Dagmar Zigackova
About
Research
Publications
2024
Co-transcriptional gene regulation in eukaryotes and prokaryotes
Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer K. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nature Reviews Molecular Cell Biology 2024, 25: 534-554. PMID: 38509203, PMCID: PMC11199108, DOI: 10.1038/s41580-024-00706-2.Peer-Reviewed Original ResearchRNA polymeraseRNA biogenesisRNA processingGene regulationDevelopment of RNA sequencingTranscription to translationRNA processing intermediatesGene expression stepsCo-transcriptional activityCellular stress responseNascent RNATranscriptional readthroughNascent transcriptsTranscriptional coordinationIntron retentionRNA foldingEukaryotesProkaryotesExpression stepsRNA sequencingTransient transcriptionGene expressionTranscriptionStress responseRNA
2022
Identification of Alternative Polyadenylation in Cyanidioschyzon merolae Through Long-Read Sequencing of mRNA
Schärfen L, Zigackova D, Reimer KA, Stark MR, Slat VA, Francoeur NJ, Wells ML, Zhou L, Blackshear PJ, Neugebauer KM, Rader SD. Identification of Alternative Polyadenylation in Cyanidioschyzon merolae Through Long-Read Sequencing of mRNA. Frontiers In Genetics 2022, 12: 818697. PMID: 35154260, PMCID: PMC8831791, DOI: 10.3389/fgene.2021.818697.Peer-Reviewed Original ResearchAlternative polyadenylationNon-model organismsRNA processing pathwaysLong-Read SequencingCyanidioschyzon merolaeSplicing statusSplicing machineryMammalian cellsRegulatory stepMRNA stabilityRed algaVolcanic hot springsGene expressionRich mediumPolyadenylationBiological importanceOrganismsSite usageProtein expressionHot springsYeastAlgaProcessing pathwaysSequencingMRNA
2019
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition
Yadav D, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky P. Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Research 2019, 48: 2091-2106. PMID: 31875226, PMCID: PMC7038937, DOI: 10.1093/nar/gkz1163.Peer-Reviewed Original ResearchConceptsDsRNA binding proteinSpecific mRNA targetsGroove sideMinor groove recognitionCytoplasmic mRNA levelsMRNA decayMRNA transportTranslational controlLoop anchorsMRNA targetsMinor groove sideMajor groove sideStaufen1Helix α1Sequence featuresDsRNABinding proteinGroove recognitionPhosphodiester backboneSpecific recognitionGuanine baseMRNA levelsPurification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and In Vitro Polyadenylation-Exosome Activation Assays
Zigáčková D, Rájecká V, Vaňáčová Š. Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and In Vitro Polyadenylation-Exosome Activation Assays. Methods In Molecular Biology 2019, 2062: 237-253. PMID: 31768980, DOI: 10.1007/978-1-4939-9822-7_12.Peer-Reviewed Original ResearchConceptsActivity of exosomesTRAMP complexExosome complexPolyadenylation complexRNA maturationRNA processingProtein complexesProtein domainsAuxiliary proteinsRNA substratesIndividual subunitsHigh processivityYeastParticular mutationAberrant formsActivation assaysRNAExosomesComplexesTRAMPWeak activityProcessivityPurificationSubunitsComplete degradation
2018
The role of 3′ end uridylation in RNA metabolism and cellular physiology
Zigáčková D, Vaňáčová Š. The role of 3′ end uridylation in RNA metabolism and cellular physiology. Philosophical Transactions Of The Royal Society B Biological Sciences 2018, 373: 20180171. PMID: 30397107, PMCID: PMC6232591, DOI: 10.1098/rstb.2018.0171.Peer-Reviewed Original ResearchConceptsRNA metabolismRegulation of stabilityCell cycle regulationNumber of pathwaysRNA maturationEukaryotic RNAOrganismal levelCellular physiologyCycle regulationRNA degradationCellular RNADiverse rolesWidespread modificationCell deathUridylationRNAMajority of modificationsCurrent knowledgeLife cycleCritical roleTheme issueRegulationPathwayMetabolismEukaryotes
2016
TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs
Ustianenko D, Pasulka J, Feketova Z, Bednarik L, Zigackova D, Fortova A, Zavolan M, Vanacova S. TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs. The EMBO Journal 2016, 35: 2179-2191. PMID: 27647875, PMCID: PMC5069555, DOI: 10.15252/embj.201694857.Peer-Reviewed Original ResearchConceptsStructured non-coding RNAsCellular RNA speciesRNA polymerase IICytoplasmic quality controlNon-coding RNAsStable secondary structureExoribonuclease DIS3L2Y-RNAsPolymerase IIStructured ncRNAsSurveillance pathwayRNA speciesWilms tumor susceptibilityRNA degradationDIS3L2Human cellsSecondary structureImmunoprecipitation methodPerlman syndromeUridylationRNAAberrant processingRNAsTumor susceptibilityUnifying feature