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
2013
Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains
Lohse M, Hernday A, Fordyce P, Noiman L, Sorrells T, Hanson-Smith V, Nobile C, DeRisi J, Johnson A. Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 7660-7665. PMID: 23610392, PMCID: PMC3651432, DOI: 10.1073/pnas.1221734110.Peer-Reviewed Original ResearchMeSH KeywordsCandida albicansChromatin ImmunoprecipitationComputational BiologyDNADNA-Binding ProteinsFungal ProteinsGene DeletionGene Expression ProfilingGene Expression Regulation, FungalGreen Fluorescent ProteinsMultigene FamilyProtein BindingProtein Interaction Domains and MotifsTranscription, GeneticConceptsSequence-specific DNA-binding proteinsDNA-binding domainWhite-opaque switchingDNA-binding proteinsTranscriptional regulatorsOpaque cellsGenome-wide chromatin immunoprecipitationHuman fungal pathogen Candida albicansSequence-specific DNA-binding domainFungal pathogen Candida albicansHeritable cell typesCis-regulatory sequencesGene regulatory proteinsRNA-binding proteinFraction of genesMajor fungal pathogenPathogen Candida albicansDeletion mutant strainAspects of biologySequence-specific mannerGene expression profilingDeep conservationCurrent annotationEvolutionary timeSmall clade