2024
SUMOylation Fine-Tunes Endothelial HEY1 in the Regulation of Angiogenesis
Ren R, Ding S, Ma K, Jiang Y, Wang Y, Chen J, Wang Y, Kou Y, Fan X, Zhu X, Qin L, Qiu C, Simons M, Wei X, Yu L. SUMOylation Fine-Tunes Endothelial HEY1 in the Regulation of Angiogenesis. Circulation Research 2024, 134: 203-222. PMID: 38166414, PMCID: PMC10872267, DOI: 10.1161/circresaha.123.323398.Peer-Reviewed Original ResearchDNA-binding capabilityElectrophoretic mobility shift assaysEndothelial cell-specific expressionMobility shift assaysHairy/EnhancerCell-specific expressionPrimary human endothelial cellsNotch pathway componentsE-box promoter elementsEndothelial cellsRegulation of angiogenesisHelix familyPostnatal vascular growthHey1 functionsTranscriptional complexChromatin immunoprecipitationE3 ligaseRTK signalingEmbryonic developmentMatrigel plug assayPromoter elementsBioinformatics analysisShift assaysSUMOylationDNA binding
2023
Antitumor active trans‑platinum complexes through metabolic stability and enhanced cellular accumulation
Menon V, Katner S, Lee D, Peterson E, Koblinski J, Farrell N. Antitumor active trans‑platinum complexes through metabolic stability and enhanced cellular accumulation. Journal Of Inorganic Biochemistry 2023, 252: 112475. PMID: 38199050, DOI: 10.1016/j.jinorgbio.2023.112475.Peer-Reviewed Original ResearchInsights into RAG Evolution from the Identification of “Missing Link” Family A RAGL Transposons
Martin E, Le Targa L, Tsakou-Ngouafo L, Fan T, Lin C, Xiao J, Huang Z, Yuan S, Xu A, Su Y, Petrescu A, Pontarotti P, Schatz D. Insights into RAG Evolution from the Identification of “Missing Link” Family A RAGL Transposons. Molecular Biology And Evolution 2023, 40: msad232. PMID: 37850912, PMCID: PMC10629977, DOI: 10.1093/molbev/msad232.Peer-Reviewed Original ResearchConceptsJawed vertebratesTransposon familyRAG1-RAG2 recombinaseRecombination signal sequencesHemichordate Ptychodera flavaMolecular domesticationSignal sequenceP. flavaDNA bindingPtychodera flavaSequence featuresTransposition activityVertebratesTransposonCritical enzymeHinge regionGenomeDomesticationFlavaProteinPivotal stepAdaptive immunityCritical intermediateRAGRAGLBedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis
Sonnenkalb L, Carter J, Spitaleri A, Iqbal Z, Hunt M, Malone K, Utpatel C, Cirillo D, Rodrigues C, Nilgiriwala K, Fowler P, Merker M, Niemann S, Consortium C, Barilar I, Battaglia S, Borroni E, Brandao A, Brankin A, Cabibbe A, Carter J, Cirillo D, Claxton P, Clifton D, Cohen T, Coronel J, Crook D, Dreyer V, Earle S, Escuyer V, Ferrazoli L, Fowler P, Gao G, Gardy J, Gharbia S, Ghisi K, Ghodousi A, Cruz A, Grandjean L, Grazian C, Groenheit R, Guthrie J, He W, Hoffmann H, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle A, Lalvani A, Lapierre S, Laurenson I, Letcher B, Lin W, Liu C, Liu D, Malone K, Mandal A, Mansjö M, Matias D, Meintjes G, de Freitas Mendes F, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser K, Ngcamu D, Hoang N, Niemann S, Nilgiriwala K, Nimmo C, Okozi N, Oliveira R, Omar S, Paton N, Peto T, Pinhata J, Plesnik S, Puyen Z, Rabodoarivelo M, Rakotosamimanana N, Rancoita P, Rathod P, Rodger G, Rodrigues C, Rodwell T, Roohi E, Santos-Lazaro D, Shah S, Kohl T, Smith G, Solano W, Spitaleri A, Supply P, Surve U, Tahseen S, Thuong N, Thwaites G, Todt K, Trovato A, Utpatel C, Van Rie A, Vijay S, Walker T, Walker S, Warren R, Werngren J, Wijkander M, Wilkinson R, Wilson D, Wintringer P, Yu X, Yang Y, Zhao Y, Yao S, Zhu B. Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis. The Lancet Microbe 2023, 4: e358-e368. PMID: 37003285, PMCID: PMC10156607, DOI: 10.1016/s2666-5247(23)00002-2.Peer-Reviewed Original ResearchConceptsMutation catalogueIn silico data analysisBedaquiline resistanceClofazimine resistanceResistance mechanismsProtein modelsClinical Mycobacterium tuberculosis complex isolatesImpaired DNA bindingClinically resistant strainsMinimum inhibitory concentrationVariants in vitroPacBio sequencingGenome sequenceGenomic rearrangementsGenomic variantsIn vitroExperimental evolutionGenotype dataTranscriptional repressorDrug resistance mechanismsClinical isolatesPhenotypic dataResistance determinantsDNA bindingProtein dimerisation
2022
DNA processing by the Kaposi's sarcoma-associated herpesvirus alkaline exonuclease SOX contributes to viral gene expression and infectious virion production
Hartenian E, Mendez A, Didychuk A, Khosla S, Glaunsinger B. DNA processing by the Kaposi's sarcoma-associated herpesvirus alkaline exonuclease SOX contributes to viral gene expression and infectious virion production. Nucleic Acids Research 2022, 51: 182-197. PMID: 36537232, PMCID: PMC9841436, DOI: 10.1093/nar/gkac1190.Peer-Reviewed Original ResearchConceptsKaposi's sarcoma-associated herpesvirusAlkaline exonucleaseInfectious virion productionViral gene expressionDNA processingStructure-guided functional analysesGene expressionDNA substrate preferenceVirion productionKingdoms of lifeCleavage of mRNAGammaherpesvirus Kaposi's sarcoma-associated herpesvirusViral DNA processingLifecycles of virusesBacteriophage LSoxS mutantFunctional conservationGenome replicationGenetic conservationSarcoma-associated herpesvirusPhage LSubstrate preferenceDNA bindingHuman gammaherpesviruses Kaposi's sarcoma-associated herpesvirusSOX activityThe Pathogenic R3052W BRCA2 Variant Disrupts Homology-Directed Repair by Failing to Localize to the Nucleus
Jimenez-Sainz J, Krysztofiak A, Garbarino J, Rogers F, Jensen RB. The Pathogenic R3052W BRCA2 Variant Disrupts Homology-Directed Repair by Failing to Localize to the Nucleus. Frontiers In Genetics 2022, 13: 884210. PMID: 35711920, PMCID: PMC9197106, DOI: 10.3389/fgene.2022.884210.Peer-Reviewed Original ResearchDominant-negative alleleDNA damage responseDNA repair functionDNA strand exchangeHomology-directed repairGenome instabilityCellular functionsDamage responseDNA bindingNegative allelesStrand exchangeRepair functionGermline missense variantsCell survivalFunction mutationsMissense variantsRAD51Pathogenic allelesSimple lossPARP inhibitorsCytoplasmProteinAllelesHomologyDNAA Two-tiered functional screen identifies herpesviral transcriptional modifiers and their essential domains
Morgens D, Nandakumar D, Didychuk A, Yang K, Glaunsinger B. A Two-tiered functional screen identifies herpesviral transcriptional modifiers and their essential domains. PLOS Pathogens 2022, 18: e1010236. PMID: 35041709, PMCID: PMC8797222, DOI: 10.1371/journal.ppat.1010236.Peer-Reviewed Original ResearchConceptsViral DNA replicationKaposi's sarcoma-associated herpesvirusViral genomeDsDNA virusesLate genesDNA replicationTranscriptional activityViral sequencesViral transcriptional activityCatalytic domainIndividual mutantsSgRNA librarySarcoma-associated herpesvirusTiling screensDNA bindingDeep sequencingBase pairsFunctional screeningCut sitePooled screeningTranscriptional modifiersDNA virusesGenomeEssential domainsGene expression
2021
Structural insights into the evolution of the RAG recombinase
Liu C, Zhang Y, Liu CC, Schatz DG. Structural insights into the evolution of the RAG recombinase. Nature Reviews Immunology 2021, 22: 353-370. PMID: 34675378, DOI: 10.1038/s41577-021-00628-6.Peer-Reviewed Original ResearchConceptsRAG recombinaseComparative genome analysisGenomes of eukaryotesProtein-DNA complexesSingle amino acid mutationAntigen receptor genesMolecular domesticationRag familyAmino acid mutationsJawed vertebratesVertebrate immunityTransposable elementsEvolutionary adaptationGenome analysisStructural biologyDNA bindingStructural insightsGene 1Acid mutationsCleavage activityRecombinaseReceptor geneStructural evidenceRecombinationAdaptive immunityProbing Microbiome Genotoxicity: A Stable Colibactin Provides Insight into Structure–Activity Relationships and Facilitates Mechanism of Action Studies
Wernke KM, Tirla A, Xue M, Surovtseva YV, Menges FS, Herzon SB. Probing Microbiome Genotoxicity: A Stable Colibactin Provides Insight into Structure–Activity Relationships and Facilitates Mechanism of Action Studies. Journal Of The American Chemical Society 2021, 143: 15824-15833. PMID: 34524796, DOI: 10.1021/jacs.1c07559.Peer-Reviewed Original ResearchConceptsFanconi anemia DNA repair pathwayBiosynthetic gene clusterDNA repair pathwaysGene clusterRepair pathwaysDNA bindingBacterial phenotypesInduces DNAGenotoxic effectsHuman microbiomeColibactinBiosynthetic precursorNatural product structuresBiological studiesPathwayStructure-activity relationshipsAction studiesGenotoxic metabolitesOrganismsOncogenesisDNATumorigenesisMicrobiomeFacilitate mechanismsPhenotypeThe peptidoglycan-associated protein NapA plays an important role in the envelope integrity and in the pathogenesis of the lyme disease spirochete
Davis MM, Brock AM, DeHart TG, Boribong BP, Lee K, McClune ME, Chang Y, Cramer N, Liu J, Jones CN, Jutras BL. The peptidoglycan-associated protein NapA plays an important role in the envelope integrity and in the pathogenesis of the lyme disease spirochete. PLOS Pathogens 2021, 17: e1009546. PMID: 33984073, PMCID: PMC8118282, DOI: 10.1371/journal.ppat.1009546.Peer-Reviewed Original ResearchConceptsPeptidoglycan-associated proteinsCell envelopeUnbiased proteomic approachCryo-electron microscopyOxidative stress responseOuter membrane vesiclesGram-negative bacteriaDps homologueEnvelope integrityProteomic approachNapA mutantOuter membraneBacterial proteinsMutant bacteriaDNA bindingCritical residuesBiological functionsLyme disease spirocheteStress responseCellular DNAMembrane vesiclesPeptidoglycanEnvelope layersBacterial pathogensCellular studiesA pentameric protein ring with novel architecture is required for herpesviral packaging
Didychuk A, Gates S, Gardner M, Strong L, Martin A, Glaunsinger B. A pentameric protein ring with novel architecture is required for herpesviral packaging. ELife 2021, 10: e62261. PMID: 33554858, PMCID: PMC7889075, DOI: 10.7554/elife.62261.Peer-Reviewed Original ResearchConceptsViral genomeAccessory factorsBind double-stranded DNAPositively charged central channelContext of KSHV infectionDouble-stranded DNA virusesPositively charged residuesOncogenic herpesvirus Kaposi's sarcoma-associated herpesvirusKaposi's sarcoma-associated herpesvirusDouble-stranded DNASarcoma-associated herpesvirusGenome packagingHomologous proteinsNascent capsidsDNA bindingProtein ringGenomePackaging motorDNA virusesCharged residuesProgeny virionsMolecular motorsCentral channelKSHV infectionMutantsChapter 9 Mechanism of glucocorticoid action in immunology—Basic concepts
Wood M, Whirledge S. Chapter 9 Mechanism of glucocorticoid action in immunology—Basic concepts. 2021, 147-170. DOI: 10.1016/b978-0-12-818508-7.00020-8.Peer-Reviewed Original ResearchGlucocorticoid receptorEpigenetic modificationsPosttranslational modificationsTranscription factorsDNA bindingTissue-specific immune responsesOverall physiologyCell typesGlucocorticoid-mediated effectsNuclear receptorsImmune cell typesFundamental processesReceptor isoformsLevels of hormonesRelative expressionReceptor actionReproductive systemChapter 9 MechanismsGlucocorticoid bioavailabilityAutoimmune diseasesGlucocorticoid actionImmune responseFetal developmentCo-factorImmune system
2020
Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6
Schmidt JM, Bleichert F. Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6. Nature Communications 2020, 11: 4263. PMID: 32848132, PMCID: PMC7450096, DOI: 10.1038/s41467-020-18067-7.Peer-Reviewed Original ResearchMeSH KeywordsAAA DomainAdenosine TriphosphateAnimalsCell Cycle ProteinsCryoelectron MicroscopyDNADrosophila melanogasterDrosophila ProteinsHydrolysisMinichromosome Maintenance ProteinsModels, MolecularOrigin Recognition ComplexProtein BindingRecombinant ProteinsReplication OriginSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsOrigin recognition complexRecognition complexReplication originsDrosophila origin recognition complexEukaryotic DNA replication initiationMetazoan origin recognition complexCryo-electron microscopy structureMcm2-7 replicative helicaseATPase siteDNA replication initiationWalker B motifMcm2-7 loadingWinged-helix domainReplicative helicaseReplication initiationMicroscopy structureDistinct DNAB motifOrigin recognitionDNA sequencesDNA bendingDNA bindingPrimary DNADNA geometryLoop regionThe DNA-binding activity of USP1-associated factor 1 is required for efficient RAD51-mediated homologous DNA pairing and homology-directed DNA repair
Liang F, Miller AS, Tang C, Maranon D, Williamson EA, Hromas R, Wiese C, Zhao W, Sung P, Kupfer GM. The DNA-binding activity of USP1-associated factor 1 is required for efficient RAD51-mediated homologous DNA pairing and homology-directed DNA repair. Journal Of Biological Chemistry 2020, 295: 8186-8194. PMID: 32350107, PMCID: PMC7294083, DOI: 10.1074/jbc.ra120.013714.Peer-Reviewed Original ResearchConceptsHomologous DNA pairingDNA-binding activityDNA pairingDNA repairDNA bindingFanconi anemia complementation group D2 proteinDamage repairHomology-directed DNA repairRAD51 recombinase activityFanconi anemia pathwayDNA damage sensitivityChromosome damage repairHR-mediated DNA repairDNA damage responseDNA damage repairHomologous recombination pathwayFactor 1FANCD2 deubiquitinationRole of DNAEfficient RAD51Deubiquitinase complexRecombinase RAD51Damage responseUAF1D2 proteinIdentification of a 22 bp DNA cis Element that Plays a Critical Role in Colony Stimulating Factor 1-Dependent Transcriptional Activation of the SPHK1 Gene
Yao GQ, Zhu M, Walker J, Insogna K. Identification of a 22 bp DNA cis Element that Plays a Critical Role in Colony Stimulating Factor 1-Dependent Transcriptional Activation of the SPHK1 Gene. Calcified Tissue International 2020, 107: 52-59. PMID: 32246175, PMCID: PMC7274855, DOI: 10.1007/s00223-020-00685-4.Peer-Reviewed Original ResearchConceptsColony stimulating factor 1Sphingosine kinase 1Bp fragmentSPHK1 promoterBp sequenceSphK1 geneDNA cis elementsProtein binding regionsSPHK1 gene expressionBp DNA fragmentStimulating factor 1Dual-luciferase reporterPutative DNATranscriptional activationTranscription factorsNuclear proteinsDNA sequencesCis elementsDNA bindingGene expressionPromoter activityDNA fragmentsKinase 1EMSAsProtein bindingSex differences in brain gene expression among suicide completers
Cabrera-Mendoza B, Fresno C, Monroy-Jaramillo N, Fries GR, Walss-Bass C, Glahn DC, Ostrosky-Wegman P, Mendoza-Morales RC, García-Dolores F, Díaz-Otañez CE, González-Sáenz EE, Genis-Mendoza AD, Martínez-Magaña JJ, Romero-Pimentel AL, Flores G, Vázquez-Roque RA, Nicolini H. Sex differences in brain gene expression among suicide completers. Journal Of Affective Disorders 2020, 267: 67-77. PMID: 32063575, DOI: 10.1016/j.jad.2020.01.167.Peer-Reviewed Original ResearchConceptsBrain gene expressionSex-specific gene expression patternsGene expressionRibonucleic protein complexesGene expression patternsGene expression profilesProtein complexesGene setsDNA bindingExpression patternsExpression profilesGenesSuicide geneBiological levelsVesicular functionCell proliferationValuable foundationDifferentiallyMicroarrayExpressionSex-specific factorsSuicide completersSuicidal brainImmune responseSex differences
2019
UAF1 DNA Binding Activity Is Critical for RAD51-Mediated Homologous DNA Pairing
Liang F, Miller A, Tang C, Sung P, Kupfer G. UAF1 DNA Binding Activity Is Critical for RAD51-Mediated Homologous DNA Pairing. Blood 2019, 134: 2497. DOI: 10.1182/blood-2019-130435.Peer-Reviewed Original ResearchHomologous DNA pairingHomologous recombinationDNA binding activityDNA repairDNA bindingDNA pairingHomologous DNAFanconi anemia DNA repair pathwayHR efficiencyFA core complexDNA damageDNA damage sensitivityDNA damage resistanceDNA-binding mutantSynaptic complex assemblyBinding activityE3 ligase activityDNA damage repairDNA repair pathwaysPresynaptic complex formationFANCD2 deubiquitinationGenome maintenanceComplex formationDeubiquitinase complexMutant proteinsAPOBEC3A Loop 1 Is a Determinant for Single-Stranded DNA Binding and Deamination
Ziegler SJ, Hu Y, Devarkar SC, Xiong Y. APOBEC3A Loop 1 Is a Determinant for Single-Stranded DNA Binding and Deamination. Biochemistry 2019, 58: 3838-3847. PMID: 31448897, PMCID: PMC7211764, DOI: 10.1021/acs.biochem.9b00394.Peer-Reviewed Original ResearchConceptsSubstrate specificityLoop 1A3 proteinsRecent structural studiesBase editing technologyEnzyme catalytic polypeptideProtein functionSubstrate recognitionDNA bindingEditing technologySsDNA recognitionSubstrate selectionNovel CRISPRDeamination activityApolipoprotein B mRNACatalytic polypeptideBiochemical levelBase editorsLoop regionInnate immune systemProteinA3ADeaminase activityA3GA3 familyARID1A‐SIN3A drives retinoic acid‐induced neuroblastoma differentiation by transcriptional repression of TERT
Bui C, Le H, Vu D, Truong K, Nguyen N, Ho M, Truong D. ARID1A‐SIN3A drives retinoic acid‐induced neuroblastoma differentiation by transcriptional repression of TERT. Molecular Carcinogenesis 2019, 58: 1998-2007. PMID: 31365169, DOI: 10.1002/mc.23091.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCell Line, TumorChild, PreschoolDNA-Binding ProteinsFemaleGene Expression Regulation, NeoplasticHumansInfantInfant, NewbornMaleNeuroblastomaRepressor ProteinsSin3 Histone Deacetylase and Corepressor ComplexTelomeraseTranscription FactorsTranscription, GeneticTretinoinConceptsEpigenetic regulationNB differentiationChromatin Remodeling ComplexKey epigenetic pathwaysChromatin immunoprecipitation-qPCRAT-rich interaction domain 1AImmature differentiation stateExact molecular mechanismsRemodeling complexRepressor complexTranscriptional repressionEpigenetic pathwaysEpigenetic dysregulationDNA bindingMolecular mechanismsMultiple cancer typesTelomerase reverse transcriptase (TERT) promoterQuantitative real-time polymerase chain reactionReverse transcriptase promoterHigh telomerase activityDifferentiation stateSwitch/Polymerase chain reactionTERT expressionDomain 1ADNA requirement in FANCD2 deubiquitination by USP1-UAF1-RAD51AP1 in the Fanconi anemia DNA damage response
Liang F, Miller AS, Longerich S, Tang C, Maranon D, Williamson EA, Hromas R, Wiese C, Kupfer GM, Sung P. DNA requirement in FANCD2 deubiquitination by USP1-UAF1-RAD51AP1 in the Fanconi anemia DNA damage response. Nature Communications 2019, 10: 2849. PMID: 31253762, PMCID: PMC6599204, DOI: 10.1038/s41467-019-10408-5.Peer-Reviewed Original ResearchConceptsFANCD2 deubiquitinationDNA damage response pathwayFanconi anemiaUSP1-UAF1 complexDNA damage toleranceDNA damage responseDamage response pathwayImportance of DNAGenome repairDamage responseResponse pathwaysUAF1DNA requirementsCellular settingsFA pathwayDNA bindingDownstream eventsDeubiquitinationRAD51AP1DNA crosslinksBiochemical systemsBone marrow failureChromosomal lesionsMultigenic diseasesMultifaceted role
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