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 ResearchConceptsRegulatory 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
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 ResearchConceptsTissue-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
2009
Response to Comment on "Human-Specific Gain of Function in a Developmental Enhancer"
Prabhakar S, Visel A, Akiyama J, Shoukry M, Lewis K, Holt A, Plajzer-Frick I, Morrison H, FitzPatrick D, Afzal V, Pennacchio L, Rubin E, Noonan J. Response to Comment on "Human-Specific Gain of Function in a Developmental Enhancer". Science 2009, 323: 714-714. DOI: 10.1126/science.1166571.Peer-Reviewed Original Research
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