2021
BACH1, the master regulator of oxidative stress, has a dual effect on CFTR expression
NandyMazumdar M, Paranjapye A, Browne J, Yin S, Leir SH, Harris A. BACH1, the master regulator of oxidative stress, has a dual effect on CFTR expression. Biochemical Journal 2021, 478: 3741-3756. PMID: 34605540, PMCID: PMC8589331, DOI: 10.1042/bcj20210252.Peer-Reviewed Original ResearchMeSH KeywordsBasic-Leucine Zipper Transcription FactorsCell Line, TumorCell ProliferationCystic Fibrosis Transmembrane Conductance RegulatorEpithelial CellsGene Expression ProfilingGene Expression RegulationGlutamate-Cysteine LigaseGlutathioneHeme Oxygenase-1HumansHydrogen PeroxideNF-E2-Related Factor 2Oxidative StressOxygenPromoter Regions, GeneticRNA, Small InterferingSignal TransductionConceptsCis-regulatory elementsTranscription factorsCFTR expressionMaster regulatorHigher-order chromatin structureOrder chromatin structureMultiple cis-regulatory elementsFine-tune expressionSpecific transcription factorsCystic fibrosis transmembrane conductance regulator (CFTR) geneCFTR gene expressionCell-specific expressionTransmembrane conductance regulator geneOxidative stressArchitectural proteinsChromatin structureLocus architectureTune expressionBTB domainCNC homolog 1SiRNA screenRegulator geneGene promoterEnvironmental cuesPhysiological oxygenKrüppel-like factor 5 regulates wound repair and the innate immune response in human airway epithelial cells
Paranjapye A, NandyMazumdar M, Browne JA, Leir SH, Harris A. Krüppel-like factor 5 regulates wound repair and the innate immune response in human airway epithelial cells. Journal Of Biological Chemistry 2021, 297: 100932. PMID: 34217701, PMCID: PMC8353497, DOI: 10.1016/j.jbc.2021.100932.Peer-Reviewed Original ResearchConceptsKrüppel-like factor 5Lung epithelial cell lineEpithelial cell lineHistone modification H3K27acEpithelial cell identityDirect gene targetsSiRNA-mediated depletionHuman airway epithelial cellsCCAAT enhancer-binding protein betaEnhancer-binding protein betaCell linesSecretion of cytokinesAirway epithelial cellsHuman lung diseasesInnate immune responseHuman airway epitheliumPseudomonas aeruginosa lipopolysaccharideFactor 5Cell identityCalu-3 cellsChIP-seqTranscription factorsRNA-seqGene targetsIL-1βThe Bromodomain Containing 8 (BRD8) transcriptional network in human lung epithelial cells
Browne JA, NandyMazumdar M, Paranjapye A, Leir SH, Harris A. The Bromodomain Containing 8 (BRD8) transcriptional network in human lung epithelial cells. Molecular And Cellular Endocrinology 2021, 524: 111169. PMID: 33476703, PMCID: PMC8035426, DOI: 10.1016/j.mce.2021.111169.Peer-Reviewed Original ResearchConceptsCCCTC-Binding FactorTranscription factorsChIP-seq peaksProcess enrichment analysisArchitectural proteinsChromatin modificationsChromatin accessibilityTranscriptional networksProtein functionLung epithelial cell lineRepressive signalsHuman lung epithelial cellsEpithelial cell lineHuman lung epithelial cell lineEnrichment analysisGene expressionLung epithelial cellsCell cycleInnate immune responseLung epithelial functionCell proliferationAntimicrobial peptidesCell linesEpithelial functionEpithelial cells
2020
Functional genomics analysis of human colon organoids identifies key transcription factors
Yin S, Ray G, Kerschner JL, Hao S, Perez A, Drumm ML, Browne JA, Leir SH, Longworth M, Harris A. Functional genomics analysis of human colon organoids identifies key transcription factors. Physiological Genomics 2020, 52: 234-244. PMID: 32390556, PMCID: PMC7311676, DOI: 10.1152/physiolgenomics.00113.2019.Peer-Reviewed Original ResearchConceptsHuman intestinal organoidsOpen chromatinTranscription factorsOpen chromatin profilesGenome-wide analysisFunctional genomic analysisCaudal type homeobox 2Open chromatin peaksKey transcription factorIntestinal epitheliumIntestinal epithelial differentiationChromatin profilesMolecular divergenceFunctional genomicsATAC-seqMotif analysisTranscriptome mappingGenomic analysisRNA-seqGenomic signaturesHuman colon organoidsFunctional overlapEpithelial transport processesType homeobox 2Organoid biology
2019
Transcriptional networks in the human epididymis
Browne JA, Leir S, Yin S, Harris A. Transcriptional networks in the human epididymis. Andrology 2019, 7: 741-747. PMID: 31050198, PMCID: PMC6688904, DOI: 10.1111/andr.12629.Peer-Reviewed Original ResearchConceptsHepatocyte nuclear factor 1Transcription factorsChIP-seqRNA-seqOpen chromatinHEE cellsTranscription factor networkCis-regulatory elementsDistinct specialized functionsGene ontology analysisSpecific transcription factorsDistinct gene expression profilesDistinct transcriptional programsNon-coding RNAsKey transcription factorSiRNA-mediated depletionHuman epididymisGene expression profilesNuclear factor 1Antiviral response genesTF targetsTranscriptional networksDNase-seqFactor networkTranscriptional programs
2018
A transcription factor network represses CFTR gene expression in airway epithelial cells.
Mutolo MJ, Leir SH, Fossum SL, Browne JA, Harris A. A transcription factor network represses CFTR gene expression in airway epithelial cells. Biochemical Journal 2018, 475: 1323-1334. PMID: 29572268, PMCID: PMC6380350, DOI: 10.1042/bcj20180044.Peer-Reviewed Original ResearchConceptsCystic fibrosisTranscription factorsAirway epitheliumEpithelial cellsCalu-3 lung epithelial cellsPrimary human bronchial epithelial cellsAirway epithelium resultsKrüppel-like factor 5Novel therapeutic targetAirway epithelial cellsEts homologous factorHuman bronchial epithelial cellsTranscription factor networkBronchial epithelial cellsLung epithelial cellsTissue-specific enhancersCystic fibrosis transmembrane conductance regulator (CFTR) geneCFTR gene expressionAirway expressionTransmembrane conductance regulator geneLung diseaseCFTR mRNA levelsPancreatic ductTherapeutic targetCF morbidity
2016
HNF1 regulates critical processes in the human epididymis epithelium
Browne JA, Yang R, Eggener SE, Leir SH, Harris A. HNF1 regulates critical processes in the human epididymis epithelium. Molecular And Cellular Endocrinology 2016, 425: 94-102. PMID: 26808453, PMCID: PMC4799753, DOI: 10.1016/j.mce.2016.01.021.Peer-Reviewed Original ResearchConceptsHepatocyte nuclear factor 1Transcription factorsHuman epididymis epithelial cellsCis-regulatory elementsChIP-seq peaksProcess enrichment analysisHNF1β transcription factorHEE cellsNuclear factor 1Luminal environmentChromatin genomeChromatin immunoprecipitationTranscriptional programsCoordinated expressionRNA-seqEpithelial transportRegulatory elementsTarget genesBioinformatics predictionCritical genesEnrichment analysisDeep sequencingEpididymis functionCritical processSperm maturation
2015
Expression profiles of human epididymis epithelial cells reveal the functional diversity of caput, corpus and cauda regions
Browne JA, Yang R, Leir SH, Eggener SE, Harris A. Expression profiles of human epididymis epithelial cells reveal the functional diversity of caput, corpus and cauda regions. Molecular Human Reproduction 2015, 22: 69-82. PMID: 26612782, PMCID: PMC4733224, DOI: 10.1093/molehr/gav066.Peer-Reviewed Original ResearchConceptsCultured epithelial cellsEpididymis functionExpression profilesHuman epididymis epithelial cellsSperm maturationDefense response processNormal sperm maturationEpithelial cellsProcess enrichment analysisGene expression profilesLuminal environmentUrogenital tract developmentFunctional diversityTranscriptional profilingCauda cellsTranscription factorsBioinformatics toolsBiological replicatesMale genital ductsSimilar transcriptomesMolecular basisEnrichment analysisHormonal signalsSAMPLES/MATERIALSDifferential expression