2022
Histone H3 proline 16 hydroxylation regulates mammalian gene expression
Liu X, Wang J, Boyer J, Gong W, Zhao S, Xie L, Wu Q, Zhang C, Jain K, Guo Y, Rodriguez J, Li M, Uryu H, Liao C, Hu L, Zhou J, Shi X, Tsai Y, Yan Q, Luo W, Chen X, Strahl B, von Kriegsheim A, Zhang Q, Wang G, Baldwin A, Zhang Q. Histone H3 proline 16 hydroxylation regulates mammalian gene expression. Nature Genetics 2022, 54: 1721-1735. PMID: 36347944, PMCID: PMC9674084, DOI: 10.1038/s41588-022-01212-x.Peer-Reviewed Original ResearchConceptsPost-translational modificationsHistone post-translational modificationsMammalian gene expressionGene expressionHistone H3Mammalian cellsDNA-templated processesTranscriptome-wide analysisTarget gene expressionHydroxylation of prolineWnt/β-cateninChromatin recruitmentHistone codeTarget genesRegulatory marksLysine residuesDirect bindingTriple-negative breast cancerΒ-cateninResidues 16H3ExpressionH3K4me3TrimethylationGenomeKap-β2/Transportin mediates β-catenin nuclear transport in Wnt signaling
Hwang WY, Kostiuk V, González DP, Lusk CP, Khokha M. Kap-β2/Transportin mediates β-catenin nuclear transport in Wnt signaling. ELife 2022, 11: e70495. PMID: 36300792, PMCID: PMC9665845, DOI: 10.7554/elife.70495.Peer-Reviewed Original ResearchConceptsNuclear transport receptorsΒ-catenin nuclear transportNuclear transportΒ-cateninExcessive WntΒ-catenin nuclear importHeterologous model systemsΒ-catenin accumulatesPrimary embryonic axisNuclear transport machineryRan-dependent mannerNuclear localization signalTCF/LEF reporterPY-NLSNuclear importLocalization signalTransport machineryTransport receptorsResponsive genesEmbryonic developmentEmbryonic axisWnt signalingKey effectorsDirect bindingHuman diseases
2021
Platelet-derived growth factor receptor beta activates Abl2 via direct binding and phosphorylation
Wu K, Wu H, Lyu W, Kim Y, Furdui CM, Anderson KS, Koleske AJ. Platelet-derived growth factor receptor beta activates Abl2 via direct binding and phosphorylation. Journal Of Biological Chemistry 2021, 297: 100883. PMID: 34144039, PMCID: PMC8259415, DOI: 10.1016/j.jbc.2021.100883.Peer-Reviewed Original ResearchConceptsAbl family kinasesFamily kinasesPlatelet-derived growth factor receptor betaGrowth factor receptor betaAbl familySrc homology 2 domainSrc homology 3 domainDiverse cellular stimuliPost-translational modificationsN-terminal halfNonreceptor tyrosine kinaseMultiple novel sitesAutoinhibited conformationSrc homologyCytoskeleton organizationCytoplasmic domainCellular stimuliKinase domainGrowth factor receptorReceptor betaKinase activityMolecular mechanismsTyrosine kinaseDirect bindingKinaseDirect binding of ESCRT protein Chm7 to phosphatidic acid–rich membranes at nuclear envelope herniations
Thaller DJ, Tong D, Marklew CJ, Ader NR, Mannino PJ, Borah S, King MC, Ciani B, Lusk CP. Direct binding of ESCRT protein Chm7 to phosphatidic acid–rich membranes at nuclear envelope herniations. Journal Of Cell Biology 2021, 220: e202004222. PMID: 33464310, PMCID: PMC7816628, DOI: 10.1083/jcb.202004222.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAmino Acid SequenceConserved SequenceEndosomal Sorting Complexes Required for TransportHydrophobic and Hydrophilic InteractionsLipid BilayersModels, BiologicalNuclear EnvelopeNuclear PorePhosphatidic AcidsProtein DomainsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsNuclear pore complex biogenesisNuclear membrane remodelingNuclear envelope herniationsLAP2-emerinNE remodelingNPC assemblyComplex biogenesisHydrophobic stretchMembrane remodelingChm7Nuclear envelopePA bindingPA metabolismFunctional importanceDirect bindingAmino acidsPhosphatidic acidMembraneBindingHeh1RecruitmentESCRTBiogenesisRemodelingYeast
2020
Munc13 binds and recruits SNAP25 to chaperone SNARE complex assembly
Sundaram R, Jin H, Li F, Shu T, Coleman J, Yang J, Pincet F, Zhang Y, Rothman JE, Krishnakumar SS. Munc13 binds and recruits SNAP25 to chaperone SNARE complex assembly. FEBS Letters 2020, 595: 297-309. PMID: 33222163, PMCID: PMC8068094, DOI: 10.1002/1873-3468.14006.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesCloning, MolecularEscherichia coliGene ExpressionGenetic VectorsLipid BilayersLiposomesMiceModels, MolecularNerve Tissue ProteinsOptical TweezersPhosphatidylcholinesPhosphatidylethanolaminesPhosphatidylserinesPolyethylene GlycolsProtein BindingProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein Interaction Domains and MotifsRecombinant Fusion ProteinsSynaptosomal-Associated Protein 25Syntaxin 1Vesicle-Associated Membrane Protein 2ConceptsSNARE complex assemblyComplex assemblyMunc13-1 MUN domainDetailed structure-function analysisSNARE protein VAMP2Syntaxin 1/Structure-function analysisSynaptic vesicle fusionOptical tweezers studiesSNARE assemblySNARE motifMUN domainMunc18-1Syntaxin-1Munc13-1FRET spectroscopyLinker regionVesicle fusionDirect bindingPhospholipid bilayersPresynaptic membraneSNAP25AssemblyBindingRecruitsIn Vitro Physical and Functional Interaction Assays to Examine the Binding of Progranulin Derivative Atsttrin to TNFR2 and Its Anti-TNFα Activity
Fu W, Hettinghouse A, Liu C. In Vitro Physical and Functional Interaction Assays to Examine the Binding of Progranulin Derivative Atsttrin to TNFR2 and Its Anti-TNFα Activity. Methods In Molecular Biology 2020, 2248: 109-119. PMID: 33185871, PMCID: PMC8112733, DOI: 10.1007/978-1-0716-1130-2_8.Peer-Reviewed Original ResearchConceptsAnti-TNFα activityAutoimmune diseasesTartrate-resistant acid phosphatase (TRAP) stainingAnti-TNFα therapyCollagen-induced arthritisInflammatory disease modelsGood therapeutic effectAcid phosphatase stainingGrowth factor-like moleculesTNF inhibitorsTherapeutic effectTNFα activityProgranulinFunctional inhibitionTNFR2AtsttrinDisease modelsPhosphatase stainingTNFRTNFαDiseaseInhibitionCritical roleDirect bindingHigh affinity
2019
Regulation of MT dynamics via direct binding of an Abl family kinase
Hu Y, Lyu W, Lowery LA, Koleske AJ. Regulation of MT dynamics via direct binding of an Abl family kinase. Journal Of Cell Biology 2019, 218: 3986-3997. PMID: 31699690, PMCID: PMC6891085, DOI: 10.1083/jcb.201812144.Peer-Reviewed Original ResearchConceptsAbl family kinasesC-terminal halfFamily kinasesMT dynamicsMT growthTubulin C-terminal tailsC-terminal tailStable reexpressionEssential regulatorCell shapeBinds microtubulesMT polymerizationAbl kinaseGenetic studiesDirect bindingFunctional interactionKinaseMicrotubulesABL2ReexpressionMT behaviorBindingRegulatorProteinGrowth
2018
MiR-221 negatively regulates innate anti-viral response
Du H, Cui S, Li Y, Yang G, Wang P, Fikrig E, You F. MiR-221 negatively regulates innate anti-viral response. PLOS ONE 2018, 13: e0200385. PMID: 30089112, PMCID: PMC6082502, DOI: 10.1371/journal.pone.0200385.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntagomirsDNA-Binding ProteinsDown-RegulationHEK293 CellsHerpesvirus 1, HumanHumansImmunity, InnateInterferon-betaMacrophagesMiceMice, Inbred C57BLMice, KnockoutMicroRNAsPromoter Regions, GeneticProtein Serine-Threonine KinasesRhabdoviridae InfectionsTranscription FactorsVesiculovirusConceptsAntiviral responseMiR-221Innate anti-viral responseInitial antiviral responseImmune cell activationMiR-221 expressionAnti-viral responseInnate antiviral responseInnate immune systemAnti-viral defenseIFNβ productionVirus infectionMultiple candidate targetsImmune systemCell activationCandidate targetsInfectionRNA-seq analysisCritical roleDirect bindingResponseMicroRNA regulatorsThe interaction between IKKα and LC3 promotes type I interferon production through the TLR9-containing LAPosome
Hayashi K, Taura M, Iwasaki A. The interaction between IKKα and LC3 promotes type I interferon production through the TLR9-containing LAPosome. Science Signaling 2018, 11 PMID: 29717061, PMCID: PMC6462218, DOI: 10.1126/scisignal.aan4144.Peer-Reviewed Original ResearchConceptsInterferon regulatory factor 7Autophagy protein LC3Type I IFN productionI interferonI IFN productionMicrotubule-associated proteinsPutative LC3Type I interferon productionEndosomal vesiclesAutophagosome formationNoncanonical autophagyToll-like receptor 9Production of IFNStimulation of TLR9Regulatory factor 7Protein LC3Direct bindingI interferon productionIFN productionEndosomesChain 3Type I interferonKinase IKKαLC3Lap formation
2017
A cell-penetrating antibody inhibits human RAD51 via direct binding
Turchick A, Hegan DC, Jensen RB, Glazer PM. A cell-penetrating antibody inhibits human RAD51 via direct binding. Nucleic Acids Research 2017, 45: 11782-11799. PMID: 29036688, PMCID: PMC5714174, DOI: 10.1093/nar/gkx871.Peer-Reviewed Original ResearchConceptsHomology-directed repairMolecular basisDirect bindingSynthetic lethal killingPre-clinical developmentBRCA2-deficient cancer cellsCell-penetrating antibodiesAnti-cancer agentsLupus autoantibodiesHuman Rad51DNA repairDNA bindingRAD51N-terminusCancer cellsSilico molecular modelingFunction mutationsCancer therapySpecific inhibitorDNANovel inhibitorsAttractive targetComplementarity-determining regionsMolecular modelingCell penetration
2016
Interaction between integrin α5 and PDE4D regulates endothelial inflammatory signalling
Yun S, Budatha M, Dahlman JE, Coon BG, Cameron RT, Langer R, Anderson DG, Baillie G, Schwartz MA. Interaction between integrin α5 and PDE4D regulates endothelial inflammatory signalling. Nature Cell Biology 2016, 18: 1043-1053. PMID: 27595237, PMCID: PMC5301150, DOI: 10.1038/ncb3405.Peer-Reviewed Original ResearchConceptsInflammatory signalingIntegrin α5Enhanced phosphodiesterase activityExtracellular matrix remodellingModulates inflammationTherapeutic targetInflammationProstacyclin secretionLipid metabolismEndothelial cellsMatrix remodellingVivo knockdownECM remodellingBasement membraneIntegrin α2Phosphodiesterase activityMolecular mechanismsRemodellingΑ5Direct bindingSignalingCellsFibronectinAtherosclerosisArtery
2015
E2F8 as a Novel Therapeutic Target for Lung Cancer
Park SA, Platt J, Lee JW, López-Giráldez F, Herbst RS, Koo JS. E2F8 as a Novel Therapeutic Target for Lung Cancer. Journal Of The National Cancer Institute 2015, 107: djv151. PMID: 26089541, PMCID: PMC4651101, DOI: 10.1093/jnci/djv151.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntineoplastic AgentsCCAAT-Enhancer-Binding ProteinsCell Line, TumorCell ProliferationCell SurvivalChromatin ImmunoprecipitationFluorescent Antibody TechniqueGene Expression Regulation, NeoplasticHumansImmunoblottingKaplan-Meier EstimateLung NeoplasmsMiceMolecular Targeted TherapyNeoplastic Stem CellsPromoter Regions, GeneticRepressor ProteinsTissue Array AnalysisUbiquitin-Protein LigasesUp-RegulationXenograft Model Antitumor AssaysConceptsTarget genesCell cycle regulationNovel therapeutic targetPromoter activity assaysCell proliferationCancer cellsExpression of UHRF1Transcription activatorAntisense morpholinoChromatin immunoprecipitationCycle regulationTherapeutic targetEmbryonic developmentE2F membersHuman lung cancer cellsMicroarray analysisInvasion analysisLung cancer cellsDirect bindingTumor growthE2F8Activity assaysPublic databasesColony formationUHRF1Endosomal regulation of contact inhibition through the AMOT:YAP pathway
Cox CM, Mandell EK, Stewart L, Lu R, Johnson DL, McCarter SD, Tavares A, Runyan R, Ghosh S, Wilson JM. Endosomal regulation of contact inhibition through the AMOT:YAP pathway. Molecular Biology Of The Cell 2015, 26: 2673-2684. PMID: 25995376, PMCID: PMC4501364, DOI: 10.1091/mbc.e15-04-0224.Peer-Reviewed Original ResearchConceptsEndosomal membranesYAP activitySubconfluent cellsOrgan growth controlTranscription coactivator YesPhosphorylation-dependent regulationIntegral membrane proteinsConfluent cellsAmot proteinsEndosomal regulationContact-mediated inhibitionCytoplasmic domainEndotubinMembrane proteinsOvergrowth phenotypeInduces translocationAngiomotinYAP interactionDirect bindingGrowth controlContact inhibitionFamily membersCell growthYAPYAP pathwayAkt Substrate of 160 kD Regulates Na+,K+-ATPase Trafficking in Response to Energy Depletion and Renal Ischemia
Alves DS, Thulin G, Loffing J, Kashgarian M, Caplan MJ. Akt Substrate of 160 kD Regulates Na+,K+-ATPase Trafficking in Response to Energy Depletion and Renal Ischemia. Journal Of The American Society Of Nephrology 2015, 26: 2765-2776. PMID: 25788531, PMCID: PMC4625659, DOI: 10.1681/asn.2013101040.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiotinylationCell LineCytoplasmDogsDynaminsEndocytosisEpithelial CellsGTPase-Activating ProteinsHumansIschemiaKidneyKidney DiseasesMadin Darby Canine Kidney CellsMaleMiceMice, KnockoutMicroscopy, FluorescencePhosphorylationProtein TransportReperfusion InjuryRNA, Small InterferingSignal TransductionSodium-Potassium-Exchanging ATPaseConceptsRenal epithelial cellsATPase traffickingIntracellular compartmentsEpithelial cell polarityEpithelial cellsBasolateral plasma membraneGlucose transporter 4Cultured epithelial cellsCell polarityRab GTPaseAkt substratePlasma membraneSubcellular distributionAS160Energy depletionDirect bindingTransporter 4TraffickingDirect roleK-ATPaseATPaseTubular soluteIntracellular accumulationCellsCompartmentsDirect Binding of Retromer to Human Papillomavirus Type 16 Minor Capsid Protein L2 Mediates Endosome Exit during Viral Infection
Popa A, Zhang W, Harrison MS, Goodner K, Kazakov T, Goodwin EC, Lipovsky A, Burd CG, DiMaio D. Direct Binding of Retromer to Human Papillomavirus Type 16 Minor Capsid Protein L2 Mediates Endosome Exit during Viral Infection. PLOS Pathogens 2015, 11: e1004699. PMID: 25693203, PMCID: PMC4334968, DOI: 10.1371/journal.ppat.1004699.Peer-Reviewed Original ResearchConceptsTrans-Golgi networkRetromer cargoTransmembrane proteinGolgi apparatusDirect bindingCoat protein complexCellular transmembrane proteinsVirus entryMinor capsid proteinCarboxy-terminal segmentProtein complexesL2 minor capsid proteinMinor capsid protein L2Early endosomesVesicular transportRetromerPlasma membraneEndosomal membranesBinding motifProtein L2Capsid proteinEndosomesL2 proteinViral componentsProtein
2011
High Throughput Sequencing Following Cross-Linked Immune Precipitation (HITS-CLIP) of Argonaute (AGO) Identifies Mir-9 As a Regulator of MMP2 in the Marrow Microenvironment (ME)
Balakrishnan I, Yang X, Torok-Storb B, Hesselberth J, Pillai M. High Throughput Sequencing Following Cross-Linked Immune Precipitation (HITS-CLIP) of Argonaute (AGO) Identifies Mir-9 As a Regulator of MMP2 in the Marrow Microenvironment (ME). Blood 2011, 118: 2392. DOI: 10.1182/blood.v118.21.2392.2392.Peer-Reviewed Original ResearchGenome-wide approachesHITS-CLIPMiRNA-mRNA interactomeMiR-9Functional nichesNext-generation sequencingHuman umbilical vein endothelial cellsGene expressionMarrow microenvironmentNew genome-wide approachDirect bindingLuciferase assayMiRNA-based regulationPost-transcriptional regulationCross-species conservationSpecific functional nichesHigh-throughput sequencingMiRNA-mRNA interactionsSmall noncoding RNAsRegulation of hematopoiesisPutative binding sitesStromal cellsCobblestone areaSequence-specific fashionCross-linked RNA
2010
Specific tyrosine phosphorylation sites on cortactin regulate Nck1-dependent actin polymerization in invadopodia
Oser M, Mader CC, Gil-Henn H, Magalhaes M, Bravo-Cordero JJ, Koleske AJ, Condeelis J. Specific tyrosine phosphorylation sites on cortactin regulate Nck1-dependent actin polymerization in invadopodia. Journal Of Cell Science 2010, 123: 3662-3673. PMID: 20971703, PMCID: PMC3037016, DOI: 10.1242/jcs.068163.Peer-Reviewed Original ResearchConceptsTyrosine phosphorylation sitesTumor cell invasionActin polymerizationPhosphorylation sitesCell invasionTyrosine 421Actin barbed endsPhosphorylation of tyrosineRegulatory switchSH2 domainMembrane protrusionsInvadopodiaCrucial residuesCortactinBarbed endsDirect bindingInvasive carcinoma cellsPhosphorylationNck1Carcinoma cellsFRET interactionsInvasionCellsPhosphotyrosineSitesAberrant overexpression and function of the miR-17-92 cluster in MLL-rearranged acute leukemia
Mi S, Li Z, Chen P, He C, Cao D, Elkahloun A, Lu J, Pelloso LA, Wunderlich M, Huang H, Luo RT, Sun M, He M, Neilly MB, Zeleznik-Le NJ, Thirman MJ, Mulloy JC, Liu PP, Rowley JD, Chen J. Aberrant overexpression and function of the miR-17-92 cluster in MLL-rearranged acute leukemia. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 3710-3715. PMID: 20133587, PMCID: PMC2840429, DOI: 10.1073/pnas.0914900107.Peer-Reviewed Original ResearchConceptsMouse bone marrow progenitor cellsMiRNA clusterTarget genesMLL fusionsBone marrow progenitor cellsMiR-17Marrow progenitor cellsCell differentiationDNA copy number amplificationsWild-type MLLProgenitor cellsRelevant target genesHistone H3 acetylationPotential target genesMLL fusion genesCopy number amplificationDevelopment of MLLH3K4 trimethylationIndividual miRNAsH3 acetylationMixed lineage leukemiaCell cycleHuman cellsDirect bindingMiRNAs
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
2002
c-Jun N-terminal Kinase (JNK) Mediates Feedback Inhibition of the Insulin Signaling Cascade*
Lee Y, Giraud J, Davis R, White M. c-Jun N-terminal Kinase (JNK) Mediates Feedback Inhibition of the Insulin Signaling Cascade*. Journal Of Biological Chemistry 2002, 278: 2896-2902. PMID: 12417588, DOI: 10.1074/jbc.m208359200.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBinding SitesCell LineConsensus SequenceCulture Media, ConditionedHumansInsulinInsulin Receptor Substrate ProteinsJNK Mitogen-Activated Protein KinasesMiceMice, KnockoutMitogen-Activated Protein Kinase 8Mitogen-Activated Protein Kinase 9Mitogen-Activated Protein KinasesMolecular Sequence DataPhosphoproteinsPhosphorylationRatsSignal TransductionTransfectionConceptsC-Jun N-terminal kinaseN-terminal kinaseDirect bindingInsulin-stimulated tyrosine phosphorylationInsulin receptor substrate-1Interaction of JNKInsulin Signaling CascadeReceptor substrate-1Mouse embryo fibroblastsActivation of JNKFeedback inhibitionNegative feedback regulatorPhosphorylation of IRS1Cellular proteinsCell-permeable peptideTyrosine phosphorylationInsulin signalSignaling cascadesIRS1 proteinJNK activitySubstrate-1Insulin stimulationEmbryo fibroblastsPhosphorylationAkt phosphorylation
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