Abstract
V(D)J recombination is responsible for assembling the functional immunoglobulin and T cell receptor genes in cells of the immune system. This specialized DNA rearrangement is initiated by the RAG1 and RAG2 proteins, lymphoid-specific factors which collaborate to make double-strand breaks at specific sites that flank segments of coding sequence. During breakage, the ends of the coding DNA are converted to DNA hairpins. Joining of the broken ends is then carried out by the non-homologous end-joining pathway, after the hairpin ends are cut open by the Artemis protein. The RAG1/2 complex can also carry out transpositional recombination, a reaction that helps to explain how the RAG proteins work, and supports previous suggestions that V(D)J recombination evolved from a mobile DNA.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Agrawal A, Eastman QM, Schatz DG (1998) Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394:744–751
Agrawal A, 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
Akamatsu Y, Monroe R, Dudley DD, Elkin SK, Gartner F, Talukder SR, Takahama Y, Alt FW, Bassing CH, Oettinger MA (2003) Deletion of the RAG2 C terminus leads to impaired lymphoid development in mice. Proc Natl Acad Sci USA 100:1209–1214
Aravind L, Koonin EV (1999) Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol 287:1023–1040
Bailin T, Mo X, Sadofsky MJ (1999) A RAG1 and RAG2 tetramer complex is active in cleavage in V(D)J recombination. Mol Cell Biol 19:4664–4671
Bassing CH, Alt FW, Hughes MM, D’Auteuil M, Wehrly TD, Woodman BB, Gartner F, White JM, Davidson L, Sleckman BP (2000) Recombination signal sequences restrict chromosomal V(D)J recombination beyond the 12/23 rule. Nature 405:583–586
Bellon SF, Rodgers KK, Schatz DG, Coleman JE, Steitz TA (1997) Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Nat Struct Biol 4:586–591
Besmer E, Mansilla-Soto J, Cassard S, Sawchuk DJ, Brown G, Sadofsky M, Lewis SM, Nussenzweig MC, Cortes P (1998) Hairpin coding end opening is mediated by RAG1 and RAG2 proteins. Mol Cell 2:817–828
Bhasin A, Goryshin IY, Reznikoff WS (1999) Hairpin formation in Tn5 transposition. J Biol Chem 274:37021–37029
Callebaut I, Mornon JP (1998) 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
Chatterji M, Tsai CL, Schatz DG (2006) Mobilization of RAG-generated signal ends by transposition and insertion in vivo. Mol Cell Biol 26:1558–1568
Clatworthy AE, Valencia MA, Haber JE, Oettinger MA (2003) V(D)J recombination and RAG-mediated transposition in yeast. Mol Cell 12:489–499
Cuomo CA, Mundy CL, Oettinger MA (1996) DNA sequence and structure requirements for cleavage of V(D)J recombination signal sequences. Mol Cell Biol 16:5683–5690
Curry JD, Geier JK, Schlissel MS (2005) Single-strand recombination signal sequence nicks in vivo: evidence for a capture model of synapsis. Nat Immunol 6:1272–1279
de Jager M, van Noort J, van Gent DC, Dekker C, Kanaar R, Wyman C (2001) Human Rad50/Mre11 is a flexible complex that can tether DNA ends. Mol Cell 8:1129–1135
Eastman QM, Leu TM, Schatz DG (1996) Initiation of V(D)J recombination in vitro obeying the 12/23 rule. Nature 380:85–88
Elkin SK, Ivanov D, Ewalt M, Ferguson CG, Hyberts SG, Sun ZY, Prestwich GD, Yuan J, Wagner G, Oettinger MA, Gozani OP (2005) A PHD finger motif in the C terminus of RAG2 modulates recombination activity. J Biol Chem 280:28701–28710
Elkin SK, Matthews AG, Oettinger MA (2003) The C-terminal portion of RAG2 protects against transposition in vitro. EMBO J 22:1931–1938
Feeney AJ, Tang A, Ogwaro KM (2000) B-cell repertoire formation: role of the recombination signal sequence in non-random V segment utilization. Immunol Rev 175:59–69
Fugmann SD, Lee AI, Shockett PE, Villey IJ, Schatz DG (2000a) The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annu Rev Immunol 18:495–527
Fugmann SD, Messier C, Novack LA, Cameron RA, Rast JP (2006) An ancient evolutionary origin of the Rag1/2 gene locus. Proc Natl Acad Sci USA 103:3728–3733
Fugmann SD, Villey IJ, Ptaszek LM, Schatz DG (2000b) Identification of two catalytic residues in RAG1 that define a single active site within the RAG1/RAG2 protein complex. Mol Cell 5:97–107
Gellert M (2002) V(D)J recombination:RAG proteins, repair factors, and regulation. Annu Rev Biochem 71:101–132
Goodarzi A, Yu Y, Riballo E, Douglas P, Walker SA, Harer C, Ye R, Marchetti C, Morrice N, Jeggo PA, Lees-Miller SP (2006) DNA-PK autophosphorylation facilitates Artemis endonuclease activity. EMBO J: in press
Han JO, Steen SB, Roth DB (1997) Ku86 is not required for protection of signal ends or for formation of nonstandard V(D)J recombination products. Mol Cell Biol 17:2226–2234
Hesse JE, Lieber MR, Mizuuchi K, Gellert M (1989) V(D)J recombination: a functional definition of the joining signals. Genes Dev 3:1053–1061
Hiom K, Gellert M (1997) A stable RAG1-RAG2-DNA complex that is active in V(D)J cleavage. Cell 88:65–72
Hiom K, Gellert M (1998) Assembly of a 12/23 paired signal complex: A critical control point in V(D)J recombination. Mol Cell 1:1011–1019
Hiom K, Melek M, Gellert M (1998) DNA transposition by the RAG1 and RAG2 proteins: A possible source of oncogenic translocations. Cell 94:463–470
Jones JM, Gellert M (2001) Intermediates in V(D)J recombination: A stable RAG1/2 complex sequesters cleaved RSS ends. Proc Natl Acad Sci USA 98:12926–12931
Jones JM, Gellert M (2002) Ordered assembly of the V(D)J synaptic complex ensures accurate recombination. EMBO J 21:4162–4171
Jones JM, Gellert M (2003) Autoubiquitylation of the V(D)J recombinase protein RAG1. Proc Natl Acad Sci USA 100:15446–15451
Jung D, Giallourakis C, Mostoslavsky R, Alt FW (2006) Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus. Annu Rev Immunol 24:541–570
Kapitonov VV, Jurka J (2005) RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3:e181
Kennedy AK, Guhathakurta A, Kleckner N, Haniford DB (1998) Tn10 transposition via a DNA hairpin intermediate. Cell 95:125–134
Kim DR, Dai Y, Mundy CL, Yang W, Oettinger MA (1999) Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase. Genes Dev 13:3070–3080
Kim DR, Oettinger MA (1998) Functional analysis of coordinated cleavage in V(D)J recombination. Mol Cell Biol 18:4679–4688
Kirch SA, Rathbun GA, Oettinger MA (1998) Dual role of RAG2 in V(D)J recombination: catalysis and regulation of ordered Ig gene assembly. EMBO J 17:4881–4886
Lafaille JJ, DeCloux A, Bonneville M, Takagaki Y, Tonegawa S (1989) Junctional sequences of T cell receptor gamma delta genes: implications for gamma delta T cell lineages and for a novel intermediate of V-(D)-J joining. Cell 59:859–870
Landree MA, Wibbenmeyer JA, Roth DB (1999) Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination. Genes Dev 13:3059–3069
Lee GS, Neiditch MB, Salus SS, Roth DB (2004) RAG proteins shepherd double-strand breaks to a specific pathway, suppressing error-prone repair, but RAG nicking initiates homologous recombination. Cell 117:171–184
Lee GS, Neiditch MB, Sinden RR, Roth DB (2002) Targeted transposition by the V(D)J recombinase. Mol Cell Biol 22:2068–2077
Lewis SM (1994) The mechanism of V(D)J joining: Lessons from molecular, immunological, and comparative analyses. Adv Immunol 56:27–150
Li Z, Dordai DI, Lee J, Desiderio S (1996) A conserved degradation signal regulates RAG-2 accumulation during cell division and links V(D)J recombination to the cell cycle. Immunity 5:575–589
Ma Y, Pannicke U, Schwarz K, Lieber MR (2002) Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell 108:781–794
Ma Y, Schwarz K, Lieber MR (2005) The Artemis:DNA-PKcs endonuclease cleaves DNA loops, flaps, and gaps. DNA Repair (Amst) 4:845–851
McBlane JF, van Gent DC, Ramsden DA, Romeo C, Cuomo CA, Gellert M, Oettinger MA (1995) Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 pro-teins and occurs in two steps. Cell 83:387–395
Melek M, Gellert M (2000) RAG1/2-mediated resolution of transposition intermediates: Two pathways and possible consequences. Cell 101:625–633
Melek M, Gellert M, van Gent DC (1998) Rejoining of DNA by the RAG1 and RAG2 proteins. Science 280:301–303
Messier TL, O’Neill JP, Hou SM, Nicklas JA, Finette BA (2003) In vivo transposition mediated by V(D)J recombinase in human T lymphocytes. EMBO J 22:1381–1388
Mizuta R, Mizuta M, Araki S, Kitamura D (2002) RAG2 is down-regulated by cytoplasmic sequestration and ubiquitin-dependent degradation. J Biol Chem 277:41423–41427
Mombaerts P, Iacomini J, Johnson RS, Herrup K, Tonegawa S, Papaioannou VE (1992) RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68:869–877
Moshous D, Callebaut I, de Chasseval R, Corneo B, Cavazzana-Calvo M, Le Deist F, Tezcan I, Sanal O, Bertrand Y, Philippe N, Fischer A, de Villartay J-P (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
Mundy CL, Patenge N, Matthews AG, Oettinger MA (2002) Assembly of the RAG1/RAG2 synaptic complex. Mol Cell Biol 22:69–77
Neiditch MB, Lee GS, Huye LE, Brandt VL, Roth DB (2002) The V(D)J recombinase efficiently cleaves and transposes signal joints. Mol Cell 9:871–878
Noordzij JG, Verkaik NS, Hartwig NG, de Groot R, van Gent DC, van Dongen JJ (2000) N-terminal truncated human RAG1 proteins can direct T-cell receptor but not immunoglobulin gene rearrangements. Blood 96:203–209
Oettinger MA, Schatz DG, Gorka C, Baltimore D (1990) RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248:1517–1523
Paull TT, Gellert M (2000) A mechanistic basis for Mre11-directed DNA joining at microhomologies. Proc Natl Acad Sci USA 97:6409–6414
Qiu JX, Kale SB, Yarnell Schultz H, Roth DB (2001) Separation-of-function mutants reveal critical roles for RAG2 in both the cleavage and joining steps of V(D)J recombination. Mol Cell 7:77–87
Raghavan SC, Tong J, Lieber MR (2006) Hybrid joint formation in human V(D)J recombination requires nonhomologous DNA end joining. DNA Repair (Amst) 5:278–285
Ramsden DA, McBlane JF, van Gent DC, Gellert M (1996) Distinct DNA sequence and structure requirements for the two steps of V(D)J recombination signal cleavage. EMBO J 15:3197–3206
Ramsden DA, Paull TT, Gellert M (1997) Cell-free V(D)J recombination. Nature 388:488–491
Ramsden DA, Wu GE (1991) Mouse κ light-chain recombination signal sequences mediate recombination more frequently than do those of λ light chain. Proc Natl Acad Sci USA 88:10721–10725
Reddy YV, Perkins EJ, Ramsden DA (2006) Genomic instability due to V(D)J recombination-associated transposition. Genes Dev 20:1575–1582
Rooney S, Alt FW, Lombard D, Whitlow S, Eckersdorff M, Fleming J, Fugmann S, Ferguson DO, Schatz DG, Sekiguchi J (2003) Defective DNA repair and increased genomic instability in Artemis-deficient murine cells. J Exp Med 197:553–565
Rooney S, Sekiguchi J, Zhu C, Cheng HL, Manis J, Whitlow S, DeVido J, Foy D, Chaudhuri J, Lombard D, Alt FW (2002) Leaky Scid phenotype associated with defective V(D)J coding end processing in Artemis-deficient mice. Mol Cell 10:1379–1390
Roth DB, Nakajima PB, Menetski JP, Bosma MJ, Gellert M (1992) V(D)J recombination in mouse thymocytes: double-strand breaks near T cell receptor d rearrangement signals. Cell 69:41–53
Roth DB, Menetski JP, Nakajima PB, Bosma MJ, Gellert M (1992) V(D)J recombination: broken DNA molecules with covalently sealed (hairpin) coding ends in scid mouse thymocytes. Cell 70:983–991
Sakano H, Huppi K, Heinrich G, Tonegawa S (1979) Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature 280:288–294
Sawchuk DJ, Weis-Garcia F, Malik S, Besmer E, Bustin M, Nussenzweig MC, Cortes P (1997) V(D)J recombination: modulation of RAG1 and RAG2 cleavage activity on 12/23 substrates by whole cell extract and DNA-bending proteins. J Exp Med 185:2025–2032
Schwarz K, Gauss GH, Ludwig L, Pannicke U, Li Z, Lindner D, Friedrich W, Seger RA, Hansen-Hagge TE, Desiderio S, Lieber MR, Bartram CR (1996) RAG mutations in human B cell-negative SCID. Science 274:97–99
Sekiguchi JA, Whitlow S, Alt FW (2001) Increased accumulation of hybrid V(D)J joins in cells expressing truncated versus full-length RAGs. Mol Cell 8:1383–1390
Shinkai Y, Rathbun G, Lam K-P, Oltz EM, Stewart V, Mendelsohn M, Charron J, Datta M, Young F, Stall AM, Alt FW (1992) RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement. Cell 68:855–867
Shockett PE, Schatz DG (1999) DNA hairpin opening mediated by the RAG1 and RAG2 proteins. Mol Cell Biol 19:4159–4166
Steen SB, Gomelsky L, Roth DB (1996) The 12/23 rule is enforced at the cleavage step of V(D)J recombination in vivo. Genes Cells 1:543–553
Steen SB, Han JO, Mundy C, Oettinger MA, Roth DB (1999) Roles of the “dispensable” portions of RAG-1 and RAG-2 in V(D)J recombination. Mol Cell Biol 19:3010–3017
Swanson PC (2002) A RAG-1/RAG-2 tetramer supports 12/23-regulated synapsis, cleavage, and transposition of V(D)J recombination signals. Mol Cell Biol 22:7790–7801
Swanson PC, Volkmer D, Wang L (2004) Full-length RAG-2, and not full-length RAG-1, specifically suppresses RAG-mediated transposition but not hybrid joint for-mation or disintegration. J Biol Chem 279:4034–4044
Tonegawa S (1983) Somatic generation of antibody diversity. Nature 302:575–581
Tsai CL, Schatz DG (2003) Regulation of RAG1/RAG2-mediated transposition by GTP and the C-terminal region of RAG2. EMBO J 22:1922–1930
van Gent DC, Hiom K, Paull TT, Gellert M (1997) Stimulation of V(D)J cleavage by high mobility group proteins. EMBO J 16:2265–2670
van Gent DC, Ramsden DA, Gellert M (1996) The RAG1 and RAG2 proteins establish the 12/23 rule in V(D)J recombination. Cell 85:107–113
Villa A, Santagata S, Bozzi F, Giliani S, Frattini A, Imberti L, Gatta LB, Ochs HD, Schwarz K, Notarangelo LD, Vezzoni P, Spanopoulou E (1998) Partial V(D)J recombination activity leads to Omenn syndrome. Cell 93:885–896
Villa A, Sobacchi C, Notarangelo LD, Bozzi F, Abinun M, Abrahamsen TG, Arkwright PD, Baniyash M, Brooks EG, Conley ME, Cortes P, Duse M, Fasth A, Filipovich AM, Infante AJ, Jones A, Mazzolari E, Muller SM, Pasic S, Rechavi G, Sacco MG, Santagata S, Schroeder ML, Seger R, Strina D, Ugazio A, Valiaho J, Vihinen M, Vogler LB, Ochs H, Vezzoni P, Friedrich W, Schwarz K (2001) V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. Blood 97:81–88
West KL, Singha NC, De Ioannes P, Lacomis L, Erdjument-Bromage H, Tempst P, Cortes P (2005) A direct interaction between the RAG2 C terminus and the core histones is required for efficient V(D)J recombination. Immunity 23:203–212
West RB, Lieber MR (1998) The RAG-HMG1 complex enforces the 12/23 rule of V(D)J recombination specifically at the double-hairpin formation step. Mol Cell Biol 18:6408–6415
Yarnell Schultz H, Landree MA, Qiu JX, Kale SB, Roth DB (2001) Joining-deficient RAG1 mutants block V(D)J recombination in vivo and hairpin opening in vitro. Mol Cell 7:65–75
Yu K, Lieber MR (2000) The nicking step in V(D)J recombination is independent of synapsis: implications for the immune repertoire. Mol Cell Biol 20:7914–7921
Yurchenko V, Xue Z, Sadofsky M (2003) The RAG1 N-terminal domain is an E3 ubiquitin ligase. Genes Dev 17:581–585
Zhou L, Mitra R, Atkinson PW, Hickman AB, Dyda F, Craig NL (2004) Transposition of hAT elements links transposable elements and V(D)J recombination. Nature 432:995–1001
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Gellert, M. (2007). V(D)J recombination: mechanism and consequences. In: Aguilera, A., Rothstein, R. (eds) Molecular Genetics of Recombination. Topics in Current Genetics, vol 17. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71021-9_16
Download citation
DOI: https://doi.org/10.1007/978-3-540-71021-9_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-71020-2
Online ISBN: 978-3-540-71021-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)