2021
TNF stimulation primarily modulates transcriptional burst size of NF‐κB‐regulated genes
Bass VL, Wong VC, Bullock ME, Gaudet S, Miller‐Jensen K. TNF stimulation primarily modulates transcriptional burst size of NF‐κB‐regulated genes. Molecular Systems Biology 2021, 17: msb202010127. PMID: 34288498, PMCID: PMC8290835, DOI: 10.15252/msb.202010127.Peer-Reviewed Original ResearchMeSH KeywordsAcetylationGene Expression RegulationNF-kappa BPromoter Regions, GeneticTumor Necrosis Factor-alphaConceptsNF-κB-regulated inflammatory genesGene expression noiseOpen chromatin environmentTranscriptional burst sizeNF-κB target genesNF-κB-regulated genesHistone 3 acetylationChromatin environmentTranscription factor NF-κBTranscriptional noiseExpression noiseTranscriptional burstingTranscript distributionFactor NF-κBGene promoterSubset of cellsIntercellular heterogeneityTNF stimulationCell heterogeneityGenesTNF protein expressionTNF activationProtein expressionTranscriptionBurst sizeCo-stimulation with opposing macrophage polarization cues leads to orthogonal secretion programs in individual cells
Muñoz-Rojas AR, Kelsey I, Pappalardo JL, Chen M, Miller-Jensen K. Co-stimulation with opposing macrophage polarization cues leads to orthogonal secretion programs in individual cells. Nature Communications 2021, 12: 301. PMID: 33436596, PMCID: PMC7804107, DOI: 10.1038/s41467-020-20540-2.Peer-Reviewed Original ResearchConceptsCo-stimulated macrophagesFunctional diversitySingle-cell RNA sequencingGlobal transcriptional programSuch functional diversityTranscriptional programsTissue homeostasisRNA sequencingEnvironmental cuesGene resultsExclusive expressionInflammatory stimuli LPSCell heterogeneityIndividual cellsPolarization cuesIndividual macrophagesTissue repairCytokine genesDiversityInnate immune cellsFighting infectionsCellsMacrophagesCuesTranscription
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 ResearchMeSH KeywordsAnimalsChromatin Assembly and DisassemblyComputational BiologyEpigenesis, GeneticGene Expression RegulationHumansNeoplasmsPhenotypeTranscription, GeneticVirus LatencyConceptsGene expression noiseExpression noisePhenotypic heterogeneityChromatin modificationsChromatin remodelingTranscriptional burstsEpigenetic controlReversible drug resistancePhenotypic diversityGene statesIdentical populationsDiseased cellsDrug resistanceCellsEukaryotesFundamental informationViral infectionVirulenceDiversityTherapeutic interventionsBetter understandingIntrinsic noiseRemodelingHeterogeneityRandom transitions