2017
Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis
De Kumar B, Parker H, Paulson A, Parrish M, Zeitlinger J, Krumlauf R. Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis. Developmental Biology 2017, 432: 151-164. PMID: 28982536, DOI: 10.1016/j.ydbio.2017.09.033.Peer-Reviewed Original ResearchConceptsTarget genesEar developmentES cellsDifferential gene expression analysisGenome-wide analysisNeural crest specificationFunctional rolePutative target genesTransgenic mouse embryosMajor signaling pathwaysNeural crest migrationRelevant target genesDown-stream componentsMouse ES cellsGene expression analysisImportant functional roleRetinoic acidEvolutionary conservationEpigenetic marksHox cofactorsMutant phenotypeMouse embryogenesisNearby genesNeural fateMouse developmentDynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cells
De Kumar B, Parker H, Parrish M, Lange J, Slaughter B, Unruh J, Paulson A, Krumlauf R. Dynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: 5838-5845. PMID: 28584089, PMCID: PMC5468655, DOI: 10.1073/pnas.1610612114.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineEmbryonic Stem CellsGene Regulatory NetworksMiceModels, GeneticNanog Homeobox ProteinSignal TransductionConceptsES cell differentiationRegulatory networksMutual repressionRegulatory regionsCell differentiationCore pluripotency networkGenome-wide mappingRegulation of pluripotencyPatterns of occupancyCell-signaling pathwaysPluripotency networkNanog bindsHox genesGenomic approachesCommon target sitesRetinoic acid treatmentTarget genesDynamic regulationES cellsMouse embryosMolecular mechanismsHOXA1GenesAlternate statesNanog
2012
Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression
Gaertner B, Johnston J, Chen K, Wallaschek N, Paulson A, Garruss A, Gaudenz K, De Kumar B, Krumlauf R, Zeitlinger J. Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression. Cell Reports 2012, 2: 1670-1683. PMID: 23260668, PMCID: PMC3572839, DOI: 10.1016/j.celrep.2012.11.024.Peer-Reviewed Original ResearchConceptsPol IIMammalian embryonic stem cellsGenes de novoDevelopmental control genesPolycomb group repressionFuture gene expressionRNA Pol IIRNA polymerase IIEmbryonic stem cellsTissue-specific fashionChromatin stateDrosophila embryosPolymerase IIExtracellular signalsDevelopmental programStages of differentiationGene expressionControl genesDevelopmental timeSynchronous inductionDynamic expressionGenesStem cellsDe novoFuture expression
2011
Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC)
Lin C, Garrett A, De Kumar B, Smith E, Gogol M, Seidel C, Krumlauf R, Shilatifard A. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC). Genes & Development 2011, 25: 1486-1498. PMID: 21764852, PMCID: PMC3143939, DOI: 10.1101/gad.2059211.Peer-Reviewed Original ResearchConceptsSuper elongation complexEmbryonic stem cellsElongation complexPol IIDifferentiation signalsDynamic transcriptional eventsMurine embryonic stem cellsRNA polymerase IIStem cellsGlobal genomic analysisTranscription elongationPolymerase IITranscriptional regulationTranscriptional activationTranscriptional eventsGenomic analysisEnvironmental cuesES cellsGene expressionHuman cellsEnvironmental stimuliGenesEssential roleActivation signalsMajor classes