2019
A 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
2017
HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets
De Kumar B, Parker H, Paulson A, Parrish M, Pushel I, Singh N, Zhang Y, Slaughter B, Unruh J, Florens L, Zeitlinger J, Krumlauf R. HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets. Genome Research 2017, 27: 1501-1512. PMID: 28784834, PMCID: PMC5580710, DOI: 10.1101/gr.219386.116.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatinGenomeHomeodomain ProteinsMiceMouse Embryonic Stem CellsProtein BindingProtein Interaction MapsProteomicsRepressor ProteinsTranscription FactorsTranscription, GeneticConceptsCross-regulatory interactionsTALE proteinsTALE membersCombinatorial binding patternsGenome-wide analysisGenome-wide basisCross-regulatory networkDiverse functional rolesMouse ES cellsHox cofactorsTALE familyFunctional diversityTransgenic reporterCombinatorial interactionsRegulatory networksHox-PbxProteomic analysisEnhancer activityHOXA1ES cellsFunctional roleProteinDistinct mechanismsBinding patternDistinct classes
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