Featured Publications
Insights into RAG Evolution from the Identification of “Missing Link” Family A RAGL Transposons
Martin E, Le Targa L, Tsakou-Ngouafo L, Fan T, Lin C, Xiao J, Huang Z, Yuan S, Xu A, Su Y, Petrescu A, Pontarotti P, Schatz D. Insights into RAG Evolution from the Identification of “Missing Link” Family A RAGL Transposons. Molecular Biology And Evolution 2023, 40: msad232. PMID: 37850912, PMCID: PMC10629977, DOI: 10.1093/molbev/msad232.Peer-Reviewed Original ResearchConceptsJawed vertebratesTransposon familyRAG1-RAG2 recombinaseRecombination signal sequencesHemichordate Ptychodera flavaMolecular domesticationSignal sequenceP. flavaDNA bindingPtychodera flavaSequence featuresTransposition activityVertebratesTransposonCritical enzymeHinge regionGenomeDomesticationFlavaProteinPivotal stepAdaptive immunityCritical intermediateRAGRAGL
2021
Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme
Liu C, Shi W, Becker ST, Schatz DG, Liu B, Yang Y. Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Science 2021, 373: 1142-1146. PMID: 34315827, PMCID: PMC9836006, DOI: 10.1126/science.abi9310.Peer-Reviewed Original ResearchConceptsCryo-electron microscopy structureRNA synthesisCoronavirus RNA synthesisNascent RNAMicroscopy structureVirus life cycleMismatch recognitionRNA substratesSubstrate specificityStructural basisMolecular mechanismsNonstructural proteinsMolecular determinantsProofreading enzymeReplication fidelityMismatch correctionAnalogue inhibitorsLife cycleExoribonucleaseExonsComplexesRNARational designProteinEnzymeSarco/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
2019
Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire
Shinoda K, Maman Y, Canela A, Schatz DG, Livak F, Nussenzweig A. Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire. Cell Reports 2019, 29: 4471-4481.e6. PMID: 31875554, PMCID: PMC8214342, DOI: 10.1016/j.celrep.2019.11.088.Peer-Reviewed Original ResearchConceptsDNA double-strand breaksRecombination signal sequencesVκ gene segmentsGene segmentsDouble-strand breaksVariable gene segmentsRAG proteinsSignal sequenceV-J rearrangementRecombination eventsSpacer regionVκ-JκRecombinationLevels of breakageComplete absenceProteinLarge fractionDeletionJκSequence
2017
New insights into the evolutionary origins of the recombination‐activating gene proteins and V(D)J recombination
Carmona LM, Schatz DG. New insights into the evolutionary origins of the recombination‐activating gene proteins and V(D)J recombination. The FEBS Journal 2017, 284: 1590-1605. PMID: 27973733, PMCID: PMC5459667, DOI: 10.1111/febs.13990.Peer-Reviewed Original ResearchConceptsTransposable elementsEvolutionary originRAG proteinsAbsence of RAG2Independent evolutionary originsBasal chordate amphioxusRecombination-activating gene (RAG) proteinsFamily of transposasesAntigen receptor genesRAG transposonChordate amphioxusJawed vertebratesSequence similarityEvolutionary relativesProteins RAG1RAG genesGene proteinRAG1Gene segmentsDiverse arrayMechanistic linkProteinRAG2Adaptive immune systemDNA cleavage reaction
2016
Collaboration of RAG2 with RAG1-like proteins during the evolution of V(D)J recombination
Carmona LM, Fugmann SD, Schatz DG. Collaboration of RAG2 with RAG1-like proteins during the evolution of V(D)J recombination. Genes & Development 2016, 30: 909-917. PMID: 27056670, PMCID: PMC4840297, DOI: 10.1101/gad.278432.116.Peer-Reviewed Original ResearchConceptsRecombination-activating gene 1Transib transposaseAbsence of RAG2RAG1/RAG2Antigen receptor genesJawed vertebratesRAG2 proteinsTransposable elementsRAG1 proteinRegulatory featuresDNA substratesGene 1RAG2Receptor geneRecombination activityProteinRecombinationTransposaseAdaptive immunityVertebratesTransposonGenesEvolutionLow levelsOrigin
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 roleMutagenesisImmunoprecipitationRepeatsRSSsRAGHistone reader BRWD1 targets and restricts recombination to the Igk locus
Mandal M, Hamel KM, Maienschein-Cline M, Tanaka A, Teng G, Tuteja JH, Bunker JJ, Bahroos N, Eppig JJ, Schatz DG, Clark MR. Histone reader BRWD1 targets and restricts recombination to the Igk locus. Nature Immunology 2015, 16: 1094-1103. PMID: 26301565, PMCID: PMC4575638, DOI: 10.1038/ni.3249.Peer-Reviewed Original Research
2014
Induction of homologous recombination between sequence repeats by the activation induced cytidine deaminase (AID) protein
Buerstedde JM, Lowndes N, Schatz DG. Induction of homologous recombination between sequence repeats by the activation induced cytidine deaminase (AID) protein. ELife 2014, 3: e03110. PMID: 25006166, PMCID: PMC4080448, DOI: 10.7554/elife.03110.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceB-LymphocytesCell LineChickensCrossing Over, GeneticCytidine DeaminaseGene ConversionGenes, ReporterGreen Fluorescent ProteinsHomologous RecombinationHumansImmunoglobulin Switch RegionLuminescent ProteinsMiceModels, GeneticMolecular Sequence DataNucleic Acid HeteroduplexesRecombinational DNA RepairRepetitive Sequences, Nucleic AcidSequence DeletionSequence Homology, Nucleic AcidSomatic Hypermutation, ImmunoglobulinConceptsHomologous recombinationCytidine deaminase proteinSequence repeatsCytidine deaminationDNA end resectionHundreds of basesAnalysis of recombinantsVertebrate cellsGene conversionRepeat recombinationEnd resectionHolliday junctionsHomologous sequencesSequence homologyReporter transgeneStrand invasionIntergenic deletionRecombinogenic activityImmunoglobulin lociRepeatsSomatic hypermutationHeteroduplex formationRecombinationProteinDeamination
2013
Cooperative recruitment of HMGB1 during V(D)J recombination through interactions with RAG1 and DNA
Little AJ, Corbett E, Ortega F, Schatz DG. Cooperative recruitment of HMGB1 during V(D)J recombination through interactions with RAG1 and DNA. Nucleic Acids Research 2013, 41: 3289-3301. PMID: 23325855, PMCID: PMC3597659, DOI: 10.1093/nar/gks1461.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesFluorescence anisotropy experimentsRAG-RSS complexesHigh mobility group box proteinAbsence of DNAGroup box proteinArchitectural proteinsPulldown experimentsRAG2 bindBox proteinSignal sequenceCooperative recruitmentComplex assemblyRecombinase complexStable integrationSequence specificitySynergistic binding effectAnisotropy experimentsAddition of DNAOrder of eventsRAG1DNAHMGB1 proteinProteinConcentration-dependent manner
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
2010
The In Vivo Pattern of Binding of RAG1 and RAG2 to Antigen Receptor Loci
Ji Y, Resch W, Corbett E, Yamane A, Casellas R, Schatz DG. The In Vivo Pattern of Binding of RAG1 and RAG2 to Antigen Receptor Loci. Cell 2010, 141: 419-431. PMID: 20398922, PMCID: PMC2879619, DOI: 10.1016/j.cell.2010.03.010.Peer-Reviewed Original ResearchConceptsJ gene segmentsRAG proteinsGene segmentsSignal sequenceLineage-specific mannerAntigen receptor lociRecombination signal sequencesLysine 4Active chromatinRAG2 bindThousands of sitesHistone 3Receptor locusDevelopmental stagesD gene segmentsDiscrete sitesCritical initial stepVivo patternRAG1BindingRAG2Beta JProteinRecombinationSpecific binding
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
2005
Biochemistry of V(D)J Recombination
Schatz DG, Spanopoulou E. Biochemistry of V(D)J Recombination. Current Topics In Microbiology And Immunology 2005, 290: 49-85. PMID: 16480039, DOI: 10.1007/3-540-26363-2_4.Peer-Reviewed Original Research
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 substratesHMG1Antigen receptor genes and the evolution of a recombinase
Schatz DG. Antigen receptor genes and the evolution of a recombinase. Seminars In Immunology 2004, 16: 245-256. PMID: 15522623, DOI: 10.1016/j.smim.2004.08.004.Peer-Reviewed Original ResearchConceptsAntigen receptor genesReceptor geneDNA repair factorsSite-specific recombination reactionRAG transposonVertebrate genomesJawed vertebratesEvolutionary implicationsRAG2 proteinsTransposable elementsRepair factorsGenesAdaptive immune systemHorizontal transmissionRAG1VertebratesGenomeImmune systemTransposonGermlineRecombinaseRAG2ProteinRecombination reactionRecombinationNew concepts in the regulation of an ancient reaction: transposition by RAG1/RAG2
Chatterji M, Tsai C, Schatz DG. New concepts in the regulation of an ancient reaction: transposition by RAG1/RAG2. Immunological Reviews 2004, 200: 261-271. PMID: 15242411, DOI: 10.1111/j.0105-2896.2004.00167.x.Peer-Reviewed Original ResearchConceptsRAG proteinsRecombination-activating gene 1Transposition activityAntigen receptor lociDNA double-stand breaksRAG1/RAG2Lymphoid-specific factorsDouble-stand breaksEndonuclease activityGene 1Chromosomal translocationsVariety of mechanismsProteinSpecific sitesRAG2Ancient reactionRecombinationRecent studiesGenome
2003
Regulation of RAG1/RAG2‐mediated transposition by GTP and the C‐terminal region of RAG2
Tsai C, Schatz DG. Regulation of RAG1/RAG2‐mediated transposition by GTP and the C‐terminal region of RAG2. The EMBO Journal 2003, 22: 1922-1930. PMID: 12682024, PMCID: PMC154477, DOI: 10.1093/emboj/cdg185.Peer-Reviewed Original ResearchConceptsFull-length RAG2RAG2 proteinsRegulatory mechanismsC-terminal regionRAG proteinsHybrid joint formationDNA recognitionDNA transpositionCleavage functionChromosomal translocationsGTPUnknown mechanismRAG2ProteinTarget DNAPhysiological concentrationsRegulationJoint formationRAGRAG1MechanismTranslocationDNAGuanineTransposition
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 dichroism