2018
Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a
Kim KY, Tanaka Y, Su J, Cakir B, Xiang Y, Patterson B, Ding J, Jung YW, Kim JH, Hysolli E, Lee H, Dajani R, Kim J, Zhong M, Lee JH, Skalnik D, Lim JM, Sullivan GJ, Wang J, Park IH. Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a. Nature Communications 2018, 9: 2583. PMID: 29968706, PMCID: PMC6030064, DOI: 10.1038/s41467-018-04818-0.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCCAAT-Enhancer-Binding ProteinsCellular ReprogrammingCellular Reprogramming TechniquesChimeraDNA MethylationEpigenesis, GeneticFemaleFibroblastsGene Knockout TechniquesHEK293 CellsHistone CodeHistone-Lysine N-MethyltransferaseHistonesHumansMaleMesodermMiceMouse Embryonic Stem CellsNeural PlateNuclear ProteinsPrimary Cell CultureRecombinant ProteinsUbiquitin-Protein LigasesConceptsEmbryonic stem cellsUnique epigenetic statesBivalent histone modificationsRecruitment of DNMT1Bivalent histone marksCell typesDNA-binding proteinsSpecialized cell typesStem cellsPluripotent stem cellsTrithorax groupBivalent domainsMesoderm specificationCOMPASS complexHeterochromatin formationEpigenetic stateCell specificationHistone marksLineage specificationHistone modificationsEpigenetic regulationSpecific lineagesDNA methylationTranscriptional marksEpigenetic changes
2016
Dnmt1 regulates the myogenic lineage specification of muscle stem cells
Liu R, Kim KY, Jung YW, Park IH. Dnmt1 regulates the myogenic lineage specification of muscle stem cells. Scientific Reports 2016, 6: 35355. PMID: 27752090, PMCID: PMC5082760, DOI: 10.1038/srep35355.Peer-Reviewed Original ResearchConceptsImportant epigenetic markKnockout mouse approachesDNA methylation patternsMuscle stem cellsDaughter DNA strandsDNMT1 regulationEpigenetic marksLineage specificationCellular identityDNA methylationMethylation patternsDNMT1 depletionMyogenic genesMyogenic differentiationLineage fidelityNegative regulatorGene expressionDNMT1Osteogenic lineageFunctional roleFunctional consequencesMouse approachDNA strandsId-1Stem cellsRegulation of the DNA Methylation Landscape in Human Somatic Cell Reprogramming by the miR-29 Family
Hysolli E, Tanaka Y, Su J, Kim KY, Zhong T, Janknecht R, Zhou XL, Geng L, Qiu C, Pan X, Jung YW, Cheng J, Lu J, Zhong M, Weissman SM, Park IH. Regulation of the DNA Methylation Landscape in Human Somatic Cell Reprogramming by the miR-29 Family. Stem Cell Reports 2016, 7: 43-54. PMID: 27373925, PMCID: PMC4945581, DOI: 10.1016/j.stemcr.2016.05.014.Peer-Reviewed Original ResearchConceptsDNA methylation stateEmbryonic stem cellsInduced pluripotent stem cellsHuman somatic cell reprogrammingSomatic cell reprogrammingMethylation stateCell reprogrammingMiR-29 familyDNA methylation landscapeImportant epigenetic regulatorsStem cellsOverexpression of Oct4Global DNA methylationMiRNA-based approachesPluripotent stem cellsMethylation landscapeHistone modificationsDNA demethylationEpigenomic changesEarly reprogrammingEpigenetic regulatorsEpigenetic differencesDNA methylationHydroxymethylation analysisReprogramming
2015
Role of Zscan4 in secondary murine iPSC derivation mediated by protein extracts of ESC or iPSC
Kwon YW, Paek JS, Cho HJ, Lee CS, Lee HJ, Park IH, Roh TY, Kang CM, Yang HM, Park YB, Kim HS. Role of Zscan4 in secondary murine iPSC derivation mediated by protein extracts of ESC or iPSC. Biomaterials 2015, 59: 102-115. PMID: 25956855, DOI: 10.1016/j.biomaterials.2015.03.031.Peer-Reviewed Original ResearchConceptsMES cellsSomatic cellsCell extractsProtein extractsGlobal gene expressionES-like cellsMouse iPS cellsPluripotent stem cellsCell-derived proteinsHistone modificationsFull reprogrammingEpigenetic statusDNA methylationZscan4Developmental potencyIPSC derivationGene expressionGenomic DNAIPS cellsAdult fibroblastsKey moleculesStem cellsProteinCellsColonies
2009
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming
Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, Gao Y, Zhang K. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nature Biotechnology 2009, 27: 353-360. PMID: 19330000, PMCID: PMC2715272, DOI: 10.1038/nbt.1530.Peer-Reviewed Original ResearchConceptsHuman CpG islandsLarge eukaryotic genomesStem cellsEmbryonic stem cellsWhole-genome analysisPluripotent stem cellsEukaryotic genomesNuclear reprogrammingCytosine methylationBisulfite sequencingDNA methylationCpG islandsMethylationPadlock probesGenomeCellsReprogrammingSequencingFibroblastsIslands