2024
Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4
Saotome M, Poduval D, Grimm S, Nagornyuk A, Gunarathna S, Shimbo T, Wade P, Takaku M. Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4. Nucleic Acids Research 2024, 52: 3607-3622. PMID: 38281186, PMCID: PMC11039999, DOI: 10.1093/nar/gkae025.Peer-Reviewed Original ResearchConceptsTranscription factorsBreast cancer cellsBinding motifTranscription factor binding motifsTranscription factor-DNA interactionsLineage-determining transcription factorsCellular reprogrammingProof-reading enzymeBasal breast cancer cellsChromatin-binding activityCancer cellsBinding site selectionEukaryotic genomesNucleosome positioningChromatin accessibilityChromatin openingGene activationCHD4Gene expressionChromatinTranscriptionBinding activityFrequent mutationsUnoccupied sitesExquisite specificity
2022
Tuft cells are key mediators of interkingdom interactions at mucosal barrier surfaces
Strine MS, Wilen CB. Tuft cells are key mediators of interkingdom interactions at mucosal barrier surfaces. PLOS Pathogens 2022, 18: e1010318. PMID: 35271673, PMCID: PMC8912186, DOI: 10.1371/journal.ppat.1010318.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsInterkingdom interactionsTuft cellsCell biologyImmune responseMicrobial activationMicrobial sensingCell abundanceMucosal barrier surfacesAntiviral adaptive immune responsesType 2 immune responsesCell heterogeneityExquisite specificityMucosal barrier integrityAdaptive immune responsesMurine norovirusHuman healthKey orchestratorsMicrobial infectionsPathogenic bacteriaBroad intraFlavivirus replicationKey mediatorContext of coinfectionTissue repairImmune evasion
2021
Pharmacological inhibition of PI5P4Kα/β disrupts cell energy metabolism and selectively kills p53-null tumor cells
Chen S, Tjin C, Gao X, Xue Y, Jiao H, Zhang R, Wu M, He Z, Ellman J, Ha Y. Pharmacological inhibition of PI5P4Kα/β disrupts cell energy metabolism and selectively kills p53-null tumor cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2002486118. PMID: 34001596, PMCID: PMC8166193, DOI: 10.1073/pnas.2002486118.Peer-Reviewed Original ResearchMeSH KeywordsAMP-Activated Protein Kinase KinasesAnimalsEnergy MetabolismHumansInsulinInsulin Receptor Substrate ProteinsMechanistic Target of Rapamycin Complex 1MiceMuscle Fibers, SkeletalNeoplasmsPhosphorylationPhosphotransferases (Alcohol Group Acceptor)Ribosomal Protein S6 Kinases, 70-kDaSignal TransductionSmall Molecule LibrariesTumor Suppressor Protein p53ConceptsP53-null tumor cellsMost human cancer cellsCell energy homeostasisCell energy metabolismTumor suppressor genePI5P4KHuman cancer cellsGenetic experimentsDifferentiated myotubesAMPK activationStructural basisKinase activityEnergy stressMetabolic regulationSuppressor geneFunction mutationsLate-onset tumorsSubstrate loopP53 tumor suppressor geneChemical probesPI3KCell typesExquisite specificityEnergy metabolismTumor cells
2020
Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans
Vormstein-Schneider D, Lin J, Pelkey K, Chittajallu R, Guo B, Arias-Garcia M, Allaway K, Sakopoulos S, Schneider G, Stevenson O, Vergara J, Sharma J, Zhang Q, Franken T, Smith J, Ibrahim L, Mastro K, Sabri E, Huang S, Favuzzi E, Burbridge T, Xu Q, Guo L, Vogel I, Sanchez V, Saldi G, Gorissen B, Yuan X, Zaghloul K, Devinsky O, Sabatini B, Batista-Brito R, Reynolds J, Feng G, Fu Z, McBain C, Fishell G, Dimidschstein J. Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans. Nature Neuroscience 2020, 23: 1629-1636. PMID: 32807948, PMCID: PMC8015416, DOI: 10.1038/s41593-020-0692-9.Peer-Reviewed Original ResearchConceptsRecombinant adeno-associated virus vectorAdeno-associated virus vectorVasoactive intestinal peptide-expressing interneuronsClasses of neuronsGene regulatory elementsGene SCN1AViral toolsNeuronal subtypesCerebral cortexViral manipulationTherapeutic interventionsVertebrate speciesNon-human primatesVirus vectorsGene expressionInterneuronsBrain regionsCircuit manipulationsExquisite specificityParvalbuminRegulatory landscapeNeuronsSCN1ASubtypesMice
2008
Substrate Discrimination among Mitogen-activated Protein Kinases through Distinct Docking Sequence Motifs*
Sheridan DL, Kong Y, Parker SA, Dalby KN, Turk BE. Substrate Discrimination among Mitogen-activated Protein Kinases through Distinct Docking Sequence Motifs*. Journal Of Biological Chemistry 2008, 283: 19511-19520. PMID: 18482985, PMCID: PMC2443660, DOI: 10.1074/jbc.m801074200.Peer-Reviewed Original ResearchConceptsDEF sitesProtein kinaseMAPK isoformsSequence requirementsMAPK signal transduction cascadePhosphorylation site motifsMAPK family membersSignal transduction cascadePeptide library screenDocking motifExtracellular stimuliMAPK interactionPhosphorylation sitesSequence motifsTransduction cascadeSite motifSubstrate specificityKey residuesSequence specificityLibrary screenUnique sequencesIndividual MAPKsCellular responsesComputational docking studiesExquisite specificity
2004
Svp1p defines a family of phosphatidylinositol 3,5‐bisphosphate effectors
Dove SK, Piper RC, McEwen RK, Yu JW, King MC, Hughes DC, Thuring J, Holmes AB, Cooke FT, Michell RH, Parker PJ, Lemmon MA. Svp1p defines a family of phosphatidylinositol 3,5‐bisphosphate effectors. The EMBO Journal 2004, 23: 1922-1933. PMID: 15103325, PMCID: PMC404323, DOI: 10.1038/sj.emboj.7600203.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAutophagy-Related ProteinsBase SequenceCloning, MolecularEndosomesEscherichia coliGene ComponentsGenetic VectorsGreen Fluorescent ProteinsMembrane ProteinsMolecular Sequence DataPhosphatidylinositol PhosphatesPhosphotransferases (Alcohol Group Acceptor)PlasmidsProtein BindingProtein FoldingProtein TransportRhinovirusSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence AlignmentSequence Analysis, DNAVacuolesConceptsFamily of phosphatidylinositolSaccharomyces cerevisiae mutantsDrosophila homologueCerevisiae mutantsMembrane recyclingVesicle recyclingVacuole enlargementVacuole membraneMultivesicular bodiesRelated proteinsLysosomal compartmentMarker proteinsExquisite specificityEffectorsProteinPhosphatidylinositolVacuolesEukaryotesCellsMutantsLocalisesGolgiHomologuesMVBGenes
2003
Phosphoinositide Recognition Domains
Lemmon MA. Phosphoinositide Recognition Domains. Traffic 2003, 4: 201-213. PMID: 12694559, DOI: 10.1034/j.1600-0854.2004.00071.x.Peer-Reviewed Original ResearchConceptsPleckstrin homology domainPhox homologyHomology domainEpsin ENTH domainENTH domainMembrane recruitmentFYVE domainBind phosphoinositidesTargeting domainsCellular phosphoinositidesCellular signalingCytoskeletal remodelingLipid bindingIntracellular traffickingStructural basisDistinct functionsExquisite specificityRecognition domainPhosphoinositideSpecificity characteristicsBilayer curvatureSignificant insightsHigh affinityDomainHomology
1988
Accuracy of in Vivo Aminoacylation Requires Proper Balance of tRNA and Aminoacyl-tRNA Synthetase
Swanson R, Hoben P, Sumner-Smith M, Uemura H, Watson L, Söll D. Accuracy of in Vivo Aminoacylation Requires Proper Balance of tRNA and Aminoacyl-tRNA Synthetase. Science 1988, 242: 1548-1551. PMID: 3144042, DOI: 10.1126/science.3144042.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthetaseAminoacyl-tRNA synthetasesProtein biosynthesisAccuracy of aminoacylationCognate aminoacyl-tRNA synthetaseAmber suppressorVivo aminoacylationGln-tRNA synthetaseCognate tRNATRNAExquisite specificityAminoacylationSynthetaseAccurate aminoacylationSynthetasesBiosynthesisIntracellular concentrationRelative levelsProper balanceComplexed formsSuppressorEscherichiaGln
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