2023
Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube
Afzal Z, Lange J, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter B, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023, 150: dev201259. PMID: 37102683, PMCID: PMC10233718, DOI: 10.1242/dev.201259.Peer-Reviewed Original ResearchConceptsNascent transcriptionDynamic regulatory interactionsHox gene expressionCis-regulatory elementsRetinoic acid response elementMouse neural tubeTranscription of genesNon-coding RNAAcid response elementSingle-molecule fluorescentRetinoic acid responseMutant embryosHOXB clusterHox expressionAxial identityHoxb genesRegulatory interactionsTranscriptional mechanismsGene expressionDependent enhancersTranscriptionResponse elementResponsive enhancerNeural tubeCompetitive interactions
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 acid
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 development
2015
Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells
De Kumar B, Parrish M, Slaughter B, Unruh J, Gogol M, Seidel C, Paulson A, Li H, Gaudenz K, Peak A, McDowell W, Fleharty B, Ahn Y, Lin C, Smith E, Shilatifard A, Krumlauf R. Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. Genome Research 2015, 25: 1229-1243. PMID: 26025802, PMCID: PMC4510006, DOI: 10.1101/gr.184978.114.Peer-Reviewed Original ResearchConceptsChromatin modificationsHomeotic clustersHox genesES cellsClustered Hox genesHomeotic gene transcriptionMouse embryonic stem cellsNoncoding RNA genesRetinoid-induced transcriptionGenome-wide approachesCis-regulatory elementsEmbryonic stem cellsTranscription stateChromatin marksHOXB clusterNoncoding genesRNA genesSegmental identityActive transcriptionNoncoding RNAsTranscription factorsEpigenetic profilesGene transcriptionEpigenetic changesBody axis