2018
Intrinsic cooperativity potentiates parallel cis-regulatory evolution
Sorrells T, Johnson A, Howard C, Britton C, Fowler K, Feigerle J, Weil P, Johnson A. Intrinsic cooperativity potentiates parallel cis-regulatory evolution. ELife 2018, 7: e37563. PMID: 30198843, PMCID: PMC6173580, DOI: 10.7554/elife.37563.Peer-Reviewed Original ResearchConceptsRegulatory sequencesGeneral transcription factor TFIIDCis-regulatory evolutionRibosomal protein genesTranscription factor TFIIDCommon interaction partnersFungal lineagesAncestral regulatorFactor TFIIDIndependent lineagesEvolutionary eventsGenomic scaleTranscription regulatorsTranscriptional activationParallel evolutionProtein geneRegulatory proteinsSecond regulatorInteraction partnersRandom mutationsFunctional sitesIntrinsic cooperativityMcm1Rap1Regulator
2015
Intersecting transcription networks constrain gene regulatory evolution
Sorrells T, Booth L, Tuch B, Johnson A. Intersecting transcription networks constrain gene regulatory evolution. Nature 2015, 523: 361-365. PMID: 26153861, PMCID: PMC4531262, DOI: 10.1038/nature14613.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBinding SitesDNA, FungalDNA-Binding ProteinsEnhancer Elements, GeneticEpistasis, GeneticEvolution, MolecularGene Expression Regulation, FungalGene Regulatory NetworksGenes, FungalKluyveromycesMating FactorPeptidesPheromonesPromoter Regions, GeneticSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription FactorsConceptsGene regulatory evolutionGene regulatory networksRegulatory DNARegulatory evolutionTranscription networksCommon ancestorRegulatory networksEpistatic interactionsSpecific genesSingle proteinMutation effectsSecond pathwayCandida albicansSuch interactionsSpecific changesSaccharomycesAncestorGenesEvolutionRegulatorProteinDNAMutationsPathwayInteraction
2012
Protein Modularity, Cooperative Binding, and Hybrid Regulatory States Underlie Transcriptional Network Diversification
Baker C, Booth L, Sorrells T, Johnson A. Protein Modularity, Cooperative Binding, and Hybrid Regulatory States Underlie Transcriptional Network Diversification. Cell 2012, 151: 80-95. PMID: 23021217, PMCID: PMC3519278, DOI: 10.1016/j.cell.2012.08.018.Peer-Reviewed Original ResearchMeSH KeywordsEvolution, MolecularFungal ProteinsGene Regulatory NetworksMembrane ProteinsPhylogenySaccharomycetalesTranscription FactorsConceptsProtein modularityAncestral modeConserved expression patternCis-regulatory sequencesNovel regulatory modeProtein-DNA interactionsRegulatory network structureMode of regulationTranscription regulationAncestral networksGene regulationModern speciesDifferent lineagesYeast speciesExpression patternsRegulatory stateRegulatory modeCooperative bindingType cellsRegulationSpeciesLineagesGenesDiversityDiversification