2024
Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals
Uebbing S, Kocher A, Baumgartner M, Ji Y, Bai S, Xing X, Nottoli T, Noonan J. Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals. Molecular Biology And Evolution 2024, 41: msae199. PMID: 39302728, PMCID: PMC11465374, DOI: 10.1093/molbev/msae199.Peer-Reviewed Original ResearchSequence evolutionRegulatory evolutionDevelopmental signaling genesEnhanced evolutionEvolutionary innovationMammalian phylogenyTranscriptional enhancersGenetic variationPhenotypic variationPleiotropic genesDevelopmental genesEnhancer elementsHoofed mammalsEnhancer sequencesActivation domainSignaling genesEvolutionary adaptationDiverse organismsGenesHuman diseasesRegulatory functionsDevelopmental processesDeveloping limbCell typesMammalsReconstructing human-specific regulatory functions in model systems
Baumgartner M, Ji Y, Noonan J. Reconstructing human-specific regulatory functions in model systems. Current Opinion In Genetics & Development 2024, 89: 102259. PMID: 39270593, PMCID: PMC11588545, DOI: 10.1016/j.gde.2024.102259.Peer-Reviewed Original Research
2022
Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome
Dutrow EV, Emera D, Yim K, Uebbing S, Kocher AA, Krenzer M, Nottoli T, Burkhardt DB, Krishnaswamy S, Louvi A, Noonan JP. Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome. Nature Communications 2022, 13: 304. PMID: 35027568, PMCID: PMC8758698, DOI: 10.1038/s41467-021-27899-w.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell DifferentiationChondrocytesChondrogenesisEmbryo, MammalianEnhancer Elements, GeneticEpigenesis, GeneticExtremitiesGene Expression ProfilingGene Expression RegulationGene Knock-In TechniquesGenomeHomeodomain ProteinsHomozygoteHumansMesodermMice, Inbred C57BLModels, GeneticPan troglodytesPromoter Regions, GeneticTime FactorsConceptsHuman Accelerated RegionsGene expressionHuman-specific sequence changesDevelopmental gene regulationSingle-cell RNA sequencingGene regulatory functionsHuman evolutionEndogenous gene expressionAlters gene expressionSkeletal patterningMolecular functionsGene regulationChondrogenic mesenchymeMouse genomeRegulatory modificationHomozygous embryosLimb developmentTranscriptional enhancersTranscription factorsRNA sequencingEnhancer activityMouse embryosRegulatory functionsAccelerated regionSequence changes
2014
Evolution of Gene Regulation in Humans
Reilly S, Noonan J. Evolution of Gene Regulation in Humans. Annual Review Of Genomics And Human Genetics 2014, 17: 1-23. DOI: 10.1146/annurev-genom-090314-045935.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsRegulatory functionsGene regulationHuman-specific genetic changesGenetic changesNovel human phenotypeNew regulatory functionInduced pluripotent stem cellsPluripotent stem cellsUnique biological featuresSpecific regulatory changesHomologous humanGenome editingGene expressionHuman phenotypesFinal online publication datePrimate cellsHuman evolutionRegulatory activityStem cellsOnline publication dateExpression levelsNonhuman primate cellsBiological featuresRegulationRegulatory innovation
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 features
2010
Genomics of Long-Range Regulatory Elements
Noonan JP, McCallion AS. Genomics of Long-Range Regulatory Elements. Annual Review Of Genomics And Human Genetics 2010, 11: 1-23. PMID: 20438361, DOI: 10.1146/annurev-genom-082509-141651.Peer-Reviewed Original ResearchConceptsRegulatory elementsGene expressionLong-range regulatory elementsCis-acting elementsHuman cell typesVertebrate genomesModel organismsSequence conservationTranscriptional regulationHuman genomeGenomic distanceRegulatory sequencesTransgenic technologyRegulatory potentialBiological functionsRegulatory functionsGenomeBiological significanceCell typesLarge-scale effortsRegulatory controlExpressionCommon setGenomicsGenes
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