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Immunoglobulin Gene Diversification ANRV260-GE39-03 ARI 21 June 2005 22:14 V I E E W R S First published online as a Review in Advance on June 21, 2005 I E N C N A D V A Immunoglobulin Gene Diversification Nancy Maizels Departments of Immunology and Biochemistry, University of Washington Medical School, Seattle, Washington 98112; email: [email protected] Annu. Rev. Genet. Key Words 2005. 39:23–46 Annu. Rev. Genet. Downloaded from arjournals.annualreviews.org antibody, deamination, mutation, recombination, repair doi: 10.1146/ by UNIVERSITY OF WASHINGTON on 09/26/05. For personal use only. annurev.genet.39.073003.110544 Abstract Copyright c 2005 by Annual Reviews. All rights Three processes alter genomic sequence and structure at the im- reserved munoglobulin genes of B lymphocytes: gene conversion, somatic hy- 0066-4197/05/1215- permutation, and class switch recombination. Though the molecular 0023$20.00 signatures of these processes differ, they occur by a shared pathway which is induced by targeted DNA deamination byaBcell–specific factor, activation induced cytidine deaminase (AID). Ubiquitous fac- tors critical for DNA repair carry out all downstream steps, creating mutations and deletions in genomic DNA. This review focuses on the genetic and biochemical mechanisms of diversification of im- munoglobulin genes. 23 ANRV260-GE39-03 ARI 21 June 2005 22:14 Contents DIVERSIFICATION CREATES A MutSα (MSH2/MSH6) and Exo1 ROBUST AND DYNAMIC Promote Switching and IMMUNE RESPONSE .......... 25 Hypermutation................ 31 MOLECULAR SIGNATURES OF UNG and MSH2 Define Two Paths Ig GENE DIVERSIFICATION . 25 to Mutagenesis ................ 32 Gene Conversion (Templated S REGIONS ARE ACTIVE Mutation) of Chicken Ig PARTNERS IN SWITCH V Regions .................... 26 RECOMBINATION............. 32 Somatic Hypermutation S Regions: A Mix of G-Rich (Nontemplated Mutation) in Repeats and Deamination Murine and Human B Cells . 26 Hotspots ..................... 32 Class Switch Recombination in G-Loops in Transcribed S Regions Mammalian B Cells ........... 26 are Deaminated by AID and A Shared Pathway Produces the Synapsed by MutSα ........... 33 Distinct Signature Outcomes of Many Factors Collaborate in Ig Gene Diversification ........ 27 Switch Recombination......... 33 AID DEAMINATES DNA DNA BREAKS AND TO INITIATE Ig GENE DIVERSIFYING Ig GENES ..... 33 DIVERSIFICATION ............ 27 Error-Prone Polymerases and AID is Expressed in Germinal Point Mutations ............... 33 Center B Cells ................ 28 A Break is Critical for Gene AID Overrides Uracil DNA Repair Conversion ................... 35 to Mutate C → UinEscherichia Breaks May Produce Somatic coli ............................ 28 Hypermutation................ 35 AID Deaminates Single-Stranded Switch Recombination Requires DNA: Transcriptional Tw o DNA Ends ............... 35 Targeting of Diversification . 29 Single-Strand Breaks, Not Hypermutation Hotspots are Double-Strand Breaks, in Deamination Hotspots......... 29 AID-Initiated Diversification . 35 PARADOXICAL MUTAGENIC TARGETING AND FUNCTIONS FOR MISTARGETING OF Annu. Rev. Genet. Downloaded from arjournals.annualreviews.org UBIQUITOUS REPAIR GENE DIVERSIFICATION. 36 by UNIVERSITY OF WASHINGTON on 09/26/05. For personal use only. FACTORS....................... 30 How is Diversification Targeted UNG Promotes Ig Gene to Ig Genes? .................. 36 Diversification ................ 30 Mistargeting: Hypermutation and NBS1 and the Translocation of MRE11/RAD50/NBS1 Proto-Oncogenes ............. 36 Complex in Ig Gene AID is But One Member of the Diversification ................ 31 APOBEC Gene Family ........ 36 24 Maizels ANRV260-GE39-03 ARI 21 June 2005 22:14 DIVERSIFICATION CREATES A These processes occur only in B cells, and ROBUST AND DYNAMIC they are regulated by developmental and envi- IMMUNE RESPONSE ronmental stimuli. They are essential, and im- Gene conversion munodeficiency results if they are impaired. The immune system must recognize an im- (templated Although the molecular signatures are dis- mense variety of different pathogens and re- mutation): tinct, all these processes are initiated by a sin- produces sequence spond dynamically as microorganisms evolve gle B cell–specific factor, activation-induced changes with during the course of infection. Toaccomplish deaminase (AID). AID is a cytidine deam- matches in germline this, lymphocytes carry out targeted and regu- donor genes or inase that carries out targeted deamination lated alterations of genomic structure and se- pseudogenes of C → Uatexpressed Ig genes. Uracil in quence. Early in B cell and T cell develop- Somatic DNA is normally repaired by conserved, ubiq- ment, antigen receptor variable (V) regions hypermutation uitous, and high-fidelity pathways, but at the are constructed by V(D)J recombination, a (nontemplated Ig genes of B lymphocytes, repair is somehow mutation): site-specific recombination process initiated diverted to ensure a mutagenic outcome. AID produces point by the lymphocyte-specific proteins RAG1 is the only B cell–specific factor involved, and mutations with no and RAG2 (8, 37), as shown in Figure 1. matches in germline downstream steps depend on ubiquitous re- Following successful V(D)J recombination, DNA pair factors that, paradoxically, promote mu- aBcell expresses an immunoglobulin (Ig) Class switch tagenesis of B cell Ig genes. This review dis- molecule composed of two distinct chains, a recombination: cusses our current mechanistic understanding heavy chain and light chain, encoded at sepa- joins a new constant of the pathways of Ig gene diversification. region to the rate alleles. The variable regions of the heavy expressed heavy and light chains together form a domain that chain variable recognizes antigen, and the heavy chain con- region, promoting MOLECULAR SIGNATURES OF stant (C) region determines how antigen is deletion of many kb Ig GENE DIVERSIFICATION removed from the body. Subsequently, B cells of chromosomal DNA increase the diversity of the repertoire and tai- The signatures of Ig gene diversification are lor Ig molecules to optimize the response to a different at different loci, in different species, specific pathogen, by modifying genomic se- and in response to distinct developmental and quence and structure of the rearranged and environmental regulation. As background, expressed Ig genes in characteristic and strik- three of the best-characterized examples are ing ways. described below. Annu. Rev. Genet. Downloaded from arjournals.annualreviews.org by UNIVERSITY OF WASHINGTON on 09/26/05. For personal use only. Figure 1 Combinatorial and mutagenic diversification of V regions. Left, combinatorial diversification at the murine κ light chain locus. In each B cell, one of many Vκ segment recombines with one of several Jκ segments to produce a functional κ variable region. Right, templated diversification at the chicken λ light chain locus. The Vλ Jλ variable region created by recombination of the single functional Vλ and Jλ segments undergoes gene conversion templated by upstream Vλ pseudogenes (ϕVλ). www.annualreviews.org • Immunoglobulin Gene Diversification 25 ANRV260-GE39-03 ARI 21 June 2005 22:14 Gene Conversion (Templated isting sequence information and inserts non- Mutation) of Chicken Ig templated (point) mutations (61, 64, 83). Hy- V Regions permutation is targeted to the transcribed V regions; the C regions and the rest of the Chickens have only a single functional light genome remain untouched. Hypermutation chain V segment, Vλ, which recombines occurs following activation with antigen, and with a single Jλ segment very early in B is coupled with selection for B cell clones that cell development. The rearranged and ex- express high-affinity antibodies. Together, hy- pressed Vλ Jλ then undergoes gene conver- permutation and clonal selection not only sion, or templated mutation. An array of increase antibody affinity, but also provide a 25 nonfunctional, “pseudo-Vλ” regions, lo- dynamic response to pathogens that are si- cated just upstream of the functional Vλ, pro- multaneously undergoing continuous muta- vide donors for sequence transfer. Diversi- tion and selection. fied Vλ regions contain tracts of sequence changes with clear matches in germline DNA (110, 127). Figure 1 compares com- Class Switch Recombination in binatorial diversification of murine V re- Mammalian B Cells gions and templated diversification of chicken V regions. Class switch recombination detaches an ex- pressed heavy chain variable (VDJ) region from one constant (C) region and joins it to Somatic Hypermutation a downstream C region, deleting the DNA (Nontemplated Mutation) in between (19, 61, 66) (Figure 2). The C Murine and Human B Cells region determines how antigen is removed from the body, and each class of C region In humans and mice, a multitude of V, D, and is specialized for clearance of specific kinds J segments recombine to create the functional of pathogens, via specific pathways (SIDE- Ig genes of the pre-immune repertoire (8, 37). BAR). Thus, switch recombination modifies Following antigen activation, the expressed how an Ig molecule removes antigen without heavy and light chain V regions are altered by affecting specificity of antigen-recognition by somatic hypermutation, which obliterates ex- literally switching C regions. Recombination junctions form within switch (S) regions, repetitive and degenerate guanine-rich re- Mammals produce four isotypes (or classes) of Ig: IgM, IgG, gions 2–10 kb in length. Recombination is µ γ ε α IgE, and IgA, encoded by the , , , and constant
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