2021
The 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
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 ResearchMeSH KeywordsComputational BiologyEpididymisGene Expression ProfilingGene Expression RegulationGene Regulatory NetworksHepatocyte Nuclear Factor 1HumansMaleSperm MaturationTranscriptomeConceptsHepatocyte 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
Region-specific microRNA signatures in the human epididymis
Browne JA, Leir SH, Eggener SE, Harris A. Region-specific microRNA signatures in the human epididymis. Asian Journal Of Andrology 2018, 20: 539-544. PMID: 30058558, PMCID: PMC6219309, DOI: 10.4103/aja.aja_40_18.Peer-Reviewed Original ResearchConceptsGene expressionSegment-specific gene expressionImportant gene networksRegionalized expression patternsRegionalized gene expressionGene ontology pathwaysSmall noncoding RNAsHuman epididymisEpithelial cellsOntology pathwaysGene networksNoncoding RNAsTarget genesHuman epididymal tissueExpression patternsSperm maturationMiR-573MiRNA expressionMiRNAsDifferentiated functionsMicroRNAsMicroRNA profilesMale fertilityLuminal environmentMiRNA signatureA novel transcriptional network for the androgen receptor in human epididymis epithelial cells
Yang R, Browne JA, Eggener SE, Leir SH, Harris A. A novel transcriptional network for the androgen receptor in human epididymis epithelial cells. Molecular Human Reproduction 2018, 24: 433-443. PMID: 30016502, PMCID: PMC6454485, DOI: 10.1093/molehr/gay029.Peer-Reviewed Original ResearchConceptsAndrogen receptorHEE cellsHuman epididymis epithelial cellsEpithelial cellsAR activationTranscriptional networksEunice Kennedy Shriver National InstituteChIP-seqProstate cancer cell linesPARTICIPANTS/MATERIALSNational InstituteSynthetic androgen R1881ROLE OF CHANCEEpididymis epitheliumDistinct androgen receptorsProstate gland epitheliumRNA-seqRunt-related transcription factor 1Single androgen receptorCancer cell linesSilico motif analysisTranscription factor 1Prostate cancerAndrogen R1881Cis-regulatory elementsA 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
2014
Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function
Browne JA, Yang R, Song L, Crawford GE, Leir SH, Harris A. Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function. Molecular Human Reproduction 2014, 20: 1198-1207. PMID: 25180270, PMCID: PMC4235575, DOI: 10.1093/molehr/gau075.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsBinding SitesCell LineChromatin Assembly and DisassemblyEpididymisEpithelial CellsGene Expression ProfilingGene Expression RegulationGene Regulatory NetworksGenome-Wide Association StudyHigh-Throughput Nucleotide SequencingHumansMalePAX2 Transcription FactorRNA InterferenceTranscription, GeneticTransfectionConceptsTranscription factor-binding sitesOpen chromatinREP cellsEpididymis epitheliumCoordinated gene expressionGenome-wide mapsSperm cell maturationHigh-throughput sequencingRNA-seq analysisCritical transcriptional regulatorPotential regulatory elementsFactor-binding sitesHEE cellsDNase I digestionRole of PAX2Chromatin mappingUrogenital tract developmentTranscriptional networksTranscriptional regulatorsCoordinated expressionRegulatory elementsMultiple genesGene expressionSilico analysisChromatin