2023
Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding
Dastidar S, De Kumar B, Lauckner B, Parrello D, Perley D, Vlasenok M, Tyagi A, Koney N, Abbas A, Nechaev S. Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding. Nature Communications 2023, 14: 7420. PMID: 37973875, PMCID: PMC10654513, DOI: 10.1038/s41467-023-43157-7.Peer-Reviewed Original Research
2021
Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube
Parker H, De Kumar B, Pushel I, Bronner M, Krumlauf R. Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube. Developmental Biology 2021, 479: 61-76. PMID: 34310923, DOI: 10.1016/j.ydbio.2021.07.014.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesBody PatterningConserved SequenceEnhancer Elements, GeneticGene ExpressionGene Expression Regulation, DevelopmentalGenes, HomeoboxHomeodomain ProteinsLampreysMyeloid Ecotropic Viral Integration Site 1 ProteinNeural CrestNeural TubePre-B-Cell Leukemia Transcription Factor 1RhombencephalonTranscription FactorsConceptsMeis genesTALE proteinsDivergence of jawedSea lamprey genomeEvolution of vertebratesNeural crest cellsLamprey genomeTALE factorsPattern of expressionPbx proteinsJawed vertebratesVertebrate evolutionDeep ancestryJawless vertebratesLamprey embryosRhombomeric domainsTransgenic reporterNeural enhancerSimilar relative positionsRegulatory interactionsPharyngeal archesReporter expressionHead developmentCrest cellsSequence alignment
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 developmentHOXA1 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 ResearchConceptsCross-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