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
NODeJ: 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
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