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
2020
Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination
Hirokawa S, Chure G, Belliveau NM, Lovely GA, Anaya M, Schatz DG, Baltimore D, Phillips R. Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination. Nucleic Acids Research 2020, 48: gkaa418-. PMID: 32449932, PMCID: PMC7337519, DOI: 10.1093/nar/gkaa418.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDNA CleavageLymphocytesNucleic Acid ConformationProtein Sorting SignalsReceptors, AntigenSingle Molecule ImagingV(D)J RecombinationVertebrates
2014
The architecture of the 12RSS in V(D)J recombination signal and synaptic complexes
Ciubotaru M, Surleac MD, Metskas LA, Koo P, Rhoades E, Petrescu AJ, Schatz DG. The architecture of the 12RSS in V(D)J recombination signal and synaptic complexes. Nucleic Acids Research 2014, 43: 917-931. PMID: 25550426, PMCID: PMC4333397, DOI: 10.1093/nar/gku1348.Peer-Reviewed Original Research
2013
RAG and HMGB1 create a large bend in the 23RSS in the V(D)J recombination synaptic complexes
Ciubotaru M, Trexler AJ, Spiridon LN, Surleac MD, Rhoades E, Petrescu AJ, Schatz DG. RAG and HMGB1 create a large bend in the 23RSS in the V(D)J recombination synaptic complexes. Nucleic Acids Research 2013, 41: 2437-2454. PMID: 23293004, PMCID: PMC3575807, DOI: 10.1093/nar/gks1294.Peer-Reviewed Original Research
2009
Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis
Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S, Steitz TA, Schatz DG. Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis. Nature Structural & Molecular Biology 2009, 16: 499-508. PMID: 19396172, PMCID: PMC2715281, DOI: 10.1038/nsmb.1593.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAnimalsBase SequenceChromosome PairingCrystallography, X-RayDNAFluorescence Resonance Energy TransferHomeodomain ProteinsMiceModels, MolecularMolecular Sequence DataNucleic Acid ConformationProtein MultimerizationProtein Structure, QuaternaryProtein Structure, TertiarySolutionsStatic Electricity
2007
Fluorescence Resonance Energy Transfer Analysis of Recombination Signal Sequence Configuration in the RAG1/2 Synaptic Complex
Ciubotaru M, Kriatchko AN, Swanson PC, Bright FV, Schatz DG. Fluorescence Resonance Energy Transfer Analysis of Recombination Signal Sequence Configuration in the RAG1/2 Synaptic Complex. Molecular And Cellular Biology 2007, 27: 4745-4758. PMID: 17470556, PMCID: PMC1951485, DOI: 10.1128/mcb.00177-07.Peer-Reviewed Original Research
2003
DNA mismatches and GC‐rich motifs target transposition by the RAG1/RAG2 transposase
Tsai C, Chatterji M, Schatz DG. DNA mismatches and GC‐rich motifs target transposition by the RAG1/RAG2 transposase. Nucleic Acids Research 2003, 31: 6180-6190. PMID: 14576304, PMCID: PMC275461, DOI: 10.1093/nar/gkg819.Peer-Reviewed Original Research
2002
Evidence of a critical architectural function for the RAG proteins in end processing, protection, and joining in V(D)J recombination
Tsai CL, Drejer AH, Schatz DG. Evidence of a critical architectural function for the RAG proteins in end processing, protection, and joining in V(D)J recombination. Genes & Development 2002, 16: 1934-1949. PMID: 12154124, PMCID: PMC186421, DOI: 10.1101/gad.984502.Peer-Reviewed Original ResearchAlanineAmino Acid SubstitutionAnimalsCell LineCysteineDNADNA NucleotidyltransferasesDNA-Binding ProteinsGene Rearrangement, B-LymphocyteGenes, RAG-1Glutamic AcidHomeodomain ProteinsHumansMacromolecular SubstancesMiceMutagenesis, Site-DirectedNuclear ProteinsNucleic Acid ConformationPhenotypeProtein Interaction MappingRecombinant Fusion ProteinsRecombination, GeneticRegulatory Sequences, Nucleic AcidSerineSubstrate SpecificityVDJ Recombinases
2001
Identification of Basic Residues in RAG2 Critical for DNA Binding by the RAG1-RAG2 Complex
Fugmann S, Schatz D. Identification of Basic Residues in RAG2 Critical for DNA Binding by the RAG1-RAG2 Complex. Molecular Cell 2001, 8: 899-910. PMID: 11684024, DOI: 10.1016/s1097-2765(01)00352-5.Peer-Reviewed Original ResearchConceptsDNA bindingRAG2 proteinsCognate DNA target sequenceDNA target sequencesResidue mutantsMolecular roleBasic residuesDNA cleavageTarget sequenceRAG1Biochemical analysisRAG2BindingCentral roleProteinRecombinationResiduesDirect involvementEssential componentComplexesMutantsCleavage reactionIdentificationRoleSequence
2000
Intermolecular V(D)J Recombination*
Tevelev A, Schatz D. Intermolecular V(D)J Recombination*. Journal Of Biological Chemistry 2000, 275: 8341-8348. PMID: 10722664, DOI: 10.1074/jbc.275.12.8341.Peer-Reviewed Original Research