2020
RNA-based CRISPR-Mediated Loss-of-Function Mutagenesis in Human Pluripotent Stem Cells
Leung AW, Broton C, Bogacheva MS, Xiao AZ, Garcia-Castro MI, Lou YR. RNA-based CRISPR-Mediated Loss-of-Function Mutagenesis in Human Pluripotent Stem Cells. Journal Of Molecular Biology 2020, 432: 3956-3964. PMID: 32339532, DOI: 10.1016/j.jmb.2020.04.017.Peer-Reviewed Original ResearchConceptsHuman pluripotent stem cellsPluripotent stem cellsTargeting efficiencyShelf cell productsTransfection protocolShort palindromic repeatsStem cellsSelection markerGenome editingPS cell linesFunction mutagenesisImproved protocolBroad applicationsPalindromic repeatsClustered RegularlyAssociated 9Human therapyEfficiencyProtocolCell productsCRISPRCrRNARegularlyApplicationsEditing
2017
Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells
Choi J, Huebner AJ, Clement K, Walsh RM, Savol A, Lin K, Gu H, Di Stefano B, Brumbaugh J, Kim SY, Sharif J, Rose CM, Mohammad A, Odajima J, Charron J, Shioda T, Gnirke A, Gygi S, Koseki H, Sadreyev RI, Xiao A, Meissner A, Hochedlinger K. Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells. Nature 2017, 548: 219-223. PMID: 28746311, PMCID: PMC5905676, DOI: 10.1038/nature23274.Peer-Reviewed Original Research
2016
DNA methylation on N6-adenine in mammalian embryonic stem cells
Wu TP, Wang T, Seetin MG, Lai Y, Zhu S, Lin K, Liu Y, Byrum SD, Mackintosh SG, Zhong M, Tackett A, Wang G, Hon LS, Fang G, Swenberg JA, Xiao AZ. DNA methylation on N6-adenine in mammalian embryonic stem cells. Nature 2016, 532: 329-333. PMID: 27027282, PMCID: PMC4977844, DOI: 10.1038/nature17640.Peer-Reviewed Original ResearchMeSH KeywordsAdenineAlkB Homolog 1, Histone H2a DioxygenaseAnimalsCell DifferentiationDNA MethylationDNA Transposable ElementsDNA-(Apurinic or Apyrimidinic Site) LyaseEnhancer Elements, GeneticEpigenesis, GeneticEvolution, MolecularGene SilencingLong Interspersed Nucleotide ElementsMammalsMiceMouse Embryonic Stem CellsUp-RegulationX ChromosomeConceptsLINE-1 transposonsEmbryonic stem cellsN6-methyladenineMammalian genomesEpigenetic silencingDNA methylationX chromosomeMammalian embryonic stem cellsEmbryonic stem cell differentiationMouse embryonic stem cellsStem cellsStem cell differentiationMammalian evolutionTranscriptional silencingEvolutionary ageGene activationDNA modificationsL1 elementsCell differentiationSilencingTransposonN6-adenineGenomeActivation signalsChromosomes
2015
Extensive Nuclear Reprogramming Underlies Lineage Conversion into Functional Trophoblast Stem-like Cells
Benchetrit H, Herman S, van Wietmarschen N, Wu T, Makedonski K, Maoz N, Tov N, Stave D, Lasry R, Zayat V, Xiao A, Lansdorp PM, Sebban S, Buganim Y. Extensive Nuclear Reprogramming Underlies Lineage Conversion into Functional Trophoblast Stem-like Cells. Cell Stem Cell 2015, 17: 543-556. PMID: 26412562, DOI: 10.1016/j.stem.2015.08.006.Peer-Reviewed Original ResearchConceptsNuclear reprogrammingEmbryonic stem cellsStem-like cellsTransient pluripotent stateStem cellsDNA methylation profilesPluripotent stem cellsPluripotent stateLineage conversionTranscriptional profilesTransient expressionMethylation profilesReprogrammingEvidence of passageMouse fibroblastsPluripotencyChimera assaysLineagesCellsHigh degreeTranscriptomeTFAP2CMethylationDifferentiationEomesAdaption by Rewiring Epigenetic Landscapes
Liu Y, Xiao A. Adaption by Rewiring Epigenetic Landscapes. Cell Stem Cell 2015, 17: 249-250. PMID: 26340521, PMCID: PMC4710369, DOI: 10.1016/j.stem.2015.08.015.Peer-Reviewed Original Research
2014
Histone Variant H2A.X Deposition Pattern Serves as a Functional Epigenetic Mark for Distinguishing the Developmental Potentials of iPSCs
Wu T, Liu Y, Wen D, Tseng Z, Tahmasian M, Zhong M, Rafii S, Stadtfeld M, Hochedlinger K, Xiao A. Histone Variant H2A.X Deposition Pattern Serves as a Functional Epigenetic Mark for Distinguishing the Developmental Potentials of iPSCs. Cell Stem Cell 2014, 15: 281-294. PMID: 25192463, DOI: 10.1016/j.stem.2014.06.004.Peer-Reviewed Original ResearchConceptsEmbryonic stem cellsLineage gene expressionHistone variant H2A.XCell lineage commitmentDevelopmental potentialMouse iPSC linesIPSC linesPluripotent stem cell (iPSC) technologyEpigenetic marksLineage genesEpigenetic mechanismsLineage commitmentLineage differentiationExtraembryonic differentiationStem cell technologyGene expressionTetraploid complementationIPSC clonesIPSC qualityStem cellsFunctional markersH2A.XDifferentiationIPSCsComplementationUsing Native Chromatin Immunoprecipitation to Interrogate Histone Variant Protein Deposition in Embryonic Stem Cells
Tseng Z, Wu T, Liu Y, Zhong M, Xiao A. Using Native Chromatin Immunoprecipitation to Interrogate Histone Variant Protein Deposition in Embryonic Stem Cells. Methods In Molecular Biology 2014, 1176: 11-22. PMID: 25030915, DOI: 10.1007/978-1-4939-0992-6_2.Peer-Reviewed Original ResearchConceptsNative chromatin immunoprecipitationHigh-throughput sequencingEmbryonic stem cellsChromatin immunoprecipitationHistone variantsMouse embryonic stem cellsGenome-wide localizationChromatin-associated factorsStem cellsProtein of interestMassive parallel sequencingHistone modificationsChromatin regionsChromatin pelletEpigenetic techniquesDNA fragmentsParallel sequencingImmunoprecipitationLibrary constructionSequencingEnzymatic digestionProtein depositionCellsH2A.XSpecific antibodiesRif1 Maintains Telomere Length Homeostasis of ESCs by Mediating Heterochromatin Silencing
Dan J, Liu Y, Liu N, Chiourea M, Okuka M, Wu T, Ye X, Mou C, Wang L, Wang L, Yin Y, Yuan J, Zuo B, Wang F, Li Z, Pan X, Yin Z, Chen L, Keefe DL, Gagos S, Xiao A, Liu L. Rif1 Maintains Telomere Length Homeostasis of ESCs by Mediating Heterochromatin Silencing. Developmental Cell 2014, 29: 7-19. PMID: 24735877, PMCID: PMC4720134, DOI: 10.1016/j.devcel.2014.03.004.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsEmbryonic Stem CellsGene DeletionGene Expression Regulation, DevelopmentalGene SilencingHeterochromatinHistonesMethylationMiceProtein BindingProtein Processing, Post-TranslationalRecombination, GeneticRNA, MessengerTelomereTelomere HomeostasisTelomere-Binding ProteinsTranscription FactorsConceptsTelomere length homeostasisEmbryonic stem cellsLength homeostasisZscan4 expressionHeterochromatic silencingHeterochromatin silencingMethylation complexChromosomal fusionsEmbryonic lethalityGenomic stabilityTelomere elongationH3K9me3 levelsSubtelomeric regionsRecombination defectsLength heterogeneityStem cellsRIF1HomeostasisSilencingExpressionZscan4HyperrecombinationShRNALethalityInteracts