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
2016
The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation
Schulte T, Mikaelsson C, Beaussart A, Kikhney A, Deshmukh M, Wolniak S, Pathak A, Ebel C, Löfling J, Fogolari F, Henriques-Normark B, Dufrêne YF, Svergun D, Nygren PÅ, Achour A. The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation. Scientific Reports 2016, 6: 32371. PMID: 27582320, PMCID: PMC5007671, DOI: 10.1038/srep32371.Peer-Reviewed Original ResearchConceptsPneumococcal biofilm formationBiofilm formationExtracellular DNAPneumococcal serine-rich repeat proteinRich repeat proteinElectrophoretic mobility shift assaysHuman pathogen Streptococcus pneumoniaeAdhesive matrix moleculesMobility shift assaysMicrobial surface componentsMajor human pathogen Streptococcus pneumoniaeN-terminal regionNon-globular structuresSerine-rich repeat proteinPathogen Streptococcus pneumoniaeHelical DNA structureRepeat proteinsHeterologous expressionCircular dichroism studiesBR domainShift assaysStructural insightsBiofilm matrixIntermolecular β-sheetsBacterial aggregationHoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix
Brown JA, Kinzig CG, DeGregorio SJ, Steitz JA. Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix. RNA 2016, 22: 743-749. PMID: 26952103, PMCID: PMC4836648, DOI: 10.1261/rna.055707.115.Peer-Reviewed Original ResearchConceptsElectrophoretic mobility shift assaysRNA triple helicesBase triplesMetastasis-associated lung adenocarcinoma transcript 1RNA stability elementMobility shift assaysTriple helixHuman metastasis-associated lung adenocarcinoma transcript 1Small molecule bindingU base triplesNucleotide compositionCellular functionsTriple-helical stabilityShift assaysLung adenocarcinoma transcript 1Stability elementEMSA resultsBiological significanceMolecule bindingRNA catalysisHelixTranscript 1Triple helix stabilityC tripleReporter
2015
Characterization of a Small‐molecule Modulator of IRE1α Activity
Salami‐Oyenuga J, Raina K, Crews C. Characterization of a Small‐molecule Modulator of IRE1α Activity. The FASEB Journal 2015, 29 DOI: 10.1096/fasebj.29.1_supplement.723.2.Peer-Reviewed Original ResearchUnfolded protein responseHuman IRE1αIRE1α activityInositol-Requiring Enzyme 1X-box binding protein 1 (XBP1) mRNAER stress conditionsEnzymatic activitySmall molecule modulatorsMechanism of regulationER stress responseHEK293T cellsThermal shift assayER stress pathwayEndoplasmic reticulum stressCellular processesER lumenUPR signalingShift assaysIRE1α activationProtein responseHuman kidney cellsIRE1α kinaseStress responseIRE1α proteinCentral player
2014
Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases
Rogers FA, Lloyd JA, Tiwari MK. Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases. Artificial DNA PNA & XNA 2014, 5: e27792. PMID: 25483840, PMCID: PMC4014521, DOI: 10.4161/adna.27792.Peer-Reviewed Original ResearchConceptsMobility gel shift assaysDNA double-strand breaksTarget sequenceGel shift assaysDouble-strand breaksGene-targeted mutagenesisActivation of apoptosisG-quadruplex formationGenomic modificationsDNA repairShift assaysReporter geneMolecular mechanismsPolypurine sequenceStrand breaksTriplex technologyTarget siteMutagenesisTriplex structureGenesGuanine baseTriplex formationGuanine basesSequenceAG30
2012
AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus
Lee N, Pimienta G, Steitz JA. AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus. RNA 2012, 18: 2073-2082. PMID: 23012480, PMCID: PMC3479396, DOI: 10.1261/rna.034900.112.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAptamers, NucleotideAU Rich ElementsBinding, CompetitiveCell Line, TumorHerpesvirus 4, HumanHeterogeneous Nuclear Ribonucleoprotein D0Heterogeneous-Nuclear Ribonucleoprotein DHost-Pathogen InteractionsHumansImmunoprecipitationMutagenesis, InsertionalProtein BindingProtein IsoformsRNA StabilityRNA, ViralConceptsAU-rich elementsProtein partnersAUF1/hnRNP DUntranslated regionBacteriophage MS2 coat proteinNovel protein partnersHigh abundanceElectrophoretic mobility shift assaysEpstein-Barr virusMS2 coat proteinStable isotope labelingMobility shift assaysInteracting proteinMolecular functionsHnRNP DAlternative splicingNoncoding RNAsShift assaysCoat proteinIsotope labelingP40 isoformRNA aptamersRNA 1AUF1UV crosslinkingIxodes scapularis JAK-STAT Pathway Regulates Tick Antimicrobial Peptides, Thereby Controlling the Agent of Human Granulocytic Anaplasmosis
Liu L, Dai J, Zhao YO, Narasimhan S, Yang Y, Zhang L, Fikrig E. Ixodes scapularis JAK-STAT Pathway Regulates Tick Antimicrobial Peptides, Thereby Controlling the Agent of Human Granulocytic Anaplasmosis. The Journal Of Infectious Diseases 2012, 206: 1233-1241. PMID: 22859824, PMCID: PMC3448968, DOI: 10.1093/infdis/jis484.Peer-Reviewed Original ResearchConceptsJAK-STAT pathwayTick salivary glandsA. phagocytophilum infectionAntimicrobial peptidesElectrophoretic mobility shift assaysPeptide-encoding genesMobility shift assaysPhagocytophilum infectionHuman granulocytic anaplasmosisGene familyTransducer activatorMammalian hostsRNA interferenceShift assaysTranscription pathwayGene expressionJAK-STATJanus kinaseGranulocytic anaplasmosisSalivary glandsPathwayGenesCritical roleAnaplasma phagocytophilumKey role
2010
The large, noncoding OLE RNA is associated with membrane biochemistry
Block K, Wallace J, Puerta‐Fernandez E, Breaker R. The large, noncoding OLE RNA is associated with membrane biochemistry. The FASEB Journal 2010, 24: 493.2-493.2. DOI: 10.1096/fasebj.24.1_supplement.493.2.Peer-Reviewed Original ResearchOLE RNAB. haloduransMembrane biochemistryMembrane-spanning proteinsHigh-throughput sequencingEnergy-generating pathwaysEscherichia coli cellsGel shift assaysNorthern blot analysisRNA fluorescenceSpecific ribonucleoproteinGram-positive bacteriaShift assaysColi cellsUnknown functionProbable binding siteSitu hybridizationBlot analysisBinding sitesHaloduransHoward Hughes Medical InstituteRNAProteinBiochemistryCells
2009
Nuclear factor erythroid 2–related factor 2 is a positive regulator of human bile salt export pump expression
Weerachayaphorn J, Cai S, Soroka CJ, Boyer JL. Nuclear factor erythroid 2–related factor 2 is a positive regulator of human bile salt export pump expression. Hepatology 2009, 50: 1588-1596. PMID: 19821532, PMCID: PMC3013376, DOI: 10.1002/hep.23151.Peer-Reviewed Original ResearchMeSH KeywordsATP Binding Cassette Transporter, Subfamily B, Member 11ATP-Binding Cassette TransportersBase SequenceHep G2 CellsHepatocytesHumansMaf Transcription FactorsMolecular Sequence DataNF-E2-Related Factor 2PyrazinesReverse Transcriptase InhibitorsRNA, MessengerSignal TransductionThionesThiophenesConceptsBile salt export pumpCholestatic liver injuryPositive transcriptional regulatorElectrophoretic mobility shift assaysHepG2 cellsBSEP expressionChromatin immunoprecipitation assaysBSEP promoterMobility shift assaysAdditional transcriptional factorsProximal promoter regionBSEP promoter activitySmall interfering RNAsFactor 2Liver injuryNuclear factorAntioxidant responsive elementTranscriptional regulatorsNrf2 transcriptional activationTranscriptional activationPositive regulatorBile salt export pump expressionNuclear farnesoid X receptorImmunoprecipitation assaysShift assays
2008
GbdR Regulates Pseudomonas aeruginosa plcH and pchP Transcription in Response to Choline Catabolites
Wargo M, Ho T, Gross M, Whittaker L, Hogan D. GbdR Regulates Pseudomonas aeruginosa plcH and pchP Transcription in Response to Choline Catabolites. Infection And Immunity 2008, 77: 1103-1111. PMID: 19103776, PMCID: PMC2643652, DOI: 10.1128/iai.01008-08.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAraC Transcription FactorBetaineCholineDNA Mutational AnalysisElectrophoretic Mobility Shift AssayGene Expression Regulation, BacterialMaleMiceMice, Inbred C57BLPhosphoric Monoester HydrolasesPhosphorylcholinePromoter Regions, GeneticPseudomonas aeruginosaPseudomonas InfectionsReverse Transcriptase Polymerase Chain ReactionSarcosineTranscription, GeneticTransferases (Other Substituted Phosphate Groups)ConceptsGlycine betainePlcH activityAraC family transcription factorElectrophoretic mobility shift assaysFamily transcription factorsEukaryotic cell membranesHemolytic phospholipase CMobility shift assaysP. aeruginosa virulenceProtein fusionsPromoter mappingTranscriptional activationTranscription factorsGbdRPhosphorylcholine phosphatasePromoter sequencesShift assaysGene expressionPromoter mutantsFeedback inductionMutantsTranscriptionPhospholipase CPrimary regulatorCell membraneTNF-&agr; Induces MMP2 Gelatinase Activity and MT1-MMP Expression in an In Vitro Model of Nucleus Pulposus Tissue Degeneration
Séguin CA, Pilliar RM, Madri JA, Kandel RA. TNF-&agr; Induces MMP2 Gelatinase Activity and MT1-MMP Expression in an In Vitro Model of Nucleus Pulposus Tissue Degeneration. Spine 2008, 33: 356-365. PMID: 18277865, DOI: 10.1097/brs.0b013e3181642a5e.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCattleElectrophoretic Mobility Shift AssayExtracellular Signal-Regulated MAP KinasesGene ExpressionImmunoblottingIn Vitro TechniquesIntervertebral DiscLuciferasesMatrix Metalloproteinase 14Matrix Metalloproteinase 2Reverse Transcriptase Polymerase Chain ReactionTumor Necrosis Factor-alphaUp-RegulationConceptsMMP-2 gelatinase activityERK MAPK pathwayTranscriptional activationMT1-MMPElectrophoretic mobility shift assaysMT1-MMP promoterMMP-2 geneMobility shift assaysSignal transduction mechanismsProtein levelsERK 1/2 activationNP tissuesTranscription factorsShift assaysMT1-MMP expressionReporter constructsTNF-alpha inductionERK MAPKGelatinase activityLuciferase constructEgr-1TNF-alpha treatmentMMP-2 activationSP-1Transduction mechanisms
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 regionDifferential Cell-Specific Modulation of HOXA10 by Estrogen and Specificity Protein 1 Response Elements
Martin R, Taylor MB, Krikun G, Lockwood C, Akbas GE, Taylor HS. Differential Cell-Specific Modulation of HOXA10 by Estrogen and Specificity Protein 1 Response Elements. The Journal Of Clinical Endocrinology & Metabolism 2007, 92: 1920-1926. PMID: 17311863, DOI: 10.1210/jc.2006-1694.Peer-Reviewed Original ResearchMeSH KeywordsBreastCells, CulturedElectrophoretic Mobility Shift AssayEstrogensFemaleGenes, ReporterHomeobox A10 ProteinsHomeodomain ProteinsHumansImmunohistochemistryLuciferasesPlasmidsReceptors, EstrogenResponse ElementsReverse Transcriptase Polymerase Chain ReactionSp1 Transcription FactorTransfectionUterusConceptsEstrogen response elementHOXA10 estrogen response elementResponse elementSp1 sitesShift assaysStage-specific expression patternsTissue specificityElectrophoretic mobility shift assaysCell typesSpecificity protein 1Mobility shift assaysAdult reproductive tractGel shift assaysDifferential cellular expressionDistinct differential expressionHox genesSp1 proteinCell-specific modulationTranscription factorsEmbryonic developmentRegulatory elementsExpression patternsReporter assaysBreast MCF-7 cellsDifferential expression
2006
Defects in E2F1/2 Expression Are Associated with Abnormalities in Cell Cycle and Differentiation in EKLF-Deficient Erythroid Cells.
Pilon A, Arcasoy M, Vayda S, Dressman H, Bieker J, Bodine D, Gallagher P. Defects in E2F1/2 Expression Are Associated with Abnormalities in Cell Cycle and Differentiation in EKLF-Deficient Erythroid Cells. Blood 2006, 108: 84. DOI: 10.1182/blood.v108.11.84.84.Peer-Reviewed Original ResearchHypersensitive sitesErythroid cellsMicroarray analysisCell cycleNumerous genesMature erythroblastsGel mobility shift assaysMicroarray dataFL cellsTranscription factor EKLFCell cycle controlMobility shift assaysΒ-globin expressionIngenuity Pathway AnalysisImmature erythroid cellsPrevious microarray analysisPrevious microarray dataE2F proteinsDefinitive erythropoiesisDNA replicationTranscription factorsColony forming assaysEKLFShift assaysTarget genesSex-lethal is a target of Bruno-mediated translational repression in promoting the differentiation of stem cell progeny during Drosophila oogenesis
Wang Z, Lin H. Sex-lethal is a target of Bruno-mediated translational repression in promoting the differentiation of stem cell progeny during Drosophila oogenesis. Developmental Biology 2006, 302: 160-168. PMID: 17067567, PMCID: PMC1904479, DOI: 10.1016/j.ydbio.2006.09.016.Peer-Reviewed Original ResearchConceptsBruno response elementCystoblast differentiationTranslational repressionElectrophoresis mobility shift assaysGermline stem cellsPotential mRNA targetsMobility shift assaysStem cell progenySex-lethalDrosophila ovaryDrosophila oogenesisMutant phenotypeBioinformatics approachMRNA targetsShift assaysType RNACDNA constructsUntranslated regionCell progenyResponse elementStem cellsNovel targetDifferentiationRepressionMS11Molecular basis underlying the poly C binding protein 1 as a regulator of the proximal promoter of mouse μ-opioid receptor gene
Malik A, Flock K, Godavarthi C, Loh H, Ko J. Molecular basis underlying the poly C binding protein 1 as a regulator of the proximal promoter of mouse μ-opioid receptor gene. Brain Research 2006, 1112: 33-45. PMID: 16904079, DOI: 10.1016/j.brainres.2006.07.019.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCarrier ProteinsCell Line, TumorDNA-Binding ProteinsElectrophoretic Mobility Shift AssayGene Expression RegulationMethionineMiceNeuroblastomaPhosphorus IsotopesPromoter Regions, GeneticProtein BindingProtein Structure, TertiaryReceptors, Opioid, muRegulatory Sequences, Nucleic AcidReverse Transcriptase Polymerase Chain ReactionRNA, MessengerRNA-Binding ProteinsTranscription, GeneticTransfectionConceptsPoly C binding protein 1Electrophoretic mobility shift assaySsDNA binding activityMu-opioid receptorsProximal promoterGene regulationBinding activityMolecular basisSsDNA-binding abilityMobility shift assayVariable domainsProtein 1Mu-opioid receptor gene expressionDNA elementsKH3 domainTransactivation domainKH1 domainSsDNA bindingShift assaysMOR gene regulationGene expressionOptimal activitySequential domainsFunctional analysisMu-opioid
2005
GATA-1 and Oct-1 Are Required for Expression of the Human α-Hemoglobin-stabilizing Protein Gene*
Gallagher PG, Liem RI, Wong E, Weiss MJ, Bodine DM. GATA-1 and Oct-1 Are Required for Expression of the Human α-Hemoglobin-stabilizing Protein Gene*. Journal Of Biological Chemistry 2005, 280: 39016-39023. PMID: 16186125, DOI: 10.1074/jbc.m506062200.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBinding SitesBlood ProteinsCell LineCloning, MolecularDNA, ComplementaryErythropoiesisGATA1 Transcription FactorGene ExpressionGlobinsHeLa CellsHumansMiceMice, TransgenicMolecular ChaperonesMolecular Sequence DataMutationOctamer Transcription Factor-1Promoter Regions, GeneticRecombinant ProteinsRNA, MessengerConceptsAlpha-hemoglobin-stabilizing proteinGATA-1AHSP promoterAHSP genePromoter/reporter plasmidsGel mobility shift assaysAHSP gene expressionChromatin immunoprecipitation assaysErythroid-specific expressionMobility shift assaysFurther genetic studiesHuman tissue culture cell linesErythroid proteinTissue culture cell linesErythroid promoterNonerythroid tissuesProtein geneImmunoprecipitation assaysRegulatory elementsShift assaysGene promoterReporter geneCandidate genesDNase IGene expressionMolecular basis for RNA kink-turn recognition by the h15.5K small RNP protein
Szewczak LB, Gabrielsen JS, Degregorio SJ, Strobel SA, Steitz JA. Molecular basis for RNA kink-turn recognition by the h15.5K small RNP protein. RNA 2005, 11: 1407-1419. PMID: 16120832, PMCID: PMC1370824, DOI: 10.1261/rna.2830905.Peer-Reviewed Original ResearchConceptsMolecular basisRNA-protein complexesMobility shift assaysKink-turn motifPotential binding sitesNucleotide analog interference mappingSmall nucleolarSnoRNP assemblyRNA-RNA contactsRNP proteinsShift assaysSnoRNAsBackbone atomsBinding sitesPreferential bindingProteinEnergetic contributionsInterference mappingMinor interactionsStructural contextPotential sitesNucleolarSitesRNAMotifIdentification of Binding Sites of EVI1 in Mammalian Cells*
Yatsula B, Lin S, Read AJ, Poholek A, Yates K, Yue D, Hui P, Perkins AS. Identification of Binding Sites of EVI1 in Mammalian Cells*. Journal Of Biological Chemistry 2005, 280: 30712-30722. PMID: 16006653, DOI: 10.1074/jbc.m504293200.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBinding SitesDNADNA-Binding ProteinsHerpes Simplex Virus Protein Vmw65HumansMDS1 and EVI1 Complex Locus ProteinMiceMolecular Sequence DataMutagenesis, Site-DirectedMutation, MissenseNIH 3T3 CellsOligonucleotide Array Sequence AnalysisProtein ConformationProto-OncogenesRecombinant Fusion ProteinsTranscription FactorsZinc FingersConceptsChromatin immunoprecipitationTarget genesN-terminal DNAPutative target genesVP16 fusion proteinTranscription start siteN-terminal domainGel shift assaysNIH 3T3 cellsZFPM2/FOG2Transcriptional activatorEndogenous genesMissense mutantsEVI1 bindsZinc fingerMammalian cellsStart siteShift assaysMutant formsFusion proteinTransactivation studiesSequence analysisGenesEVI1Binding sitesMOLECULAR MECHANISMS REGULATING HUMAN CYP4B1 LUNG-SELECTIVE EXPRESSION
Poch M, Cutler N, Yost G, Hines R. MOLECULAR MECHANISMS REGULATING HUMAN CYP4B1 LUNG-SELECTIVE EXPRESSION. Drug Metabolism And Disposition 2005, 33: 1174-1184. PMID: 15900016, DOI: 10.1124/dmd.105.004523.Peer-Reviewed Original ResearchConceptsDistal regulatory elementsRegulatory elementsTransient expressionCompetitive electrophoretic mobility shift assaysDNA/protein binding assaysKrüppel-like factor (KLF) familyElectrophoretic mobility shift assaysTranscription factor recognition sequenceChromatin immunoprecipitation assaysTranscription factor sitesProximal elementMobility shift assaysHepG2 hepatoblastoma cellsProtein binding assaysSp1 bindingSp1 elementImmunoprecipitation assaysNuclear proteinsKidney-derived cellsFactor familyShift assaysFactor sitesMutagenesis studiesRegulatory mechanismsMolecular mechanisms
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