2022
The three-dimensional landscape of cortical chromatin accessibility in Alzheimer’s disease
Bendl J, Hauberg M, Girdhar K, Im E, Vicari J, Rahman S, Fernando M, Townsley K, Dong P, Misir R, Kleopoulos S, Reach S, Apontes P, Zeng B, Zhang W, Voloudakis G, Brennand K, Nixon R, Haroutunian V, Hoffman G, Fullard J, Roussos P. The three-dimensional landscape of cortical chromatin accessibility in Alzheimer’s disease. Nature Neuroscience 2022, 25: 1366-1378. PMID: 36171428, PMCID: PMC9581463, DOI: 10.1038/s41593-022-01166-7.Peer-Reviewed Original ResearchConceptsOpen chromatin regionsCis-regulatory domainsChromatin accessibilitySpecific enhancer-promoter interactionsTranscription factor regulatory networksEnhancer-promoter interactionsATAC-seq librariesChromatin regionsLysosomal genesNonneuronal nucleiRegulatory networksThree-dimensional structureGenomeThree-dimensional landscapeRegulatory effectsAlzheimer's diseaseCommunity-based analysisUSF2GenesDysregulationRepertoireTFAD casesLandscapeDomain
2017
In utero exposure to maternal smoking is associated with DNA methylation alterations and reduced neuronal content in the developing fetal brain
Chatterton Z, Hartley B, Seok M, Mendelev N, Chen S, Milekic M, Rosoklija G, Stankov A, Trencevsja-Ivanovska I, Brennand K, Ge Y, Dwork A, Haghighi F. In utero exposure to maternal smoking is associated with DNA methylation alterations and reduced neuronal content in the developing fetal brain. Epigenetics & Chromatin 2017, 10: 4. PMID: 28149327, PMCID: PMC5270321, DOI: 10.1186/s13072-017-0111-y.Peer-Reviewed Original ResearchMeSH KeywordsBrainDNA MethylationFemaleFetal DevelopmentFetusGestational AgeGTP-Binding Protein alpha Subunits, Gq-G11HumansImmunohistochemistryInduced Pluripotent Stem CellsMaleMaternal ExposureNeural Stem CellsNeuronsPregnancyPregnancy Trimester, SecondPromoter Regions, GeneticSmokingSuccinate DehydrogenaseTubulinConceptsMaternal smokingDorsolateral prefrontal cortexNeuronal contentCortical gray matterFetal brain growthDifferentiation of neuronsBehavioral problemsFalse discovery correctionSignificant DMRsSmoking exposureGestational ageSecond trimesterUtero exposurePrenatal exposureCortical developmentFetal brainExposure altersSmokingBrain growthGray matterCell proportionFetusesPrefrontal cortexDNA methylationMethylation profiles
2014
A Role for Noncoding Variation in Schizophrenia
Roussos P, Mitchell A, Voloudakis G, Fullard J, Pothula V, Tsang J, Stahl E, Georgakopoulos A, Ruderfer D, Charney A, Okada Y, Siminovitch K, Worthington J, Padyukov L, Klareskog L, Gregersen P, Plenge R, Raychaudhuri S, Fromer M, Purcell S, Brennand K, Robakis N, Schadt E, Akbarian S, Sklar P. A Role for Noncoding Variation in Schizophrenia. Cell Reports 2014, 9: 1417-1429. PMID: 25453756, PMCID: PMC4255904, DOI: 10.1016/j.celrep.2014.10.015.Peer-Reviewed Original ResearchMeSH KeywordsArthritis, RheumatoidCalcium Channels, L-TypeDatabases, GeneticDNA, IntergenicEnhancer Elements, GeneticGene Expression RegulationGenetic LociGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansMolecular Sequence AnnotationOrgan SpecificityPolymorphism, Single NucleotidePromoter Regions, GeneticProtein BindingRisk FactorsSchizophreniaConceptsExpression quantitative trait lociGenome-wide significant lociCommon variant lociQuantitative trait lociPluripotent stem cell-derived neuronsDistal regulatory elementsStem cell-derived neuronsPotential physical interactionsCell-derived neuronsRegulatory element sequencesPotential functional roleGenome architectureChromosomal loopingTranscriptional regulationFunctional annotationTrait lociSignificant lociNoncoding SNPsRegulatory elementsNoncoding variationsRisk lociVariant lociUnknown functionFunctional linkElement sequences