2022
Taming the transposon: H3K9me3 turns foe to friend in human development
Chitrakar A, Noon M, Xiao AZ. Taming the transposon: H3K9me3 turns foe to friend in human development. Cell Stem Cell 2022, 29: 1009-1010. PMID: 35803220, PMCID: PMC9484580, DOI: 10.1016/j.stem.2022.06.010.Peer-Reviewed Original Research
2018
N 6 -methyladenine DNA Modification in Glioblastoma
Xie Q, Wu TP, Gimple RC, Li Z, Prager BC, Wu Q, Yu Y, Wang P, Wang Y, Gorkin DU, Zhang C, Dowiak AV, Lin K, Zeng C, Sui Y, Kim LJY, Miller TE, Jiang L, Lee-Poturalski C, Huang Z, Fang X, Zhai K, Mack SC, Sander M, Bao S, Kerstetter-Fogle AE, Sloan AE, Xiao AZ, Rich JN. N 6 -methyladenine DNA Modification in Glioblastoma. Cell 2018, 175: 1228-1243.e20. PMID: 30392959, PMCID: PMC6433469, DOI: 10.1016/j.cell.2018.10.006.Peer-Reviewed Original ResearchMeSH KeywordsAdenineAdultAgedAlkB Homolog 1, Histone H2a DioxygenaseAnimalsAstrocytesBrain NeoplasmsCell HypoxiaChildDNA MethylationEpigenomicsFemaleGlioblastomaHeterochromatinHistonesHumansKaplan-Meier EstimateMaleMiceMiddle AgedNeoplastic Stem CellsRNA InterferenceRNA, Small InterferingTumor Suppressor Protein p53ConceptsDNA modificationsHeterochromatic histone modificationsRegulation of transcriptionNovel DNA modificationChromatin accessibilityEpigenetic marksHistone modificationsTranscriptional silencingEpigenetic modificationsGenetic driversHuman diseasesOncogenic pathwaysTumor cell proliferationPotential therapeutic targetALKBH1Cell proliferationTumor-bearing miceCritical roleTherapeutic targetDNAHuman tissuesHuman glioblastoma modelGlioblastoma modelGlioblastomaSilencing
2017
Quality control towards the application of induced pluripotent stem cells
Lin K, Xiao AZ. Quality control towards the application of induced pluripotent stem cells. Current Opinion In Genetics & Development 2017, 46: 164-169. PMID: 28823985, DOI: 10.1016/j.gde.2017.07.006.Peer-Reviewed Original Research
2015
Adaption 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 ResearchRoles for Histone Acetylation in Regulation of Telomere Elongation and Two‐cell State in Mouse ES Cells
Dan J, Yang J, Liu Y, Xiao A, Liu L. Roles for Histone Acetylation in Regulation of Telomere Elongation and Two‐cell State in Mouse ES Cells. Journal Of Cellular Physiology 2015, 230: 2337-2344. PMID: 25752831, PMCID: PMC4711819, DOI: 10.1002/jcp.24980.Peer-Reviewed Original ResearchConceptsHistone acetylation levelsES cellsHistone acetylationHistone hypoacetylationHistone hyperacetylationTelomere elongationAcetylation levelsWild-type ES cellsRepressive DNA methylationRepressive epigenetic marksTelomere length maintenanceTwo-cell stateMouse ES cellsMammalian telomeresHeterochromatic stateEpigenetic marksHistone methylationLength maintenanceEpigenetic modificationsDNA methylationTelomere recombinationHistone deacetylase inhibitorsSpecific genesGene expressionTelomeres
2014
The Developmental Potential of iPSCs Is Greatly Influenced by Reprogramming Factor Selection
Buganim Y, Markoulaki S, van Wietmarschen N, Hoke H, Wu T, Ganz K, Akhtar-Zaidi B, He Y, Abraham BJ, Porubsky D, Kulenkampff E, Faddah DA, Shi L, Gao Q, Sarkar S, Cohen M, Goldmann J, Nery JR, Schultz MD, Ecker JR, Xiao A, Young RA, Lansdorp PM, Jaenisch R. The Developmental Potential of iPSCs Is Greatly Influenced by Reprogramming Factor Selection. Cell Stem Cell 2014, 15: 295-309. PMID: 25192464, PMCID: PMC4170792, DOI: 10.1016/j.stem.2014.07.003.Peer-Reviewed Original ResearchAnimalsCell LineCellular ReprogrammingChimeraChromosomes, Human, Pair 8DNA MethylationEmbryonic Stem CellsEnhancer Elements, GeneticGene Expression ProfilingGenomeHistonesHumansInduced Pluripotent Stem CellsKruppel-Like Factor 4Mice, Inbred C57BLMice, Inbred DBARNA, MessengerTranscription FactorsTrisomyHistone 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
2009
Dephosphorylation of the C-terminal Tyrosyl Residue of the DNA Damage-related Histone H2A.X Is Mediated by the Protein Phosphatase Eyes Absent*
Krishnan N, Jeong DG, Jung SK, Ryu SE, Xiao A, Allis CD, Kim SJ, Tonks NK. Dephosphorylation of the C-terminal Tyrosyl Residue of the DNA Damage-related Histone H2A.X Is Mediated by the Protein Phosphatase Eyes Absent*. Journal Of Biological Chemistry 2009, 284: 16066-16070. PMID: 19351884, PMCID: PMC2713548, DOI: 10.1074/jbc.c900032200.Peer-Reviewed Original ResearchMeSH KeywordsCell Line, TumorDNA DamageDNA-Binding ProteinsElectrochemistryHistonesHumansIntracellular Signaling Peptides and ProteinsMetalsNuclear ProteinsPhosphorylationProtein Structure, TertiaryProtein Tyrosine Phosphatase, Non-Receptor Type 1Protein Tyrosine PhosphatasesRNA InterferenceSubstrate SpecificityTransfectionTyrosineConceptsEyes AbsentDNA damage responseTyr-142Damage responseTyrosyl residuesProtein tyrosine phosphataseDNA damage repairAtypical kinaseHistone H2A.X.Haloacid dehalogenaseMammalian cellsHistone H2A.XDisplayed specificityElevated basal phosphorylationPhosphorylation statusRNA interferenceDamage repairPhysiological substratesH2A.XNovel roleBasal phosphorylationImportant regulatorDephosphorylationResiduesWSTFA distinct H2A.X isoform is enriched in Xenopus laevis eggs and early embryos and is phosphorylated in the absence of a checkpoint
Shechter D, Chitta RK, Xiao A, Shabanowitz J, Hunt DF, Allis CD. A distinct H2A.X isoform is enriched in Xenopus laevis eggs and early embryos and is phosphorylated in the absence of a checkpoint. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 749-754. PMID: 19131518, PMCID: PMC2630098, DOI: 10.1073/pnas.0812207106.Peer-Reviewed Original ResearchConceptsDNA damageEarly embryosSignificance of phosphorylationTerminal consensus sequenceExogenous DNA damageDNA damage responseCell-free egg extractsPhospho-specific antibodiesEarly cell cyclesFrog Xenopus laevisMulticellular organismsH2A variantsXenopus tropicalisDamage responseUnannotated isoformsMammalian cellsHistone H2A.XSomatic cellsCheckpoint conditionsXenopus laevis eggsAquatic speciesEgg extractsConsensus sequenceCell cycleH2A.X
2008
WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity
Xiao A, Li H, Shechter D, Ahn SH, Fabrizio LA, Erdjument-Bromage H, Ishibe-Murakami S, Wang B, Tempst P, Hofmann K, Patel DJ, Elledge SJ, Allis CD. WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity. Nature 2008, 457: 57-62. PMID: 19092802, PMCID: PMC2854499, DOI: 10.1038/nature07668.Peer-Reviewed Original ResearchConceptsDNA damage responseIntrinsic tyrosine kinase activityTyrosine kinase activityDamage responseKinase activityWilliams-Beuren syndrome transcription factorDouble-strand break responseNew regulatory mechanismWICH complexKinase foldEukaryotic cellsTranscription factorsWSTFKnowledge of domainsGenomic instabilityBreak responseSequence homologyRegulatory mechanismsCell deathPrecise rolePhosphorylationRepair processNew mechanismChromatinImportant role
2004
Linking the epigenetic ‘language’ of covalent histone modifications to cancer
Hake SB, Xiao A, Allis CD. Linking the epigenetic ‘language’ of covalent histone modifications to cancer. British Journal Of Cancer 2004, 90: 761-769. PMID: 14970850, PMCID: PMC2410168, DOI: 10.1038/sj.bjc.6601575.Peer-Reviewed Original ResearchConceptsCovalent histone modificationsHistone modificationsMethylation of DNAChromatin reorganisationEpigenetic modulationCovalent modificationHuman biologyHuman cancersMultistep processMethylationRecent findingsChromatinHuman healthHistonesEpigeneticsPhosphorylationBiologyAcetylationDNAModificationPotential therapyCarcinogenesisMajor partCancer