2020
Cancer-specific mutation of GATA3 disrupts the transcriptional regulatory network governed by Estrogen Receptor alpha, FOXA1 and GATA3
Takaku M, Grimm S, De Kumar B, Bennett B, Wade P. Cancer-specific mutation of GATA3 disrupts the transcriptional regulatory network governed by Estrogen Receptor alpha, FOXA1 and GATA3. Nucleic Acids Research 2020, 48: 4756-4768. PMID: 32232341, PMCID: PMC7229857, DOI: 10.1093/nar/gkaa179.Peer-Reviewed Original ResearchConceptsRegulatory networksAltered chromatin architectureTranscriptional regulatory networksDifferential gene expressionEpithelial cell biologyTranscription factor FOXA1Mammary epithelial cellsEstrogen receptor alphaCancer-specific mutationsMammary gland developmentChromatin architectureChromatin localizationGenomic localizationReceptor alphaMutant cellsGenomic analysisNetwork downstreamGene setsCell biologyEstrogen receptorGene expressionGATA3 mutationsGland developmentSimilar mutationsFOXA1
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
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 ResearchMeSH KeywordsAnimalsEvolution, MolecularGene Expression RegulationGene Regulatory NetworksGenes, HomeoboxHumansMultigene FamilyRNA, Long NoncodingTranscriptional Activation