2020
Prioritizing 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
2014
Post-translational Regulation of the Type III Inositol 1,4,5-Trisphosphate Receptor by miRNA-506*
Ananthanarayanan M, Banales JM, Guerra MT, Spirli C, Munoz-Garrido P, Mitchell-Richards K, Tafur D, Saez E, Nathanson MH. Post-translational Regulation of the Type III Inositol 1,4,5-Trisphosphate Receptor by miRNA-506*. Journal Of Biological Chemistry 2014, 290: 184-196. PMID: 25378392, PMCID: PMC4281721, DOI: 10.1074/jbc.m114.587030.Peer-Reviewed Original ResearchConceptsReporter activityMiR-506Trisphosphate receptorPost-translational regulationMiR-506 mimicsCell linesMiR-506 inhibitorEpigenetic regulationMiRNA regulationType III inositolFibrotic signatureMiR-506 expressionType III isoformCholangiocyte cell lineHEK293 cellsSitu hybridizationProtein levelsControl cellsInsP3R3H69 cellsRegulationSignalingExpressionCellsInositol
2012
Parathyroid hormone-related protein activates Wnt signaling to specify the embryonic mammary mesenchyme
Hiremath M, Dann P, Fischer J, Butterworth D, Boras-Granic K, Hens J, Van Houten J, Shi W, Wysolmerski J. Parathyroid hormone-related protein activates Wnt signaling to specify the embryonic mammary mesenchyme. Development 2012, 139: 4239-4249. PMID: 23034629, PMCID: PMC3478689, DOI: 10.1242/dev.080671.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsbeta CateninCell DifferentiationFemaleGene Expression Regulation, DevelopmentalKeratinocytesLymphoid Enhancer-Binding Factor 1Mammary Glands, AnimalMesodermMiceMice, KnockoutParathyroid Hormone-Related ProteinReceptors, Parathyroid HormoneThrombospondinsWnt ProteinsWnt Signaling PathwayConceptsLoss of PTHrPOverexpression of PTHrPHormone-related proteinMammary mesenchymeΒ-cateninEmbryonic mammary mesenchymeWnt pathwayWnt/β-cateninEmbryonic mammary developmentCanonical Wnt pathwayPTHrPMammary developmentMammary budAbnormal differentiationReduced expressionBasal keratinocytesVentral skinReporter activityBud cellsMarkersCanonical WntInappropriate differentiationAbolished expressionMesenchyme markersOverexpressionLead induces an osteoarthritis‐like phenotype in articular chondrocytes through disruption of TGF‐β signaling
Holz JD, Beier E, Sheu T, Ubayawardena R, Wang M, Sampson ER, Rosier RN, Zuscik M, Puzas JE. Lead induces an osteoarthritis‐like phenotype in articular chondrocytes through disruption of TGF‐β signaling. Journal Of Orthopaedic Research® 2012, 30: 1760-1766. PMID: 22517267, PMCID: PMC3839422, DOI: 10.1002/jor.22117.Peer-Reviewed Original ResearchConceptsLead treatmentOsteoarthritis-like phenotypeNormal chondrocyte phenotypeDose-dependent mannerArticular chondrocytesTGF-β signalingActive caspase-3MMP13 activityLead exposureHigher level leadType II collagenVivo exposureCollagen levelsNovel targetType X collagenCaspase-3Articular surfaceEnvironmental toxinsLead toxicityII collagenReporter activityTreatmentArticular cartilageDosePhenotypic shift
2007
Identification and Functional Analysis of a Novel Human CYP2E1 Far Upstream Enhancer
Shadley J, Divakaran K, Munson K, Hines R, Douglas K, McCarver D. Identification and Functional Analysis of a Novel Human CYP2E1 Far Upstream Enhancer. Molecular Pharmacology 2007, 71: 1630-1639. PMID: 17353354, DOI: 10.1124/mol.106.031302.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBinding SitesCells, CulturedCytochrome P-450 CYP2E1Enhancer Elements, GeneticGATA4 Transcription FactorGene Expression Regulation, EnzymologicGenetic VariationHepatocytesHumansMolecular Sequence DataPromoter Regions, GeneticRepetitive Sequences, Nucleic AcidSteroidogenic Factor 1Trans-ActivatorsTranscriptional ActivationConceptsElectrophoretic mobility shift assaysEnhancer sequencesCompetitive electrophoretic mobility shift assaysSupershift electrophoretic mobility shift assaysFunctional regulatory elementsGATA family membersMobility shift assaysGreater luciferase activityOrphan nuclear receptorSteroidogenic factor 1Luciferase reporter activityGATA sequencesFetoprotein transcription factorGATA familyChromatin immunoprecipitationTranscription factorsNuclear proteinsRegulatory elementsShift assaysRegulatory mechanismsFunctional analysisPromoter constructsDirect repeatsReporter activityUpstream region
2006
An autoregulatory element maintains HOXA10 expression in endometrial epithelial cells
Kelly M, Daftary G, Taylor HS. An autoregulatory element maintains HOXA10 expression in endometrial epithelial cells. American Journal Of Obstetrics And Gynecology 2006, 194: 1100-1107. PMID: 16580301, DOI: 10.1016/j.ajog.2005.12.025.Peer-Reviewed Original ResearchConceptsEndometrial epithelial cellsHOXA10 expressionProgesterone receptorAutoregulatory elementRegulatory regionsEpithelial cellsGene expressionBT-20 cellsSteroid-induced gene expressionReporter gene expressionEndometrial receptivityIshikawa cellsSex steroidsBase pair elementSteroid receptorsAlternative molecular mechanismsStromal cellsHOXA10 proteinReporter constructsExpression increasesMolecular mechanismsReceptorsReporter activityDirect bindingHOXA10
2004
A HOXA10 Estrogen Response Element (ERE) is Differentially Regulated by 17 Beta-estradiol and Diethylstilbestrol (DES)
Akbas GE, Song J, Taylor HS. A HOXA10 Estrogen Response Element (ERE) is Differentially Regulated by 17 Beta-estradiol and Diethylstilbestrol (DES). Journal Of Molecular Biology 2004, 340: 1013-1023. PMID: 15236964, DOI: 10.1016/j.jmb.2004.05.052.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceCell Line, TumorCell NucleusDiethylstilbestrolDNA-Binding ProteinsElectrophoretic Mobility Shift AssayEstradiolEstrogen Receptor alphaEstrogen Receptor betaGene Expression RegulationHomeobox A10 ProteinsHomeodomain ProteinsHumansLigandsProtein BindingReceptors, EstrogenResponse ElementsSubstrate SpecificityConceptsEstrogen response elementHOXA10 estrogen response elementConsensus estrogen response elementHox gene expressionHOXA10 geneEndometrial adenocarcinoma cell lineMolecular mechanismsSRC-1Ligand-specific activationGene expressionMüllerian duct differentiationReporter activityAdenocarcinoma cell lineFemale reproductive tractReporter expressionLigand specificityLuciferase reporter activityIshikawa cellsResponse elementEstrogen regulationEstrogen diethylstilbestrolHOXA10 expressionDevelopmental gene expressionDevelopmental anomaliesDuct differentiation
2003
GCNF‐dependent repression of BMP‐15 and GDF‐9 mediates gamete regulation of female fertility
Lan Z, Gu P, Xu X, Jackson KJ, DeMayo FJ, O'Malley BW, Cooney AJ. GCNF‐dependent repression of BMP‐15 and GDF‐9 mediates gamete regulation of female fertility. The EMBO Journal 2003, 22: 4070-4081. PMID: 12912906, PMCID: PMC175795, DOI: 10.1093/emboj/cdg405.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBone Morphogenetic Protein 15Bone Morphogenetic ProteinsCHO CellsCricetinaeDNA-Binding ProteinsEgg ProteinsFemaleFertilityGene Expression RegulationGrowth Differentiation Factor 9IntegrasesIntercellular Signaling Peptides and ProteinsMembrane GlycoproteinsMiceMice, KnockoutMice, TransgenicModels, BiologicalNuclear Receptor Subfamily 6, Group A, Member 1OocytesOvaryReceptors, Cell SurfaceReceptors, Cytoplasmic and NuclearRepressor ProteinsTransforming Growth Factor betaTransgenesViral ProteinsZona PellucidaZona Pellucida GlycoproteinsConceptsGerm cell nuclear factorBMP-15Bone morphogenetic protein 15New regulatory pathwayFemale fertilityGDF-9Growth differentiation factor 9DR0 elementsDifferentiation factor 9Knockout mouse modelSomatic cellsGene promoterRegulatory pathwaysReproductive defectsReporter activityFemale reproductionMolecular studiesFactor 9Paracrine communicationProtein 15Nuclear factorAberrant steroidogenesisExpressionOocytesPrimary defectCRALBP transcriptional regulation in ciliary epithelial, retinal Müller and retinal pigment epithelial cells
Kennedy BN, Li C, Ortego J, Coca-Prados M, Sarthy VP, Crabb JW. CRALBP transcriptional regulation in ciliary epithelial, retinal Müller and retinal pigment epithelial cells. Experimental Eye Research 2003, 76: 257-260. PMID: 12565814, DOI: 10.1016/s0014-4835(02)00308-1.Peer-Reviewed Original ResearchConceptsTranscriptional regulationBinding Protein FunctionsCell-specific expressionPromoter analysisProtein functionRepressor elementEnhancer elementsPromoter constructsReporter activityRetinal pigment epithelial cellsPigment epithelial cellsCiliary epitheliumEpithelial cellsVisual cycleRPE cellsBPRegulationRetinal pigment epitheliumCellsMüller cellsGenesMutationsRLBP1 geneEpitheliumWildtype
2001
Autostimulation of the Epstein-Barr Virus BRLF1 Promoter Is Mediated through Consensus Sp1 and Sp3 Binding Sites
Ragoczy T, Miller G. Autostimulation of the Epstein-Barr Virus BRLF1 Promoter Is Mediated through Consensus Sp1 and Sp3 Binding Sites. Journal Of Virology 2001, 75: 5240-5251. PMID: 11333906, PMCID: PMC114930, DOI: 10.1128/jvi.75.11.5240-5251.2001.Peer-Reviewed Original ResearchMeSH KeywordsB-LymphocytesBase SequenceBinding SitesCell Line, TransformedDNA-Binding ProteinsGene DeletionGene Expression Regulation, ViralHerpesvirus 4, HumanHeterotrimeric GTP-Binding ProteinsHumansImmediate-Early ProteinsMolecular Sequence DataMutagenesis, Site-DirectedPromoter Regions, GeneticProtein BindingReceptors, Cell SurfaceSp1 Transcription FactorSp3 Transcription FactorTrans-ActivatorsTranscription FactorsViral ProteinsVirus ActivationConceptsSp1/Sp3 siteLytic cycleSp3 transcription factorsBinding of Sp1Transcriptional start siteSite-directed mutagenesisGel shift analysisBRLF1 promoterReporter-based assaysEpstein–Barr virus Rta proteinCellular Sp1Own geneConsensus Sp1Transcriptional activationCellular proteinsTranscription factorsStart siteDNA bindingOwn expressionMutagenesis studiesRta proteinSp1Reporter activityTranscription factor Zif268B cells
2000
Transcriptional Activation of the Cyclooxygenase-2 Gene in Endotoxin-treated RAW 264.7 Macrophages*
Wadleigh D, Reddy S, Kopp E, Ghosh S, Herschman H. Transcriptional Activation of the Cyclooxygenase-2 Gene in Endotoxin-treated RAW 264.7 Macrophages*. Journal Of Biological Chemistry 2000, 275: 6259-6266. PMID: 10692422, DOI: 10.1074/jbc.275.9.6259.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAnimalsCCAAT-Enhancer-Binding ProteinsCyclic AMPCyclooxygenase 2DNA-Binding ProteinsDrosophila ProteinsEndotoxinsGenes, ReporterI-kappa B ProteinsIsoenzymesJNK Mitogen-Activated Protein KinasesLipopolysaccharidesMacrophagesMAP Kinase Kinase Kinase 1MiceMitogen-Activated Protein KinasesMutationNuclear ProteinsPhosphorylationPromoter Regions, GeneticProstaglandin-Endoperoxide SynthasesProtein Serine-Threonine KinasesProteinsProto-Oncogene Proteins c-junSignal TransductionTranscriptional ActivationConceptsTranscriptional activationCis-acting transcriptional regulatory elementsReporter activityRas-independent pathwayTranscriptional regulatory elementsCis-acting elementsDominant-negative formDominant-negative expression vectorCyclic AMP response elementC-Jun phosphorylationElement-binding proteinAMP response elementImmediate early genesRAW 264.7 macrophagesTranscription factorsRaf-1E-boxRegulatory elementsAlpha mutantsCOX-2 promoterGene expressionCOX-2 reporterExpression vectorCyclic AMP response element-binding proteinC-Jun
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