2016
Origin and evolution of developmental enhancers in the mammalian neocortex
Emera D, Yin J, Reilly SK, Gockley J, Noonan JP. Origin and evolution of developmental enhancers in the mammalian neocortex. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: e2617-e2626. PMID: 27114548, PMCID: PMC4868431, DOI: 10.1073/pnas.1603718113.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBiological EvolutionComputer SimulationEnhancer Elements, GeneticGene Expression Regulation, DevelopmentalHumansMiceModels, GeneticMorphogenesisNeocortexSpecies SpecificityTranscription FactorsConceptsRegulatory elementsDe novo birthMammalian stem lineageNovel regulatory sequencesWeak evolutionary constraintsMammalian neocortexBackground genomic sequencesDevelopmental enhancersEvolutionary constraintsMorphological innovationsStem lineageEutherian mammalsGenomic sequencesRegulatory sequencesPhylogenetic originComplex enhancerCell signalingGenomic backgroundMouse corticogenesisCell migrationMammalsMammalian forebrainEnhancerGenesLife cycle
2015
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment
Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nature Communications 2015, 6: 6404. PMID: 25752243, PMCID: PMC4355952, DOI: 10.1038/ncomms7404.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAutism Spectrum DisorderChromatin Assembly and DisassemblyDNA-Binding ProteinsGene Expression Regulation, DevelopmentalGene Knockdown TechniquesGene Regulatory NetworksHumansMiceModels, NeurologicalNervous SystemNeural Stem CellsTranscription FactorsConceptsASD risk genesRisk genesRegulatory networksAncient gene regulatory networksHuman neural stem cellsLoss of CHD8Specific regulatory networksGene regulatory networksCo-expression networkAutism risk genesEmbryonic mouse cortexChromatin modifiersIdentification of recurrentChromodomain-HelicaseChd8 knockdownNeural stem cellsMouse neurodevelopmentCHD8Human brain developmentFunction mutationsGenesStem cellsHuman neurodevelopmentNovo lossBrain developmentEvolutionary changes in promoter and enhancer activity during human corticogenesis
Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, Sarro R, Rakic P, Noonan JP. Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science 2015, 347: 1155-1159. PMID: 25745175, PMCID: PMC4426903, DOI: 10.1126/science.1260943.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCerebral CortexEnhancer Elements, GeneticEpigenesis, GeneticEvolution, MolecularGene Expression Regulation, DevelopmentalHumansMacaca mulattaMiceOrganogenesisPromoter Regions, GeneticRatsConceptsCorrelated gene expression patternsSimilar transcription factorsGene expression patternsCommon regulatory mechanismHuman cortical evolutionPotential regulatory changesEvolutionary changeEpigenetic profilingEvolutionary expansionTranscription factorsGenetic mechanismsSite enrichmentEnhancer activityDevelopmental processesExpression patternsHuman corticogenesisRegulatory mechanismsMouse corticogenesisHuman higher cognitionCortical evolutionPromoterCorticogenesisCoordinated patternNeuronal proliferationEnhancer
2013
The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb
Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP. The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb. Cell 2013, 154: 185-196. PMID: 23827682, PMCID: PMC3785101, DOI: 10.1016/j.cell.2013.05.056.Peer-Reviewed Original ResearchMeSH KeywordsAcetylationAnimalsBiological EvolutionEnhancer Elements, GeneticExtremitiesGene Expression Regulation, DevelopmentalGenetics, MedicalGenome-Wide Association StudyHistonesHumansMacaca mulattaMiceOrganogenesisPromoter Regions, GeneticTranscriptomeConceptsCis-regulatory evolutionHistone modification H3K27acGenome-wide viewMouse limb developmentRegulatory activityGain of activityMost enhancersGene regulationEmbryonic limbLimb developmentHuman lineageEnhancer activityHuman embryonic tissuesGene expressionEmbryonic tissuesRegulatory functionsPromoterH3K27acMolecular driversGenetic causeHeterogeneous genetic causesEnhancerQuantitative readoutMorphological evolutionAnatomical featuresThe genomic landscape of cohesin-associated chromatin interactions
DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP. The genomic landscape of cohesin-associated chromatin interactions. Genome Research 2013, 23: 1224-1234. PMID: 23704192, PMCID: PMC3730097, DOI: 10.1101/gr.156570.113.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesCCCTC-Binding FactorCell Cycle ProteinsChromatinChromatin ImmunoprecipitationChromosomal Proteins, Non-HistoneEnhancer Elements, GeneticGene Expression Regulation, DevelopmentalGenomeHistonesLimb BudsMiceMice, Inbred C57BLOrgan SpecificityPromoter Regions, GeneticProtein SubunitsRepressor ProteinsConceptsPaired-end tag sequencingGenome-wide scaleInsulator protein CTCFChromatin interaction analysisEnhancer-promoter interactionsEnhancer-promoter communicationEmbryonic stem cellsChromatin stateProtein CTCFChromatin interactionsTag sequencingDNA loopsRegulatory architectureMouse limbRegulatory outputMouse embryosGenomic landscapeMultiple tissuesCohesinStem cellsCTCFPromoterDemarcate regionsInteraction analysisGenome
2012
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb
Cotney J, Leng J, Oh S, DeMare LE, Reilly SK, Gerstein MB, Noonan JP. Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. Genome Research 2012, 22: 1069-1080. PMID: 22421546, PMCID: PMC3371702, DOI: 10.1101/gr.129817.111.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatinE1A-Associated p300 ProteinEmbryo, MammalianEnhancer Elements, GeneticExtremitiesGene Expression ProfilingGene Expression Regulation, DevelopmentalHistonesMiceNucleosomesOrgan SpecificityConceptsTissue-specific gene expressionChromatin state signatureActive developmental enhancersChromatin stateDevelopmental enhancersGene expressionEmbryonic tissuesHistone modification profilingOpen chromatin stateGenome-wide profilingEmbryonic cell typesMultiple embryonic tissuesGene expression differencesWhole transcriptome analysisH3K27me3 depletionEmbryonic forelimbChromatin profilingNucleosome displacementPutative enhancersEmbryonic limbMammalian embryosH3K27ac enrichmentRegulatory sequencesRegulatory elementsEnhancer discovery
2008
Human-Specific Gain of Function in a Developmental Enhancer
Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, FitzPatrick DR, Afzal V, Pennacchio LA, Rubin EM, Noonan JP. Human-Specific Gain of Function in a Developmental Enhancer. Science 2008, 321: 1346-1350. PMID: 18772437, PMCID: PMC2658639, DOI: 10.1126/science.1159974.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBinding SitesBody PatterningConserved SequenceEmbryonic DevelopmentEnhancer Elements, GeneticEvolution, MolecularExtremitiesGene Expression ProfilingGene Expression Regulation, DevelopmentalHumansLimb BudsMacaca mulattaMiceMice, TransgenicMolecular Sequence DataMutationPan troglodytesPAX9 Transcription FactorSelection, GeneticTranscription FactorsConceptsExpression domainsHuman-specific substitutionsHuman-specific gainsGain of functionOrthologous elementsDevelopmental enhancersAncestral stateGene regulationNoncoding sequencesTerrestrial vertebratesHuman enhancersSynthetic enhancersEnhancer sequencesGene expressionRegulatory functionsDevelopmental stagesVivo analysisEnhancerVivo evidenceTransgenic miceSequenceVertebratesDomainRegulationSubstitution