2020
Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit
Britton C, Sorrells T, Johnson A. Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit. Science 2020, 367: 96-100. PMID: 31896718, PMCID: PMC8284397, DOI: 10.1126/science.aax5217.Peer-Reviewed Original Research
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
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
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