2017
Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis
De Kumar B, Parker H, Paulson A, Parrish M, Zeitlinger J, Krumlauf R. Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis. Developmental Biology 2017, 432: 151-164. PMID: 28982536, DOI: 10.1016/j.ydbio.2017.09.033.Peer-Reviewed Original ResearchConceptsTarget genesEar developmentES cellsDifferential gene expression analysisGenome-wide analysisNeural crest specificationFunctional rolePutative target genesTransgenic mouse embryosMajor signaling pathwaysNeural crest migrationRelevant target genesDown-stream componentsMouse ES cellsGene expression analysisImportant functional roleRetinoic acidEvolutionary conservationEpigenetic marksHox cofactorsMutant phenotypeMouse embryogenesisNearby genesNeural fateMouse developmentHOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets
De Kumar B, Parker H, Paulson A, Parrish M, Pushel I, Singh N, Zhang Y, Slaughter B, Unruh J, Florens L, Zeitlinger J, Krumlauf R. HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets. Genome Research 2017, 27: 1501-1512. PMID: 28784834, PMCID: PMC5580710, DOI: 10.1101/gr.219386.116.Peer-Reviewed Original ResearchConceptsCross-regulatory interactionsTALE proteinsTALE membersCombinatorial binding patternsGenome-wide analysisGenome-wide basisCross-regulatory networkDiverse functional rolesMouse ES cellsHox cofactorsTALE familyFunctional diversityTransgenic reporterCombinatorial interactionsRegulatory networksHox-PbxProteomic analysisEnhancer activityHOXA1ES cellsFunctional roleProteinDistinct mechanismsBinding patternDistinct classes
2015
Roles 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
2011
Cell cycle adaptations of embryonic stem cells
Ballabeni A, Park IH, Zhao R, Wang W, Lerou PH, Daley GQ, Kirschner MW. Cell cycle adaptations of embryonic stem cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 19252-19257. PMID: 22084091, PMCID: PMC3228440, DOI: 10.1073/pnas.1116794108.Peer-Reviewed Original ResearchMeSH KeywordsAdaptation, BiologicalAnaphase-Promoting Complex-CyclosomeAnimalsCell CycleCell Cycle ProteinsCell DifferentiationCell LineChromatinCyclin-Dependent Kinase 2Embryonic Stem CellsFlow CytometryImmunoblottingImmunoprecipitationMiceReal-Time Polymerase Chain ReactionUbiquitin-Protein Ligase ComplexesUbiquitinationConceptsHigh CDK activityCDK activityES cellsAPC/C activityUbiquitin ligase APC/CCell cycle adaptationsAPC/CEmbryonic stem cellsRapid cell cyclesMouse ES cellsMCM proteinsMitotic exitFactor Cdt1Emi1 proteinDNA replicationSomatic cellsCell cycleKey adaptationGap phaseS phaseC enzymesLevels of cyclinG1 phaseNormal progressionStem cells
2009
Klf4 Interacts Directly with Oct4 and Sox2 to Promote Reprogramming
Wei Z, Yang Y, Zhang P, Andrianakos R, Hasegawa K, Lyu J, Chen X, Bai G, Liu C, Pera M, Lu W. Klf4 Interacts Directly with Oct4 and Sox2 to Promote Reprogramming. Stem Cells 2009, 27: 2969-2978. PMID: 19816951, DOI: 10.1002/stem.231.Peer-Reviewed Original ResearchConceptsInduced pluripotent stemEndogenous KLF4Sets of transcription factorsInduced pluripotent stem cellsTandem zinc fingerEmbryonic stemDominant negative mutantInduced iPS cellsMouse ES cellsSomatic cell reprogrammingWild-type Klf4Zinc fingerPluripotent stemTranscription factorsC-terminusIPS cellsInhibit reprogrammingEctopic expressionTarget genesNanog promoterSomatic cellsSOX2Cell reprogrammingES cellsKLF4
2008
Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells
Liang J, Wan M, Zhang Y, Gu P, Xin H, Jung SY, Qin J, Wong J, Cooney AJ, Liu D, Songyang Z. Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nature Cell Biology 2008, 10: 731-739. PMID: 18454139, DOI: 10.1038/ncb1736.Peer-Reviewed Original ResearchConceptsES cell fateRepression complexMouse ES cellsCell fateTranscription factorsES cellsTranscriptional repression complexES cell differentiationEssential transcription factorEmbryonic stem cellsSub-stoichiometric levelsHistone deacetylase activityNuRD complexRepressor complexEndogenous NanogProtein complexesGene transcriptionTarget genesDeacetylase activityNanogNuRDGenesStem cellsCellsComplexes
2003
Disruption of the genomic imprint in trans with homologous recombination at Snrpn in ES cells
Tsai T, Bressler J, Jiang Y, Beaudet AL. Disruption of the genomic imprint in trans with homologous recombination at Snrpn in ES cells. Genesis 2003, 37: 151-161. PMID: 14666508, DOI: 10.1002/gene.10237.Peer-Reviewed Original ResearchConceptsPaternal alleleImprinting centerMaternal alleleSomatic mammalian cellsTrans-acting factorsActivation of expressionSNURF-SNRPN geneMouse ES cellsChromatin domainsGenomic imprintsImprinted domainMammalian cellsHomologous recombinationGene targetingHomologous associationES cellsComplete demethylationSNURF-SNRPNPrader-Willi syndromeExon 2AllelesGenesRecombinantsCellsDomainMyocardin Is a Critical Serum Response Factor Cofactor in the Transcriptional Program Regulating Smooth Muscle Cell Differentiation
Du KL, Ip HS, Li J, Chen M, Dandre F, Yu W, Lu MM, Owens GK, Parmacek MS. Myocardin Is a Critical Serum Response Factor Cofactor in the Transcriptional Program Regulating Smooth Muscle Cell Differentiation. Molecular And Cellular Biology 2003, 23: 2425-2437. PMID: 12640126, PMCID: PMC150745, DOI: 10.1128/mcb.23.7.2425-2437.2003.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCell DifferentiationCells, CulturedCOS CellsDNA, ComplementaryGene Expression Regulation, DevelopmentalHumansMiceMicrofilament ProteinsMolecular Sequence DataMuscle ProteinsMuscle, SmoothMuscle, Smooth, VascularMyocardiumNuclear ProteinsOrgan SpecificityPromoter Regions, GeneticRatsRNA, Small InterferingSequence AlignmentSerum Response FactorStem CellsTrans-ActivatorsTranscriptional ActivationConceptsSerum response factorExpression of myocardinTranscriptional programsSerum Response Factor CofactorMyocardin geneSRF DNA-binding domainSmooth muscle cell lineageFunction of myocardinSmooth muscle cell differentiationDNA-binding domainMuscle cell lineageMuscle cell differentiationTranscription factor myocardinTranscriptional regulatory elementsUndifferentiated mouse ES cellsEmbryonic stem cellsMouse ES cellsAlpha promoter activitySmooth muscle alpha-actinSM22 alphaMuscle alpha-actinMutant proteinsVisceral SMCsEmbryonic developmentRegulatory elements
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