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 ResearchConceptsCis-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 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