2021
Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes
Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, Niklason LE, Montgomery RR, Eisenbarth SC, Chen S, Williams A, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, Pyle AM, van Dijk D, Wilen CB. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLOS Biology 2021, 19: e3001143. PMID: 33730024, PMCID: PMC8007021, DOI: 10.1371/journal.pbio.3001143.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionSARS-CoV-2Human bronchial epithelial cellsInterferon-stimulated genesCell state changesAcute respiratory syndrome coronavirus 2 infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectionSyndrome coronavirus 2 infectionCell tropismCoronavirus 2 infectionCoronavirus disease 2019Onset of infectionCell-intrinsic expressionCourse of infectionAir-liquid interface culturesHost-viral interactionsBronchial epithelial cellsSingle-cell RNA sequencingCell typesIL-1Disease 2019Human airwaysDevelopment of therapeuticsDrug AdministrationViral replication
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 ResearchConceptsGene 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 values
2014
Probing the effect of promoters on noise in gene expression using thousands of designed sequences
Sharon E, van Dijk D, Kalma Y, Keren L, Manor O, Yakhini Z, Segal E. Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Research 2014, 24: 1698-1706. PMID: 25030889, PMCID: PMC4199362, DOI: 10.1101/gr.168773.113.Peer-Reviewed Original ResearchConceptsExpression noiseGene expressionMean expression levelTranscription factorsPromoter sequencesExpression levelsGene expression noisePromoter DNA sequencesMore transcription factorsNucleosome-disfavoring sequencesHigher expression noiseDifferent promoter sequencesNonspecific DNA bindingOne-dimensional slidingCellular functionsHigh-throughput methodNative promoterDNA sequencesDNA bindingSynthetic promotersPromoterIdentical cellsTarget siteSequence
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