2024
Machine-guided design of cell-type-targeting cis-regulatory elements
Gosai S, Castro R, Fuentes N, Butts J, Mouri K, Alasoadura M, Kales S, Nguyen T, Noche R, Rao A, Joy M, Sabeti P, Reilly S, Tewhey R. Machine-guided design of cell-type-targeting cis-regulatory elements. Nature 2024, 634: 1211-1220. PMID: 39443793, PMCID: PMC11525185, DOI: 10.1038/s41586-024-08070-z.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsCell typesActivation of off-target cellsGene expressionCell type-specific expressionSynthetic cis-regulatory elementsCell-type specificityHuman genomeUnique cell typeTissue identityBiotechnological applicationsTissue specificityIn vitro validationCell linesCre activitySequenceGenesNatural sequenceDevelopmental timeExpressionCellsGenomeTested in vivoMotifOff-target cellsSomatic mosaicism in schizophrenia brains reveals prenatal mutational processes
Maury E, Jones A, Seplyarskiy V, Nguyen T, Rosenbluh C, Bae T, Wang Y, Abyzov A, Khoshkhoo S, Chahine Y, Zhao S, Venkatesh S, Root E, Voloudakis G, Roussos P, Network B, Park P, Akbarian S, Brennand K, Reilly S, Lee E, Sunyaev S, Walsh C, Chess A. Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes. Science 2024, 386: 217-224. PMID: 39388546, PMCID: PMC11490355, DOI: 10.1126/science.adq1456.Peer-Reviewed Original ResearchConceptsTranscription factor binding sitesWhole-genome sequencingOpen chromatinMutational processesSomatic mutationsFactor binding sitesSchizophrenia casesSchizophrenia risk genesSomatic mosaicismSomatic variantsRisk genesG mutationGene expressionGermline mutationsBinding sitesGenesMutationsIncreased somatic mutationsChromatinMosaic somatic mutationsPrenatal neurogenesisContext of schizophreniaBrain neuronsSchizophrenia brainVariantsMassively parallel approaches for characterizing noncoding functional variation in human evolution
Rong S, Root E, Reilly S. Massively parallel approaches for characterizing noncoding functional variation in human evolution. Current Opinion In Genetics & Development 2024, 88: 102256. PMID: 39217658, DOI: 10.1016/j.gde.2024.102256.Peer-Reviewed Original ResearchCis-regulatory elementsFunction of cis-regulatory elementsImpact of sequence variantsHigh-throughput approachNoncoding variationGenome functionNoncoding regionsSequence variantsPhenotypic consequencesCRISPR screensGenetic basisGenetic variantsGenetic differencesDiverse phenotypesGene expressionRegulatory functionsHuman evolutionFunctional variationGenomeUnique phenotypePhenotypeRegulatory impactModel systemVariantsGenesMulticenter integrated analysis of noncoding CRISPRi screens
Yao D, Tycko J, Oh J, Bounds L, Gosai S, Lataniotis L, Mackay-Smith A, Doughty B, Gabdank I, Schmidt H, Guerrero-Altamirano T, Siklenka K, Guo K, White A, Youngworth I, Andreeva K, Ren X, Barrera A, Luo Y, Yardımcı G, Tewhey R, Kundaje A, Greenleaf W, Sabeti P, Leslie C, Pritykin Y, Moore J, Beer M, Gersbach C, Reddy T, Shen Y, Engreitz J, Bassik M, Reilly S. Multicenter integrated analysis of noncoding CRISPRi screens. Nature Methods 2024, 21: 723-734. PMID: 38504114, PMCID: PMC11009116, DOI: 10.1038/s41592-024-02216-7.Peer-Reviewed Original ResearchCis-regulatory elementsCRISPR interferenceSingle guide RNADetection of cis-regulatory elementsGuide RNAsCandidate cis-regulatory elementsNoncoding cis-regulatory elementsDNA strand biasGene regulatory landscapeCis-regulatory mechanismsNoncoding genomeNoncoding elementsTranscribed regionsStrand biasHuman cell linesCRISPR screensFunctional characterizationTranscriptional effectsGenomeK562 cellsRegulatory landscapeCell linesConsortium effortCharacterization CenterRNA
2021
Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak
Siddle K, Krasilnikova L, Moreno G, Schaffner S, Vostok J, Fitzgerald N, Lemieux J, Barkas N, Loreth C, Specht I, Tomkins-Tinch C, Paull J, Schaeffer B, Taylor B, Loftness B, Johnson H, Schubert P, Shephard H, Doucette M, Fink T, Lang A, Baez S, Beauchamp J, Hennigan S, Buzby E, Ash S, Brown J, Clancy S, Cofsky S, Gagne L, Hall J, Harrington R, Gionet G, DeRuff K, Vodzak M, Adams G, Dobbins S, Slack S, Reilly S, Anderson L, Cipicchio M, DeFelice M, Grimsby J, Anderson S, Blumenstiel B, Meldrim J, Rooke H, Vicente G, Smith N, Messer K, Reagan F, Mandese Z, Lee M, Ray M, Fisher M, Ulcena M, Nolet C, English S, Larkin K, Vernest K, Chaluvadi S, Arvidson D, Melchiono M, Covell T, Harik V, Brock-Fisher T, Dunn M, Kearns A, Hanage W, Bernard C, Philippakis A, Lennon N, Gabriel S, Gallagher G, Smole S, Madoff L, Brown C, Park D, MacInnis B, Sabeti P. Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak. Cell 2021, 185: 485-492.e10. PMID: 35051367, PMCID: PMC8695126, DOI: 10.1016/j.cell.2021.12.027.Peer-Reviewed Original ResearchConceptsVaccinated individualsPublic health responseEpidemiological dataHealth responseComprehensive public health responseFirst large outbreakHigh vaccination ratesDelta variant outbreakOutbreak-associated casesVaccination ratesCOVID-19 casesDelta variantRobust public health responseVariant outbreakLarge outbreakMultiple settingsOutbreakIndividualsCasesInfectionOnward impactResponseSynthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows
Lagerborg KA, Normandin E, Bauer MR, Adams G, Figueroa K, Loreth C, Gladden-Young A, Shaw BM, Pearlman LR, Berenzy D, Dewey HB, Kales S, Dobbins ST, Shenoy ES, Hooper D, Pierce VM, Zachary KC, Park DJ, MacInnis BL, Tewhey R, Lemieux JE, Sabeti PC, Reilly SK, Siddle KJ. Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows. Nature Microbiology 2021, 7: 108-119. PMID: 34907347, PMCID: PMC8923058, DOI: 10.1038/s41564-021-01019-2.Peer-Reviewed Original ResearchDetection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells
Jagoda E, Xue JR, Reilly SK, Dannemann M, Racimo F, Huerta-Sanchez E, Sankararaman S, Kelso J, Pagani L, Sabeti PC, Capellini TD. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Molecular Biology And Evolution 2021, 39: msab304. PMID: 34662402, PMCID: PMC8760939, DOI: 10.1093/molbev/msab304.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsGene expressionPutative cis-regulatory elementsParallel reporter assaysImmune transcription factorsReporter gene expressionExpression of genesGenic targetsSelective sweepsMPRA dataInnate immune pathwaysPositive selectionTranscription factorsEndogenous sequencesReporter assaysAntiviral defenseDriver variantsGenetic variantsFunctional significanceImmune pathwaysWhite blood cell countGenesModern humansPotential immune responseBlood cell countGenome-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 linesFunctional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation
Khetan S, Kales S, Kursawe R, Jillette A, Ulirsch JC, Reilly SK, Ucar D, Tewhey R, Stitzel ML. Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation. Nature Communications 2021, 12: 5242. PMID: 34475398, PMCID: PMC8413311, DOI: 10.1038/s41467-021-25514-6.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphismsTranscriptional activationEndoplasmic reticulum (ER) stress conditionsTranscriptional stress responseCis-regulatory effectsParallel reporter assaysT2D single nucleotide polymorphismsHigh linkage disequilibriumMultiple single nucleotide polymorphismsT2D genetic riskT2D-associated single nucleotide polymorphismsMIN6 β-cellsChromatin accessibilityCandidate single nucleotide polymorphismsT2D geneticsHuman genomeAssociation signalsRepetitive elementsFunctional characterizationNuclear elementsMolecular mechanismsReporter assaysStress responseAssociation studiesDirect characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH
Reilly SK, Gosai SJ, Gutierrez A, Mackay-Smith A, Ulirsch JC, Kanai M, Mouri K, Berenzy D, Kales S, Butler GM, Gladden-Young A, Bhuiyan RM, Stitzel ML, Finucane HK, Sabeti PC, Tewhey R. Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH. Nature Genetics 2021, 53: 1166-1176. PMID: 34326544, PMCID: PMC8925018, DOI: 10.1038/s41588-021-00900-4.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingBayes TheoremClustered Regularly Interspaced Short Palindromic RepeatsDelta-5 Fatty Acid DesaturaseDeoxyribonuclease IFatty Acid DesaturasesFlow CytometryGATA1 Transcription FactorHumansIn Situ Hybridization, FluorescenceK562 CellsLIM Domain ProteinsModels, GeneticPolymorphism, Single NucleotideProto-Oncogene ProteinsQuantitative Trait LociRegulatory Sequences, Nucleic AcidRNA, Guide, CRISPR-Cas SystemsConceptsCis-regulatory elementsGenome-wide association signalsGenome functionEpigenetic mappingComplex genetic associationsFunctional dissectionNearest geneGenetic variationAssociation signalsNative transcriptsTarget genesCausal variantsMultiple genesEndogenous functionsReporter assaysGenesCre activitySitu hybridizationGenetic associationFlow cytometryLociTranscriptsHierarchical Bayesian modelReaction fluorescenceHybridization
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 discoveryEnhancerEvolutionPrioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features
Ray JP, de Boer CG, Fulco CP, Lareau CA, Kanai M, Ulirsch JC, Tewhey R, Ludwig LS, Reilly SK, Bergman DT, Engreitz JM, Issner R, Finucane HK, Lander ES, Regev A, Hacohen N. Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features. Nature Communications 2020, 11: 1237. PMID: 32144282, PMCID: PMC7060350, DOI: 10.1038/s41467-020-15022-4.Peer-Reviewed Original ResearchConceptsChromatin accessible regionsGenome-wide association studiesDisease-associated lociGenetic variantsCausal genetic variantsDisease-associated variantsComplex traitsGenetic variationRegulatory regionsGenomic featuresCausal variantsRegulatory potentialAssociation studiesReporter activityDisease-associated haplotypeLinkage disequilibriumCommon variantsTight linkage disequilibriumExperimental assaysCell linesImmune cell linesLociAccessible regionsTNFAIP3TNFAIP3 locus
2018
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay
Tewhey R, Kotliar D, Park D, Liu B, Winnicki S, Reilly S, Andersen K, Mikkelsen T, Lander E, Schaffner S, Sabeti P. Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay. Cell 2018, 172: 1132-1134. PMID: 29474912, DOI: 10.1016/j.cell.2018.02.021.Peer-Reviewed Original Research
2016
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay
Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC. Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay. Cell 2016, 165: 1519-1529. PMID: 27259153, PMCID: PMC4957403, DOI: 10.1016/j.cell.2016.04.027.Peer-Reviewed Original ResearchConceptsNon-coding variantsCausal allelesCis-expression quantitative trait lociReporter assaysHundreds of lociQuantitative trait lociParallel reporter assaysNon-coding polymorphismsTrait lociControl regionGene expressionRegulatory functionsDifferential expressionHuman traitsHuman biologyAlters expressionAllelesLociProstaglandin EP4 receptorTraitsExpressionRisk allelesVariantsDirect identificationDirect evidenceEvolution 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
2015
Evolutionary 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 ResearchConceptsCorrelated 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
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