Key Points
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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.
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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.
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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.
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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.
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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.
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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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References
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).
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).
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.
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.
Lewis, S. M. The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. Adv. Immunol. 56, 27–150 (1994).
Swanson, P. C. The bounty of RAGs: recombination signal complexes and reaction outcomes. Immunol. Rev. 200, 90–114 (2004).
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).
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).
Jones, J. M. & Gellert, M. Ordered assembly of the V(D)J synaptic complex ensures accurate recombination. EMBO J. 21, 4162–4171 (2002).
Gellert, M. V(D)J recombination: RAG proteins, repair factors, and regulation. Annu. Rev. Biochem. 71, 101–132 (2002).
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).
Hesslein, D. G. & Schatz, D. G. Factors and forces controlling V(D)J recombination. Adv. Immunol. 78, 169–232 (2001).
Yancopoulos, G. D. & Alt, F. W. Regulation of the assembly and expression of variable-region genes. Annu. Rev. Immunol. 4, 339–368 (1986).
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).
Goldmit, M. & Bergman, Y. Monoallelic gene expression: a repertoire of recurrent themes. Immunol. Rev. 200, 197–214 (2004).
Krangel, M. S. T cell development: better living through chromatin. Nature Immunol. 8, 687–694 (2007).
Schlissel, M. S. Regulating antigen-receptor gene assembly. Nature Rev. Immunol. 3, 890–899 (2003).
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.
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).
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).
McBlane, F. & Boyes, J. Stimulation of V(D)J recombination by histone acetylation. Curr. Biol. 10, 483–486 (2000).
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).
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).
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).
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).
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).
Kondilis-Mangum, H. D. et al. Transcription-dependent mobilization of nucleosomes at accessible TCR gene segments in vivo. J. Immunol. 184, 6970–6977 (2010).
Kaplan, N. et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458, 362–366 (2009).
Segal, E. & Widom, J. What controls nucleosome positions? Trends Genet. 25, 335–343 (2009).
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).
Segal, E. & Widom, J. Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr. Opin. Struct. Biol. 19, 65–71 (2009).
Chowdhury, D. & Sen, R. Regulation of immunoglobulin heavy-chain gene rearrangements. Immunol. Rev. 200, 182–196 (2004).
Krangel, M. S. Mechanics of T cell receptor gene rearrangement. Curr. Opin. Immunol. 21, 133–139 (2009).
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).
Schlissel, M. S. Regulation of activation and recombination of the murine Igκ locus. Immunol. Rev. 200, 215–223 (2004).
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.
Abarrategui, I. & Krangel, M. S. Noncoding transcription controls downstream promoters to regulate T-cell receptor α recombination. EMBO J. 26, 4380–4390 (2007).
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).
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).
Bolland, D. J. et al. Antisense intergenic transcription in V(D)J recombination. Nature Immunol. 5, 630–637 (2004).
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).
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).
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).
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).
Oettinger, M. A. How to keep V(D)J recombination under control. Immunol. Rev. 200, 165–181 (2004).
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).
Osipovich, O. et al. Targeted inhibition of V(D)J recombination by a histone methyltransferase. Nature Immunol. 5, 309–316 (2004).
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).
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).
Smale, S. T. The establishment and maintenance of lymphocyte identity through gene silencing. Nature Immunol. 4, 607–615 (2003).
Workman, J. L. Nucleosome displacement in transcription. Genes Dev. 20, 2009–2017 (2006).
Li, B., Carey, M. & Workman, J. L. The role of chromatin during transcription. Cell 128, 707–719 (2007).
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
Shogren-Knaak, M. et al. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311, 844–847 (2006).
Zhang, Y. et al. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol. Cell 24, 559–568 (2006).
Wang, X. et al. Regulation of Tcrb recombination ordering by c-Fos-dependent RAG deposition. Nature Immunol. 9, 794–801 (2008).
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).
Hesslein, D. G. et al. Pax5 is required for recombination of transcribed, acetylated, 5′ IgH V gene segments. Genes Dev. 17, 37–42 (2003).
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).
Kosak, S. T. & Groudine, M. Form follows function: the genomic organization of cellular differentiation. Genes Dev. 18, 1371–1384 (2004).
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).
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.
Skok, J. A. et al. Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes. Nature Immunol. 8, 378–387 (2007).
Hewitt, S. L. et al. RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci. Nature Immunol. 10, 655–664 (2009).
Goldmit, M. et al. Epigenetic ontogeny of the Igk locus during B cell development. Nature Immunol. 6, 198–203 (2005).
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).
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).
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).
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).
Singh, N., Bergman, Y., Cedar, H. & Chess, A. Biallelic germline transcription at the κ immunoglobulin locus. J. Exp. Med. 197, 743–750 (2003).
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).
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).
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).
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).
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.
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).
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).
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).
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).
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.
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.
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).
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).
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).
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.
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).
Ji, Y. et al. Promoters, enhancers, and transcription target RAG1 binding during V(D)J recombination. J. Exp. Med. 207, 2809–2816 (2010).
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).
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).
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).
Matthews, A. G. W. & Oettinger, M. A. RAG: a recombinase diversified. Nature Immunol. 10, 817–821 (2009).
Corneo, B. et al. Rag mutations reveal robust alternative end joining. Nature 449, 483–486 (2007).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Oestreich, K. J. et al. Regulation of TCR β gene assembly by a promoter/enhancer holocomplex. Immunity 24, 381–391 (2006).
Spicuglia, S. et al. Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes. Mol. Cell 10, 1479–1487 (2002).
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).
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).
McMillan, R. E. & Sikes, M. L. Differential activation of dual promoters alters Dβ2 germline transcription during thymocyte development. J. Immunol. 180, 3218–3228 (2008).
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).
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).
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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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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DOI: https://doi.org/10.1038/nri2941
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