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 ResearchMeSH KeywordsAnimalsDNADNA-Binding ProteinsGenes, HomeoboxHomeodomain ProteinsHumansModels, GeneticProtein BindingConceptsProtein 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 alterationDrosophilaGenes
2020
A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins
Singh N, De Kumar B, Paulson A, Parrish M, Zhang Y, Florens L, Conaway J, Si K, Krumlauf R. A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins. Genes & Development 2020, 34: 1680-1696. PMID: 33184220, PMCID: PMC7706710, DOI: 10.1101/gad.342329.120.Peer-Reviewed Original ResearchConceptsC-terminal motifAncestral activityFunctional analysisDNA-binding patternsGenome-wide analysisDNA-binding regionLow sequence similarityDNA-binding experimentsAmino acid sequenceSix-amino acid motifAncestral functionPbx proteinsEvolutionary noveltyGene duplicationFunctional diversificationHoxa1 proteinMouse proteinProtein functionSequence similarityFunctional evolutionAcid sequenceChimeric proteinMouse cellsHoxb1Structural predictions
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 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