2015
Noise in gene expression is coupled to growth rate
Keren L, van Dijk D, Weingarten-Gabbay S, Davidi D, Jona G, Weinberger A, Milo R, Segal E. Noise in gene expression is coupled to growth rate. Genome Research 2015, 25: 1893-1902. PMID: 26355006, PMCID: PMC4665010, DOI: 10.1101/gr.191635.115.Peer-Reviewed Original ResearchMeSH KeywordsCell CycleEnvironmentGene ExpressionGene Expression Regulation, FungalGene-Environment InteractionModels, BiologicalPromoter Regions, GeneticSaccharomyces cerevisiaeSingle-Cell AnalysisTranscriptional ActivationConceptsGene expression noiseExpression noiseGene expressionGlobal changeLower growth rateDifferent growth ratesDifferent cell cycle stagesAverage gene expressionNutrient-poor conditionsEnvironmental conditionsCell cycle stageOverall high variabilityGrowth rateMost promotersCell cycle heterogeneityCellular regulationPromoter featuresDisplay elevated levelsExpression variabilityBiological functionsExpression distributionPhenotypic implicationsAsynchronous populationIdentical cellsExpression valuesSlow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage
van Dijk D, Dhar R, Missarova AM, Espinar L, Blevins WR, Lehner B, Carey LB. Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage. Nature Communications 2015, 6: 7972. PMID: 26268986, PMCID: PMC4557116, DOI: 10.1038/ncomms8972.Peer-Reviewed Original ResearchMeSH KeywordsCell ProliferationDNA DamageDNA-Directed RNA PolymerasesFlow CytometryFungal ProteinsGene Expression Regulation, FungalRNA, FungalYeastsConceptsTranscriptional stress responseDNA damageDNA damage responseIsogenic populationsRNA polymerase fidelityDamage responseTranscriptional differencesIsogenic cellsEnvironmental stressCell variabilityStress responseGrowth ratePolymerase fidelityCulture conditionsPolymerase error rateOxidative stressCellsSuch cellsSame environmentTranscriptomeTransposonSubpopulationsTranscriptsGenotypicStress
2013
Promoter Sequence Determines the Relationship between Expression Level and Noise
Carey LB, van Dijk D, Sloot PM, Kaandorp JA, Segal E. Promoter Sequence Determines the Relationship between Expression Level and Noise. PLOS Biology 2013, 11: e1001528. PMID: 23565060, PMCID: PMC3614515, DOI: 10.1371/journal.pbio.1001528.Peer-Reviewed Original ResearchMeSH KeywordsAlcohol DehydrogenaseBacterial ProteinsBase SequenceBinding SitesCation Transport ProteinsEnzyme InductionGene ExpressionGene Expression Regulation, FungalGene LibraryGenes, ReporterKineticsLuminescent ProteinsModels, GeneticPromoter Regions, GeneticProtein BindingSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription FactorsConceptsTranscriptional burstsUnique transcriptional statesTranscription factor activitySingle target geneExpression levelsMechanism of repressionAbility of cellsTF activityGene expression levelsExtracellular cuesTranscriptional statesTranscriptional regulationPromoter DNAPromoter sequencesSingle TFCell variabilityTarget genesRegulatory mechanismsExpression changesZap1Diverse mechanismsNative targetsFactor activityExpression increasesGenes