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Recombination centres and the orchestration of V(D)J recombination

Nature Reviews Immunology volume 11, pages 251–263 (2011)Cite this article

Subjects

Key Points

  • V(D)J recombination, which assembles antigen receptor genes during lymphocyte development, is initiated when the recombination activating gene 1 (RAG1) and RAG2 proteins bind and cleave genomic DNA at recombination signal sequences that lie adjacent to antigen receptor gene segments.

  • Modulation of chromatin structure, histone modifications and transcriptional activity determine the accessibility of recombination signal sequences for binding by RAG1 and RAG2 and thereby help to dictate the developmentally ordered sequence of V(D)J recombination events.

  • V(D)J recombination is also controlled by the association of antigen receptor genes with active or inactive nuclear compartments and by changes in the higher order chromatin architecture (such as looping and contraction) of antigen receptor genes.

  • The RAG proteins associate with a small region of highly active chromatin in each antigen receptor locus, forming recombination centres within which V(D)J recombination might be regulated.

  • The interaction of the RAG2 plant homeodomain (PHD) finger with trimethylated histone H3 lysine 4 (H3K4me3; a modification found in active chromatin) is important for efficient V(D)J recombination and results in the association of RAG2 with many thousands of sites in the genome.

  • The ectopic recruitment and activity of RAG1 and RAG2 at loci that do not encode antigen receptors contributes to genome instability and the development of lymphoid malignancies.

Abstract

The initiation of V(D)J recombination by the recombination activating gene 1 (RAG1) and RAG2 proteins is carefully orchestrated to ensure that antigen receptor gene assembly occurs in the appropriate cell lineage and in the proper developmental order. Here we review recent advances in our understanding of how DNA binding and cleavage by the RAG proteins are regulated by the chromatin structure and architecture of antigen receptor genes. These advances suggest novel mechanisms for both the targeting and the mistargeting of V(D)J recombination, and have implications for how these events contribute to genome instability and lymphoid malignancy.

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Figure 1: The structure of antigen receptor genes.
Figure 2: Mechanism of V(D)J recombination.
Figure 3: The recombination centre model.
Figure 4: The nonamer-first model for RSS recognition.

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References

  1. Mills, K. D., Ferguson, D. O. & Alt, F. W. The role of DNA breaks in genomic instability and tumorigenesis. Immunol. Rev. 194, 77–95 (2003).

    Article  CAS  PubMed  Google Scholar 

  2. Lieber, M. R., Yu, K. F. & Raghavan, S. C. Roles of nonhomologous DNA end joining, V(D)J recombination, and class switch recombination in chromosomal translocations. DNA Repair 5, 1234–1245 (2006).

    Article  CAS  PubMed  Google Scholar 

  3. Tsai, A. G. et al. Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity. Cell 135, 1130–1142 (2008). This study proposed, and provided support for, the fascinating idea that RAG and AID collaborate to create DNA nicks and breaks at methylated CpG sequences.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Yancopoulos, G. D. & Alt, F. W. Developmentally controlled and tissue-specific expression of unrearranged VH gene segments. Cell 40, 271–281 (1985). This classic study provided the first evidence for, and proposed, the accessibility model for the control of V(D)J recombination.

    Article  CAS  PubMed  Google Scholar 

  5. Lewis, S. M. The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. Adv. Immunol. 56, 27–150 (1994).

    Article  CAS  PubMed  Google Scholar 

  6. Swanson, P. C. The bounty of RAGs: recombination signal complexes and reaction outcomes. Immunol. Rev. 200, 90–114 (2004).

    Article  CAS  PubMed  Google Scholar 

  7. Fugmann, S. D. & Schatz, D. G. Identification of basic residues in RAG2 critical for DNA binding by the RAG1–RAG2 complex. Mol. Cell 8, 899–910 (2001).

    Article  CAS  PubMed  Google Scholar 

  8. Mundy, C. L., Patenge, N., Matthews, A. G. W. & Oettinger, M. A. Assembly of the RAG1/RAG2 synaptic complex. Mol. Cell. Biol. 22, 69–77 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Jones, J. M. & Gellert, M. Ordered assembly of the V(D)J synaptic complex ensures accurate recombination. EMBO J. 21, 4162–4171 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Gellert, M. V(D)J recombination: RAG proteins, repair factors, and regulation. Annu. Rev. Biochem. 71, 101–132 (2002).

    Article  CAS  PubMed  Google Scholar 

  11. Cobb, R. M., Oestreich, K. J., Osipovich, O. A. & Oltz, E. M. Accessibility control of V(D)J recombination. Adv. Immunol. 91, 45–109 (2006).

    Article  CAS  PubMed  Google Scholar 

  12. Hesslein, D. G. & Schatz, D. G. Factors and forces controlling V(D)J recombination. Adv. Immunol. 78, 169–232 (2001).

    Article  CAS  PubMed  Google Scholar 

  13. Yancopoulos, G. D. & Alt, F. W. Regulation of the assembly and expression of variable-region genes. Annu. Rev. Immunol. 4, 339–368 (1986).

    Article  CAS  PubMed  Google Scholar 

  14. Jung, D., Giallourakis, C., Mostoslavsky, R. & Alt, F. W. Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus. Annu. Rev. Immunol. 24, 541–570 (2006).

    Article  CAS  PubMed  Google Scholar 

  15. Goldmit, M. & Bergman, Y. Monoallelic gene expression: a repertoire of recurrent themes. Immunol. Rev. 200, 197–214 (2004).

    Article  CAS  PubMed  Google Scholar 

  16. Krangel, M. S. T cell development: better living through chromatin. Nature Immunol. 8, 687–694 (2007).

    Article  CAS  Google Scholar 

  17. Schlissel, M. S. Regulating antigen-receptor gene assembly. Nature Rev. Immunol. 3, 890–899 (2003).

    Article  CAS  Google Scholar 

  18. Stanhope-Baker, P., Hudson, K. M., Shaffer, A. L., Constantinescu, A. & Schlissel, M. S. Cell type-specific chromatin structure determines the targeting of V(D)J recombinase activity in vitro. Cell 85, 887–897 (1996). This classic study demonstrated that chromatin structure is a critical determinant of DNA cutting by RAG.

    Article  CAS  PubMed  Google Scholar 

  19. Kwon, J., Imbalzano, A. N., Matthews, A. & Oettinger, M. A. Accessibility of nucleosomal DNA to V(D)J cleavage is modulated by RSS positioning and HMG1. Mol. Cell 2, 829–839 (1998).

    Article  CAS  PubMed  Google Scholar 

  20. Golding, A., Chandler, S., Ballestar, E., Wolffe, A. P. & Schlissel, M. S. Nucleosome structure completely inhibits in vitro cleavage by the V(D)J recombinase. EMBO J. 18, 3712–3723 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. McBlane, F. & Boyes, J. Stimulation of V(D)J recombination by histone acetylation. Curr. Biol. 10, 483–486 (2000).

    Article  CAS  PubMed  Google Scholar 

  22. Kwon, J., Morshead, K. B., Guyon, J. R., Kingston, R. E. & Oettinger, M. A. Histone acetylation and hSWI/SNF remodeling act in concert to stimulate V(D)J cleavage of nucleosomal DNA. Mol. Cell 6, 1037–1048 (2000).

    Article  CAS  PubMed  Google Scholar 

  23. Patenge, N., Elkin, S. K. & Oettinger, M. A. ATP-dependent remodeling by SWI/SNF and ISWI proteins stimulates V(D)J cleavage of 5 S arrays. J. Biol. Chem. 279, 35360–35367 (2004).

    Article  CAS  PubMed  Google Scholar 

  24. Nightingale, K. P. et al. Acetylation increases access of remodelling complexes to their nucleosome targets to enhance initiation of V(D)J recombination. Nucl. Acids Res. 35, 6311–6321 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Du, H., Ishii, H., Pazin, M. J. & Sen, R. Activation of 12/23-RSS-dependent RAG cleavage by hSWI/SNF complex in the absence of transcription. Mol. Cell 31, 641–649 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Baumann, M., Mamais, A., McBlane, F., Xiao, H. & Boyes, J. Regulation of V(D)J recombination by nucleosome positioning at recombination signal sequences. EMBO J. 22, 5197–5207 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kondilis-Mangum, H. D. et al. Transcription-dependent mobilization of nucleosomes at accessible TCR gene segments in vivo. J. Immunol. 184, 6970–6977 (2010).

    Article  CAS  PubMed  Google Scholar 

  28. Kaplan, N. et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458, 362–366 (2009).

    Article  CAS  PubMed  Google Scholar 

  29. Segal, E. & Widom, J. What controls nucleosome positions? Trends Genet. 25, 335–343 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zhang, Y. et al. Intrinsic histone–DNA interactions are not the major determinant of nucleosome positions in vivo. Nature Struct. Mol. Biol. 16, 847–852 (2009).

    Article  CAS  Google Scholar 

  31. Segal, E. & Widom, J. Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr. Opin. Struct. Biol. 19, 65–71 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Chowdhury, D. & Sen, R. Regulation of immunoglobulin heavy-chain gene rearrangements. Immunol. Rev. 200, 182–196 (2004).

    Article  CAS  PubMed  Google Scholar 

  33. Krangel, M. S. Mechanics of T cell receptor gene rearrangement. Curr. Opin. Immunol. 21, 133–139 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Jhunjhunwala, S., van Zelm, M. C., Peak, M. M. & Murre, C. Chromatin architecture and the generation of antigen receptor diversity. Cell 138, 435–448 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Schlissel, M. S. Regulation of activation and recombination of the murine Igκ locus. Immunol. Rev. 200, 215–223 (2004).

    Article  CAS  PubMed  Google Scholar 

  36. Abarrategui, I. & Krangel, M. S. Regulation of T cell receptor-α gene recombination by transcription. Nature Immunol. 7, 1109–1115 (2006). This study provided the first direct support for the long held idea that transcriptional elongation is important for creating accessibility for V(D)J recombination.

    Article  CAS  Google Scholar 

  37. Abarrategui, I. & Krangel, M. S. Noncoding transcription controls downstream promoters to regulate T-cell receptor α recombination. EMBO J. 26, 4380–4390 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Sikes, M. L., Meade, A., Tripathi, R., Krangel, M. S. & Oltz, E. M. Regulation of V(D)J recombination: a dominant role for promoter positioning in gene segment accessibility. Proc. Natl Acad. Sci. USA 99, 12309–12314 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Fernex, C., Capone, M. & Ferrier, P. The V(D)J recombinational and transcriptional activities of the immunoglobulin heavy-chain intronic enhancer can be mediated through distinct protein-binding sites in a transgenic substrate. Mol. Cell. Biol. 15, 3217–3226 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Bolland, D. J. et al. Antisense intergenic transcription in V(D)J recombination. Nature Immunol. 5, 630–637 (2004).

    Article  CAS  Google Scholar 

  41. Bolland, D. J. et al. Antisense intergenic transcription precedes Igh D-to-J recombination and is controlled by the intronic enhancer Eμ. Mol. Cell. Biol. 27, 5523–5533 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Chakraborty, T. et al. Repeat organization and epigenetic regulation of the DH-Cμ domain of the immunoglobulin heavy-chain gene locus. Mol. Cell 27, 842–850 (2007).

    Article  CAS  PubMed  Google Scholar 

  43. Osipovich, O. A., Subrahmanyam, R., Pierce, S., Sen, R. & Oltz, E. M. Cutting edge: SWI/SNF mediates antisense Igh transcription and locus-wide accessibility in B cell precursors. J. Immunol. 183, 1509–1513 (2009).

    Article  CAS  PubMed  Google Scholar 

  44. Giallourakis, C. C. et al. Elements between the IgH variable (V) and diversity (D) clusters influence antisense transcription and lineage-specific V(D)J recombination. Proc. Natl Acad. Sci. USA 107, 22207–22212 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Oettinger, M. A. How to keep V(D)J recombination under control. Immunol. Rev. 200, 165–181 (2004).

    Article  CAS  PubMed  Google Scholar 

  46. Chakraborty, T. et al. A 220-nucleotide deletion of the intronic enhancer reveals an epigenetic hierarchy in immunoglobulin heavy chain locus activation. J. Exp. Med. 206, 1019–1027 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Osipovich, O. et al. Targeted inhibition of V(D)J recombination by a histone methyltransferase. Nature Immunol. 5, 309–316 (2004).

    CAS  Google Scholar 

  48. Morshead, K. B., Ciccone, D. N., Taverna, S. D., Allis, C. D. & Oettinger, M. A. Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4. Proc. Natl Acad. Sci. USA 100, 11577–11582 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Johnson, K. et al. B cell-specific loss of histone 3 lysine 9 methylation in the VH locus depends on Pax5. Nature Immunol. 5, 853–861 (2004).

    Article  CAS  Google Scholar 

  50. Smale, S. T. The establishment and maintenance of lymphocyte identity through gene silencing. Nature Immunol. 4, 607–615 (2003).

    Article  CAS  Google Scholar 

  51. Workman, J. L. Nucleosome displacement in transcription. Genes Dev. 20, 2009–2017 (2006).

    Article  CAS  PubMed  Google Scholar 

  52. Li, B., Carey, M. & Workman, J. L. The role of chromatin during transcription. Cell 128, 707–719 (2007).

    Article  CAS  PubMed  Google Scholar 

  53. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).

    Article  CAS  PubMed  Google Scholar 

  54. Shogren-Knaak, M. et al. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311, 844–847 (2006).

    Article  CAS  PubMed  Google Scholar 

  55. Zhang, Y. et al. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol. Cell 24, 559–568 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Wang, X. et al. Regulation of Tcrb recombination ordering by c-Fos-dependent RAG deposition. Nature Immunol. 9, 794–801 (2008).

    Article  CAS  Google Scholar 

  57. Zhang, Z. X. et al. Transcription factor Pax5 (BSAP) transactivates the RAG-mediated VH-to-DJH rearrangement of immunoglobulin genes. Nature Immunol. 7, 616–624 (2006).

    Article  CAS  Google Scholar 

  58. Hesslein, D. G. et al. Pax5 is required for recombination of transcribed, acetylated, 5′ IgH V gene segments. Genes Dev. 17, 37–42 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Jackson, A., Kondilis, H. D., Khor, B., Sleckman, B. P. & Krangel, M. S. Regulation of T cell receptor β allelic exclusion at a level beyond accessibility. Nature Immunol. 6, 189–197 (2005).

    Article  CAS  Google Scholar 

  60. Kosak, S. T. & Groudine, M. Form follows function: the genomic organization of cellular differentiation. Genes Dev. 18, 1371–1384 (2004).

    Article  CAS  PubMed  Google Scholar 

  61. Reddy, K. L., Zullo, J. M., Bertolino, E. & Singh, H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452, 243–247 (2008).

    Article  CAS  PubMed  Google Scholar 

  62. Kosak, S. T. et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296, 158–162 (2002). This paper provided the first evidence that V(D)J recombination is associated with contraction and movement away from the nuclear periphery of the recombining locus.

    Article  CAS  PubMed  Google Scholar 

  63. Skok, J. A. et al. Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes. Nature Immunol. 8, 378–387 (2007).

    Article  CAS  Google Scholar 

  64. Hewitt, S. L. et al. RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci. Nature Immunol. 10, 655–664 (2009).

    Article  CAS  Google Scholar 

  65. Goldmit, M. et al. Epigenetic ontogeny of the Igk locus during B cell development. Nature Immunol. 6, 198–203 (2005).

    Article  CAS  Google Scholar 

  66. Schlimgen, R. J., Reddy, K. L., Singh, H. & Krangel, M. S. Initiation of allelic exclusion by stochastic interaction of Tcrb alleles with repressive nuclear compartments. Nature Immunol. 9, 802–809 (2008).

    Article  CAS  Google Scholar 

  67. Hewitt, S. L. et al. Association between the Igk and Igh immunoglobulin loci mediated by the 3′ Igk enhancer induces 'decontraction' of the Igh locus in pre-B cells. Nature Immunol. 9, 396–404 (2008).

    Article  CAS  Google Scholar 

  68. Roldan, E. et al. Locus 'decontraction' and centromeric recruitment contribute to allelic exclusion of the immunoglobulin heavy-chain gene. Nature Immunol. 6, 31–41 (2005).

    Article  CAS  Google Scholar 

  69. Jia, J., Kondo, M. & Zhuang, Y. Germline transcription from T-cell receptor Vβ gene is uncoupled from allelic exclusion. EMBO J. 26, 2387–2399 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Singh, N., Bergman, Y., Cedar, H. & Chess, A. Biallelic germline transcription at the κ immunoglobulin locus. J. Exp. Med. 197, 743–750 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Amin, R. H. et al. Biallelic, ubiquitous transcription from the distal germline Igκ locus promoter during B cell development. Proc. Natl Acad. Sci. USA 106, 522–527 (2009).

    Article  CAS  PubMed  Google Scholar 

  72. Fitzsimmons, S. P., Bernstein, R. M., Max, E. E., Skok, J. A. & Shapiro, M. A. Dynamic changes in accessibility, nuclear positioning, recombination, and transcription at the Igκ locus. J. Immunol. 179, 5264–5273 (2007).

    Article  CAS  PubMed  Google Scholar 

  73. Sayegh, C., Jhunjhunwala, S., Riblet, R. & Murre, C. Visualization of looping involving the immunoglobulin heavy-chain locus in developing B cells. Genes Dev. 19, 322–327 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Fuxa, M. et al. Pax5 induces V-to-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene. Genes Dev. 18, 411–422 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Jhunjhunwala, S. et al. The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions. Cell 133, 265–279 (2008). This landmark study provided the highest resolution picture to date of the higher order chromatin architecture and dynamics of an antigen receptor locus.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Shih, H. Y. & Krangel, M. S. Distinct contracted conformations of the Tcra/Tcrd locus during Tcra and Tcrd recombination. J. Exp. Med. 207, 1835–1841 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Callebaut, I. & Mornon, J. P. The V(D)J recombination activating protein RAG2 consists of a six-bladed propeller and a PHD fingerlike domain, as revealed by sequence analysis. Cell. Mol. Life Sci. 54, 880–891 (1998).

    Article  CAS  PubMed  Google Scholar 

  78. Elkin, S. K. et al. A PHD finger motif in the C terminus of RAG2 modulates recombination activity. J. Biol. Chem. 280, 28701–28710 (2005).

    Article  CAS  PubMed  Google Scholar 

  79. West, K. L. et al. A direct interaction between the RAG2 C terminus and the core histones is required for efficient V(D)J recombination. Immunity 23, 203–212 (2005).

    Article  CAS  PubMed  Google Scholar 

  80. Matthews, A. G. et al. RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature 450, 1106–1110 (2007). This study provided a high resolution structure for the PHD finger of RAG2 bound to H3K4me3, as well as evidence for the biological importance of this interaction.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Liu, Y., Subrahmanyam, R., Chakraborty, T., Sen, R. & Desiderio, S. 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 (2007). This study demonstrated that the RAG2 PHD finger binds H3K4me3 and provided evidence for the biological importance of this interaction.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Gomez, C. A. et al. Mutations in conserved regions of the predicted RAG2 kelch repeats block initiation of V(D)J recombination and result in primary immunodeficiencies. Mol. Cell. Biol. 20, 5653–5664 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Shimazaki, N., Tsai, A. G. & Lieber, M. R. H3K4me3 stimulates the V(D)J RAG complex for both nicking and hairpinning in trans in addition to tethering in cis: implications for translocations. Mol. Cell 34, 535–544 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Grundy, G. J., Yang, W. & Gellert, M. Autoinhibition of DNA cleavage mediated by RAG1 and RAG2 is overcome by an epigenetic signal in V(D)J recombination. Proc. Natl Acad. Sci. USA 107, 22487–22492 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Ji, Y. et al. The in vivo pattern of binding of RAG1 and RAG2 to antigen receptor loci. Cell 141, 419–431 (2010). This study demonstrated that the binding of RAG1 and RAG2 to antigen receptor loci is developmentally regulated, lineage restricted and focused on small, highly active regions of chromatin referred to as recombination centres.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Zhao, S., Gwyn, L. M., De, P. & Rodgers, K. K. A non-sequence-specific DNA binding mode of RAG1 is inhibited by RAG2. J. Mol. Biol. 387, 744–758 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Ji, Y. et al. Promoters, enhancers, and transcription target RAG1 binding during V(D)J recombination. J. Exp. Med. 207, 2809–2816 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Grazini, U. et al. The RING domain of RAG1 ubiquitylates histone H3: a novel activity in chromatin-mediated regulation of V(D)J joining. Mol. Cell 37, 282–293 (2010).

    Article  CAS  PubMed  Google Scholar 

  89. Raghavan, S. C., Swanson, P. C., Wu, X., Hsieh, C. L. & Lieber, M. R. A non-B-DNA structure at the Bcl-2 major breakpoint region is cleaved by the RAG complex. Nature 428, 88–93 (2004).

    Article  CAS  PubMed  Google Scholar 

  90. Lee, G. S., Neiditch, M. B., Salus, S. S. & Roth, D. B. RAG proteins shepherd double-strand breaks to a specific pathway, suppressing error-prone repair, but RAG nicking initiates homologous recombination. Cell 117, 171–184 (2004).

    Article  CAS  PubMed  Google Scholar 

  91. Matthews, A. G. W. & Oettinger, M. A. RAG: a recombinase diversified. Nature Immunol. 10, 817–821 (2009).

    Article  CAS  Google Scholar 

  92. Corneo, B. et al. Rag mutations reveal robust alternative end joining. Nature 449, 483–486 (2007).

    Article  CAS  PubMed  Google Scholar 

  93. Cui, X. & Meek, K. Linking double-stranded DNA breaks to the recombination activating gene complex directs repair to the nonhomologous end-joining pathway. Proc. Natl Acad. Sci. USA 104, 17046–17051 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Raval, P., Kriatchko, A. N., Kumar, S. & Swanson, P. C. Evidence for Ku70/Ku80 association with full-length RAG1. Nucl. Acids Res. 36, 2060–2072 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Curry, J. D., Geier, J. K. & Schlissel, M. S. Single-strand recombination signal sequence nicks in vivo: evidence for a capture model of synapsis. Nature Immunol. 6, 1272–1279 (2005).

    Article  CAS  Google Scholar 

  96. Yin, F. F. et al. Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis. Nature Struct. Mol. Biol. 16, 499–508 (2009).

    Article  CAS  Google Scholar 

  97. Yu, K. F. & Lieber, M. R. Mechanistic basis for coding end sequence effects in the initiation of V(D)J recombination. Mol. Cell. Biol. 19, 8094–8102 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Franchini, D. M., Benoukraf, T., Jaeger, S., Ferrier, P. & Payet-Bornet, D. Initiation of V(D)J recombination by Dβ-associated recombination signal sequences: a critical control point in TCRβ gene assembly. PLoS ONE 4, e4575 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Sikes, M. L., Gomez, R. J., Song, J. & Oltz, E. M. A developmental stage-specific promoter directs germline transcription of DβJβ gene segments in precursor T lymphocytes. J. Immunol. 161, 1399–1405 (1998).

    CAS  PubMed  Google Scholar 

  100. Merelli, I. et al. RSSsite: a reference database and prediction tool for the identification of cryptic recombination signal sequences in human and murine genomes. Nucl. Acids Res. 38, W262–W267 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Zhao, J., Bacolla, A., Wang, G. & Vasquez, K. M. Non-B DNA structure-induced genetic instability and evolution. Cell. Mol. Life Sci. 67, 43–62 (2010).

    Article  CAS  PubMed  Google Scholar 

  102. Yamane, A. et al. Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes. Nature Immunol. 12, 62–69 (2010).

    Article  CAS  Google Scholar 

  103. Staszewski, O. et al. Activation-induced cytidine deaminase induces reproducible DNA breaks at many non-Ig loci in activated B cells. Mol. Cell 41, 232–242 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Leu, T. M. & Schatz, D. G. rag-1 and rag-2 are components of a high-molecular-weight complex, and association of rag-2 with this complex is rag-1 dependent. Mol. Cell. Biol. 15, 5657–5670 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Lin, W.-C. & Desiderio, S. Cell cycle regulation of V(D)J recombination-activating protein RAG-2. Proc. Natl Acad. Sci. USA 91, 2733–2737 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Lee, J. & Desiderio, S. Cyclin A/CDK2 regulates V(D)J recombination by coordinating RAG-2 accumulation and DNA repair. Immunity 11, 771–781 (1999).

    Article  CAS  PubMed  Google Scholar 

  107. Fugmann, S. D., Lee, A. I., Shockett, P. E., Villey, I. J. & Schatz, D. G. The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annu. Rev. Immunol. 18, 495–527 (2000).

    Article  CAS  PubMed  Google Scholar 

  108. De, P. & Rodgers, K. K. Putting the pieces together: identification and characterization of structural domains in the V(D)J recombination protein RAG1. Immunol. Rev. 200, 70–82 (2004).

    Article  CAS  PubMed  Google Scholar 

  109. Mathieu, N., Hempel, W. M., Spicuglia, S., Verthuy, C. & Ferrier, P. Chromatin remodeling by the T cell receptor (TCR)-β gene enhancer during early T cell development: implications for the control of TCR-β locus recombination. J. Exp. Med. 192, 625–636 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Bouvier, G. et al. Deletion of the mouse T-cell receptor β gene enhancer blocks α-β T-cell development. Proc. Natl Acad. Sci. USA 93, 7877–7881 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Bories, J. C., Demengeot, J., Davidson, L. & Alt, F. W. Gene-targeted deletion and replacement mutations of the T-cell receptor β-chain enhancer: the role of enhancer elements in controlling V(D)J recombination accessibility. Proc. Natl Acad. Sci. USA 93, 7871–7876 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Oestreich, K. J. et al. Regulation of TCR β gene assembly by a promoter/enhancer holocomplex. Immunity 24, 381–391 (2006).

    Article  CAS  PubMed  Google Scholar 

  113. Spicuglia, S. et al. Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes. Mol. Cell 10, 1479–1487 (2002).

    Article  CAS  PubMed  Google Scholar 

  114. Whitehurst, C. E., Chattopadhyay, S. & Chen, J. Control of V(D)J recombinational accessibility of the Dβ1 gene segment at the TCRβ locus by a germline promoter. Immunity 10, 313–322 (1999).

    Article  CAS  PubMed  Google Scholar 

  115. Whitehurst, C. E., Schlissel, M. S. & Chen, J. Deletion of germline promoter PDβ1 from the TCRβ locus causes hypermethylation that impairs Dβ1 recombination by multiple mechanisms. Immunity 13, 703–714 (2000).

    Article  CAS  PubMed  Google Scholar 

  116. McMillan, R. E. & Sikes, M. L. Differential activation of dual promoters alters Dβ2 germline transcription during thymocyte development. J. Immunol. 180, 3218–3228 (2008).

    Article  CAS  PubMed  Google Scholar 

  117. McMillan, R. E. & Sikes, M. L. Promoter activity 5′ of Dβ2 is coordinated by E47, Runx1, and GATA-3. Mol. Immunol. 46, 3009–3017 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Osipovich, O. et al. Essential function for SWI-SNF chromatin-remodeling complexes in the promoter-directed assembly of Tcrb genes. Nature Immunol. 8, 809–816 (2007).

    Article  CAS  Google Scholar 

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Acknowledgements

The authors wish to thank E. Oltz, G. Teng, K. Shetty and J. Banerjee for comments on the manuscript. We apologize that not all of the relevant literature could be cited owing to space constraints.

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  1. Department of Immunobiology and Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, 06520-8011, Connecticut, USA

    David G. Schatz

  2. Department of Immunology & Microbiology, School of Medicine, Xi'an JiaoTong University, Xian Shaanxi, 710049, China

    Yanhong Ji

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Glossary

V(D)J recombination

Somatic rearrangement of variable (V), diversity (D) and joining (J) regions of the genes that encode antigen receptors, leading to repertoire diversity of immunoglobulins and T cell receptors.

Chromosomal translocation

An aberration of chromosome structure in which a portion of one chromosome is broken off and becomes attached to another.

Non-homologous end joining

(NHEJ). A DNA repair process that joins broken DNA ends (double strand breaks) without using homologous DNA as a template. Components of this pathway include the proteins Ku70 (also known as XRCC6), Ku80 (also known as XRCC5), Artemis, X-ray repair cross-complementing protein 4 (XRCC4), DNA ligase IV and the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs).

Chromatin

The combination of DNA, histones and other proteins that comprises eukaryotic chromosomes. The basic repeating unit of chromatin is the nucleosome, which consists of an octamer of histone proteins around which ∼146 base pairs of DNA is wound.

Allelic exclusion

In theory, every B cell has the potential to produce two immunoglobulin heavy chains and two immunoglobulin light chains. In practice, however, a B cell produces only one immunoglobulin heavy chain and the majority produce only one immunoglobulin light chain. Similarly, most T cells produce only a single T cell receptor β-chain protein. The process by which the production of two different chains is prevented is known as allelic exclusion. Allelic exclusion is accomplished primarily through regulated V(D)J recombination.

Germline transcription

Transcription of unrearranged antigen receptor gene loci that begins before or coincident with their activation. It is not thought to produce functional protein, and the promoter and initiation sites are often lost in the subsequent rearrangement events.

Nucleosome

The fundamental structural unit of eukaryotic chromosomes. It consists of pairs of each of the core histones (H2A, H2B, H3 and H4), thereby creating the histone octamer, and a single molecule of the linker histone H1. The nucleosome spans ∼146 base pairs of DNA.

Chromatin remodelling complex

An enzymatic complex that remodels the DNA–nucleosome architecture and thus can determine transcriptional activity. The SWI–SNF ATPase is an example of a complex that remodels chromatin.

Antisense transcription

Transcription in the opposite direction and of the opposite strand from that used to generate the normal product of a gene. It is not thought to generate a protein product but instead might alter chromatin structure either directly (via the act of transcription) or indirectly (via the antisense RNA produced).

Heterochromatin

High-density regions in the nucleus that are thought to contain compacted chromatin structures associated with silent genes.

DNase I hypersensitive site

A site of nuclease sensitivity when nuclei from cells are exposed to limiting concentrations of the enzyme DNase I. The digested regions of DNA correspond to sites of open DNA, which might be transcription factor binding sites or areas of altered nucleosome conformation.

Bromodomain

A module of ∼110 amino acids that is found in several transcriptional regulators. A bromodomain consists of a four-helix bundle with a single binding pocket for Nɛ-acetyl-lysine on histone tails.

Pro-B cell

A cell in the earliest stage of B cell development in the bone marrow. Pro-B cells are characterized by incomplete immunoglobulin heavy chain rearrangements and are defined as CD19+ and cytoplasmic IgM− or, sometimes, as B220+CD43+ (by the Hardy classification scheme).

Pericentric heterochromatin

Regions of very densely packed chromatin fibres located near the centromere of each chromosome. These regions are typically inactive and often cluster to form discrete clumps in the nucleus.

Fluorescence in situ hybridization

(FISH). The use of fluorescent probes to visually label specific DNA sequences in the nuclei of cells that are in the interphase or metaphase stages of mitosis.

Chromatin immunoprecipitation

An experimental technique that analyses direct binding of an endogenous transcription factor to chromatin by fixation with formaldehyde followed by immunoprecipitation with a transcription factor-specific antibody. Gene-specific enrichment is then assessed by polymerase chain reaction analysis of the immunoprecipitated DNA.

Recombination centre

A region of an antigen receptor locus that is characterized by strong binding of recombination activating gene 1 (RAG1) and RAG2 and high levels of germline transcription, RNA polymerase II, histone acetylation and trimethylated histone H3 lysine 4 (H3K4me3).

Cryptic RSS

A region of DNA that resembles a true recombination signal sequence (RSS) in some of its functionally important sequence features but does not lie adjacent to an antigen receptor gene segment.

Homologous recombination

Genetic recombination that occurs between regions of DNA with long stretches of homology. This occurs with a low frequency in somatic cells and at a much higher frequency in germ cells.

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Schatz, D., Ji, Y. Recombination centres and the orchestration of V(D)J recombination. Nat Rev Immunol 11, 251–263 (2011). https://doi.org/10.1038/nri2941

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