2021
Structural visualization of transcription activated by a multidrug-sensing MerR family regulator
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B. Structural visualization of transcription activated by a multidrug-sensing MerR family regulator. Nature Communications 2021, 12: 2702. PMID: 33976201, PMCID: PMC8113463, DOI: 10.1038/s41467-021-22990-8.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsBacterial ProteinsBase SequenceBinding SitesCloning, MolecularCryoelectron MicroscopyCrystallography, X-RayDNA, BacterialDNA-Binding ProteinsDNA-Directed RNA PolymerasesEscherichia coliGene ExpressionGene Expression Regulation, BacterialGenetic VectorsModels, MolecularNucleic Acid ConformationPromoter Regions, GeneticProtein BindingProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein Interaction Domains and MotifsRecombinant ProteinsTranscription Elongation, GeneticTranscription Initiation, GeneticConceptsMerR family regulatorsFamily regulatorCryo-electron microscopy structureBacterial RNA polymerase holoenzymeRegulation of transcriptionRNA polymerase holoenzymePromoter openingTranscription regulationMicroscopy structureTranscription initiationPolymerase holoenzymeRNA elongationTranscriptional regulatorsMerR familyDNA remodelingSpacer DNAPromoter recognitionPromoter elementsCellular signalsSpacer promoterInitial transcriptionTranscription processTranscriptionPromoterRegulator
2004
Cloning of Apoptosis-Related Genes by Representational Difference Analysis of cDNA
Hubank M, Bryntesson F, Regan J, Schatz DG. Cloning of Apoptosis-Related Genes by Representational Difference Analysis of cDNA. Methods In Molecular Biology 2004, 282: 255-273. PMID: 15105570, DOI: 10.1385/1-59259-812-9:255.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsApoptosisCell SeparationCloning, MolecularDNA, ComplementaryFlow CytometryGene Expression ProfilingSequence Analysis, DNAConceptsRepresentational difference analysisApoptosis-related genesComplementary DNA representational difference analysisCDNA-RDAGene expressionDifferential gene expression analysisIdentification of genesKey target genesExpression levelsGene expression analysisLow-abundance transcriptsGene microarray analysisModel organismsTranscriptional differencesTarget genesExpression analysisDifferential displayMicroarray analysisGene microarrayCDNA fragmentsCDNA ampliconsGenesBase pairsSerial analysisPolymerase chain reaction amplification
2003
A Functional Analysis of the Spacer of V(D)J Recombination Signal Sequences
Lee AI, Fugmann SD, Cowell LG, Ptaszek LM, Kelsoe G, Schatz DG. A Functional Analysis of the Spacer of V(D)J Recombination Signal Sequences. PLOS Biology 2003, 1: e1. PMID: 14551903, PMCID: PMC212687, DOI: 10.1371/journal.pbio.0000001.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesSignal sequenceGene segmentsProtein-DNA interactionsLevel of recombinationDegree of conservationParticular functional importanceJ gene segmentsAntigen receptor genesSpacer variantsRAG proteinsRecombination machineryRSS activityInactive pseudogeneRSS functionSpacer sequencesFunctional analysisInteraction surfaceFunctional importanceLymphocyte developmentNumerous complex interactionsBiochemical assaysDistinct cooperationReceptor geneHeptamer
2002
RAG1-DNA Binding in V(D)J Recombination SPECIFICITY AND DNA-INDUCED CONFORMATIONAL CHANGES REVEALED BY FLUORESCENCE AND CD SPECTROSCOPY*
Ciubotaru M, Ptaszek LM, Baker GA, Baker SN, Bright FV, Schatz DG. RAG1-DNA Binding in V(D)J Recombination SPECIFICITY AND DNA-INDUCED CONFORMATIONAL CHANGES REVEALED BY FLUORESCENCE AND CD SPECTROSCOPY*. Journal Of Biological Chemistry 2002, 278: 5584-5596. PMID: 12488446, DOI: 10.1074/jbc.m209758200.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBinding SitesCircular DichroismCloning, MolecularDNADNA NucleotidyltransferasesDNA-Binding ProteinsEscherichia coliGenes, RAG-1Homeodomain ProteinsKineticsMiceOligodeoxyribonucleotidesProtein ConformationRecombinant ProteinsRecombination, GeneticSubstrate SpecificityTransfectionTransposasesVDJ RecombinasesConceptsRecombination signal sequencesConformational changesSynaptic complex formationAbsence of DNAAssembly of immunoglobulinMajor conformational changesIntrinsic protein fluorophoresProtein intrinsic fluorescenceSolvent-exposed environmentRAG2 proteinsRAG1/2 complexSingle DNA moleculesRAG1 proteinSignal sequenceAcrylamide quenching studiesT-cell receptor genesStrep-tagRecombination specificityDNA moleculesProtein fluorophoresRAG1Receptor geneProteinIntrinsic fluorescenceCircular dichroismInducible Gene Expression Using an Autoregulatory, Tetracycline‐Controlled System
Shockett P, Schatz D. Inducible Gene Expression Using an Autoregulatory, Tetracycline‐Controlled System. Current Protocols In Molecular Biology 2002, 60: 16.14.1-16.14.9. PMID: 18265300, DOI: 10.1002/0471142727.mb1614s60.Peer-Reviewed Original ResearchConceptsInducible gene expressionSelectable markerGene expressionSecond selectable markerCell linesFibroblast cell lineTransient transfectionGene protein expressionResultant clonesStable linesMarker plasmidPlasmidProtein expressionAdherent cellsTransactivatorExpressionTransfectionCellsTargetGenesSupport protocolClonesLinesMarkersAutoregulatory
2000
Cell-cycle-regulated DNA double-strand breaks in somatic hypermutation of immunoglobulin genes
Papavasiliou F, Schatz D. Cell-cycle-regulated DNA double-strand breaks in somatic hypermutation of immunoglobulin genes. Nature 2000, 408: 216-221. PMID: 11089977, DOI: 10.1038/35041599.Peer-Reviewed Original ResearchConceptsDNA double-strand breaksDouble-strand breaksSomatic hypermutationRepair of DSBsVariable region promotersImmunoglobulin variable region genesDNA replicationHomologous recombinationHeterologous promoterSpecific residuesVariable genesNearby mutationsRegion promoterVariable region genesImmunoglobulin genesHeterologous sequencesChromosomal translocationsPoint mutationsGenesRegion genesMutationsHypermutationTranscriptionPromoterB-cell tumors
1999
DNA Hairpin Opening Mediated by the RAG1 and RAG2 Proteins
Shockett P, Schatz D. DNA Hairpin Opening Mediated by the RAG1 and RAG2 Proteins. Molecular And Cellular Biology 1999, 19: 4159-4166. PMID: 10330156, PMCID: PMC104375, DOI: 10.1128/mcb.19.6.4159.Peer-Reviewed Original Research
1994
Identifying differences in mRNA expression by representational difference analysis of cDNA
Hubank M, Schatz DG. Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucleic Acids Research 1994, 22: 5640-5648. PMID: 7838717, PMCID: PMC310128, DOI: 10.1093/nar/22.25.5640.Peer-Reviewed Original Research
1991
Selective expression of RAG-2 in chicken B cells undergoing immunoglobulin gene conversion
Carlson L, Oettinger M, Schatz D, Masteller E, Hurley E, McCormack W, Baltimore D, Thompson C. Selective expression of RAG-2 in chicken B cells undergoing immunoglobulin gene conversion. Cell 1991, 64: 201-208. PMID: 1986866, DOI: 10.1016/0092-8674(91)90221-j.Peer-Reviewed Original ResearchMeSH KeywordsActinsAnimalsB-LymphocytesBlotting, NorthernBursa of FabriciusCell LineChickensCloning, MolecularFlow CytometryGene ConversionGene ExpressionGene Expression RegulationGenes, ImmunoglobulinHumansMolecular Sequence DataNucleic Acid HybridizationRecombination, GeneticRNA, MessengerSpleenThymus GlandConceptsIg gene conversionGene conversionChicken B cellsRAG-2 mRNARAG-2Cis-acting DNA elementsChicken B cell lineRAG-1Mammalian B cellsIntrachromosomal gene conversionImmunoglobulin gene conversionRAG-2 expressionB cell developmentIg diversificationRAG-1 mRNADNA elementsCell developmentB cell linesBursa of FabriciusB cellsPhenotypic characteristicsSelective expressionCell linesBursal lymphocytesMRNA
1989
The V(D)J recombination activating gene, RAG-1
Schatz D, Oettinger M, Baltimore D. The V(D)J recombination activating gene, RAG-1. Cell 1989, 59: 1035-1048. PMID: 2598259, DOI: 10.1016/0092-8674(89)90760-5.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBiological EvolutionCell LineCloning, MolecularDNA NucleotidyltransferasesGene Expression RegulationGene LibraryGene Rearrangement, T-LymphocyteGenes, ImmunoglobulinGenomic LibraryHumansMiceMolecular Sequence DataNucleic Acid HybridizationOligonucleotide ProbesReceptors, Antigen, T-CellRecombination, GeneticSequence Homology, Nucleic AcidT-LymphocytesTransfectionVDJ Recombinases