2024
Hox Genes
Duraiswamy A, Senkumar L, De Kumar B. Hox Genes. 2024 DOI: 10.1016/b978-0-12-822563-9.00196-7.Peer-Reviewed Original ResearchHox genesAberrant expression of HOX genesCell fate determinationExpression of Hox genesFate determinationTissue homeostasisMetastatic behavior of tumorsCell migrationGenesDevelopmental eventsDevelopmental defectsHoxCancer progressionAberrant expressionMetastatic behaviorBehavior of tumorsCellsDisease progressionDisease prognosisProteinHomeostasisOrganogenesisPrognosis
2021
The Hox protein conundrum: The “specifics” of DNA binding for Hox proteins and their partners
De Kumar B, Darland D. The Hox protein conundrum: The “specifics” of DNA binding for Hox proteins and their partners. Developmental Biology 2021, 477: 284-292. PMID: 34102167, PMCID: PMC8846413, DOI: 10.1016/j.ydbio.2021.06.002.Peer-Reviewed Original ResearchConceptsProtein binding specificityHox proteinsAnterior-posterior body axisTranscription factor-DNA interactionsBinding specificityHox protein functionMulti-protein interactionsHomeodomain transcription factorHomeotic genesSegmental identityUnique target specificityProtein functionTranscription factorsCooperative binding modelGene expressionBody axisMolecular characterizationTarget specificityProteinDNAMouse systemRecent studiesSubsequent alterationDrosophilaGenes
2019
Hox genes: Downstream “effectors” of retinoic acid signaling in vertebrate embryogenesis
Nolte C, De Kumar B, Krumlauf R. Hox genes: Downstream “effectors” of retinoic acid signaling in vertebrate embryogenesis. Genesis 2019, 57: e23306. PMID: 31111645, DOI: 10.1002/dvg.23306.Peer-Reviewed Original ResearchConceptsHox genesAxial patterningHox gene expressionAnteroposterior axisBasic body planGene regulatory networksVertebrate embryogenesisAnimal developmentPatterning of cellsVertebrate developmentBody planAxial specificationRegulatory networksCombinatorial codeTissue contextGene expressionDirect effectorVertebrate planHematopoietic systemGenesReproductive organsRegulatory processesEmbryogenesisDifferential responseRetinoic acidA Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates
Parker H, De Kumar B, Green S, Prummel K, Hess C, Kaufman C, Mosimann C, Wiedemann L, Bronner M, Krumlauf R. A Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates. Nature Communications 2019, 10: 1189. PMID: 30867425, PMCID: PMC6416258, DOI: 10.1038/s41467-019-09197-8.Peer-Reviewed Original ResearchConceptsNeural crestHox genesAncestral mechanismRegulatory circuitsUpstream regulatory componentsNeural crest patterningAncient paraloguesPbx proteinsJawed vertebratesAncient conservationExtant vertebratesAncestral activityRegulatory interactionsHOX2 genesRegulatory componentsVertebratesJaw formationGenesGnathostomesEnhancerHoxLampreyParaloguesImportant roleHoxa2
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
2017
Dynamic 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 ResearchConceptsES 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
2016
HOXs and lincRNAs: Two sides of the same coin
De Kumar B, Krumlauf R. HOXs and lincRNAs: Two sides of the same coin. Science Advances 2016, 2: e1501402. PMID: 27034976, PMCID: PMC4805430, DOI: 10.1126/sciadv.1501402.Peer-Reviewed Original Research
2013
Insights from transcriptional profiling the mouse hindbrain: Novel feedback between retinoids and Hox genes
Yurieva M, De Kumar B, Krumlauf R. Insights from transcriptional profiling the mouse hindbrain: Novel feedback between retinoids and Hox genes. The FASEB Journal 2013, 27: 966.1-966.1. DOI: 10.1096/fasebj.27.1_supplement.966.1.Peer-Reviewed Original ResearchHox genesTranscriptional profilingTranscription factorsDpc mouse embryosGene expression patternsKey transcription factorVertebrate hindbrainHindbrain patterningLaser capture microscopyHox familyFunctional validationMouse embryosExpression patternsGene expressionWild typeRhombomeresMouse hindbrainIndividual rhombomeresSingle rhombomereGenesNovel targetRetinoid metabolismHindbrainAnimal lethalityProfiling
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