturesLociCell linesDeletionGenesRegulationVivo contributionRecent evidenceMegadomainsAutosomesFIRREMutantsChromosomesMain driversBiologySuperloops
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 ResearchConceptsInduced pluripotencyHuman cellsEmbryonic patterning genesComplementary functional analysesPre-implantation stagesPatterning genesDevelopmental regulatorsEpigenomic analysisMolecular principlesNovel regulatorFunctional analysisIntegrative analysisIntercellular heterogeneityMolecular underpinningsPluripotencyDisease modelingCell platformRegulatorCellsDistinct wavesDonor variabilityGenes
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
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 questionsCDKN1C