2011
miRNA Regulatory Circuits in ES Cells Differentiation: A Chemical Kinetics Modeling Approach
Luo Z, Xu X, Gu P, Lonard D, Gunaratne PH, Cooney AJ, Azencott R. miRNA Regulatory Circuits in ES Cells Differentiation: A Chemical Kinetics Modeling Approach. PLOS ONE 2011, 6: e23263. PMID: 22039400, PMCID: PMC3198445, DOI: 10.1371/journal.pone.0023263.Peer-Reviewed Original ResearchConceptsES cell differentiationMRNA genesRepressive interactionsCell differentiationTarget mRNA genesEmbryonic stem cellsGene regulationRegulatory circuitsTranslation inhibitionMRNA targetsGene MES cellsMiRNAs inhibitorsMicroarray dataGenesMiRNAsStem cellsGene GProtein expressionDirect degradationMRNADifferentiationImportant roleCellsMicroRNAs
2008
Novel MicroRNA Candidates and miRNA-mRNA Pairs in Embryonic Stem (ES) Cells
Gu P, Reid J, Gao X, Shaw C, Creighton C, Tran P, Zhou X, Drabek R, Steffen D, Hoang D, Weiss M, Naghavi A, El-daye J, Khan M, Legge G, Wheeler D, Gibbs R, Miller J, Cooney A, Gunaratne P. Novel MicroRNA Candidates and miRNA-mRNA Pairs in Embryonic Stem (ES) Cells. PLOS ONE 2008, 3: e2548. PMID: 18648548, PMCID: PMC2481296, DOI: 10.1371/journal.pone.0002548.Peer-Reviewed Original ResearchConceptsMiRNA-mRNA pairsEmbryonic stem cellsES cellsMiRNA candidatesPost-transcriptional gene regulationTranscriptional gene regulationCore regulatory networkLoss of repressionMiRNA target predictionOpposite expression trendsStem cellsES cell differentiationNovel candidatesNovel miRNAsGene regulationSmall RNAsMiRNA maturationGene networksTranscript sequencesRegulatory networksExpression trendsSilico searchMicroRNA candidatesCell differentiationTarget predictionNanog 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
2007
Nuclear Receptors in Regulation of Mouse ES Cell Pluripotency and Differentiation
Mullen EM, Gu P, Cooney AJ. Nuclear Receptors in Regulation of Mouse ES Cell Pluripotency and Differentiation. PPAR Research 2007, 2007: 61563. PMID: 18274628, PMCID: PMC2233893, DOI: 10.1155/2007/61563.Peer-Reviewed Original ResearchNuclear receptorsES cellsES cell phenotypeES cell pluripotencyLIF/STAT3Embryonic stem cellsTranscription factor Sox2Different cell typesCell pluripotencyPluripotent phenotypeFactor Sox2Differentiated cellsCell typesStem cellsCell phenotypeGreat therapeutic potentialPhenotypeCellsDifferentiationReceptorsImportant processPluripotency
2005
Orphan Nuclear Receptor GCNF Is Required for the Repression of Pluripotency Genes during Retinoic Acid-Induced Embryonic Stem Cell Differentiation
Gu P, LeMenuet D, Chung A, Mancini M, Wheeler DA, Cooney AJ. Orphan Nuclear Receptor GCNF Is Required for the Repression of Pluripotency Genes during Retinoic Acid-Induced Embryonic Stem Cell Differentiation. Molecular And Cellular Biology 2005, 25: 8507-8519. PMID: 16166633, PMCID: PMC1265758, DOI: 10.1128/mcb.25.19.8507-8519.2005.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBlotting, NorthernBlotting, WesternCell DifferentiationCell LineCell NucleusChromatin ImmunoprecipitationDNA-Binding ProteinsDown-RegulationEmbryo, MammalianFemaleFibroblast Growth Factor 4GenotypeHomeodomain ProteinsIn Situ HybridizationMaleMiceMice, TransgenicMicroscopy, FluorescenceModels, GeneticNanog Homeobox ProteinNuclear Receptor Subfamily 6, Group A, Member 1Octamer Transcription Factor-3PhenotypePlasmidsProtein BindingReceptors, Cytoplasmic and NuclearResponse ElementsReverse Transcriptase Polymerase Chain ReactionSignal TransductionSOXB1 Transcription FactorsStem CellsTime FactorsTrans-ActivatorsTransfectionTretinoinConceptsLoss of repressionES cell differentiationPluripotency genesCell differentiationTranscription factorsEmbryonic developmentES cellsEmbryonic stem cell pluripotencyEmbryonic stem cell differentiationEarly mouse embryonic developmentStem cell pluripotencyMouse embryonic developmentPluripotency gene expressionEarly embryonic developmentInitiation of differentiationStem cell differentiationRetinoic acidCell pluripotencyNanog geneGenes Oct4Somatic cellsUndifferentiated stateGene expressionGCNFRepressionOrphan Nuclear Receptor LRH-1 Is Required To Maintain Oct4 Expression at the Epiblast Stage of Embryonic Development
Gu P, Goodwin B, Chung A, Xu X, Wheeler DA, Price RR, Galardi C, Peng L, Latour AM, Koller BH, Gossen J, Kliewer SA, Cooney AJ. Orphan Nuclear Receptor LRH-1 Is Required To Maintain Oct4 Expression at the Epiblast Stage of Embryonic Development. Molecular And Cellular Biology 2005, 25: 3492-3505. PMID: 15831456, PMCID: PMC1084298, DOI: 10.1128/mcb.25.9.3492-3505.2005.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBlastocystCell DifferentiationDNA-Binding ProteinsDown-RegulationEmbryo, MammalianEmbryonic DevelopmentGene Expression Regulation, DevelopmentalGene SilencingGenes, LethalMiceOctamer Transcription Factor-3Receptors, Cytoplasmic and NuclearResponse ElementsStem CellsTranscription FactorsUp-RegulationConceptsInner cell massEpiblast stageES cellsOct4 expressionOrphan nuclear receptor LRH-1Embryonic developmentLRH-1Proximal enhancerCell lineagesNuclear receptor LRH-1Developmental stagesGerm cell lineagePluripotent cell lineageDifferentiation time pointsEmbryonic stem cellsReporter gene expressionEssential roleUndifferentiated ES cellsCell massSF-1 response elementExpression of Oct4Early developmental stagesOct4 geneDistal enhancerProximal promoter