2024
Tet2 Loss in Hematopoietic Stem Cells Triggers Chromatin Reorganization through DNA Methylation Shifts
Roy R, Pillai M, Boddu P. Tet2 Loss in Hematopoietic Stem Cells Triggers Chromatin Reorganization through DNA Methylation Shifts. Blood 2024, 144: 1812. DOI: 10.1182/blood-2024-211494.Peer-Reviewed Original ResearchTopologically associating domainsDisruption of TAD boundariesTopologically associating domains boundariesTAD boundariesMutant cellsChromatin organizationChromatin compartmentsDNA methylationLT-HSCsKO cellsEnhancer-promoterHigher-order chromatin organizationTet2 lossStudy of chromatin organizationGene expressionMethyl-seq dataHypermethylated differentially methylated regionsPaired-end readsWT cellsGene regulatory networksConversion of 5-methylcytosineDifferentially Methylated RegionsMyelodysplastic syndromeCompartment shiftsChanges to DNA methylationVPS13B is localized at the interface between Golgi cisternae and is a functional partner of FAM177A1
Ugur B, Schueder F, Shin J, Hanna M, Wu Y, Leonzino M, Su M, McAdow A, Wilson C, Postlethwait J, Solnica-Krezel L, Bewersdorf J, De Camilli P. VPS13B is localized at the interface between Golgi cisternae and is a functional partner of FAM177A1. Journal Of Cell Biology 2024, 223: e202311189. PMID: 39331042, PMCID: PMC11451052, DOI: 10.1083/jcb.202311189.Peer-Reviewed Original ResearchConceptsLipid transportGolgi complex proteinGolgi subcompartmentsGolgi membranesGolgi cisternaeProtein familyFunctional partnersGolgi complexKO cellsComplex proteinsFAM177A1GolgiVPS13BAdjacent membranesMutationsProteinCohen syndromeLipidOrthologsInteractorsBrefeldinMembraneOrganellesSubcompartmentsDevelopmental disorders
2022
Transport studies with the polymorphic TAP molecules in chickens
Palmer E, Migalska M, Wise D, Tregaskes C, Kaufman J. Transport studies with the polymorphic TAP molecules in chickens. Molecular Immunology 2022, 150: 28. DOI: 10.1016/j.molimm.2022.05.095.Peer-Reviewed Original ResearchTAP genesPeptide motifsKO cellsTransport assaysPeptide translocationDouble KO cellsExpressed class I moleculeChicken cell linesCell linesCRISPR-Cas9 technologyTAP2 genesSequence variationB12 cellsMutant geneResponse to infectious diseasesChicken MHCGenetic associationTranslocation specificityGenesPermeabilised cellsCell surfaceTranslocationTransport peptideRecombination levelsHaplotypesMHC class II-restricted-presentationMHC class II and DM molecules in chickens: different yet again
Wise D, Halabi S, Afrache H, Fakiola M, Parker A, Kaufman J. MHC class II-restricted-presentationMHC class II and DM molecules in chickens: different yet again. Molecular Immunology 2022, 150: 32-33. DOI: 10.1016/j.molimm.2022.05.108.Peer-Reviewed Original ResearchIntestinal epithelial cellsClass II moleculesKO cellsClass II A genesII moleculesClass I systemResistance to infectious diseasesRT-PCRBF2 genesWestern blottingDM locusClass II BI systemA geneChicken MHCGenetic associationTapasin geneCRISPR-Cas9DMB1Tissue section stainingGenesBLB2Closely-linkedB2-microglobulinGut tissueCombinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS
Shi X, Reinstadler B, Shah H, To TL, Byrne K, Summer L, Calvo SE, Goldberger O, Doench JG, Mootha VK, Shen H. Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS. Nature Communications 2022, 13: 2483. PMID: 35513392, PMCID: PMC9072411, DOI: 10.1038/s41467-022-30126-9.Peer-Reviewed Original ResearchConceptsDe novo purine biosynthesisMitochondrial iron uptakeStructure-guided mutagenesisNovo purine biosynthesisMetabolic stateMitochondrial glutathione transportGlutathione importGenetic interactionsGenetic perturbationsDifferent metabolic environmentsFitness defectsLack of substrateGene interactionsMitochondrial OXPHOSMitochondrial membranePurine biosynthesisCarrier familyTransport assaysKO cellsIron uptakeGlutathione transportTransport activityIron homeostasisGlutathione homeostasisGenes
2021
Loss of ATRX confers DNA repair defects and PARP inhibitor sensitivity
Garbarino J, Eckroate J, Sundaram RK, Jensen RB, Bindra RS. Loss of ATRX confers DNA repair defects and PARP inhibitor sensitivity. Translational Oncology 2021, 14: 101147. PMID: 34118569, PMCID: PMC8203843, DOI: 10.1016/j.tranon.2021.101147.Peer-Reviewed Original ResearchPARP inhibitor sensitivityInhibitor sensitivityKey DNA damage response pathwaysDNA damage response pathwayFunction of ATRXHR-defective cellsDamage response pathwayAlpha thalassemia/mental retardation syndrome XDNA repair defectsLoss of ATRXHistone chaperonesHistone variantsReplication stressMental retardation syndrome XModel cell lineResponse pathwaysEpistatic interactionsDNA repairGene targetingAtaxia telangiectasiaKO cellsIsocitrate dehydrogenase 1DDR defectsMolecular markersRepair defects
2020
The NBDY Microprotein Regulates Cellular RNA Decapping
Na Z, Luo Y, Schofield JA, Smelyansky S, Khitun A, Muthukumar S, Valkov E, Simon MD, Slavoff SA. The NBDY Microprotein Regulates Cellular RNA Decapping. Biochemistry 2020, 59: 4131-4142. PMID: 33059440, PMCID: PMC7682656, DOI: 10.1021/acs.biochem.0c00672.Peer-Reviewed Original ResearchConceptsP-bodiesNonsense-mediated decay factorsKO cellsSmall open reading framesCytoplasmic ribonucleoprotein granulesOpen reading frameSubstrate transcriptsCellular transcriptomeRibonucleoprotein granulesTarget transcriptsRNA stabilityKnockout cellsUTR lengthReading frameGlobal profilingProteogenomic identificationMacromolecular complexesHuman RNACellular RNACytoplasmic RNAGene stabilityAmino acidsCell growthMicroproteinsTranscriptsNeuronal Calcium Sensor 1 (NCS1) as a Potential Drug Target for Treatment of Wolfram Syndrome
Fischer T, Nguyen L, Ehrlich B. Neuronal Calcium Sensor 1 (NCS1) as a Potential Drug Target for Treatment of Wolfram Syndrome. The FASEB Journal 2020, 34: 1-1. DOI: 10.1096/fasebj.2020.34.s1.00556.Peer-Reviewed Original ResearchNeuronal calcium sensor-1Wolfram syndromeHigh glucose treatmentDiabetes mellitusFunction of WFS1Lack of therapyGlucose treatmentCalcium-dependent protease calpainMajority of casesRat insulinoma cellsBaseline calciumCalcium binding proteinOptical atrophyKO cellsGlucose toxicityCalcium responseCalcium homeostasisPathophysiological consequencesCTRL cellsPhospho-AktDiscovery of drugsPotential drug targetsProtease calpainGenetic causeProtein expression
2019
ATG2 transports lipids to promote autophagosome biogenesis
Valverde DP, Yu S, Boggavarapu V, Kumar N, Lees JA, Walz T, Reinisch KM, Melia TJ. ATG2 transports lipids to promote autophagosome biogenesis. Journal Of Cell Biology 2019, 218: 1787-1798. PMID: 30952800, PMCID: PMC6548141, DOI: 10.1083/jcb.201811139.Peer-Reviewed Original ResearchConceptsProtein-mediated lipid transferLipid transferLipid transfer proteinTransfers lipidsAutophagosome biogenesisAutophagosome membraneDonor membranesN-terminal fragmentDifferent organellesAutophagy proteinsAutophagosome formationKO cellsContact sitesSpecific machineryLipid homeostasisClear functionAtg2BiogenesisProteinDelivery of lipidsLipidsATG2AMembraneOrganellesAutophagosomes
2009
C/EBPε directs granulocytic-vs-monocytic lineage determination and confers chemotactic function via Hlx
Halene S, Gaines P, Sun H, Zibello T, Lin S, Khanna-Gupta A, Williams SC, Perkins A, Krause D, Berliner N. C/EBPε directs granulocytic-vs-monocytic lineage determination and confers chemotactic function via Hlx. Experimental Hematology 2009, 38: 90-103.e4. PMID: 19925846, PMCID: PMC2827304, DOI: 10.1016/j.exphem.2009.11.004.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBone Marrow CellsCCAAT-Enhancer-Binding ProteinsCell DifferentiationCell LineChemotaxis, LeukocyteGene ExpressionGranulocyte-Macrophage Colony-Stimulating FactorGranulocytesHematopoietic Stem CellsHomeodomain ProteinsMiceMice, KnockoutMonocytesMyelopoiesisNeutrophilsReceptors, ChemokineTranscription FactorsTransduction, GeneticConceptsKO cellsNew regulatory functionCommon myeloid progenitorsNeutrophil-specific granule deficiencyProgenitor cell lineCell linesRestoration of expressionDifferentiated cell linesSpecific granule deficiencyLineage-specific cell surface antigensLineage decisionsLineage determinationEpsilon geneCCAAT enhancerDeficiency phenotypeRegulatory functionsChemotaxis defectIntermediate cell typeKO bone marrowPerformed expressionNeutrophil differentiationCell typesFunctional studiesNeutrophil maturationMyeloid progenitors
2005
Insulin Receptor Substrate 2 Plays Diverse Cell-specific Roles in the Regulation of Glucose Transport*
Sadagurski M, Weingarten G, Rhodes C, White M, Wertheimer E. Insulin Receptor Substrate 2 Plays Diverse Cell-specific Roles in the Regulation of Glucose Transport*. Journal Of Biological Chemistry 2005, 280: 14536-14544. PMID: 15705592, DOI: 10.1074/jbc.m410227200.Peer-Reviewed Original ResearchMeSH KeywordsAdenoviridaeAnimalsBiological TransportDeoxyglucoseEpidermisFibroblastsGenotypeGlucoseHomozygoteImmunoblottingImmunoprecipitationInsulin Receptor Substrate ProteinsIntracellular Signaling Peptides and ProteinsKeratinocytesMiceMice, KnockoutPhosphatidylinositol 3-KinasesPhosphoproteinsSkinThymidineTime FactorsConceptsIRS-2Glucose transportInsulin receptor substrate-2 proteinInsulin-induced glucose transportInsulin receptor substrate 2Insulin-stimulated glucose transportIRS-1 proteinCell specific associationIRS-2 proteinClassical insulin target tissuesCell-specific mannerSkin epidermal keratinocytesIRS-PICell-specific rolePositive regulatorInsulin target tissuesCell physiologyDermal fibroblastsKO cellsEpidermal keratinocytesAkt activationPhosphatidylinositolSubstrate 2Insulin receptorProtein
2000
Essential Role of Insulin Receptor Substrate-2 in Insulin Stimulation of Glut4 Translocation and Glucose Uptake in Brown Adipocytes*
Fasshauer M, Klein J, Ueki K, Kriauciunas K, Benito M, White M, Kahn C. Essential Role of Insulin Receptor Substrate-2 in Insulin Stimulation of Glut4 Translocation and Glucose Uptake in Brown Adipocytes*. Journal Of Biological Chemistry 2000, 275: 25494-25501. PMID: 10829031, DOI: 10.1074/jbc.m004046200.Peer-Reviewed Original ResearchMeSH KeywordsAdipocytesAdipose Tissue, BrownAnimalsArabidopsis ProteinsAzo CompoundsBiological TransportCell DifferentiationCell MembraneCells, CulturedColoring AgentsDose-Response Relationship, DrugGlucoseGlucose Transporter Type 4ImmunoblottingInsulinInsulin Receptor Substrate ProteinsIntracellular Signaling Peptides and ProteinsMiceMice, KnockoutMonosaccharide Transport ProteinsMuscle ProteinsPhosphatidylinositol 3-KinasesPhosphoproteinsPhosphorylationPlant ProteinsPlasmidsPotassium ChannelsPrecipitin TestsProtein Serine-Threonine KinasesProto-Oncogene ProteinsProto-Oncogene Proteins c-aktRetroviridaeSignal TransductionSubcellular FractionsTime FactorsConceptsInsulin-stimulated GLUT4 translocationGLUT4 translocationInsulin-induced glucose uptakeIRS-2Plasma membraneDownstream effectorsWild typeInsulin receptor substrate (IRS) proteinsBrown adipocyte cell lineInsulin stimulationGlycogen synthase kinase-3IRS-2-associated phosphatidylinositolGlucose uptakeAkt-dependent phosphorylationInsulin receptor substrate 2Synthase kinase-3Brown adipocytesMajor downstream effectorActivity of AktMature brown adipocytesAdipocyte cell lineSubstrate proteinsWild-type counterpartsKO cellsKinase 3
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