2013
Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression
Miller-Jensen K, Skupsky R, Shah PS, Arkin AP, Schaffer DV. Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression. PLOS Computational Biology 2013, 9: e1003135. PMID: 23874178, PMCID: PMC3708878, DOI: 10.1371/journal.pcbi.1003135.Peer-Reviewed Original ResearchConceptsGenomic contextGene expressionSp1 mutationPromoter sequencesStochastic phenotypeEukaryotic gene expressionForward genetic screenBasal expressionHIV-1 gene expressionViral gene expressionCore promoter regionSingle-cell experimentsGene expression levelsGenetic screenHIV LTR promoterPhenotypic noiseAbsence of TatTranscription factorsPromoter elementsGenomic integrationPositive feedback loopGenetic elementsRelevant model systemPromoter regionGenetic selection
2012
Chromatin accessibility at the HIV LTR promoter sets a threshold for NF-κB mediated viral gene expression
Miller-Jensen K, Dey SS, Pham N, Foley JE, Arkin AP, Schaffer DV. Chromatin accessibility at the HIV LTR promoter sets a threshold for NF-κB mediated viral gene expression. Integrative Biology 2012, 4: 661-671. PMID: 22555315, PMCID: PMC3362694, DOI: 10.1039/c2ib20009k.Peer-Reviewed Original ResearchConceptsChromatin accessibilityGene expressionChromatin environmentIntegration sitesHigher-order chromatin structureDifferent genomic environmentsLTR promoterRepressive histone marksDifferent chromatin environmentsOrder chromatin structureGene expression regulationTranscription factor inputsSame transcription factorDifferential gene expressionLevels of RelASelective gene expressionViral gene expressionViral integration sitesTranscription factor activationHIV gene regulationGenomic environmentHIV LTR promoterHistone marksChromatin featuresChromatin structure