2022
A transcriptional cycling model recapitulates chromatin-dependent features of noisy inducible transcription
Bullock ME, Moreno-Martinez N, Miller-Jensen K. A transcriptional cycling model recapitulates chromatin-dependent features of noisy inducible transcription. PLOS Computational Biology 2022, 18: e1010152. PMID: 36084132, PMCID: PMC9491597, DOI: 10.1371/journal.pcbi.1010152.Peer-Reviewed Original ResearchMeSH KeywordsChromatinHIV InfectionsHIV-1HumansNF-kappa BTranscription, GeneticTranscriptional ActivationVirus LatencyConceptsGene expression noiseExpression noiseTranscriptional burstingPromoter statesDifferent chromatin environmentsChromatin environmentChromatin statePause releaseTranscription factor NFChromatin accessibilityChromatin remodelingTranscriptional noiseChromatin locationsInducible transcriptionSubstantial phenotypic heterogeneityTranscriptional activationTranscription factorsTranscript distributionPolymerase complexTarget genesPolymerase bindingGene expressionPromoter activityViral activationBiological processes
2017
Systems analysis of latent HIV reversal reveals altered stress kinase signaling and increased cell death in infected T cells
Fong LE, Sulistijo ES, Miller-Jensen K. Systems analysis of latent HIV reversal reveals altered stress kinase signaling and increased cell death in infected T cells. Scientific Reports 2017, 7: 16179. PMID: 29170390, PMCID: PMC5701066, DOI: 10.1038/s41598-017-15532-0.Peer-Reviewed Original ResearchConceptsInfected T cellsT cellsT cell reservoirCell deathPMA/ionomycinCD3/CD28Phosphorylation of IκBαViral protein expressionPhosphorylation signaturesHIV eradicationLatent CD4HIV reactivationLatent reservoirLatent HIVActivation of p38Latent infectionClinical strategiesViral latencyViral expressionProtein expressionUninfected cellsInfected cellsDeathCD4Cell reservoir
2015
Distinct promoter activation mechanisms modulate noise-driven HIV gene expression
Chavali AK, Wong VC, Miller-Jensen K. Distinct promoter activation mechanisms modulate noise-driven HIV gene expression. Scientific Reports 2015, 5: 17661. PMID: 26666681, PMCID: PMC4678399, DOI: 10.1038/srep17661.Peer-Reviewed Original ResearchA passive-flow microfluidic device for imaging latent HIV activation dynamics in single T cells
Ramji R, Wong VC, Chavali AK, Gearhart LM, Miller-Jensen K. A passive-flow microfluidic device for imaging latent HIV activation dynamics in single T cells. Integrative Biology 2015, 7: 998-1010. PMID: 26138068, PMCID: PMC4558391, DOI: 10.1039/c5ib00094g.Peer-Reviewed Original Research
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
2011
Varying virulence: epigenetic control of expression noise and disease processes
Miller-Jensen K, Dey SS, Schaffer DV, Arkin AP. Varying virulence: epigenetic control of expression noise and disease processes. Trends In Biotechnology 2011, 29: 517-525. PMID: 21700350, DOI: 10.1016/j.tibtech.2011.05.004.Peer-Reviewed Original ResearchConceptsGene expression noiseExpression noisePhenotypic heterogeneityChromatin modificationsChromatin remodelingTranscriptional burstsEpigenetic controlReversible drug resistancePhenotypic diversityGene statesIdentical populationsDiseased cellsDrug resistanceCellsEukaryotesFundamental informationViral infectionVirulenceDiversityTherapeutic interventionsBetter understandingIntrinsic noiseRemodelingHeterogeneityRandom transitions
2009
Control of Stochastic Gene Expression by Host Factors at the HIV Promoter
Burnett JC, Miller-Jensen K, Shah PS, Arkin AP, Schaffer DV. Control of Stochastic Gene Expression by Host Factors at the HIV Promoter. PLOS Pathogens 2009, 5: e1000260. PMID: 19132086, PMCID: PMC2607019, DOI: 10.1371/journal.ppat.1000260.Peer-Reviewed Original Research