2024
PIWI-interacting RNAs: who, what, when, where, why, and how
Haase A, Ketting R, Lai E, van Rij R, Siomi M, Svoboda P, van Wolfswinkel J, Wu P. PIWI-interacting RNAs: who, what, when, where, why, and how. The EMBO Journal 2024, 1-5. PMID: 39327528, DOI: 10.1038/s44318-024-00253-8.Peer-Reviewed Original ResearchPIWI-interacting RNAsPiRNA biologySelfish genetic elementsAdult mammalian testisGerm cell biologyRegulate gene expressionPIWI proteinsMammalian testisGenetic elementsEvolutionary biologistsAntiviral defenseGene expressionCell biologyBiologyPIWIRNATestisGeneticistsBiologistsProteinGermPlanariaDefenseExpressionBiochemists
2023
Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy
Poulet A, Kratkiewicz A, Li D, van Wolfswinkel J. Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy. Science Advances 2023, 9: eadh4887. PMID: 37801496, PMCID: PMC10558129, DOI: 10.1126/sciadv.adh4887.Peer-Reviewed Original ResearchConceptsAdult pluripotent stem cellsPluripotent stem cellsStem cell genesStem cellsCell genesPluripotency-related gene expressionStem cell-specific genesTissue-specific genesCell-specific genesTissue-specific promotersChromatin stateChromatin organizationRegenerative organismsChromatin analysisConstitutive genesRegulatory logicTranscription factorsGene expressionSequence featuresGenesDefault statePromoterLong-term maintenanceCellsISWI
2022
MtING2 encodes an ING domain PHD finger protein which affects Medicago growth, flowering, global patterns of H3K4me3, and gene expression
Jaudal M, Mayo‐Smith M, Poulet A, Whibley A, Peng Y, Zhang L, Thomson G, Trimborn L, Jacob Y, van Wolfswinkel J, Goldstone D, Wen J, Mysore K, Putterill J. MtING2 encodes an ING domain PHD finger protein which affects Medicago growth, flowering, global patterns of H3K4me3, and gene expression. The Plant Journal 2022, 112: 1029-1050. PMID: 36178149, PMCID: PMC9828230, DOI: 10.1111/tpj.15994.Peer-Reviewed Original ResearchConceptsGene-edited mutantsGene expressionWinter-annual ArabidopsisWild-type plantsPlant homeodomain (PHD) fingerStrong mutant phenotypePHD finger proteinChIP-seq analysisRNA sequencing experimentsExpression of activatorsPHD fingerMutant phenotypeFinger proteinMedicago truncatulaImportant physiological roleAbnormal leavesInsertion mutantsMutant studiesEpigenetic mechanismsMost plantsSmall seedsGrowth genesKey regulatorWild typeMutants
2016
A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes
Carmell M, Dokshin G, Skaletsky H, Hu Y, van Wolfswinkel J, Igarashi K, Bellott D, Nefedov M, Reddien P, Enders G, Uversky V, Mello C, Page D. A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes. ELife 2016, 5: e19993. PMID: 27718356, PMCID: PMC5098910, DOI: 10.7554/elife.19993.Peer-Reviewed Original ResearchConceptsDedicated germlineMajor eukaryotic lineagesDNA damage repairGerm cell markersEukaryotic lineagesDiverse eukaryotesEukaryotic evolutionMulticellular organismsMulticellular animalsSexual reproductionEarly eukaryotesGenomic integrityPhylogenetic analysisAncient familyReproductive cellsDamage repairGene expressionEukaryotesHeritable genomeGerm cellsProteinStem cellsGCNAGermlineCell markers
2012
Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of Caenorhabditis elegans
Kamminga LM, van Wolfswinkel JC, Luteijn MJ, Kaaij LJ, Bagijn MP, Sapetschnig A, Miska EA, Berezikov E, Ketting RF. Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of Caenorhabditis elegans. PLOS Genetics 2012, 8: e1002702. PMID: 22829772, PMCID: PMC3400576, DOI: 10.1371/journal.pgen.1002702.Peer-Reviewed Original ResearchConceptsHENN-1G RNAAGO proteinsSRNA moleculesSmall RNAsGene expressionC. elegans piRNAsGermline-expressed genesSequence-specific recruitmentDifferent RNAi pathwaysGlobal gene expression analysisGlobal gene expressionLoss of methylationGene expression analysisEndogenous RNAiRNAi pathwayC. elegansRNA classesRNA displayGene activityRNA interferenceExpression analysisSequence specificityTarget RNARNA
2010
The role of small non-coding RNAs in genome stability and chromatin organization
van Wolfswinkel JC, Ketting RF. The role of small non-coding RNAs in genome stability and chromatin organization. Journal Of Cell Science 2010, 123: 1825-1839. PMID: 20484663, DOI: 10.1242/jcs.061713.Peer-Reviewed Original ResearchConceptsSmall non-coding RNAsNon-coding RNAsSmall-interfering RNAChromatin-related mechanismsPost-transcriptional regulationNew regulatory mechanismNon-coding RNAChromatin regulationGenome stabilityChromatin organizationRegulatory potentialGene expressionRegulatory mechanismsRNARNA contentInitial discoveryRegulationEukaryotesMicroRNAsMechanismExpressionCellsDiscovery