2021
Genome-wide functional screen of 3′UTR variants uncovers causal variants for human disease and evolution
Griesemer D, Xue JR, Reilly SK, Ulirsch JC, Kukreja K, Davis JR, Kanai M, Yang DK, Butts JC, Guney MH, Luban J, Montgomery SB, Finucane HK, Novina CD, Tewhey R, Sabeti PC. Genome-wide functional screen of 3′UTR variants uncovers causal variants for human disease and evolution. Cell 2021, 184: 5247-5260.e19. PMID: 34534445, PMCID: PMC8487971, DOI: 10.1016/j.cell.2021.08.025.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesCausal variantsEvolutionary adaptationGenome-wide functional screenDiverse molecular mechanismsHuman evolutionary adaptationBase-pair resolutionParallel reporterHuman cell linesMiRNA sitesTranscriptional changesFunctional screenAllelic replacementSimple sequenceMolecular mechanismsAssociation studiesRich elementsPair resolutionHuman diseasesPhenotype associationsHuman traitsUntranslated region variantsGenetic variantsRegulatory activityCell lines
2020
Massively parallel discovery of human-specific substitutions that alter enhancer activity
Uebbing S, Gockley J, Reilly SK, Kocher AA, Geller E, Gandotra N, Scharfe C, Cotney J, Noonan JP. Massively parallel discovery of human-specific substitutions that alter enhancer activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 118: e2007049118. PMID: 33372131, PMCID: PMC7812811, DOI: 10.1073/pnas.2007049118.Peer-Reviewed Original ResearchConceptsHuman-specific substitutionsHuman-gained enhancersGenetic changesEnhancer functionEnhancer activityHuman-specific genetic changesHuman evolutionGene regulatory elementsBackground genetic variationAncestral functionRegulatory evolutionEnhancer assaysGenetic variationRegulatory elementsNeural stem cellsHuman traitsNovel activityNonadditive wayRegulatory activityStem cellsFunctional impactDifferential activityParallel discoveryEnhancerEvolution
2016
Evolution of Gene Regulation in Humans.
Reilly SK, Noonan JP. Evolution of Gene Regulation in Humans. Annual Review Of Genomics And Human Genetics 2016, 17: 45-67. PMID: 27147089, DOI: 10.1146/annurev-genom-090314-045935.Peer-Reviewed Original ResearchConceptsRegulatory functionsGene regulationHuman-specific genetic changesGenetic changesNovel human phenotypeNew regulatory functionInduced pluripotent stem cellsPluripotent stem cellsUnique biological featuresSpecific regulatory changesHomologous humanGenome editingGene expressionHuman phenotypesPrimate cellsHuman evolutionRegulatory activityStem cellsExpression levelsNonhuman primate cellsBiological featuresRegulationRegulatory innovationCellsHumans
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