Immunoglobulin Gene Rearrangements

Abstract

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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References

Agrawal A and Schatz DG (1997) RAG1 and RAG2 form a stable postcleavage synaptic complex with DNA containing signal ends in V(D)J recombination. Cell 89: 43–53.

Agrawal A, Eastman QM and Schatz DG (1998) Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394: 744–751.

Bergeron S, Madathiparambil T and Swanson PC (2005) Both high mobility group (HMG)‐boxes and the acidic tail of HMGB1 regulate recombination‐activating gene (RAG)‐mediated recombination signal synapsis and cleavage in vitro. Journal of Biological Chemistry 280: 31314–31324.

Bertocci B, DeSmet A, Weill J‐C and Reynaud CA (2006) Non‐overlapping functions of polX family DNA polymerases, pol m, pol l, and TdT, during immunoglobulin V(D)J recombination in vivo. Immunity 25: 31–41.

Bransteitter R, Pham P, Scharff MD and Goodman MF (2003) Activation‐induced cytidine deaminase deaminates deoxycytidine on single‐stranded DNA but requires the action of RNase. Proceedings of the National Academy of Sciences of the USA 100: 4102–4107.

Curry JD, Geier JK and Schlissel MS (2005) Single‐strand recombination signal sequence nicks in vivo: evidence for a capture model of synapsis. Nature Immunology 6: 1272–1279.

Daniels GA and Lieber MR (1995) RNA:DNA complex formation upon transcription of immunoglobulin switch regions: implications for the mechanism and regulation of class switch recombination. Nucleic Acids Research 23: 5006–5011.

DiNoia J and Neuberger MS (2002) Altering the pathway of immunoglobulin hypermutation by inhibiting uracil‐DNA glycosylase. Nature 419: 43–48.

Downs JA and Jackson SP (2004) A means to a DNA end: the many roles of Ku. Nature Reviews. Molecular Cell Biology 5: 367–378.

Drejer‐Teel AH, Fugmann SD and Schatz DG (2007) The beyond 12/23 restriction is imposed at the nicking and pairing steps of DNA cleavage during V(D)J recombination. Molecular and Cellular Biology 27: 6288–6299.

Dudley DD, Chaudhuri J, Bassing CH and Alt FW (2005) Mechanism and control of V(D)J recombination versus class switch recombination: similarities and differences. Advances in Immunology 86: 43–112.

Ferguson DO, Sekiguchi JM, Chang S et al. (2000) The nonhomologous end‐joining pathway of DNA repair is required for genomic stability and the suppression of translocations. Proceedings of the National Academy of Sciences of the USA 97: 6630–6633.

Fugmann SD, Lee AI, Shockett PE, Villey IJ and Schatz DG (2000) The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annual Review of Immunology 18: 495–527.

Gellert M (2002) V(D)J recombination: RAG proteins, repair factors, and regulation. Annual Review of Biochemistry 71: 101–132.

van Gent DC, McBlane JF, Ramsden DA et al. (1995) Initiation of V(D)J recombination in a cell‐free system. Cell 81: 925–934.

Gottlieb T and Jackson SP (1993) The DNA‐dependent protein kinase: requirement for DNA ends and association with Ku antigen. Cell 72: 131–142.

Grawunder U, Wilm M, Wu X et al. (1997) Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells. Nature 388: 492–495.

Han L and Yu K (2008) Altered kinetics of nonhomologous end joining and class switch recombination in ligase IV–deficient B cells. Journal of Experimental Medicine 205: 2745–2753.

Hawwari A, Bock C and Krangel MS (2005) Regulation of T cell receptor alpha gene assembly by a complex hierarchy of germline Jalpha promoters. Nature Immunology 6: 481–489.

Hiom K, Melek M and Gellert M (1998) DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94: 463–470.

Lieber MR (2006) The polymerases for V(D)J recombination. Immunity 25: 7–9.

Lieber MR (2008) The mechanism of human nonhomologous DNA end joining. Journal of Biological Chemistry 283: 1–5.

Liu Y, Subrahmanyam R, Chakraborty T, Sen R and Desiderio S (2007) A plant homeodomain in RAG‐2 that binds hypermethylated lysine 4 of histone H3 is necessary for efficient antigen‐receptor‐gene rearrangement. Immunity 27: 561–571.

Ma Y, Pannicke U, Schwarz K and Lieber MR (2002) Hairpin opening and overhang processing by an Artemis:DNA‐PKcs complex in V(D)J recombination and in nonhomologous end joining. Cell 108: 781–794.

Mahowald GK, Baron JM and Sleckman BP (2008) Collateral damage from antigen receptor gene diversification. Cell 135: 1009–1012.

Matthews AG, Kuo AJ, Ramon‐Maiques S et al. (2007) RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature 450: 1106–1110.

Moshous D, Callebaut I, Chasseval RD et al. (2001) Artemis, a novel DNA double‐strand break repair/V(D)J recombination protein, is mutated in human severe combined immune deficiency. Cell 105: 177–186.

Muramatsu M, Sankaranand V, Anant S et al. (1999) Specific expression of activation‐induced cytidine deaminase (AID), a novel member of the RNA‐editing deaminase family in germinal center B cells. Journal of Biological Chemistry 274: 18470–18476.

Oettinger MA, Schatz DG, Gorka C and Baltimore D (1990) Rag‐1 and Rag‐2, adjacent genes that synergistically activate V(D)J recombination. Science 248: 1517–1523.

Petersen‐Mahrt SK, Harris RS and Neuberger MS (2002) AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature 418: 99–103.

Rada C, Williams GT, Nilsen H et al. (2002) Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG‐deficient mice. Current Biology 12: 1748–1755.

Reaban ME and Griffin JA (1990) Induction of RNA‐stabilized DNA conformers by transcription of an immunoglobulin switch region. Nature 348: 342–344.

Roth D and Wilson J (1988) Illegitimate recombination in mammalian cells. In: Kucherlapapti R and Smith GR (eds) Genetic Recombination, pp. 621–653. Washington, DC: American Society for Microbiology.

Roth DB, Zhu C and Gellert M (1993) Characterization of broken DNA molecules associated with V(D)J recombination. Proceedings of the National Academy of Sciences of the USA 90: 10788–10792.

Schatz DG, Oettinger MA and Baltimore D (1989) The V(D)J recombination activating gene, RAG‐1. Cell 59: 1035–1048.

Schatz DG (2004) V(D)J recombination. Immunological Review 200: 5–11.

Schlissel M (2004a) The spreading influence of chromatin modification. Nature Genetics 36: 438–440.

Schlissel MS (2004b) Regulation of activation and recombination of the murine Igkappa locus. Immunological Review 200: 215–223.

Schlissel M, Constantinescu A, Morrow T and Peng A (1993) Double‐strand signal sequence breaks in V(D)J recombination are blunt, 5′‐phosphorylated, RAG‐dependent, and cell cycle regulated. Genes & Development 7: 2520–2532.

Schwarz K, Gauss GH, Ludwig L et al. (1996) RAG mutations in human B cell‐negative SCID. Science 274: 97–99.

Shimazaki N, Tsai AG and Lieber MR (2009) H3K4me3 stimulates V(D)J RAG complex for both nicking and hairpinning in trans in addition to tethering in Cis: implications for translocations. Molecular Cell 34: 535–544.

Shlyakhtenko LS, Gilmore J, Kriatchko AN et al. (2009) Molecular mechanism underlying RAG1/RAG2 synaptic complex formation. Journal of Biological Chemistry 284: 20956–20965.

Soulas‐Sprauel P, Rivera‐Munoz P, Malivert L et al. (2007) V(D)J and immunoglobulin class switch recombinations: a paradigm to study the regulation of DNA end‐joining. Oncogene 26: 7780–7791.

Stavnezer J (1996) Immunoglobulin class switching. Current Opinion in Immunology 8: 199–205.

Tonegawa S (1983) Somatic generation of antibody diversity. Nature 302: 575–581.

Tsai AG, Lu H, Raghavan SC et al. (2008) Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity. Cell 135: 1130–1142.

Villa A, Sobacchi C, Notarangelo L et al. (2001) V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. Blood 97: 81–88.

Wang JH, Alt FW, Gostissa M et al. (2008) Oncogenic transformation in the absence of Xrcc4 targets peripheral B cells that have undergone editing and switching. Journal of Experimental Medicine 205: 3079–3090.

Wilson TE, Grawunder U and Lieber MR (1997) Yeast DNA ligase IV mediates non‐homologous DNA end joining. Nature 388: 495–498.

Yan CT, Boboila C, Souza EK et al. (2007) IgH class switching and translocations use a robust non‐classical end‐joining pathway. Nature 449: 478–482.

Yu K and Lieber MR (2000) The nicking step of V(D)J recombination is independent of synapsis: implications for the immune repertoire. Molecular and Cellular Biology 20: 7914–7921.

Yu K and Lieber MR (2003) Nucleic acid structures and enzymes in the immunoglobulin class switch recombination mechanism. DNA Repair 2: 1163–1174.

Yu K, Chedin F, Hsieh C‐L, Wilson TE and Lieber MR (2003) R‐loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nature Immunology 4: 442–451.

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. http://www.els.net [doi: 10.1002/9780470015902.a0000596.pub2]