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
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