Featured Publications
Transposon molecular domestication and the evolution of the RAG recombinase
Zhang Y, Cheng TC, Huang G, Lu Q, Surleac MD, Mandell JD, Pontarotti P, Petrescu AJ, Xu A, Xiong Y, Schatz DG. Transposon molecular domestication and the evolution of the RAG recombinase. Nature 2019, 569: 79-84. PMID: 30971819, PMCID: PMC6494689, DOI: 10.1038/s41586-019-1093-7.Peer-Reviewed Original ResearchConceptsRAG1-RAG2 recombinaseMolecular domesticationRAG recombinaseCryo-electron microscopy structureTwo-tiered mechanismAmino acid residuesJawed vertebratesMicroscopy structureEvolutionary adaptationDNA substratesTransposition activityAcid residuesDomesticationDNA cleavageAcidic regionDiverse repertoireAdaptive immune systemRecombinaseTransposonCell receptorTransposasePivotal eventRecombinationCleavageVertebrates
2024
The Role of RAG in V(D)J Recombination
Xiao J, Martin E, Wang K, Schatz D. The Role of RAG in V(D)J Recombination. 2024 DOI: 10.1016/b978-0-128-24465-4.00019-3.Peer-Reviewed Original ResearchRecombination signal sequencesRecombination activating geneV(D)J recombinationDNA cleavageConserved sequence elementsNonhomologous end-joining pathwayLymphoid-specific proteinsAntigen receptor gene segmentsEnd-joining pathwayPair of hairpinsReceptor gene segmentsTransposable elementsDomain architectureSequence elementsLocus structureSignal sequenceTransposition mechanismTranscriptional regulationJawed vertebratesTransposase activityActive genesPosttranslational modificationsEnhancer elementsProtein structureCell cycle
2021
Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) activity is required for V(D)J recombination
Chen CC, Chen BR, Wang Y, Curman P, Beilinson HA, Brecht RM, Liu CC, Farrell RJ, de Juan-Sanz J, Charbonnier LM, Kajimura S, Ryan TA, Schatz DG, Chatila TA, Wikstrom JD, Tyler JK, Sleckman BP. Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) activity is required for V(D)J recombination. Journal Of Experimental Medicine 2021, 218: e20201708. PMID: 34033676, PMCID: PMC8155808, DOI: 10.1084/jem.20201708.Peer-Reviewed Original ResearchConceptsRAG2 gene expressionSarco/endoplasmic reticulum Ca2Gene expressionEndoplasmic reticulum Ca2ER Ca2ER transmembrane proteinExpression of SERCA3Mature B cellsER lumenCytosolic Ca2Transmembrane proteinCRISPR/PreB cellsDNA cleavageB cellsReticulum Ca2SERCA proteinATPase activityProteinProfound blockATP2A2 mutationsRAG1Recombination
2018
DNA melting initiates the RAG catalytic pathway
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H. DNA melting initiates the RAG catalytic pathway. Nature Structural & Molecular Biology 2018, 25: 732-742. PMID: 30061602, PMCID: PMC6080600, DOI: 10.1038/s41594-018-0098-5.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesDNA meltingCryo-EM structureBase-specific contactsSignal sequenceDNA transpositionSubstrate bindingRetroviral integrationRAG endonucleaseDimer openingTerminal sequenceGTG sequenceDNA cleavageScissile phosphateDNAUniversal mechanismPiston-like movementSequenceActive siteHeptamerRetrotransposonsCatalytic pathwayTransposonComplexesEndonuclease
2016
The Role of RAG in V(D)J Recombination
Carmona L, Schatz D. The Role of RAG in V(D)J Recombination. 2016, 99-106. DOI: 10.1016/b978-0-12-374279-7.05012-8.Peer-Reviewed Original ResearchRecombination signal sequencesTransposable elementsCell cycle-dependent mannerAntigen receptor gene segmentsLymphoid-specific proteinsDNA cleavageCycle-dependent mannerReceptor gene segmentsRAG cleavageRAG proteinsTranslational regulationPosttranslational modificationsSignal sequenceNonhomologous endRAG activitySequence elementsEnhancer elementsTransposition mechanismCell cycleLymphocyte developmentGene segmentsPair of hairpinsBlunt endsRecombinationRAG2
2015
Recruitment of RAG1 and RAG2 to Chromatinized DNA during V(D)J Recombination
Shetty K, Schatz DG. Recruitment of RAG1 and RAG2 to Chromatinized DNA during V(D)J Recombination. Molecular And Cellular Biology 2015, 35: 3701-3713. PMID: 26303526, PMCID: PMC4589606, DOI: 10.1128/mcb.00219-15.Peer-Reviewed Original ResearchConceptsConserved heptamerRAG2 proteinsChromatin immunoprecipitationNonamer elementsRecombination substratesSignal sequenceNonamer sequencesMutant formsCryptic RSSsRAG1DNA cleavageGene segmentsChromatinCell linesRAG2ProteinRecruitmentRecombinationSequenceMajor roleMutagenesisImmunoprecipitationRepeatsRSSsRAGSingle-molecule analysis of RAG-mediated V(D)J DNA cleavage
Lovely GA, Brewster RC, Schatz DG, Baltimore D, Phillips R. Single-molecule analysis of RAG-mediated V(D)J DNA cleavage. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: e1715-e1723. PMID: 25831509, PMCID: PMC4394307, DOI: 10.1073/pnas.1503477112.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesSingle-molecule assaysSame DNA moleculeAntigen receptor genesConsensus recombination signal sequencesSingle-molecule analysisHigh mobility group box protein 1Individual molecular eventsSignal sequenceSingle-molecule levelGene productsDNA bindingMolecular eventsLymphocyte developmentDNA moleculesDNA cleavageProtein 1Synapse formationSynaptic complexReceptor geneCleavageRAGAssaysRAG1/2ComplexesMapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2* ♦
Zhang YH, Shetty K, Surleac MD, Petrescu AJ, Schatz DG. Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2* ♦. Journal Of Biological Chemistry 2015, 290: 11802-11817. PMID: 25745109, PMCID: PMC4424321, DOI: 10.1074/jbc.m115.638627.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCatalytic DomainDNA-Binding ProteinsGene Expression RegulationGenome, HumanHEK293 CellsHomeodomain ProteinsHumansInterferometryMaleMiceMice, Inbred C57BLMolecular Sequence DataMutationNuclear ProteinsProtein BindingProtein Interaction MappingProtein Structure, SecondaryThymus GlandV(D)J RecombinationVDJ RecombinasesConceptsRegion of RAG1Α-helixZinc finger regionResidues N-terminalActive siteAcidic amino acidsPulldown assaysAccessory factorsHermes transposaseProteins RAG1Finger regionRAG activityQuantitative Western blottingC-terminusRAG endonucleaseN-terminalCatalytic functionRAG1Amino acidsDNA cleavageRAG2Nuclear concentrationRecombination activityCatalytic centerBiolayer interferometryChapter 2 The Mechanism of V(D)J Recombination
Little A, Matthews A, Oettinger M, Roth D, Schatz D. Chapter 2 The Mechanism of V(D)J Recombination. 2015, 13-34. DOI: 10.1016/b978-0-12-397933-9.00002-3.ChaptersLymphocyte developmentNonhomologous end-joining pathwayRegulation of recombinationAntigen receptor lociEnd-joining pathwayDNA repair proteinsRecombination-activating gene 1RAG proteinsDNA breaksRecombinase machineryFunctional antigen receptorEnd processingReceptor locusGenetic instabilityGene 1Recombinase activityChromosomal translocationsDNA cleavageProtein 1Diverse repertoireRepair stepsBox protein 1Antigen receptorHigh mobility group box protein 1Recombination
2011
V(D)J Recombination: Mechanisms of Initiation
Schatz DG, Swanson PC. V(D)J Recombination: Mechanisms of Initiation. Annual Review Of Genetics 2011, 45: 167-202. PMID: 21854230, DOI: 10.1146/annurev-genet-110410-132552.Peer-Reviewed Original ResearchConceptsProtein-DNA complexesUbiquitin ligase activityHistone recognitionDomain organizationRAG proteinsRAG2 proteinsLigase activityT-cell receptor genesRecombination signalsDNA breaksHeptamer sequenceLymphocyte developmentDNA breakageDNA cleavageGene segmentsFunctional significanceProper repairReceptor geneRAG1ProteinRecombinationMechanism of initiationComplexesRecent advancesGenes
2007
The Beyond 12/23 Restriction Is Imposed at the Nicking and Pairing Steps of DNA Cleavage during V(D)J Recombination
Drejer-Teel AH, Fugmann SD, Schatz DG. The Beyond 12/23 Restriction Is Imposed at the Nicking and Pairing Steps of DNA Cleavage during V(D)J Recombination. Molecular And Cellular Biology 2007, 27: 6288-6299. PMID: 17636023, PMCID: PMC2099602, DOI: 10.1128/mcb.00835-07.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesDNA cleavageGene segmentsDNA cleavage stepRecombination-activating gene 1Dbeta gene segmentVariable region exonsJbeta gene segmentsRAG proteinsDNA elementsSignal sequenceDirect VbetaRegion exonsGene 1Oligonucleotide substratesLocus sequenceDistinct combinationsProteinRecombinationCleavageNickingCleavage stepSequenceDifferent stepsExons
2006
Mobilization of RAG-Generated Signal Ends by Transposition and Insertion In Vivo
Chatterji M, Tsai CL, Schatz DG. Mobilization of RAG-Generated Signal Ends by Transposition and Insertion In Vivo. Molecular And Cellular Biology 2006, 26: 1558-1568. PMID: 16449665, PMCID: PMC1367191, DOI: 10.1128/mcb.26.4.1558-1568.2006.Peer-Reviewed Original ResearchConceptsRAG proteinsVertebrate cellsTransposition eventsEnd fragmentsFull-length RAG2Embryonic kidney cell lineHuman embryonic kidney cell lineTarget site duplicationsGenome instabilityHuman genomeSignal endsKidney cell lineGenomic instabilityTranslocation eventsSite duplicationsChromosomal translocationsDNA cleavageComplex rearrangementsChromosome deletionsEssential roleProteinCell linesEpisomesDeletionAssays
2004
Synapsis of Recombination Signal Sequences Located in cis and DNA Underwinding in V(D)J Recombination
Ciubotaru M, Schatz DG. Synapsis of Recombination Signal Sequences Located in cis and DNA Underwinding in V(D)J Recombination. Molecular And Cellular Biology 2004, 24: 8727-8744. PMID: 15367690, PMCID: PMC516766, DOI: 10.1128/mcb.24.19.8727-8744.2004.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesDNA substratesSignal sequenceDNA distortionHigh mobility group proteinsProtein conformational changesSame DNA moleculeDouble-strand DNA cleavageRAG proteinsRAG2 proteinsDNA underwindingGroup proteinsSite of cleavagePreferred substrateConformational changesDNA moleculesDNA cleavageProteinRelaxed substrateUnderwindingRecombinationCleavageSequenceSuch substratesHMG1
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
1999
Detection of RAG Protein-V(D)J Recombination Signal Interactions Near the Site of DNA Cleavage by UV Cross-Linking
Eastman Q, Villey I, Schatz D. Detection of RAG Protein-V(D)J Recombination Signal Interactions Near the Site of DNA Cleavage by UV Cross-Linking. Molecular And Cellular Biology 1999, 19: 3788-3797. PMID: 10207102, PMCID: PMC84213, DOI: 10.1128/mcb.19.5.3788.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesRAG proteinsRAG2 proteinsDNA cleavageHeptamer elementSite of cleavageActive site organizationRAG1-RAG2RAG1 proteinSignal sequenceDouble-strand cleavageSite-specific interactionsSame nucleotideRecognition surfaceProteinRAG1UV CrossSignal interactionsSite organizationCleavageSequenceComplexesSitesClose proximityNucleotides
1998
Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system
Agrawal A, Eastman Q, Schatz D. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 1998, 394: 744-751. PMID: 9723614, DOI: 10.1038/29457.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsAntibodiesBinding SitesB-LymphocytesCatalysisCell LineDNADNA Transposable ElementsDNA, CircularDNA-Binding ProteinsDrug Resistance, MicrobialEvolution, MolecularGene Rearrangement, B-LymphocyteGene Rearrangement, T-LymphocyteHigh Mobility Group ProteinsHomeodomain ProteinsImmune SystemMiceMolecular Sequence DataReceptors, Antigen, T-CellRecombination, GeneticRestriction MappingTransposasesVertebratesConceptsT-cell receptor genesRecombination signalsSequence-specific DNA recognitionAncestral receptor geneComponent gene segmentsSite-specific recombination reactionPiece of DNAEvolutionary divergenceJawless vertebratesRecombination-activating geneTransposable elementsDNA recognitionRetroviral integrationGermline insertionDNA moleculesGenesShort duplicationsDNA cleavageRAG1Gene segmentsTransposition reactionRAG2Receptor geneTarget DNA moleculesTarget DNA
1997
Nicking is asynchronous and stimulated by synapsis in 12/23 rule-regulated V(D)J cleavage
Eastman Q, Schatz D. Nicking is asynchronous and stimulated by synapsis in 12/23 rule-regulated V(D)J cleavage. Nucleic Acids Research 1997, 25: 4370-4378. PMID: 9336470, PMCID: PMC147051, DOI: 10.1093/nar/25.21.4370.Peer-Reviewed Original Research
1996
RAG1 Mediates Signal Sequence Recognition and Recruitment of RAG2 in V(D)J Recombination
Difilippantonio M, McMahan C, Eastman Q, Spanopoulou E, Schatz D. RAG1 Mediates Signal Sequence Recognition and Recruitment of RAG2 in V(D)J Recombination. Cell 1996, 87: 253-262. PMID: 8861909, DOI: 10.1016/s0092-8674(00)81343-4.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCell LineDNA NucleotidyltransferasesDNA-Binding ProteinsGenes, ImmunoglobulinHomeodomain ProteinsHumansMacromolecular SubstancesMolecular Sequence DataNuclear ProteinsProtein BindingProteinsRecombinant ProteinsRecombination, GeneticSalmonellaSequence AlignmentStructure-Activity RelationshipTranscriptional ActivationTransfectionConceptsDNA bindingAbsence of RAG2Signal sequence recognitionRegion of RAG1RAG2 proteinsBacterial invertasesSequence similarityRecombination signalsSpecific binding interactionsRAG1Sequence recognitionDNA cleavageRAG2Binding interactionsProteinBindingRecombinationRecent studiesSignal recognitionInvertaseHeptamerRecruitmentCleavageLocalizationVivo