Immunoglobulin Gene Rearrangements


V(D)J and class switch recombination are two deoxyribonucleic acid (DNA) recombination processes that occur at immunoglobulin genes during the generation of B cells and the attendant rearrangement of immunoglobulin heavy and light chain loci. V(D)J occurs during early B‐ and T‐cell development whereas class switch recombination occurs exclusively in mature B cells. V(D)J recombination achieves the assembly of new exons that encode the portion of the antigen receptor that binds antigen. Class switch recombination changes the constant portion of the heavy chain of the antibody from IgM to IgG, IgA or IgE. V(D)J recombination occurs in the bone marrow for pre‐B cells and in the thymus for pre‐T cells. Class switch recombination occurs in the germinal centres in the spleen, lymph nodes and Peyer's patches.

Key Concepts:

  • V(D)J recombination occurs only in vertebrates, because these are the only organisms that have lymphocytes and that generate B and T cells with antigen receptors.

  • V(D)J recombination is done by the RAG1 and RAG2 proteins, which bind at recombination signal sequences (RSS) that consist of heptamer and nonamer recognition sequences.

  • The RAG complex (consisting of RAG1 and RAG2, along with HMGB1) is only expressed in pre‐B cells and pre‐T cells.

  • Class switch recombination requires activation‐induced deaminase (AID).

  • AID acts only on single‐stranded DNA.

  • For class switch regions, single‐stranded DNA is generated by the formation of R‐loops at the switch regions.

  • Switch regions consist of unit repeats (25–80 bp in length) that are 40–50% G on the nontemplate strand, making them prone to form R‐loops.

  • Occasionally, the RAG complex or AID act at off‐target sites, thereby triggering double‐strand breaks that can cause the chromosomal translocations that initiate many types of lymphomas or lymphoid leukaemias.

Keywords: V(D)J recombination; class switch recombination

Figure 1.

Summary of components and steps of V(D)J recombination. A single V and J are depicted, though combinatorial diversity is achieved using numerous V and J segments. A signal sequence is adjacent to each V or J coding segment. Within each signal, the nonamer of each signal is located furthest from its coding segment, whereas the heptamer is directly adjacent to the coding segment. Figure provide more detail for all of the correspondingly numbered steps. RAG represents the RAG1, RAG2, HMGB1 complex. Ku is the Ku70/86 heterodimer. Terminal deoxynucleotidyltransferase (TdT) is not an essential component for V(D)J recombination, but is a lymphoid‐specific enzyme which is present in pre‐B and pre‐T cells during most of the period in which they carry out this process. The nuclease for hairpin opening is Artemis:DNA‐PKcs, and it may also trim the coding ends before joining. The polymerases involved are TdT, pol μ and pol λ. In the bottom line of the diagram, the coding joint has dashed lines on either side of the junction to depict nucleotide loss and addition, resulting in junctional diversity. RAG, recombination‐activating gene; HMG, high‐mobility group protein B1 and DNA‐PKcs, DNA‐dependent protein kinase (catalytic subunit).

Figure 2.

Model for the nicking and hairpin formation phases of V(D)J recombination. The RAG1, RAG2, HMGB1 complex is depicted as a single green oval. At the cleavage step, the signal ends are blunt and have a 5′‐phosphate and 3′‐OH. Nicking can occur before synapsis. The coding ends after step 4 are hairpinned at their termini.

Figure 3.

Model for roles of Ku and DNA‐dependent protein kinase catalytic subunit (DNA‐PKcs) in the end joining of V(D)J recombination.

Figure 4.

Model for the DNA end‐joining phase of V(D)J recombination. Terminal deoxynucleotidyltransferase (TdT) template‐independent nucleotide addition can occur at the 3′‐OH of any of the four DNA ends, but is only relevant to the immune system at the coding ends where it contributes as a major factor to junctional diversification. In addition to RAG‐1 and RAG‐2, TdT is the only other lymphoid‐specific component, but unlike RAGs, TdT is not essential for the cutting and joining to occur. The nuclease for resecting nucleotides from each end is probably Artemis:DNA‐PKcs. The polymerases for fill‐in synthesis are pol μ and pol λ, but pol μ can also add template‐independently. The blunt signal ends are ligated together and also the aligned coding ends.

Figure 5.

Class switch recombination at the immunoglobulin heavy‐chain locus. Unlike V(D)J recombination, which occurs at all three immunoglobulin loci (heavy chain, kappa chain and lambda chain) and all three T‐cell receptor loci (α/δ, β and γ), class switch recombination only occurs at the IgH locus. The right‐angle arrows represent internal promoters called sterile transcript promoters. The transcripts from these do not encode protein because of stop codons. This suggests that transcription may be important for the mechanism of class switch recombination. The ovals represent the G‐rich repetitive class switch sequences. Recombination occurs between switch sequences. Not all of the sterile transcript promoters are active at any one time. The cytokine stimulation of B cells in the peripheral lymphoid tissues determines which promoters are active.

Figure 6.

Aspects of the Mechanism of Class Switch Recombination. R‐loops form at the switch regions because these regions are G‐rich on the nontemplate DNA strand, thereby encoding G‐rich transcripts that form cause R‐loop formation. AID converts Cs to Us at regions of ssDNA. Uracil DNA glycosylase (UDG) removes the U, resulting in an abasic site. AP endonuclease (APE) nicks the DNA 5′ of the abasic sites.



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Further Reading

Max E (2008) Immunoglobulins: molecular genetics. In: Paul WE (ed.) Fundamental Immunology, pp. 192–236. Philadelphia: Lippincott Williams Wilkins. (ISBN: 0781765196).

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Lieber, Michael(Dec 2009) Immunoglobulin Gene Rearrangements. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000596.pub2]