2020
Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis
VanOudenhove J, Yankee T, Wilderman A, Cotney J. Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis. Circulation Research 2020, 127: e184-e209. PMID: 32772801, PMCID: PMC7554226, DOI: 10.1161/circresaha.120.316704.Peer-Reviewed Original ResearchMeSH KeywordsChromatinEnhancer Elements, GeneticEpigenomicsGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Regulatory NetworksGenetic VariationHeartHeart Defects, CongenitalHistone CodeHomeobox Protein Nkx-2.5HumansNAV1.5 Voltage-Gated Sodium ChannelOrganogenesisRegulatory Sequences, Ribonucleic AcidT-Box Domain ProteinsTranscriptomeConceptsRegulatory sequencesHeart enhancersHeart organogenesisGene expression network analysisWeighted gene coexpression networkGene expression dynamicsGene expression networksPutative disease genesWhole-genome sequencing dataGene coexpression networksExpression network analysisDisease-relevant genesGenome sequencing dataRare sequence alterationsHeart-specific expressionClear genetic componentChromatin stateTranscriptomic dynamicsHistone modificationsFunctional annotationExpression networksExpression dynamicsGene modulesCoexpression networkGenetic variation
2018
High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development
Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Reports 2018, 23: 1581-1597. PMID: 29719267, PMCID: PMC5965702, DOI: 10.1016/j.celrep.2018.03.129.Peer-Reviewed Original ResearchMeSH KeywordsDatabases, Nucleic AcidEmbryo, MammalianEmbryonic DevelopmentEpigenesis, GeneticFaceGene Expression Regulation, DevelopmentalHumansSkullConceptsRegulatory sequencesEmbryonic developmentEmbryonic craniofacial developmentEmbryonic craniofacial tissueGene regulatory programsNormal facial variationHuman embryonic developmentCraniofacial abnormalitiesEpigenomic annotationsEpigenomic atlasCraniofacial developmentIntronic sequencesCraniofacial tissuesRegulatory programsCraniofacial researchersMultiple tissuesCell typesSignificant enrichmentSystematic identificationCommon variantsCausal regionOrofacial cleftingEmbryonic periodSequenceCraniofacial complex
2017
Precocious Phenotypic Transcription‐Factor Expression During Early Development
VanOudenhove J, Medina R, Ghule P, Lian J, Stein J, Zaidi S, Stein G. Precocious Phenotypic Transcription‐Factor Expression During Early Development. Journal Of Cellular Biochemistry 2017, 118: 953-958. PMID: 27591551, PMCID: PMC5336526, DOI: 10.1002/jcb.25723.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell DifferentiationCell LineageCore Binding Factor Alpha 2 SubunitEmbryonic Stem CellsEpithelial-Mesenchymal TransitionGene Expression Regulation, DevelopmentalHumansOrgan SpecificityUp-RegulationConceptsPhenotypic transcription factorsTranscription factorsPrecocious expressionRUNX1 transcription factorTranscriptional controlLineage identityGene expressionNovel roleBiological importanceMesenchymal transitionEarly differentiationMesenchymal differentiationTransient upregulationDetailed mechanistic studiesExpressionDifferentiationMechanistic studiesRUNX1RoleUpregulationFurther studies
2016
Transient RUNX1 Expression during Early Mesendodermal Differentiation of hESCs Promotes Epithelial to Mesenchymal Transition through TGFB2 Signaling
VanOudenhove J, Medina R, Ghule P, Lian J, Stein J, Zaidi S, Stein G. Transient RUNX1 Expression during Early Mesendodermal Differentiation of hESCs Promotes Epithelial to Mesenchymal Transition through TGFB2 Signaling. Stem Cell Reports 2016, 7: 884-896. PMID: 27720906, PMCID: PMC5106514, DOI: 10.1016/j.stemcr.2016.09.006.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsHESC differentiationMesendodermal lineage commitmentPhenotypic transcription factorsLoss of repressionRUNX1 depletionMesenchymal transitionEmbryonic stem cellsLoss of RUNX1Mesendodermal lineagesMesendodermal differentiationLineage commitmentTranscription factorsBiochemical approachesEpithelial genesCell motilityFunctional analysisEpithelial marker expressionRUNX1 expressionStem cellsRUNX1TGFB2DifferentiationEarly eventsCandidate factorsGenome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation
Grandy R, Whitfield T, Wu H, Fitzgerald M, VanOudenhove J, Zaidi S, Montecino M, Lian J, van Wijnen A, Stein J, Stein G. Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation. Molecular And Cellular Biology 2016, 36: 615-627. PMID: 26644406, PMCID: PMC4751694, DOI: 10.1128/mcb.00877-15.Peer-Reviewed Original ResearchMeSH KeywordsCell CycleCell DifferentiationCell LineChromatinDNA MethylationDNA-Binding ProteinsEpigenesis, GeneticGene Expression Regulation, DevelopmentalGenome-Wide Association StudyHistone-Lysine N-MethyltransferaseHistonesHuman Embryonic Stem CellsHumansMyeloid-Lymphoid Leukemia ProteinNeoplasm ProteinsConceptsHuman embryonic stem cellsBivalent genesHistone modificationsCell cycleCell cycle-dependent fashionPluripotent cell cycleRepressive histone modificationsPosttranslational histone modificationsH3K4me3/H3K27me3Maintenance of pluripotencyHistone modification signaturesMethylation/demethylationLevels of H3K4me3Embryonic stem cellsInduction of differentiationChromatin regulationChromatin modifiersEpigenetic landscapeCell identityModification signaturesLineage commitmentGenomic enrichmentGene promoterProgeny cellsMolecular mechanisms