2019
Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum
Wang Z, López-Giráldez F, Wang J, Trail F, Townsend JP. Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum. MBio 2019, 10: 10.1128/mbio.02119-19. PMID: 31822585, PMCID: PMC6904875, DOI: 10.1128/mbio.02119-19.Peer-Reviewed Original ResearchConceptsGene expressionMating lociFungal diversityResponsive genesSexual developmentSecondary metabolism gene clustersGenome-wide gene expressionMating-type genesRich fungal diversitySecondary metabolism pathwaysModel filamentous fungusSecondary metabolic pathwaysWide gene expressionNumerous secondary metabolitesGene expression responsesHistidine kinaseLife cycleSexual reproductionHomothallic speciesDevelopmental genesEvolutionary biologistsHeterokaryon incompatibilityAsexual reproductionDistinct morphological stagesEvolutionary historyThe Ulp2 SUMO protease promotes transcription elongation through regulation of histone sumoylation
Ryu H, Su D, Wilson‐Eisele N, Zhao D, López‐Giráldez F, Hochstrasser M. The Ulp2 SUMO protease promotes transcription elongation through regulation of histone sumoylation. The EMBO Journal 2019, 38: e102003. PMID: 31313851, PMCID: PMC6694223, DOI: 10.15252/embj.2019102003.Peer-Reviewed Original ResearchConceptsSmall ubiquitin-like modifierRNA polymerase IIC-terminal domainHistone sumoylationTranscription elongationActive genesSUMO proteaseRNAPII C-terminal domainChromatin regulatory mechanismsTranscriptional elongation defectsUbiquitin-like modifierCtk1 kinaseH2B ubiquitylationEukaryotic proteinsNucleosome associationElongation defectsPolySUMO chainsPolymerase IITranscript elongationCUP1 geneUlp2Saccharomyces cerevisiaeRegulatory mechanismsImpaired associationSerine 2Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa
Wang Z, Miguel-Rojas C, Lopez-Giraldez F, Yarden O, Trail F, Townsend JP. Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa. MBio 2019, 10: 10.1128/mbio.00192-19. PMID: 30914504, PMCID: PMC6437048, DOI: 10.1128/mbio.00192-19.Peer-Reviewed Original ResearchMeSH KeywordsCarbonCulture MediaGene Expression ProfilingGene Expression Regulation, FungalMetabolic Networks and PathwaysNeurospora crassaNitrogenSpores, FungalConceptsDevelopmental regulatory genesVegetative growthAsexual reproductionConidial germinationRegulatory genesNutritional environmentLife historyNitrogen metabolismLife-history decisionsMode of reproductionAdaptive life historiesKnockout of genesGenome-wide transcriptomicsEarly life historySexual developmentMetabolic gene expressionReproductive dispersalSexual reproductionDevelopmental genesMetabolic genesNeurospora crassaDiverse ecosystemsNutrient conditionsGene expressionMajor switch
2014
Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa
Lehr NA, Wang Z, Li N, Hewitt DA, López-Giráldez F, Trail F, Townsend JP. Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa. PLOS ONE 2014, 9: e110398. PMID: 25329823, PMCID: PMC4203796, DOI: 10.1371/journal.pone.0110398.Peer-Reviewed Original ResearchConceptsNeurospora crassaSexual reproductionN. crassaGenetic basisThree-dimensional fruiting bodiesSexual spore productionN. crassa geneBody developmentDiverse life historiesGenome-wide transcriptomicsSexual developmentStudy of meiosisGene expression differencesList of genesGene expression levelsMeiotic machineryMeiosis genesOrthologous genesSporulation genesNeurospora speciesGlomerella graminicolaEvolutionary timeAnimal taxaPerithecium formationLife history
2013
Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa
Wang Z, Lopez-Giraldez F, Lehr N, Farré M, Common R, Trail F, Townsend JP. Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa. MSphere 2013, 13: 154-169. PMID: 24243796, PMCID: PMC3910948, DOI: 10.1128/ec.00248-13.Peer-Reviewed Original ResearchMeSH KeywordsDNA-Binding ProteinsFungal ProteinsGene DeletionGene Expression Regulation, DevelopmentalGene Expression Regulation, FungalGenes, Mating Type, FungalGenome, FungalNeurospora crassaSpores, FungalUp-RegulationConceptsPerithecial developmentNeurospora crassaGene expressionSexual developmentBody developmentFruiting-body developmentMost upregulated genesReverse genetics approachGlobal gene expressionSimilar expression patternsSame developmental stageMulticellular organismsSexual crossingMat AUnclassified proteinsDevelopmental traitsN. crassaKnockout analysisTranscriptomic landscapeType genesUpregulated genesGenetic basisDiverse functionsExpression patternsStage specificity
2012
Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology
Sikhakolli UR, López-Giráldez F, Li N, Common R, Townsend JP, Trail F. Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology. Fungal Genetics And Biology 2012, 49: 663-673. PMID: 22705880, DOI: 10.1016/j.fgb.2012.05.009.Peer-Reviewed Original ResearchMeSH KeywordsApoptosisCluster AnalysisComputational BiologyEcosystemFruiting Bodies, FungalFusariumGene Expression ProfilingGene Expression Regulation, FungalLipid MetabolismMating FactorPeptidesPhenotypeTranscriptomeConceptsF. graminearumOrthologous genesLife historyFusarium graminearumF. verticillioidesGene expressionSexual developmentStage-specific gene expressionSpecies' life historyDifferent life historiesPrevious morphological analysesMorphological developmentLife cycleSexual sporesCereal pathogensUnclassified proteinsFunctional assignmentTranscriptional programsTranscriptome analysisTranscriptional analysisType genesEcological characteristicsApoptotic processFusarium speciesGraminearumSex-specific gene expression during asexual development of Neurospora crassa
Wang Z, Kin K, López-Giráldez F, Johannesson H, Townsend JP. Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics And Biology 2012, 49: 533-543. PMID: 22626843, PMCID: PMC3397379, DOI: 10.1016/j.fgb.2012.05.004.Peer-Reviewed Original ResearchConceptsMating-type genesAsexual developmentMating typesNeurospora crassaGene expressionSex-specific gene expressionFungal life historyLight-responsive genesOverall gene expressionExpression levelsDifferent mating typesExpression of pheromonePheromone genesHigh expression levelsMat AType genesLife historyResponse genesExpression differencesDevelopment stagesGenesClonal developmentImpact of lightReceptor geneCrassa
2010
Multi-targeted priming for genome-wide gene expression assays
Adomas AB, Lopez-Giraldez F, Clark TA, Wang Z, Townsend JP. Multi-targeted priming for genome-wide gene expression assays. BMC Genomics 2010, 11: 477. PMID: 20716356, PMCID: PMC3091673, DOI: 10.1186/1471-2164-11-477.Peer-Reviewed Original ResearchMeSH KeywordsDNA PrimersGene Expression ProfilingGene Expression Regulation, FungalGenes, FungalMetabolic Networks and PathwaysMyceliumNeurospora crassaNitrogenOligonucleotide Array Sequence AnalysisReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionReverse TranscriptionRNA, FungalRNA, MessengerSaccharomyces cerevisiaeSequence Analysis, RNAConceptsGene expressionGene expression assaysNeurospora crassaRibosomal RNAExpression assaysMost protein-coding genesEarly sexual developmentGenome-wide gene expressionTransfer RNA genesProtein-coding genesNitrogen starvation responseGenome of SaccharomycesPreponderance of genesGlobal gene expressionResponse of SaccharomycesCommon sequence motifsSexual developmentDetailed expression profilesReverse transcriptionRNA genesStarvation responseTag sequencingSequence motifsTransfer RNATranscriptomic assaysLOX: inferring Level Of eXpression from diverse methods of census sequencing
Zhang Z, López-Giráldez F, Townsend JP. LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics 2010, 26: 1918-1919. PMID: 20538728, PMCID: PMC2905554, DOI: 10.1093/bioinformatics/btq303.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyExpressed Sequence TagsGene Expression ProfilingGene Expression Regulation, FungalOligonucleotide Array Sequence AnalysisSoftwareConceptsTranscriptomic sequencing data