Transposon Molecular Domestication and the Evolution of the RAG Recombinase

[1]  F. Alt,et al.  DNA melting initiates the RAG catalytic pathway , 2018, Nature Structural & Molecular Biology.

[2]  S. Desiderio,et al.  The RAG-2 Inhibitory Domain Gates Accessibility of the V(D)J Recombinase to Chromatin , 2018, Molecular and Cellular Biology.

[3]  Z. Zhou,et al.  Cracking the DNA Code for V(D)J Recombination. , 2018, Molecular cell.

[4]  E. Betrán,et al.  Transposable Element Domestication As an Adaptation to Evolutionary Conflicts. , 2017, Trends in genetics : TIG.

[5]  E. Koonin,et al.  Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery. , 2017, Current opinion in microbiology.

[6]  D. Schatz,et al.  New insights into the evolutionary origins of the recombination‐activating gene proteins and V(D)J recombination , 2017, The FEBS journal.

[7]  Marius A. Micluţa,et al.  Roles of the C-terminal domains of topoisomerase IIα and topoisomerase IIβ in regulation of the decatenation checkpoint , 2017, Nucleic acids research.

[8]  D. Agard,et al.  MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy , 2017, Nature Methods.

[9]  A. Xu,et al.  The RAG transposon is active through the deuterostome evolution and domesticated in jawed vertebrates , 2017, bioRxiv.

[10]  D. Schatz,et al.  Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination , 2016, Cell.

[11]  E. Lindahl,et al.  Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 , 2016, bioRxiv.

[12]  Richard L. Frock,et al.  Detecting DNA double-stranded breaks in mammalian genomes by linear amplification–mediated high-throughput genome-wide translocation sequencing , 2016, Nature Protocols.

[13]  Hao Wu,et al.  Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures , 2015, Cell.

[14]  C. Mason,et al.  Genomic DNA transposition induced by human PGBD5 , 2015, bioRxiv.

[15]  Kai Zhang,et al.  Gctf: Real-time CTF determination and correction , 2015, bioRxiv.

[16]  Min-Sung Kim,et al.  Assembly Pathway and Characterization of the RAG1/2-DNA Paired and Signal-end Complexes* , 2015, The Journal of Biological Chemistry.

[17]  D. Schatz,et al.  Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2*♦ , 2015, The Journal of Biological Chemistry.

[18]  Matthias J. Brunner,et al.  Atomic accuracy models from 4.5 Å cryo-electron microscopy data with density-guided iterative local refinement , 2015, Nature Methods.

[19]  Min-Sung Kim,et al.  Crystal structure of the V(D)J recombinase RAG1–RAG2 , 2015, Nature.

[20]  Nathaniel Echols,et al.  EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy , 2015, Nature Methods.

[21]  S. Desiderio,et al.  An autoregulatory mechanism imposes allosteric control on the V(D)J recombinase by histone H3 methylation. , 2015, Cell reports.

[22]  F. Alt,et al.  Molecular biology of B cells , 2015 .

[23]  S. Lewis,et al.  The Origin of V(D)J Diversification , 2015 .

[24]  D. Roth,et al.  RAG2's acidic hinge restricts repair-pathway choice and promotes genomic stability. , 2013, Cell reports.

[25]  Janusz M. Bujnicki,et al.  QA-RecombineIt: a server for quality assessment and recombination of protein models , 2013, Nucleic Acids Res..

[26]  A. Petrescu,et al.  Structural Determinants at the Interface of the ARC2 and Leucine-Rich Repeat Domains Control the Activation of the Plant Immune Receptors Rx1 and Gpa21[C][W][OA] , 2013, Plant Physiology.

[27]  D. Rio,et al.  The Human THAP9 Gene Encodes an Active P-Element DNA Transposase , 2013, Science.

[28]  Sjors H.W. Scheres,et al.  RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[29]  D. Schatz,et al.  A Dual Interaction between the DNA Damage Response Protein MDC1 and the RAG1 Subunit of the V(D)J Recombinase* , 2012, The Journal of Biological Chemistry.

[30]  D. Schatz,et al.  V(D)J recombination: mechanisms of initiation. , 2011, Annual review of genetics.

[31]  J. V. Moran,et al.  Dynamic interactions between transposable elements and their hosts , 2011, Nature Reviews Genetics.

[32]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[33]  S. Fugmann.  The origins of the Rag genes--from transposition to V(D)J recombination. , 2010, Seminars in immunology.

[34]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[35]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[36]  D. Schatz,et al.  Structure of the RAG1 nonamer-binding domain with DNA reveals a dimer that mediates DNA synapsis , 2009, Nature Structural &Molecular Biology.

[37]  Z. Izsvák,et al.  Molecular domestication of transposable elements: From detrimental parasites to useful host genes , 2009, Cellular and Molecular Life Sciences.

[38]  Leonardo G. Trabuco,et al.  Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. , 2008, Structure.

[39]  J. Danska,et al.  Chromosomal reinsertion of broken RSS ends during T cell development , 2007, The Journal of experimental medicine.

[40]  Barbara Corneo,et al.  Rag mutations reveal robust alternative end joining , 2007, Nature.

[41]  P. Swanson,et al.  Identification and Characterization of a Gain-of-Function RAG-1 Mutant , 2006, Molecular and Cellular Biology.

[42]  D. Ramsden,et al.  Genomic instability due to V(D)J recombination-associated transposition. , 2006, Genes & development.

[43]  D. Schatz,et al.  Mobilization of RAG-Generated Signal Ends by Transposition and Insertion In Vivo , 2006, Molecular and Cellular Biology.

[44]  P. Swanson,et al.  RAG and HMGB1 proteins: purification and biochemical analysis of recombination signal complexes. , 2006, Methods in enzymology.

[45]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[46]  J. Jurka,et al.  RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons , 2005, PLoS biology.

[47]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[48]  D. Schatz,et al.  New concepts in the regulation of an ancient reaction: transposition by RAG1/RAG2 , 2004, Immunological reviews.

[49]  M. Gellert,et al.  The taming of a transposon: V(D)J recombination and the immune system , 2004, Immunological reviews.

[50]  J. Nicklas,et al.  In vivo transposition mediated by V(D)J recombinase in human T lymphocytes , 2003, The EMBO journal.

[51]  G. S. Lee,et al.  The V(D)J recombinase efficiently cleaves and transposes signal joints. , 2002, Molecular cell.

[52]  M. Gellert.  V(D)J recombination: RAG proteins, repair factors, and regulation. , 2002, Annual review of biochemistry.

[53]  M. Gellert,et al.  DNA Transposition by the RAG1 and RAG2 Proteins A Possible Source of Oncogenic Translocations , 1998, Cell.

[54]  David G. Schatz,et al.  Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system , 1998, Nature.

[55]  D. Schatz,et al.  Mechanism of V(D)J recombination. , 1996, Current opinion in immunology.

[56]  C. Thompson,et al.  New insights into V(D)J recombination and its role in the evolution of the immune system. , 1995, Immunity.

[57]  S. Lewis,et al.  The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. , 1994, Advances in immunology.

[58]  Y. Shoenfeld,et al.  [The T cell receptor]. , 1985, Harefuah.

[59]  Hitoshi Sakano,et al.  Sequences at the somatic recombination sites of immunoglobulin light-chain genes , 1979, Nature.

[60]  L. Sinzellea,et al.  Molecular domestication of transposable elements : From detrimental parasites to useful host genes , 2022 .