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 alterationDrosophilaGenesGenome-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
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
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