2024
Structural basis for transcription activation by the nitrate-responsive regulator NarL
Kompaniiets D, He L, Wang D, Zhou W, Yang Y, Hu Y, Liu B. Structural basis for transcription activation by the nitrate-responsive regulator NarL. Nucleic Acids Research 2024, 52: 1471-1482. PMID: 38197271, PMCID: PMC10853779, DOI: 10.1093/nar/gkad1231.Peer-Reviewed Original ResearchTranscription activation complexC-terminal domainTranscription activationAlpha C-terminal domainStructural basisGlobal transcription factorCryo-EM structureDetailed mechanistic understandingPromoter DNATranscription initiationBinds DNATranscription assaysTranscription factorsActivation complexÅ resolutionNarLDimer bindsMolecular mechanismsNovel mechanismActivation mechanismMechanistic understandingDNAStress factorsPromoterActivation
2016
The Role of UAF1 in the Fanconi Anemia Pathway Regulation of Homologous Recombination-Mediated Genome Maintenance
Liang F, Longerich S, Tang C, Buzovestsky O, Xiong Y, Maranon D, Wiese C, Miller A, Sung P, Kupfer G. The Role of UAF1 in the Fanconi Anemia Pathway Regulation of Homologous Recombination-Mediated Genome Maintenance. Blood 2016, 128: 1041. DOI: 10.1182/blood.v128.22.1041.1041.Peer-Reviewed Original ResearchHomologous recombinationGenome maintenanceDNA damageFA DNA repair pathwayCancer-prone genetic diseasesFanconi anemiaDNA damage hypersensitivityFunctional synergySynaptic complex assemblyProtein complex formationRad51 presynaptic filamentD-loop reactionDNA repair functionDNA damage repairDNA binding activityCell linesFANCD2 ubiquitinationGenome stabilityComplex formationRAD51 recombinaseHuman cell linesBinds DNAPresynaptic filamentRecombinase RAD51UAF1DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos
Surovtsev IV, Campos M, Jacobs-Wagner C. DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: e7268-e7276. PMID: 27799522, PMCID: PMC5135302, DOI: 10.1073/pnas.1616118113.Peer-Reviewed Original ResearchConceptsParA ATPase activityParA gradientCellular physiologyATP bindingBinds DNAIntracellular patterningChromosomal lociATP hydrolysisIntracellular transportInside cellsMultiple copiesMultiple cargoesDNA fluctuationsATPase activityIntracellular patternMacromolecular componentsCargoDNAPatterningMinimal systemBindingSignature patternsParBCargo dynamicsCellsPromotion of RAD51-Mediated Homologous DNA Pairing by the RAD51AP1-UAF1 Complex
Liang F, Longerich S, Miller AS, Tang C, Buzovetsky O, Xiong Y, Maranon DG, Wiese C, Kupfer GM, Sung P. Promotion of RAD51-Mediated Homologous DNA Pairing by the RAD51AP1-UAF1 Complex. Cell Reports 2016, 15: 2118-2126. PMID: 27239033, PMCID: PMC5381662, DOI: 10.1016/j.celrep.2016.05.007.Peer-Reviewed Original ResearchConceptsHomologous recombinationFanconi anemia DNA damage response pathwayDNA damage response pathwaySmall ubiquitin-like modifierDNA damage hypersensitivityHomologous DNA pairingSUMO-interacting motifDamage response pathwayUbiquitin-like modifierFANCD2 ubiquitinationGenome maintenanceComplex formationNucleoprotein intermediatesRAD51 recombinaseDNA pairingProtein complexesBinds DNAAccessory factorsResponse pathwaysHomologous DNADNA repairLike domainUAF1RAD51RAD51AP1
2012
The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub
Trofka A, Schwendinger-Schreck J, Brend T, Pontius W, Emonet T, Holley SA. The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub. Development 2012, 139: 940-947. PMID: 22278920, PMCID: PMC3274355, DOI: 10.1242/dev.073544.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBasic Helix-Loop-Helix Transcription FactorsBiological ClocksBody PatterningComputer SimulationDimerizationDNAGene Expression Regulation, DevelopmentalGene Knockdown TechniquesGene Regulatory NetworksRecombinant Fusion ProteinsRepressor ProteinsTranscription FactorsZebrafishZebrafish ProteinsConceptsZebrafish segmentation clockSegmentation clockBinds DNACis-regulatory sequencesDNA-binding heterodimersTranscriptional negative feedbackGenetic experimentsHer7Regulatory sequencesDNA bindingHes6Vivo assaysDNAHomodimerHeterodimersDistinct preferenceEmergent functionsNetwork hubsNegative feedbackComputational analysisClockDimersSequestrationProteinRegulation
1997
Parvovirus initiation factor PIF: a novel human DNA-binding factor which coordinately recognizes two ACGT motifs
Christensen J, Cotmore S, Tattersall P. Parvovirus initiation factor PIF: a novel human DNA-binding factor which coordinately recognizes two ACGT motifs. Journal Of Virology 1997, 71: 5733-5741. PMID: 9223459, PMCID: PMC191825, DOI: 10.1128/jvi.71.8.5733-5741.1997.Peer-Reviewed Original ResearchConceptsDNA-binding factorsACGT motifGel mobility shift assaysReplication initiation processMobility shift assaysHigher-order multimersParvovirus initiation factorSame cellular factorHeLa S3 cellsMouse genomeBinds DNADNA replicationACGT sequenceInitiation factorsOrigin sequencesShift assaysMinimal originMutant oligonucleotidesATP hydrolysisMobility shiftDNase ICellular factorsEssential cofactorMobility assaysSingle binding site
1991
Heterodimers of the Zebra and Fos Basic Domains Bind DNA with the Specificity of Zebra
Taylor N, Kolman J, Miller G. Heterodimers of the Zebra and Fos Basic Domains Bind DNA with the Specificity of Zebra. Experimental Biology And Medicine 1991, 99-103. DOI: 10.1007/978-1-4612-0405-3_15.Peer-Reviewed Original Research
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