2019
The 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: embj2019102003. 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 2
2018
Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO protease
Ryu HY, López-Giráldez F, Knight J, Hwang SS, Renner C, Kreft SG, Hochstrasser M. Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO protease. Nature Communications 2018, 9: 5417. PMID: 30575729, PMCID: PMC6303320, DOI: 10.1038/s41467-018-07836-0.Peer-Reviewed Original ResearchConceptsRibosome biogenesisSUMO modification pathwayUlp2 SUMO proteaseSmall nucleolar RNAsSUMO-specific proteasesSnoRNA genesCCR4 deadenylaseDistinct adaptive mechanismsRibosomal proteinsCellular evolutionChromosome INucleolar RNAsRibosome formationSUMO proteaseAdaptive advantageExtended passagingRapid adaptationLong-term adaptationBiogenesisAdaptive mechanismsMutationsProteaseAneuploidyDisomyRegulatory shift
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 assays