Synopses & Reviews
V(D)J Recombination: for the community of immunologists and developmental biologists, the molecular route by which B and T lymphocytes acquire their unique function of affording adaptive immunity. Yet, for many--from experienced scientists to trainees--it represents a (rather too) sophisticated process whose true insight is excessively demanding. However, when not simply considered as a private ground for a few aficionados, it can be seen as a way of understanding how mature lymphocytes carry on their basic functions. For the group of aficionados--which includes this editor--it is an elegant paradigm featuring many fascinating evolutionary achievements of which the biological world alone has the secret. These include a subtle biochemical principle most likely hijacked some 470 million years ago from an ancestral gene invader and since then cleverly adapted by jawed vertebrates to precisely cleave and rearrange their antigen receptor (Ig and TCR) loci. This invader would itself have assigned the services of the nonhomologous end joining (NHEJ) DNA repair machinery as well as various DNA polymerases or transferases to work in concert with developmental clues in lymphoid cell lineages to generate an immune repertoire and efficient host surveillance while avoiding autoimmunity. Recently, important new refinements in these systems have emerged, continuing to challenge our knowledge and beliefs. These are just the topics covered by the senior authors--all established leaders in this field--and their colleagues, whilst writing the various chapters in this book. They lead us through the latest findings concerning the biochemical properties of the V(D)J recombinase (Swanson), it's buried and potentially harmful transposase and translocase activities (Oettinger; Roth), the increasing importance of NHEJ whose dysfunction causes severe forms of immune deficiencies (de Villartay), and the numerous facets in the control of gene rearrangement via non-coding RNA transcription and exquisitely regulated changes in chromosomal structure (Corcoran; Feeney; Jouvin-Marche; Krangel; Oltz and Spicuglia). Burning progress on regulatory aspects has included the large-scale dynamics and nuclear compartmentalization of Ig and TCR loci (Singh), the anticipated--but difficult to ascertain--role of dedicated transcription factors (Zhang), the relationships between structural properties of the recombination core apparatus and its cell cycle phase-dependant accumulation/degradation or connection to the chromatin template (Desiderio), the evolution of these regulatory aspects throughout the phylogeny (Hsu), and how abnormalities in the recombination apparatus/process can contribute to lymphoid malignancies (Macintyre). Overall, this book represents a tour over this, in all respects, vital process and I would like to greatly acknowledge the efforts of these eminent colleagues for concisely describing its so many aspects. We believe that every advance in this field contributes to strengthening knowledge of fundamental importance both academically and clinically. Together, we hope that the result is an attractive book which will captivate its readers and encourage some to pursue further digging in this seemingly inexhaustible mine of biological resources.
Synopsis
V(D)J Recombination: for the community of immunologists and developmental biologists, the molecular route by which B and T lymphocytes acquire their unique function of affording adaptive immunity. Yet, for many--from experienced scientists to trainees--it represents a (rather too) sophisticated process whose true insight is excessively demanding. However, when not simply considered as a private ground for a few aficionados, it can be seen as a way of understanding how mature lymphocytes carry on their basic functions. For the group of aficionados--which includes this editor--it is an elegant paradigm featuring many fascinating evolutionary achievements of which the biological world alone has the secret. These include a subtle biochemical principle most likely hijacked some 470 million years ago from an ancestral gene invader and since then cleverly adapted by jawed vertebrates to precisely cleave and rearrange their antigen receptor (Ig and TCR) loci. This invader would itself have assigned the services of the nonhomologous end joining (NHEJ) DNA repair machinery as well as various DNA polymerases or transferases to work in concert with developmental clues in lymphoid cell lineages to generate an immune repertoire and efficient host surveillance while avoiding autoimmunity.
Synopsis
V(D)J Recombination: for the community of immunologists and developmental biologists, the molecular route by which B and T lymphocytes acquire their unique function of affording adaptive immunity. Yet, for many--from experienced scientists to trainees--it represents a (rather too) sophisticated process whose true insight is excessively demanding. However, when not simply considered as a private ground for a few aficionados, it can be seen as a way of understanding how mature lymphocytes carry on their basic functions. For the group of aficionados--which includes this editor--it is an elegant paradigm featuring many fascinating evolutionary achievements of which the biological world alone has the secret. These include a subtle biochemical principle most likely hijacked some 470 million years ago from an ancestral gene invader and since then cleverly adapted by jawed vertebrates to precisely cleave and rearrange their antigen receptor (Ig and TCR) loci. This invader would itself have assigned the services of the nonhomologous end joining (NHEJ) DNA repair machinery as well as various DNA polymerases or transferases to work in concert with developmental clues in lymphoid cell lineages to generate an immune repertoire and efficient host surveillance while avoiding autoimmunity.
About the Author
PIERRE FERRIER is a Principal Investigator and Research Director at the Centre d'Immunologie de Marseille-Luminy (CIML), France. He has also worked as a Director of Marseille-Nice Genopole, a local consortium of more than twenty laboratories aimed at developing high-throughput research techniques in genomics. Main research interests include the analysis of the molecular mechanisms responsible for the control of gene expression and recombination programs during hematopoietic cell development and pathogenesis. He is a member of several national and international scientific organizations including the Institut National de la Santé et de la Recherche Médicale (Inserm), the Agence Nationale de la Recherche (ANR), the Association pour la Recherche sur le Cancer (ARC), the Human Frontier Science Program Organization (HFSPO), and the Université Virtuelle Médicale de Monaco (UVMM). Pierre Ferrier received his academic degrees from Montpellier (MD) and Marseille (PhD) Universities, France. He was a post-doctoral fellow (1986-90) in the laboratory of Prof. F.W. Alt at the Columbia University College of Physicians and Surgeons, New York, NY, USA.
Table of Contents
1. Early Steps of V(D)J Rearangement: Insights from Biochemical Studies of RAG-RSS Complexes..... 1 Patrick C. Swanson, Sushil Kumar and Prafulla Raval Abstract..... 1 Introduction..... 1 Assembly and Organization of Single Site and Synaptic RAG-RSS Complexes..... 3 Insights into RAG-Mediated RSS Recognition and Cleavage Mechanisms..... 5 Elements Guiding Enforcement of the 12/23 Rule..... 8 Transcription Factor-Assisted Targeting of Antigen Receptor Loci..... 10 Conclusions and Future Directions..... 11 2. Regulation of RAG Transposition..... 16 Adam G.W. Matthews and Marjorie A. Oettinger Abstract..... 16 Introduction..... 16 Biochemistry of V(D)J Recombination..... 16 Overview of RAG Transposition..... 19 Regulation of RAG Transposition..... 24 Current Understanding of how RAG Transposition is Regulated..... 24 Additional Potential Regulatory Mechanisms..... 25 Summary..... 27 3. Recent Insights into the Formation of RAG-Induced Chromosomal Translocations..... 32 Vicky L. Brandt and David B. Roth Abstract..... 32 Introduction..... 32 Overview of the V(D)J Recombination Reaction..... 33 Potential Mechanisms of RAG-Mediated Translocations..... 34 Mistaken Identities: Substrate Selection Errors..... 34 The Ends that Got Away: Errors in Joining..... 36 4. V(D)J Recombination Deficiencies..... 46 Jean-Pierre de Villartay Abstract..... 46 Introduction..... 46 RAG1 and RAG2 Deficiencies..... 47 T-B-SCID with Radiosensitivity..... 50 5. Large-Scale Chromatin Remodeling at the Immunoglobulin Heav y Chain Locus: A Paradigm for Multigene Regulation..... 59 Daniel J. Bolland, Andrew L. Wood and Anne E. Corcoran Abstract..... 59 Introduction..... 60 Chromatin Remodeling..... 62 Intergenic Transcription..... 63 Intergenic Transcription in the Mouse Igh Locus V Region..... 63 Antisense Transcription..... 64 Antisense Transcription in the Igh Locus V Region..... 64 Antisense and Intergenic Transcription in the Igh D Region..... 66 Subnuclear Relocalisation..... 66 3-Dimensional Alterations in Chromatin Structure..... 67 Transcription Factories..... 68 Biased Recombination Frequency Explainedby Numerous Mechanisms..... 68 Allelic Choice and Allelic Exclusion..... 68 Other Antigen Receptor Loci..... 69 Future Directions..... 69 6. Genetic and Epigenetic Control of V Gene Rearangement Frequency..... 73 Ann J. Feeney Abstract..... 73 Introduction..... 73 Sequence Variation in RSS Can Greatly Affect Recombination..... 74 RSS Is Not Always Responsible for Unequal Rearrangement.....75 Chromatin as the Gatekeeper of Accessibility..... 75 Role of Transcription Factors in Controlling Rearrangement..... 77 Conclusions..... 79 7. Dynamic aspects of TCRa gene recombination: qualitative and quantitative assessments of the TCRa chain repertoire in Man and mouse..... 82 Evelyne Jouvin-Marche, Patrizia Fuschiotti and Patrice Noël Marche Abstract..... 82 Introduction..... 82 Complexity of mouse and human TCRAD locus..... 83 Analysis of human and mouse TCRA-chain diversity..... 84 Comparison between the frequencies of rearrangements in thymus and peripheral T-lymphocytes..... 85 The size of the mouse and human TCRa repertoire..... 87 Conclusion..... 90 8. Germline Transcription: A Key Regulator of Accessibility and Recombination..... 93 Iratxe Abarrategui and Michael S. Krangel Abstract..... 93 Introduction..... 93 A Brief History of Germline Transcription and V(D)J Recombination..... 94 Disruption of Chromatin by Transcription..... 95 Regulation of V(D)J Recombination by Transcription..... 97 Future Directions..... 99 9. Dynamic Regulation of Antigen Receptor Gene Assembly..... 103 Lance R. Thomas, Robin Milley Cobb and Eugene M. Oltz Abstract..... 103 Introduction..... 103 Developmental Control of V(D)J Recombination..... 104 Genetic Control of Recombinase Accessibility..... 105 Chromatin Accessibility Control Mechanisms for V(D)J Recombination..... 107 Control of V(D)J Recombination by Nuclear Compartmentalization..... 109 Primary Activation of Antigen Receptor Loci for D to J Rearrangement..... 109 Long-Range Control of V(D)J Recombination.....111 Allelic Exclusion.....111 Concluding Remarks..... 113 10. Molecular Genetics at the T-Cell Receptor b Locus: Insights into the Regulation of V(D)J Recombination.....116 Marie Bonnet, Pierre Ferrier and Salvatore Spicuglia Abstract..... 116 Introduction..... 116 Overview of the Tcrb Genomic Structure and Recombination Properties.....117 Tcrb-RSSs and Rearrangement Efficiency..... 117 Cis-Regulatory Elements at the Tcrb Locus..... 119 Trans-Regulators of Tcrb Locus Expression/Recombination..... 122 Chromatin Accessibility..... 123 Allelic Exclusion at the Tcrb Locus..... 126 Conclusion and Future Direction.....128 11. Molecular Pa thways and Mechanisms Regulating the Recombination of Immunoglobulin Genes during B-Lymphocyte Development..... 133 Kristen Johnson, Karen L. Reddy and Harinder Singh Abstract..... 133 Introduction..... 133 B-Cell Fate Specification and the Joining of D-to-JH Segments..... 137 B-Cell Fate Commitment and V-to-DJH Rearrangement..... 138 The Pre-B-Cell Checkpoint and the Induction of Light-Chain Recombination..... 141 Allelic Exclusion..... 143 Perspectives..... 144 12. Regulation of V(D)J recombinationby E-protein transcription factors..... 148 Mary Elizabeth Jones and Yuan Zhuang Abstract..... 148 Introduction..... 148 Transcriptional Control of Ig and TCR Antigen Receptor and Their Associated Genes..... 149 Induction of Ig and TCR Gene Rearrangement..... 150 Regulation of the Developmental Window for V(D)J Recombination.....150 Concluding Remarks..... 153 13. Temporal and Spatial Regulation of V(D)J Recombination: Interactions of Extrinsic Factors with the RAG Complex..... 157 Yun Liu, Li Zhang and Stephen Desiderio Abstract..... 157 Functional Organization of RAG-1 and RAG-2..... 157 Temporal Regulation of V(D)J Recombination through Interactions with the RAG-2 Non-Core Region..... 158 Locus Specificity: General Remarks..... 159 Epigenetic Modifications of Possible Relevance to V(D)J Recombination..... 159 DNA Methylation..... 159 Nucleosome Phasing..... 159 Histone Acetylation..... 160 Histone H3 K9 Methylation..... 160 Histone H3 K4 Methylation.....160 Direct Recognition of Modified Histone H3 by the V(D)J Recombinase..... 160 Evidence for Allosteric Regulation of V(D)J Recombinase Activity by Histone H3 Trimethylated at Lysine 4..... 161 Future Directions: Deposition and Integration of Epigenetic Signals Controlling V(D)J Recombination..... 162 14. V(D)J Recombination: Of Mice and Sharks..... 166 Ellen Hsu Abstract..... 166 Introduction..... 166 V(D)J Rearrangement..... 168 V(D)J Rearrangement Patterns..... 172 Rabbit..... 172 Multiple IgH Loci in Other Vertebrate Species..... 173 Summary..... 176 15. Normal and Pa thological V(D)J Recombination: Contribution to the Understanding of Human Lymphoid Malignancies..... 180 Saïda Dadi, Sandrine Le Noir, Vahid Asnafi, Kheïra Beldjord and Elizabeth A. Macintyre Abstract..... 180 Introduction..... 180 Diagnostic Clonality Analysis..... 181 Recombinase Mediated Oncogenesis..... 185 Conclusion..... 190