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 biologyBiologyPIWIRNATestisGeneticistsBiologistsProteinGermPlanariaDefenseExpressionBiochemistsA comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals
Konstantinidou P, Loubalova Z, Ahrend F, Friman A, Almeida M, Poulet A, Horvat F, Wang Y, Losert W, Lorenzi H, Svoboda P, Miska E, van Wolfswinkel J, Haase A. A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals. Cell Reports 2024, 43: 114777. PMID: 39302833, DOI: 10.1016/j.celrep.2024.114777.Peer-Reviewed Original ResearchPIWI-interacting RNAsPiwi-interacting RNA clustersPiRNA clustersPiRNA biologySilencing mobile genetic elementsGenomic piRNA clustersSingle-stranded precursorsMobile genetic elementsSafeguarding genome integrityGerm cell biologySpecies-specific variationGenome invadersTranscriptional readthroughTransposon insertionGenetic elementsGenome integrityRetroviral invasionMolecular mechanismsCell biologyRNAMammalsSpeciesBiologyTransposonReadthroughGene-edited Mtsoc1 triple mutant Medicago plants do not flower
Poulet A, Zhao M, Peng Y, Tham F, Jaudal M, Zhang L, van Wolfswinkel J, Putterill J. Gene-edited Mtsoc1 triple mutant Medicago plants do not flower. Frontiers In Plant Science 2024, 15: 1357924. PMID: 38469328, PMCID: PMC10926907, DOI: 10.3389/fpls.2024.1357924.Peer-Reviewed Original ResearchTriple mutant linesSingle mutantsFlowering timeMutant linesMultiple gene duplication eventsGene duplication eventsSOC1-like genesModel Arabidopsis thalianaMADS transcription factorsWild-type backgroundRegulation of floweringOptimal flowering timeNon-flowering plantsShort-day photoperiodCRISPR-Cas9 gene editingGene expression analysisDuplication eventsArabidopsis thalianaSOC1 genesDelayed floweringFloral promotersCrop productionFlower developmentFlowering pathwayMedicago truncatula
2023
piRNA generation is associated with the pioneer round of translation in stem cells
Parambil S, Li D, Zelko M, Poulet A, van Wolfswinkel J. piRNA generation is associated with the pioneer round of translation in stem cells. Nucleic Acids Research 2023, 52: 2590-2608. PMID: 38142432, PMCID: PMC10954484, DOI: 10.1093/nar/gkad1212.Peer-Reviewed Original ResearchSMEDWI-1Pioneer roundStem cellsPlanarian stem cellsStem cell maintenanceStem cell stateNon-coding transcriptsPiRNA pathwayPIWI proteinsTransposon repressionBiogenesis pathwayPiRNA generationGenomic integritySmall RNAsCell maintenanceSuch transcriptsCell statesCytoplasmic poolTranscriptsCell coloniesCell healthPiRNAsDynamic poolTranscriptomeCellsChromatin 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 maintenanceCellsISWIInsights in piRNA targeting rules
van Wolfswinkel J. Insights in piRNA targeting rules. Wiley Interdisciplinary Reviews - RNA 2023, 15: e1811. PMID: 37632327, PMCID: PMC10895071, DOI: 10.1002/wrna.1811.Peer-Reviewed Original ResearchPIWI-interacting RNAsTarget transcriptsProtein-RNA interactionsRNA-RNA interactionsPotential target transcriptsPIWI proteinsProtein-RNARNA interactionsSequence complementarityCells of animalsTranscriptionEffective downregulationStructural studiesProteinPIWITransposonGermlineStem cellsRNATargetCleavageDownregulationDefenseThe Histone Chaperone Network Is Highly Conserved in Physarum polycephalum
Poulet A, Rousselot E, Téletchéa S, Noirot C, Jacob Y, van Wolfswinkel J, Thiriet C, Duc C. The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum. International Journal Of Molecular Sciences 2023, 24: 1051. PMID: 36674565, PMCID: PMC9864664, DOI: 10.3390/ijms24021051.Peer-Reviewed Original ResearchConceptsHistone chaperonesEukaryotic treeChaperone networkBranching eukaryotesChaperone interactionsYeast complexCellular lifeDiverse proteinsPlant kingdomChaperone expressionRNA sequencingChaperonesKey residuesFunctional domainsHistonesCell cycleS phaseChromatinPhysarum polycephalumPlantsDistinct patternsEukaryotesOrthologuesCladeConserved
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 typeMutantsNODeJ: an ImageJ plugin for 3D segmentation of nuclear objects
Dubos T, Poulet A, Thomson G, Péry E, Chausse F, Tatout C, Desset S, van Wolfswinkel JC, Jacob Y. NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects. BMC Bioinformatics 2022, 23: 216. PMID: 35668354, PMCID: PMC9169307, DOI: 10.1186/s12859-022-04743-6.Peer-Reviewed Original ResearchConceptsImageJ pluginCommand-line optionsChromatin organizationThree-dimensional imaging technologyArabidopsis thaliana nucleiDNA FISH experimentsNodeJSSource codePublic datasetsProgram segmentsReduced processing timePluginProcessing timeAbiotic stressesHeterochromatin domainsLaplacian convolutionFISH experimentsSubnuclear structuresCellular processesHigh-throughput analysisPlant systemsProcessing methodsDiverse setImaging technologyImages
2021
PIWI-mediated control of tissue-specific transposons is essential for somatic cell differentiation
Li D, Taylor D, van Wolfswinkel J. PIWI-mediated control of tissue-specific transposons is essential for somatic cell differentiation. Cell Reports 2021, 37: 109776. PMID: 34610311, PMCID: PMC8532177, DOI: 10.1016/j.celrep.2021.109776.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsPIWI proteinsCell differentiationDefective cell differentiationLineage-specific genesSubset of transposonsAdult pluripotent stem cellsSomatic cell differentiationStem cell systemStem cell biologyPluripotent stem cellsTransposon derepressionAnimal germlineSpecific chromatinRegenerative animalsPlanarian neoblastsCell biologyTransposonStem cellsProteinDifferentiationIntricate interplayCell systemAddition causesTissue dysfunction
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
2014
Single-Cell Analysis Reveals Functionally Distinct Classes within the Planarian Stem Cell Compartment
van Wolfswinkel JC, Wagner DE, Reddien PW. Single-Cell Analysis Reveals Functionally Distinct Classes within the Planarian Stem Cell Compartment. Cell Stem Cell 2014, 15: 326-339. PMID: 25017721, PMCID: PMC4171737, DOI: 10.1016/j.stem.2014.06.007.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptional profilingDistinct cellular compartmentsGene expression fingerprintPluripotent stem cellsStem cell compartmentProliferative cell populationDistinct classesTranscriptional profilingCellular compartmentsPlanarian neoblastsExpression fingerprintsBroad lineagesEpidermal cellsNeoblastsStem cellsCell compartmentLineagesCell populationsCell analysisCellsCompartmentsPlanariansFlatwormsRegenerationHomeostasisPiwi and Potency: PIWI Proteins in Animal Stem Cells and Regeneration
van Wolfswinkel JC. Piwi and Potency: PIWI Proteins in Animal Stem Cells and Regeneration. Integrative And Comparative Biology 2014, 54: 700-713. PMID: 24948137, DOI: 10.1093/icb/icu084.Peer-Reviewed Original ResearchConceptsPIWI proteinsSomatic stem cellsStem cellsDifferent animal phylaGerm cell lineageStem cell systemAnimal stem cellsAnimal germlineGermline developmentAncestral roleAnimal phylaDiverse animalsCell lineagesDifferentiation potentialProteinGermlineCell systemCellsSuch cellsPiwiPiRNAsPhylaLineagesTransposonAvailable revealsWhole-Body Acoel Regeneration Is Controlled by Wnt and Bmp-Admp Signaling
Srivastava M, Mazza-Curll K, van Wolfswinkel J, Reddien P. Whole-Body Acoel Regeneration Is Controlled by Wnt and Bmp-Admp Signaling. Current Biology 2014, 24: 1107-1113. PMID: 24768051, DOI: 10.1016/j.cub.2014.03.042.Peer-Reviewed Original ResearchConceptsWhole-body regenerationMolecular mechanismsLast common ancestorEarly branching positionDorsal-ventral axisYears of evolutionEnigmatic phylumBilaterian evolutionMolecular resourcesUnderlying molecular mechanismsSystemic RNAiAccessible embryosCommon ancestorHofsteniaPhylogenetic analysisVentral cellsAcoelsMolecular studiesTranscriptomePhylaRNAiPlanariansAncestorBranching positionModel systemMUT-14 and SMUT-1 DEAD Box RNA Helicases Have Overlapping Roles in Germline RNAi and Endogenous siRNA Formation
Phillips C, Montgomery B, Breen P, Roovers E, Rim Y, Ohsumi T, Newman M, van Wolfswinkel J, Ketting R, Ruvkun G, Montgomery T. MUT-14 and SMUT-1 DEAD Box RNA Helicases Have Overlapping Roles in Germline RNAi and Endogenous siRNA Formation. Current Biology 2014, 24: 839-844. PMID: 24684932, PMCID: PMC4010136, DOI: 10.1016/j.cub.2014.02.060.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCaenorhabditis elegansCaenorhabditis elegans ProteinsDEAD-box RNA HelicasesFluoroimmunoassayGerm CellsImmunoprecipitationMolecular Sequence DataReal-Time Polymerase Chain ReactionRNA InterferenceRNA, Small InterferingSaccharomyces cerevisiaeSequence AlignmentSequence Analysis, DNAConceptsSiRNA formationMutator fociClass genesDEAD-box RNA helicasesBox RNA helicasesElegans genesEndogenous siRNAsSiRNA amplificationMutant displaysP granulesNuclear peripheryRNA helicasesMissense mutantsMutant proteinsDouble mutantMUT-16Target mRNAsRNAiGerm cellsGenesEarly stepsGermline genesSiRNAsMutantsWidespread loss
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
2009
The Argonaute CSR-1 and Its 22G-RNA Cofactors Are Required for Holocentric Chromosome Segregation
Claycomb J, Batista P, Pang K, Gu W, Vasale J, van Wolfswinkel J, Chaves D, Shirayama M, Mitani S, Ketting R, Conte D, Mello C. The Argonaute CSR-1 and Its 22G-RNA Cofactors Are Required for Holocentric Chromosome Segregation. Cell 2009, 139: 123-134. PMID: 19804758, PMCID: PMC2766185, DOI: 10.1016/j.cell.2009.09.014.Peer-Reviewed Original ResearchConceptsArgonaute CSR-1Chromosome segregationHolocentric chromosomesCSR-1Protein-coding genesProper chromosome segregationProtein-coding domainsDRH-3EGO-1C. elegansSmall RNAsTarget lociTarget mRNAsSpindle polesDevelopmental timingMetaphase plateDiverse processesChromosomesKinetochoresProtein levelsProper organizationElegansChromatinDicerGenomeCDE-1 Affects Chromosome Segregation through Uridylation of CSR-1-Bound siRNAs
van Wolfswinkel JC, Claycomb JM, Batista PJ, Mello CC, Berezikov E, Ketting RF. CDE-1 Affects Chromosome Segregation through Uridylation of CSR-1-Bound siRNAs. Cell 2009, 139: 135-148. PMID: 19804759, DOI: 10.1016/j.cell.2009.09.012.Peer-Reviewed Original ResearchConceptsCDE-1Chromosome segregationCSR-1RNAi pathwaySimilar sorting mechanismsMitotic chromosome segregationEndogenous RNAi pathwaysEGO-1Argonaute proteinsMitotic chromosomesSiRNA levelsC. elegansConserved natureSorting mechanismSiRNAsUridylationChromosomesInappropriate loadingProteinPathwaySegregationElegansRNAiMammalsGenes
2005
Assessment of potency of allergenic activity of low molecular weight compounds based on IL-1α and IL-18 production by a murine and human keratinocyte cell line
Van Och F, Van Loveren H, Van Wolfswinkel J, Machielsen A, Vandebriel R. Assessment of potency of allergenic activity of low molecular weight compounds based on IL-1α and IL-18 production by a murine and human keratinocyte cell line. Toxicology 2005, 210: 95-109. PMID: 15840424, DOI: 10.1016/j.tox.2005.01.004.Peer-Reviewed Original ResearchConceptsLocal lymph node assayPotency of allergensCytokine productionMurine local lymph node assayGuinea pig maximisation testIL-18 productionProduction of cytokinesLymph node assayHuman keratinocyte cell line HaCaT.Cell linesKeratinocyte cell line HaCaT.Assessment of potencyPresent studyIL-1αIL-1alphaStimulation indexHuman keratinocyte cell lineAnimal modelsAllergen concentrationsKeratinocyte cell lineDose-response dataVivo modelAllergenic potencyAllergenic activitySkin sensitisation