2021
Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression
Singh N, De Kumar B, Paulson A, Parrish M, Scott C, Zhang Y, Florens L, Krumlauf R. Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression. Journal Of Developmental Biology 2021, 9: 6. PMID: 33546292, PMCID: PMC7931043, DOI: 10.3390/jdb9010006.Peer-Reviewed Original ResearchHistone marksGenome-wide binding analysisRepressive histone marksActive histone marksTranscriptional repressor RESTExpression of Hoxb1Specific regulatory functionsEmbryonic stem cellsAnimal developmentGene repressionHoxb1 functionGene regulationNeural fateRepressor RESTRepressive roleTranscription factorsHoxb1Diverse DNATarget genesReporter geneGene expressionRegulatory functionsStem cellsMotifBinding analysis
2018
Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits Leukemogenesis
Qian P, De Kumar B, He X, Nolte C, Gogol M, Ahn Y, Chen S, Li Z, Xu H, Perry J, Hu D, Tao F, Zhao M, Han Y, Hall K, Peak A, Paulson A, Zhao C, Venkatraman A, Box A, Perera A, Haug J, Parmely T, Li H, Krumlauf R, Li L. Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits Leukemogenesis. Cell Stem Cell 2018, 22: 740-754.e7. PMID: 29727682, DOI: 10.1016/j.stem.2018.04.012.Peer-Reviewed Original ResearchConceptsHoxb expressionHematopoietic stem cellsDNA methylationCoordinate regulationLoss of HSCsCis-regulatory elementsSpecific DNA methylationDNA methylome analysisHox genesHOXB clusterHox expressionEpigenetic regulationDNA methyltransferasesMethylome analysisHoxb genesCluster expressionLT-HSCsRetinoid signalingNormal hematopoiesisGenesStem cellsLeukemogenesisMethylationReconstitution capacityRegulation
2016
The Methylation-Sensitive Enhancer Derare Maintains Hematopoietic Stem Cells through Regulation of Hoxb Cluster
Qian P, De Kumar B, Ahn Y, Nolte C, Paulson A, He X, Li Z, Perry J, Zhao M, Tao F, Krumlauf R, Li L. The Methylation-Sensitive Enhancer Derare Maintains Hematopoietic Stem Cells through Regulation of Hoxb Cluster. Blood 2016, 128: 725. DOI: 10.1182/blood.v128.22.725.725.Peer-Reviewed Original ResearchHematopoietic stem cellsHoxB gene expressionGene expressionLT-HSCsHOXB clusterHOXB cluster genesCluster genesHoxb genesCluster gene expressionChIP-seq analysisCis-regulatory elementsTrans-acting factorsFunctional hematopoietic stem cellsNext-generation sequencing technologiesStem cellsDNA methylation analysisCancer Genome Atlas (TCGA) projectHematopoietic cell typesLong-term reconstitution capacityHSC maintenancePutative enhancersTranscriptome analysisRegulatory networksRNA-seqGenetic regulatory networks
2015
A Conserved Cis-Regulatory Retinoic Acid Responsive Element Is Essential for Maintenance of Primitive Hematopoietic Stem Cells through Regulation of Hoxb Cluster
Qian P, Ahn Y, De Kumar B, Nolte C, He X, Paulson A, Perry J, Li Z, Krumlauf R, Li L. A Conserved Cis-Regulatory Retinoic Acid Responsive Element Is Essential for Maintenance of Primitive Hematopoietic Stem Cells through Regulation of Hoxb Cluster. Blood 2015, 126: 2377. DOI: 10.1182/blood.v126.23.2377.2377.Peer-Reviewed Original ResearchRetinoic acid responsive elementHOXB clusterHematopoietic stem cellsAcid-responsive elementPrimitive hematopoietic stem cellsLT-HSCsHox clustersHox genesHigh-throughput transcriptome analysisResponsive elementIndividual Hox genesCell typesMultiple Hox genesStem cell maintenanceFunctional hematopoietic stem cellsHoxB gene expressionStem cellsMultiple blood cell typesNervous system developmentCentral nervous system developmentLong-term reconstitution capacityHOXB cluster genesKnockout mouse modelBlood cell typesVertebrate species
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