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