2024
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue
Farzad N, Enninful A, Bao S, Zhang D, Deng Y, Fan R. Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. Nature Protocols 2024, 19: 3389-3425. PMID: 38943021, DOI: 10.1038/s41596-024-01013-y.Peer-Reviewed Original ResearchTn5 transpositionDeterministic barcodingGenome-wide profiling of histone modificationsProfiling of histone modificationsTransposase-accessible chromatin sequencingEpigenomic profiling methodsGenome-wide profilingSingle-base resolutionGene regulation programsGenomic DNA locusNext-generation sequencingDNA lociBioinformatics skillsLibrary preparationDNA barcodingChromatin accessibilityChromatin sequencingHistone modificationsEpigenome sequencingEpigenetic landscapeEpigenetic mapsCellular functionsEpigenetic markersCustom pipelineBarcoding
2023
Epigenetic markers and therapeutic targets for metastasis
Kravitz C, Yan Q, Nguyen D. Epigenetic markers and therapeutic targets for metastasis. Cancer And Metastasis Reviews 2023, 42: 427-443. PMID: 37286865, PMCID: PMC10595046, DOI: 10.1007/s10555-023-10109-y.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEpigenomic alterationsLineage integrityTherapeutic targetEpigenetic markersCancer cellsGenetic aberrationsCurrent knowledgeHuman tumorsMalignant cell cloneTumor progressionDNANumber of discoveriesCell clonesDisseminated diseaseCertain organsPrimary tumorTherapeutic responseMetastatic cancerEpigenomeChromatinHistonesLiquid biopsyAlterationsClonesTarget
2015
Baseline Chromatin Modification Levels May Predict Interindividual Variability in Ozone-Induced Gene Expression
McCullough S, Bowers E, On D, Morgan D, Dailey L, Hines R, Devlin R, Diaz-Sanchez D. Baseline Chromatin Modification Levels May Predict Interindividual Variability in Ozone-Induced Gene Expression. Toxicological Sciences 2015, 150: 216-224. PMID: 26719369, PMCID: PMC4838038, DOI: 10.1093/toxsci/kfv324.Peer-Reviewed Original ResearchConceptsChromatin modificationsH3 lysine 4 trimethylationSpecific chromatin modificationsChromatin modification statesLysine 4 trimethylationUnmodified H3Human bronchial epithelial cellsModification statesTotal H3H3K27 acetylationCellular signalsGene inductionPrimary human bronchial epithelial cellsKey regulatorGene expressionEpigenetic markersBronchial epithelial cellsTraditional toxicological paradigmModification levelsRelative abundanceAir-liquid interface modelTrimethylationEpithelial cellsH3Specific modifications
2014
Feasibility of using an epigenetic marker of risk for lung cancer, methylation of p16, to promote smoking cessation among US veterans
Shofer S, Beyea M, Li S, Bastian LA, Wahidi MM, Kelley M, Lipkus IM. Feasibility of using an epigenetic marker of risk for lung cancer, methylation of p16, to promote smoking cessation among US veterans. BMJ Open Respiratory Research 2014, 1: e000032. PMID: 25478181, PMCID: PMC4212704, DOI: 10.1136/bmjresp-2014-000032.Peer-Reviewed Original ResearchLung cancer riskLung cancerSmoking cessationCancer riskMethylated p16Time of enrollmentAcceptance of testingCent of participantsAirway obstructionActive smokersCurrent smokersCessation assistanceTobacco exposureCessation ratesUS veteransEpigenetic markersSmokersMethylation of p16P16 methylationCancerP16SmokingEducational materialsRiskEducational presentationsEpigenetic regulation of OPA1 sensitizes hepatocellular carcinoma to sorafenib‐induced apoptosis (59.1)
Puszyk W, Dong H, Zhao F, Shisgal P, Cabrera R, Neslon D, Liu C. Epigenetic regulation of OPA1 sensitizes hepatocellular carcinoma to sorafenib‐induced apoptosis (59.1). The FASEB Journal 2014, 28 DOI: 10.1096/fasebj.28.1_supplement.59.1.Peer-Reviewed Original ResearchDNA methylationHepatocellular carcinomaEpigenetic regulationProtein OPA1HCC cellsMitochondrial fragmentationGene promoterC releaseEpigenetic analysisXenograft tumor growthEpigenetic markersSorafenib-induced apoptosisAkt pathwayOPA1HCC xenograft tumor growthHepatocellular carcinoma cellsNovel therapeutic targetExpression levelsTumorigenesis of HCCIdentification of patientsPathogenesis of HCCOPA1 knockdownApoptosisPrimary hepatocytesSensitivity of HCCChild Abuse, Depression, and Methylation in Genes Involved With Stress, Neural Plasticity, and Brain Circuitry
Weder N, Zhang H, Jensen K, Yang BZ, Simen A, Jackowski A, Lipschitz D, Douglas-Palumberi H, Ge M, Perepletchikova F, O'Loughlin K, Hudziak JJ, Gelernter J, Kaufman J. Child Abuse, Depression, and Methylation in Genes Involved With Stress, Neural Plasticity, and Brain Circuitry. Journal Of The American Academy Of Child & Adolescent Psychiatry 2014, 53: 417-424.e5. PMID: 24655651, PMCID: PMC4126411, DOI: 10.1016/j.jaac.2013.12.025.Peer-Reviewed Original ResearchConceptsTubulin Polymerization Promoting ProteinCandidate genesEpigenetic changesMethylation sitesGenome-wide methylation studyMultiple methylation sitesK BeadChip arraySaliva-derived DNAEpigenetic mechanismsK BeadChipBeadChip arrayEpigenetic markersStress responseMethylation studiesCpG sitesGenesNeural circuitry developmentMethylationId-3Whole genome testingNeural plasticityGRIN1Genome testingPlasticityGlutamate receptors
2010
Bridging Environment and DNA: Activity-Induced Epigenetic Modification in the Adult Brain
Ma D, Guo J, Ming G, Song H. Bridging Environment and DNA: Activity-Induced Epigenetic Modification in the Adult Brain. Research And Perspectives In Alzheimer's Disease 2010, 113-123. DOI: 10.1007/978-3-642-16602-0_10.Peer-Reviewed Original ResearchEpigenetic modificationsDNA methylationDNA methylation landscapeStable epigenetic markerMechanisms of neural plasticityLearning-related stimuliDemethylation machineryMethylation landscapeNeuronal genomeEpigenetic markersGene expressionPsychiatric disordersDNAActivity-dependent inductionNeural plasticityExternal cuesNeuronal activityPotential therapeutic interventionsGenesSensory informationAdult brainSensory experienceBrainGenomeNeuronal properties
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