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  • Review Article
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Immunoglobulin class-switch DNA recombination: induction, targeting and beyond

Nature Reviews Immunology volume 12, pages 517–531 (2012)Cite this article

Subjects

Key Points

  • T cell-dependent and T cell-independent primary class-switch DNA recombination (CSR)-inducing stimuli induce activation-induced cytidine deaminase (AID) in a B cell differentiation stage-specific manner. AID expression is further enhanced by secondary CSR-inducing stimuli — namely, interleukin-4, transforming growth factor-β and interferon-γ — through interplay between transcription factors.

  • Targeting of the CSR machinery is made possible by the specific richness of 5′-AGCT-3′ repeats in all S regions and the high avidity of 14-3-3 adaptors for such repeats. Targeting is orchestrated by germline IH-S-CH transcription and epigenetic changes in the S regions that are to undergo recombination; these processes are induced by primary and secondary CSR-inducing stimuli.

  • Histone modifications and factors involved in germline IH-S-CH transcription have an important and active role in the recruitment of 14-3-3 adaptors and AID to S region DNA and in the stabilization of these CSR factors.

  • Proper adaptors (such as 14-3-3 proteins and replication protein A), which do not possess enzymatic activity, function as scaffold proteins for other CSR factors. In addition, enzymes (such as REV1) can function as scaffold elements in CSR.

  • Scaffold proteins that can directly interact with modified histones transduce crucial epigenetic information to AID and other enzymatic effectors of CSR.

Abstract

Class-switch DNA recombination (CSR) of the immunoglobulin heavy chain (IGH) locus is central to the maturation of the antibody response and crucially requires the cytidine deaminase AID. CSR involves changes in the chromatin state and the transcriptional activation of the IGH locus at the upstream and downstream switch (S) regions that are to undergo S–S DNA recombination. In addition, CSR involves the induction of AID expression and the targeting of CSR factors to S regions by 14-3-3 adaptors, and it is facilitated by the transcription machinery and by histone modifications. In this Review, we focus on recent advances regarding the induction and targeting of CSR and outline an integrated model of the assembly of macromolecular complexes that transduce crucial epigenetic information to enzymatic effectors of the CSR machinery.

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Figure 1: CSR entails DNA deletion.
Figure 2: Enzymes and scaffold elements in CSR.
Figure 3: CSR-inducing stimuli and the interplay of transcription factors.
Figure 4: Targeting of the CSR machinery.

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Acknowledgements

We apologize that owing to space limitations only a fraction of the relevant literature was cited. We thank all other members of the Casali laboratory for careful evaluation of this manuscript. Work on class-switch DNA recombination in the Casali laboratory has been supported by US National Institutes of Health grants AI 079705, AI 045011 and AI 060573. T. Mai has been supported by grant T32 CA 009054.

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  1. Institute for Immunology and Department of Medicine, School of Medicine, University of California, Irvine, 92697-4120, California, USA

    Zhenming Xu, Hong Zan, Egest J. Pone, Thach Mai & Paolo Casali

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  1. Zhenming Xu
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  3. Egest J. Pone
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Correspondence to Paolo Casali.

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Supplementary information

Supplementary information S1 (figure)

5′-AGCT-3′ repeats in S region DNA. (PDF 907 kb)

Glossary

BCR signalling

(B cell receptor signalling). Signals triggered by the binding of an antigen to the membrane-bound immunoglobulin of the BCR complex and the subsequent phosphorylation of the BCR components CD79a and CD79b at their ITAM motifs. This leads to the activation of tyrosine kinases, secondary messengers and signalling pathways (such as the NF-κB and MAPK pathways). BCR signalling is important for diverse B cell processes, including development, survival, activation, proliferation and differentiation.

Hyper-IgM syndrome

(HIGM syndrome). Syndromes characterized by elevated levels of IgM and decreased or absent levels of IgG, IgA and IgE, resulting from the impairment or ablation of class-switch recombination.

Activation-induced cytidine deaminase

(AID). A member of the AID and APOBEC family of cytidine or cytosine deaminases that catalyses the deamination of deoxycytosines to deoxyuracils, thereby initiating immunoglobulin class-switch recombination, somatic hypermutation and gene conversion.

Uracil DNA glycosylase

(UNG). An enzyme that removes uracil bases from DNA by cleaving N-glycosidic bonds and thereby initiates the base excision repair pathway that removes deoxyuracils from the genome.

Base excision repair

(BER). A DNA repair pathway that replaces damaged bases through a multistep process involving the excision of damaged bases by DNA glycosylases, nicking of the abasic sites by apurinic/apyrimidinic endonucleases, filling in of the single-stranded DNA gaps by DNA polymerases (such as DNA polymerase-β) and ligation by DNA ligases.

Mismatch repair

(MMR). A DNA repair system that recognizes and repairs mismatched DNA base pairs that result from DNA damage or from the erroneous insertion, deletion or misincorporation of bases during DNA replication or recombination.

Classical non-homologous end joining

(C-NHEJ). A DNA repair process that joins together non-homologous DNA ends using the four core components KU70, KU86, XRCC4 and DNA ligase IV, and additional components such as DNA-PKcs and Artemis.

Alternative end joining

(A-EJ). A double-strand break (DSB) repair process that occurs in the absence of certain classical non-homologous end joining components and is thought to depend on the MRN complex, CTIP and/or PARP1 to generate a microhomology region between the ends of DSBs for end joining.

Homologous recombination

A DNA recombination mechanism whereby extensive homology between two different DNA regions allows for the annealing of complementary strands from the two different regions. The enzymatic resolution of this hybrid intermediate leads to recombination between the two different DNA regions.

Primary CSR-inducing stimuli

Stimuli that induce the expression of AID, 14-3-3 adaptors and other important class-switch recombination (CSR) factors, thereby enabling CSR. These stimuli are triggered by the engagement of CD40 (a T cell-dependent stimulus) or by dual TLR–BCR, TACI–BCR or TLR–TACI engagement (T cell-independent stimuli). Primary stimuli enable secondary CSR-inducing stimuli to induce germline IH-S-CH transcription and histone modifications in selected switch regions.

Secondary CSR-inducing stimuli

These are cytokines — namely, IL-4 and TGFβ, and IFNγ in mice but not humans — that cannot induce AID but are required for directing switching to IgG, IgA and/or IgE. These stimuli select the acceptor switch region(s) through the induction of germline IH-S-CH transcription and the enrichment of specific histone modifications. They also enhance the expression of AID induced by primary class-switch recombination (CSR)-inducing stimuli.

T cell-dependent antibody responses

Antibody responses to protein antigens that require recognition of the antigen by T helper cells and cooperation between antigen-specific B and T cells. These responses lead to the generation of high-affinity antibodies and long-term memory.

TACI

A TNF receptor family member specific for B cell-activating factor (BAFF) and a proliferation-inducing ligand (APRIL) that activates signalling pathways (such as the NF-κB pathway) through TRAF adaptors.

T cell-independent antibody responses

Antibody responses to certain repetitive microbial constituents that occur in the absence of T cell help.

Chromosomal translocations

Aberrant chromosome structures that result from the breaking and joining of a chromosome (or part of a chromosome) to another chromosome through improper DSB ligation. These translocations frequently occur in cancers.

RNA exosome

A eukaryotic multiprotein complex comprised of a ring-like nine-subunit core (containing six different RNase subunits and three distinct RNA-binding subunits) and three additional subunits with RNase activities. It degrades erroneous RNA molecules, thereby enforcing RNA quality control. It also degrades non-erroneous RNA molecules, thereby maintaining their normal half-life and exposing the DNA strands of transcribed S regions for AID to deaminate.

5′-RGYW-3′ hotspot

A DNA motif that is frequently mutated during somatic hypermutation (SHM) as a result of the intrinsic preference of the SHM machinery for targeting this motif. R represents a purine; Y represents a pyrimidine; and W represents either A or T.

R-loop

A nucleic acid structure in which an RNA strand hybridizes with a complementary strand in a double-stranded DNA molecule and displaces the other DNA strand (which is typically rich in deoxyguanines), thereby forming a loop of up to hundreds of nucleotides.

14-3-3 adaptor proteins

A family of seven evolutionarily conserved and highly homologous adaptor proteins that form homodimers, heterodimers and/or tetramers and bind to a multitude of protein and DNA ligands. 14-3-3 proteins regulate diverse cell homeostasis events, such as signal transduction, survival, cell cycle progression and DNA replication, as well as cell differentiation processes, such as class-switch recombination.

Histone modifications

Post-translational chemical modifications of histones, including methylation, acetylation and phosphorylation. These modifications are inserted by histone-modifying enzymes and can actively mediate specific biological processes by interacting with selected effector proteins, including scaffold proteins that recruit and/or stabilize downstream factors. Histone modifications also determine chromatin accessibilities for DNA replication, repair and recombination.

Scaffold proteins

Multidomain proteins or multisubunit protein oligomers that, by switching the conformation of their ligands, coordinate the spatiotemporal organization of macromolecular complexes. This can bring enzymes into proximity with their substrates and eventually leads to specific biological information outputs.

REV1

A translesion DNA polymerase that bypasses DNA lesions using its dCMP transferase activity to mediate DNA repair. REV1 also possesses scaffold functions to recruit or stabilize other DNA repair factors.

Histone code hypothesis

A hypothesis postulating that distinct histone modifications that act alone, sequentially or combinatorially form a 'histone code' that is read by effector proteins to mediate biological processes.

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Xu, Z., Zan, H., Pone, E. et al. Immunoglobulin class-switch DNA recombination: induction, targeting and beyond. Nat Rev Immunol 12, 517–531 (2012). https://doi.org/10.1038/nri3216

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