1
|
Johnston R, Mathias B, Crowley SJ, Schmidt HA, White LS, Mosammaparast N, Green AM, Bednarski JJ. Nuclease-independent functions of RAG1 direct distinct DNA damage responses in B cells. EMBO Rep 2023; 24:e55429. [PMID: 36382770 PMCID: PMC9827558 DOI: 10.15252/embr.202255429] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022] Open
Abstract
Developing B cells generate DNA double-stranded breaks (DSBs) to assemble immunoglobulin receptor (Ig) genes necessary for the expression of a mature B cell receptor. These physiologic DSBs are made by the RAG endonuclease, which is comprised of the RAG1 and RAG2 proteins. In pre-B cells, RAG-mediated DSBs activate the ATM kinase to coordinate canonical and non-canonical DNA damage responses (DDR) that trigger DSB repair and B cell developmental signals, respectively. Whether this broad cellular response is distinctive to RAG DSBs is poorly understood. To delineate the factors that direct DDR signaling in B cells, we express a tetracycline-inducible Cas9 nuclease in Rag1-deficient pre-B cells. Both RAG- and Cas9-mediated DSBs at Ig genes activate canonical DDR. In contrast, RAG DSBs, but not Cas9 DSBs, induce the non-canonical DDR-dependent developmental program. This unique response to RAG DSBs is, in part, regulated by non-core regions of RAG1. Thus, B cells trigger distinct cellular responses to RAG DSBs through unique properties of the RAG endonuclease that promotes activation of B cell developmental programs.
Collapse
Affiliation(s)
- Rachel Johnston
- Department of PediatricsWashington University School of MedicineSt. LouisMOUSA
| | - Brendan Mathias
- Department of PediatricsWashington University School of MedicineSt. LouisMOUSA
| | - Stephanie J Crowley
- Department of PediatricsWashington University School of MedicineSt. LouisMOUSA
| | - Haley A Schmidt
- Department of PediatricsWashington University School of MedicineSt. LouisMOUSA
| | - Lynn S White
- Department of PediatricsWashington University School of MedicineSt. LouisMOUSA
| | - Nima Mosammaparast
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisMOUSA
| | - Abby M Green
- Department of PediatricsWashington University School of MedicineSt. LouisMOUSA
| | - Jeffrey J Bednarski
- Department of PediatricsWashington University School of MedicineSt. LouisMOUSA
| |
Collapse
|
2
|
Bai W, Zhao B, Gu M, Dong J. Alternative end-joining in BCR gene rearrangements and translocations. Acta Biochim Biophys Sin (Shanghai) 2022; 54:782-795. [PMID: 35593472 PMCID: PMC9828324 DOI: 10.3724/abbs.2022051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) occur during antigen receptor gene recombination, namely V(D)J recombination in developing B lymphocytes and class switch recombination (CSR) in mature B cells. Repair of these DSBs by classical end-joining (c-NHEJ) enables the generation of diverse BCR repertoires for efficient humoral immunity. Deletion of or mutation in c-NHEJ genes in mice and humans confer various degrees of primary immune deficiency and predisposition to lymphoid malignancies that often harbor oncogenic chromosomal translocations. In the absence of c-NHEJ, alternative end-joining (A-EJ) catalyzes robust CSR and to a much lesser extent, V(D)J recombination, but the mechanisms of A-EJ are only poorly defined. In this review, we introduce recent advances in the understanding of A-EJ in the context of V(D)J recombination and CSR with emphases on DSB end processing, DNA polymerases and ligases, and discuss the implications of A-EJ to lymphoid development and chromosomal translocations.
Collapse
Affiliation(s)
- Wanyu Bai
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Bo Zhao
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Mingyu Gu
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Junchao Dong
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China,Correspondence address. Tel: +86-20-87330571; E-mail:
| |
Collapse
|
3
|
Christie SM, Fijen C, Rothenberg E. V(D)J Recombination: Recent Insights in Formation of the Recombinase Complex and Recruitment of DNA Repair Machinery. Front Cell Dev Biol 2022; 10:886718. [PMID: 35573672 PMCID: PMC9099191 DOI: 10.3389/fcell.2022.886718] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
V(D)J recombination is an essential mechanism of the adaptive immune system, producing a diverse set of antigen receptors in developing lymphocytes via regulated double strand DNA break and subsequent repair. DNA cleavage is initiated by the recombinase complex, consisting of lymphocyte specific proteins RAG1 and RAG2, while the repair phase is completed by classical non-homologous end joining (NHEJ). Many of the individual steps of this process have been well described and new research has increased the scale to understand the mechanisms of initiation and intermediate stages of the pathway. In this review we discuss 1) the regulatory functions of RAGs, 2) recruitment of RAGs to the site of recombination and formation of a paired complex, 3) the transition from a post-cleavage complex containing RAGs and cleaved DNA ends to the NHEJ repair phase, and 4) the potential redundant roles of certain factors in repairing the break. Regulatory (non-core) domains of RAGs are not necessary for catalytic activity, but likely influence recruitment and stabilization through interaction with modified histones and conformational changes. To form long range paired complexes, recent studies have found evidence in support of large scale chromosomal contraction through various factors to utilize diverse gene segments. Following the paired cleavage event, four broken DNA ends must now make a regulated transition to the repair phase, which can be controlled by dynamic conformational changes and post-translational modification of the factors involved. Additionally, we examine the overlapping roles of certain NHEJ factors which allows for prevention of genomic instability due to incomplete repair in the absence of one, but are lethal in combined knockouts. To conclude, we focus on the importance of understanding the detail of these processes in regards to off-target recombination or deficiency-mediated clinical manifestations.
Collapse
Affiliation(s)
- Shaun M. Christie
- *Correspondence: Shaun M. Christie, ; Carel Fijen, ; Eli Rothenberg,
| | - Carel Fijen
- *Correspondence: Shaun M. Christie, ; Carel Fijen, ; Eli Rothenberg,
| | - Eli Rothenberg
- *Correspondence: Shaun M. Christie, ; Carel Fijen, ; Eli Rothenberg,
| |
Collapse
|
4
|
Libri A, Marton T, Deriano L. The (Lack of) DNA Double-Strand Break Repair Pathway Choice During V(D)J Recombination. Front Genet 2022; 12:823943. [PMID: 35082840 PMCID: PMC8785701 DOI: 10.3389/fgene.2021.823943] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023] Open
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that can be mended via several DNA repair pathways. Multiple factors can influence the choice and the restrictiveness of repair towards a given pathway in order to warrant the maintenance of genome integrity. During V(D)J recombination, RAG-induced DSBs are (almost) exclusively repaired by the non-homologous end-joining (NHEJ) pathway for the benefit of antigen receptor gene diversity. Here, we review the various parameters that constrain repair of RAG-generated DSBs to NHEJ, including the peculiarity of DNA DSB ends generated by the RAG nuclease, the establishment and maintenance of a post-cleavage synaptic complex, and the protection of DNA ends against resection and (micro)homology-directed repair. In this physiological context, we highlight that certain DSBs have limited DNA repair pathway choice options.
Collapse
Affiliation(s)
- Alice Libri
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| | - Timea Marton
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| |
Collapse
|
5
|
The CRL4VPRBP(DCAF1) E3 ubiquitin ligase directs constitutive RAG1 degradation in a non-lymphoid cell line. PLoS One 2021; 16:e0258683. [PMID: 34648572 PMCID: PMC8516306 DOI: 10.1371/journal.pone.0258683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/02/2021] [Indexed: 11/19/2022] Open
Abstract
The development of B and T lymphocytes critically depends on RAG1/2 endonuclease activity to mediate antigen receptor gene assembly by V(D)J recombination. Although control of RAG1/2 activity through cell cycle- and ubiquitin-dependent degradation of RAG2 has been studied in detail, relatively little is known about mechanisms regulating RAG1 stability. We recently demonstrated that VprBP/DCAF1, a substrate adaptor for the CRL4 E3 ubiquitin ligase complex, is required to maintain physiological levels of RAG1 protein in murine B cells by facilitating RAG1 turnover. Loss of VprBP/DCAF1 in vivo results in elevated RAG1 expression, excessive V(D)J recombination, and immunoglobulin light chain repertoire skewing. Here we show that RAG1 is constitutively degraded when ectopically expressed in a human fibroblast cell line. Consistent with our findings in murine B cells, RAG1 turnover under these conditions is sensitive to loss of VprBP, as well as CRL4 or proteasome inhibition. Further evidence indicates that RAG1 degradation is ubiquitin-dependent and that RAG1 association with the CRL4VPRBP/DCAF1 complex is independent of CUL4 activation status. Taken together, these findings suggest V(D)J recombination co-opts an evolutionarily conserved and constitutively active mechanism to ensure rapid RAG1 turnover to restrain excessive RAG activity.
Collapse
|
6
|
Beilinson HA, Glynn RA, Yadavalli AD, Xiao J, Corbett E, Saribasak H, Arya R, Miot C, Bhattacharyya A, Jones JM, Pongubala JM, Bassing CH, Schatz DG. The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination. J Exp Med 2021; 218:e20210250. [PMID: 34402853 PMCID: PMC8374863 DOI: 10.1084/jem.20210250] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/30/2021] [Accepted: 07/30/2021] [Indexed: 11/29/2022] Open
Abstract
Immunoglobulin and T cell receptor gene assembly depends on V(D)J recombination initiated by the RAG1-RAG2 recombinase. The RAG1 N-terminal region (NTR; aa 1-383) has been implicated in regulatory functions whose influence on V(D)J recombination and lymphocyte development in vivo is poorly understood. We generated mice in which RAG1 lacks ubiquitin ligase activity (P326G), the major site of autoubiquitination (K233R), or its first 215 residues (Δ215). While few abnormalities were detected in R1.K233R mice, R1.P326G mice exhibit multiple features indicative of reduced recombination efficiency, including an increased Igκ+:Igλ+ B cell ratio and decreased recombination of Igh, Igκ, Igλ, and Tcrb loci. Previous studies indicate that synapsis of recombining partners during Igh recombination occurs through two pathways: long-range scanning and short-range collision. We find that R1Δ215 mice exhibit reduced short-range Igh and Tcrb D-to-J recombination. Our findings indicate that the RAG1 NTR regulates V(D)J recombination and lymphocyte development by multiple pathways, including control of the balance between short- and long-range recombination.
Collapse
Affiliation(s)
- Helen A. Beilinson
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Rebecca A. Glynn
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Anurupa Devi Yadavalli
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Jianxiong Xiao
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Elizabeth Corbett
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Huseyin Saribasak
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Rahul Arya
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Charline Miot
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Anamika Bhattacharyya
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC
| | - Jessica M. Jones
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC
| | - Jagan M.R. Pongubala
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Craig H. Bassing
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David G. Schatz
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| |
Collapse
|
7
|
Abstract
V(D)J recombination assembles and diversifies Ig and T cell receptor genes in developing B and T lymphocytes. The reaction is initiated by the RAG1-RAG2 protein complex which binds and cleaves at discrete gene segments in the antigen receptor loci. To identify mechanisms that regulate V(D)J recombination, we used proximity-dependent biotin identification to analyze the interactomes of full-length and truncated forms of RAG1 in pre-B cells. This revealed an association of RAG1 with numerous nucleolar proteins in a manner dependent on amino acids 216 to 383 and allowed identification of a motif required for nucleolar localization. Experiments in transformed pre-B cell lines and cultured primary pre-B cells reveal a strong correlation between disruption of nucleoli, reduced association of RAG1 with a nucleolar marker, and increased V(D)J recombination activity. Mutation of the RAG1 nucleolar localization motif boosts recombination while removal of the first 215 amino acids of RAG1, required for efficient egress from nucleoli, reduces recombination activity. Our findings indicate that nucleolar sequestration of RAG1 is a negative regulatory mechanism in V(D)J recombination and identify regions of the RAG1 N-terminal region that control nucleolar association and egress.
Collapse
|
8
|
The RAG-2 Inhibitory Domain Gates Accessibility of the V(D)J Recombinase to Chromatin. Mol Cell Biol 2018; 38:MCB.00159-18. [PMID: 29760281 DOI: 10.1128/mcb.00159-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/01/2018] [Indexed: 02/06/2023] Open
Abstract
Accessibility of antigen receptor loci to RAG is correlated with the presence of H3K4me3, which binds to a plant homeodomain (PHD) in the RAG-2 subunit and promotes V(D)J recombination. A point mutation in the PHD, W453A, eliminates binding of H3K4me3 and impairs recombination. The debilitating effect of the W453A mutation is ameliorated by second-site mutations that locate an inhibitory domain in the interval from residues 352 through 405 of RAG-2. Disruption of the inhibitory domain stimulates V(D)J recombination within extrachromosomal substrates and at endogenous antigen receptor loci. Association of RAG-1 and RAG-2 with chromatin at the IgH locus in B cell progenitors is dependent on recognition of H3K4me3 by the PHD. Strikingly, disruption of the inhibitory domain permits association of RAG with the IgH locus in the absence of H3K4me3 binding. Thus, the inhibitory domain acts as a gate that prohibits RAG from accessing the IgH locus unless RAG-2 is engaged by H3K4me3.
Collapse
|
9
|
Schabla NM, Perry GA, Palmer VL, Swanson PC. VprBP (DCAF1) Regulates RAG1 Expression Independently of Dicer by Mediating RAG1 Degradation. THE JOURNAL OF IMMUNOLOGY 2018; 201:930-939. [PMID: 29925675 DOI: 10.4049/jimmunol.1800054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/03/2018] [Indexed: 12/21/2022]
Abstract
The assembly of Ig genes in developing B lymphocytes by V(D)J recombination is initiated by the RAG1-RAG2 endonuclease complex. We previously identified an interaction between RAG1 and viral protein R binding protein (VprBP) (also known as DNA damage binding protein 1 cullin 4-associated factor 1 [DCAF1]), a substrate receptor for the cullin 4-really interesting new gene (RING) E3 ubiquitin ligase (CRL4). We report in this article that in mice, B cell-intrinsic loss of VprBP increases RAG1 protein levels and disrupts expression of the endoribonuclease Dicer, which is essential for microRNA maturation. Rag1/2 transcription is known to be derepressed by loss of microRNA-mediated suppression of phosphatase and tensin homolog, raising the possibility that the elevated level of RAG1 observed in VprBP-deficient B cells is caused indirectly by the loss of Dicer. However, we show that VprBP restrains RAG1 expression posttranscriptionally and independently of Dicer. Specifically, loss of VprBP stabilizes RAG1 protein, which we show is normally degraded via a mechanism requiring both 20S proteasome and cullin-RING E3 ubiquitin ligase activity. Furthermore, we show that RAG1 stabilization through small molecule inhibition of cullin-RING E3 ubiquitin ligase activation promotes V(D)J recombination in a murine pre-B cell line. Thus, in addition to identifying a role for VprBP in maintaining Dicer levels in B cells, our findings reveal the basis for RAG1 turnover and provide evidence that the CRL4VprBP(DCAF1) complex functions to maintain physiological levels of V(D)J recombination.
Collapse
Affiliation(s)
- N Max Schabla
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178
| | - Greg A Perry
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178
| | - Victoria L Palmer
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178
| | - Patrick C Swanson
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178
| |
Collapse
|
10
|
Hewitt SL, Wong JB, Lee JH, Nishana M, Chen H, Coussens M, Arnal SM, Blumenberg LM, Roth DB, Paull TT, Skok JA. The Conserved ATM Kinase RAG2-S365 Phosphorylation Site Limits Cleavage Events in Individual Cells Independent of Any Repair Defect. Cell Rep 2018; 21:979-993. [PMID: 29069605 PMCID: PMC5662208 DOI: 10.1016/j.celrep.2017.09.084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 08/23/2017] [Accepted: 09/25/2017] [Indexed: 12/03/2022] Open
Abstract
Many DNA lesions associated with lymphoid malignancies are linked to off-target cleavage by the RAG1/2 recombinase. However, off-target cleavage has mostly been analyzed in the context of DNA repair defects, confounding any mechanistic understanding of cleavage deregulation. We identified a conserved SQ phosphorylation site on RAG2 365 to 366 that is involved in feedback control of RAG cleavage. Mutation of serine 365 to a non-phosphorylatable alanine permits bi-allelic and bi-locus RAG-mediated breaks in the same cell, leading to reciprocal translocations. This phenomenon is analogous to the phenotype we described for ATM kinase inactivation. Here, we establish deregulated cleavage itself as a driver of chromosomal instability without the associated repair defect. Intriguingly, a RAG2-S365E phosphomimetic rescues the deregulated cleavage of ATM inactivation, reducing the incidence of reciprocal translocations. These data support a model in which feedback control of cleavage and maintenance of genome stability involves ATM-mediated phosphorylation of RAG2.
Collapse
Affiliation(s)
- Susannah L Hewitt
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Jason B Wong
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Ji-Hoon Lee
- Howard Hughes Medical Institute, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | | | - Hongxi Chen
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Marc Coussens
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Suzzette M Arnal
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Lili M Blumenberg
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - David B Roth
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tanya T Paull
- Howard Hughes Medical Institute, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
11
|
Bonnet M, Sarmento LM, Martins AC, Sobral D, Silva J, Demengeot J. iRAGu: A Novel Inducible and Reversible Mouse Model for Ubiquitous Recombinase Activity. Front Immunol 2017; 8:1525. [PMID: 29176980 PMCID: PMC5686385 DOI: 10.3389/fimmu.2017.01525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 10/27/2017] [Indexed: 11/17/2022] Open
Abstract
Developing lymphocytes express the recombination activating genes (RAGs) 1 and 2 products that form a site specific recombinase complex (RAG), introducing double strand DNA breaks (DSBs) at recombination signal sequences (RSSs) flanking the V, D, and J gene segments in the antigen receptor loci. The subsequent steps in the reaction consist in the ligation of DSBs by ubiquitous enzymes of the non-homologous end joining DNA repair pathway. This mutagenesis process is responsible for the generation of the very large clonal diversity of T and B lymphocytes, itself allowing the recognition of a virtually open-ended antigenic universe. Sequences resembling RSS are found at high frequency all over the genome, and involved in RAG mediated illegitimate recombination and translocations. Hence, natural and induced ectopic activity of RAG is a threat to the genome only recently underscored. Here, we report and characterize a novel mouse transgenic system for which ubiquitous expression of the recombinase is inducible. In this system, the RAG1 protein is constitutively expressed and functional, while the RAG2 protein, coupled to the estrogen receptor, becomes functionally active upon 4-hydroxytamoxifen (TAM) administration. We describe two transgenic lines. The first one, when introgressed into an endogenous Rag2−/− genetic background is faithfully recapitulating lymphocyte development, repertoire dynamics and cryptic rearrangements, in a TAM-dependent manner. In this model, deprivation of TAM is followed by lymphocyte development arrest, evidencing the reversibility of the system. The second transgenic line is leaky, as the transgenes promote lymphocyte differentiation in absence of TAM treatment. Upon TAM-induction defects in lymphocytes composition and global health reveals the deleterious effect of uncontrolled RAG activity. Overall, this novel transgenic model provides a tool where RAG activity can be specifically manipulated to assess the dynamics of lymphocyte differentiation and the challenges imposed by the recombinase on the vertebrate genome.
Collapse
Affiliation(s)
- Marie Bonnet
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | | | - Joana Silva
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | |
Collapse
|
12
|
Rommel PC, Oliveira TY, Nussenzweig MC, Robbiani DF. RAG1/2 induces genomic insertions by mobilizing DNA into RAG1/2-independent breaks. J Exp Med 2017; 214:815-831. [PMID: 28179379 PMCID: PMC5339680 DOI: 10.1084/jem.20161638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/09/2016] [Accepted: 12/12/2016] [Indexed: 11/23/2022] Open
Abstract
Rommel et al. reveal a novel RAG1/2-mediated insertion pathway, which has the potential to destabilize the lymphocyte genome and shares features with DNA insertions observed in human cancer. The RAG recombinase (RAG1/2) plays an essential role in adaptive immunity by mediating V(D)J recombination in developing lymphocytes. In contrast, aberrant RAG1/2 activity promotes lymphocyte malignancies by causing chromosomal translocations and DNA deletions at cancer genes. RAG1/2 can also induce genomic DNA insertions by transposition and trans-V(D)J recombination, but only few such putative events have been documented in vivo. We used next-generation sequencing techniques to examine chromosomal rearrangements in primary murine B cells and discovered that RAG1/2 causes aberrant insertions by releasing cleaved antibody gene fragments that subsequently reintegrate into DNA breaks induced on a heterologous chromosome. We confirmed that RAG1/2 also mobilizes genomic DNA into independent physiological breaks by identifying similar insertions in human lymphoma and leukemia. Our findings reveal a novel RAG1/2-mediated insertion pathway distinct from DNA transposition and trans-V(D)J recombination that destabilizes the genome and shares features with reported oncogenic DNA insertions.
Collapse
Affiliation(s)
- Philipp C Rommel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065 .,Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| |
Collapse
|
13
|
Lescale C, Deriano L. The RAG recombinase: Beyond breaking. Mech Ageing Dev 2016; 165:3-9. [PMID: 27863852 DOI: 10.1016/j.mad.2016.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/04/2016] [Accepted: 11/11/2016] [Indexed: 11/17/2022]
Abstract
DNA double-strand breaks (DSBs) are commonly seen as lesions that threaten genome integrity and contribute to cancer and aging processes. However, in the context of antigen receptor gene assembly, known as V(D)J recombination, DSBs are obligatory intermediates that allow the establishment of genetic diversity and adaptive immunity. V(D)J recombination is initiated when the lymphoid-restricted recombination-activating genes RAG1 and RAG2 are expressed and form a site-specific endonuclease (the RAG nuclease or RAG recombinase). Here, we discuss the ability of the RAG nuclease to minimize the risks of genome disruption by coupling the breakage and repair steps of the V(D)J reaction. This implies that the RAG genes, derived from an ancient transposon, have undergone strong selective pressure to prohibit transposition in favor of promoting controlled DNA end joining in cis by the ubiquitous DNA damage response and DNA repair machineries. We also discuss the idea that, in addition to being essential for the rearrangement of antigen receptor genes, RAG-mediated DSBs could impact cellular processes and outcomes by affecting genetic and epigenetic programs.
Collapse
Affiliation(s)
- Chloé Lescale
- Department of Immunology and Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Ludovic Deriano
- Department of Immunology and Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.
| |
Collapse
|
14
|
Rodgers KK. Riches in RAGs: Revealing the V(D)J Recombinase through High-Resolution Structures. Trends Biochem Sci 2016; 42:72-84. [PMID: 27825771 DOI: 10.1016/j.tibs.2016.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/04/2016] [Accepted: 10/17/2016] [Indexed: 12/15/2022]
Abstract
Development of the adaptive immune system is dependent on V(D)J recombination, which forms functional antigen receptor genes through rearrangement of component gene segments. The V(D)J recombinase, comprising recombination-activating proteins RAG1 and RAG2, guides the initial DNA cleavage events to the recombination signal sequence (RSS), which flanks each gene segment. Although the enzymatic steps for RAG-mediated endonucleolytic activity were established over two decades ago, only recently have high-resolution structural studies of the catalytically active core regions of the RAG proteins shed light on conformational requirements for the reaction. While outstanding questions remain, we have a clearer picture of how RAG proteins function in generating the diverse repertoires of antigen receptors, the underlying foundation of the adaptive immune system.
Collapse
Affiliation(s)
- Karla K Rodgers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA.
| |
Collapse
|
15
|
Abstract
V(D)J recombination, the mechanism responsible for generating antigen receptor diversity, has the potential to generate aberrant DNA rearrangements in developing lymphocytes. Indeed, the recombinase has been implicated in several different kinds of errors leading to oncogenic transformation. Here we review the basic aspects of V(D)J recombination, mechanisms underlying aberrant DNA rearrangements, and the types of aberrant events uncovered in recent genomewide analyses of lymphoid neoplasms.
Collapse
|
16
|
Lescale C, Abramowski V, Bedora-Faure M, Murigneux V, Vera G, Roth DB, Revy P, de Villartay JP, Deriano L. RAG2 and XLF/Cernunnos interplay reveals a novel role for the RAG complex in DNA repair. Nat Commun 2016; 7:10529. [PMID: 26833222 PMCID: PMC4740868 DOI: 10.1038/ncomms10529] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/22/2015] [Indexed: 12/22/2022] Open
Abstract
XRCC4-like factor (XLF) functions in classical non-homologous end-joining (cNHEJ) but is dispensable for the repair of DNA double-strand breaks (DSBs) generated during V(D)J recombination. A long-standing hypothesis proposes that, in addition to its canonical nuclease activity, the RAG1/2 proteins participate in the DNA repair phase of V(D)J recombination. Here we show that in the context of RAG2 lacking the C-terminus domain (Rag2c/c mice), XLF deficiency leads to a profound lymphopenia associated with a severe defect in V(D)J recombination and, in the absence of p53, increased genomic instability at V(D)J sites. In addition, Rag2c/cXLF−/−p53−/− mice develop aggressive pro-B cell lymphomas bearing complex chromosomal translocations and gene amplifications involving Igh and c-myc/pvt1 loci. Our results reveal an unanticipated functional interplay between the RAG complex and XLF in repairing RAG-induced DSBs and maintaining genome integrity during antigen receptor gene assembly. Antigen receptor diversity relies on careful DNA cleavage and repair. Here the authors identify a functional interplay between RAG2 and XLF during V(D)J recombination, revealing an important role for the RAG complex in repairing induced DNA double-strand breaks and maintaining genome integrity.
Collapse
Affiliation(s)
- Chloé Lescale
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
| | - Vincent Abramowski
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - Marie Bedora-Faure
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
| | - Valentine Murigneux
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
| | - Gabriella Vera
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - David B Roth
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Patrick Revy
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - Jean-Pierre de Villartay
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - Ludovic Deriano
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
| |
Collapse
|
17
|
Xu K, Liu H, Shi Z, Song G, Zhu X, Jiang Y, Zhou Z, Liu X. Disruption of the RAG2 zinc finger motif impairs protein stability and causes immunodeficiency. Eur J Immunol 2015; 46:1011-9. [PMID: 26692406 DOI: 10.1002/eji.201545896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 11/18/2015] [Accepted: 12/15/2015] [Indexed: 12/28/2022]
Abstract
Although the RAG2 core domain is the minimal region required for V(D)J recombination, the noncore region also plays important roles in the regulation of recombination, and mutations in this region are often related to severe combined immunodeficiency. A complete understanding of the functions of the RAG2 noncore region and the potential contributions of its individual residues has not yet been achieved. Here, we show that the zinc finger motif within the noncore region of RAG2 is indispensable for maintaining the stability of the RAG2 protein. The zinc finger motif in the noncore region of RAG2 is highly conserved from zebrafish to humans. Knock-in mice carrying a zinc finger mutation (C478Y) exhibit decreased V(D)J recombination efficiency and serious impairment in T/B-cell development due to RAG2 instability. Further studies also reveal the importance of the zinc finger motif for RAG2 stability. Moreover, mice harboring a RAG2 noncore region mutation (N474S), which is located near C478 but is not zinc-binding, exhibit no impairment in either RAG2 stability or T/B-cell development. Taken together, our findings contribute to defining critical functions of the RAG2 zinc finger motif and provide insights into the relationships between the mutations within this motif and immunodeficiency diseases.
Collapse
Affiliation(s)
- Ke Xu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haifeng Liu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhubing Shi
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guangrong Song
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoyan Zhu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuzhang Jiang
- Department of Medical Laboratory, Huaian First People's Hospital, Nanjing Medical University, Huaian, Jiangsu, China
| | - Zhaocai Zhou
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaolong Liu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
18
|
RAG1-mediated ubiquitylation of histone H3 is required for chromosomal V(D)J recombination. Cell Res 2015; 25:181-92. [PMID: 25572281 DOI: 10.1038/cr.2015.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 08/26/2014] [Accepted: 10/21/2014] [Indexed: 12/22/2022] Open
Abstract
RAG1 and RAG2 proteins are key components in V(D)J recombination. The core region of RAG1 is capable of catalyzing the recombination reaction; however, the biological function of non-core RAG1 remains largely unknown. Here, we show that in a murine-model carrying the RAG1 ring-finger conserved cysteine residue mutation (C325Y), V(D)J recombination was abrogated at the cleavage step, and this effect was accompanied by decreased mono-ubiquitylation of histone H3. Further analyses suggest that un-ubiquitylated histone H3 restrains RAG1 to the chromatin by interacting with the N-terminal 218 amino acids of RAG1. Our data provide evidence for a model in which ubiquitylation of histone H3 mediated by the ring-finger domain of RAG1 triggers the release of RAG1, thus allowing its transition into the cleavage phase. Collectively, our findings reveal that the non-core region of RAG1 facilitates chromosomal V(D)J recombination in a ubiquitylation-dependent pathway.
Collapse
|
19
|
|
20
|
An autoregulatory mechanism imposes allosteric control on the V(D)J recombinase by histone H3 methylation. Cell Rep 2014; 10:29-38. [PMID: 25543141 DOI: 10.1016/j.celrep.2014.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 09/29/2014] [Accepted: 11/25/2014] [Indexed: 01/15/2023] Open
Abstract
V(D)J recombination is initiated by a specialized transposase consisting of the subunits RAG-1 and RAG-2. The susceptibility of gene segments to DNA cleavage by the V(D)J recombinase is correlated with epigenetic modifications characteristic of active chromatin, including trimethylation of histone H3 on lysine 4 (H3K4me3). Engagement of H3K4me3 by a plant homeodomain (PHD) in RAG-2 promotes recombination in vivo and stimulates DNA cleavage by RAG in vitro. We now show that H3K4me3 acts allosterically at the PHD finger to relieve autoinhibition imposed by a separate domain within RAG-2. Disruption of this autoinhibitory domain was associated with constitutive increases in recombination frequency, DNA cleavage activity, substrate binding affinity, and catalytic rate, thus mimicking the stimulatory effects of H3K4me3. Our observations support a model in which allosteric control of RAG is enforced by an autoinhibitory domain whose action is relieved by engagement of active chromatin.
Collapse
|
21
|
Parkinson NJ, Roddis M, Ferneyhough B, Zhang G, Marsden AJ, Maslau S, Sanchez-Pearson Y, Barthlott T, Humphreys IR, Ladell K, Price DA, Ponting CP, Hollander G, Fischer MD. Violation of the 12/23 rule of genomic V(D)J recombination is common in lymphocytes. Genome Res 2014; 25:226-34. [PMID: 25367293 PMCID: PMC4315296 DOI: 10.1101/gr.179770.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
V(D)J genomic recombination joins single gene segments to encode an extensive repertoire of antigen receptor specificities in T and B lymphocytes. This process initiates with double-stranded breaks adjacent to conserved recombination signal sequences that contain either 12- or 23-nucleotide spacer regions. Only recombination between signal sequences with unequal spacers results in productive coding genes, a phenomenon known as the “12/23 rule.” Here we present two novel genomic tools that allow the capture and analysis of immune locus rearrangements from whole thymic and splenic tissues using second-generation sequencing. Further, we provide strong evidence that the 12/23 rule of genomic recombination is frequently violated under physiological conditions, resulting in unanticipated hybrid recombinations in ∼10% of Tcra excision circles. Hence, we demonstrate that strict adherence to the 12/23 rule is intrinsic neither to recombination signal sequences nor to the catalytic process of recombination and propose that nonclassical excision circles are liberated during the formation of antigen receptor diversity.
Collapse
Affiliation(s)
| | - Matthew Roddis
- Systems Biology Laboratory UK, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Ben Ferneyhough
- Systems Biology Laboratory UK, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Gang Zhang
- Systems Biology Laboratory UK, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Adam J Marsden
- Systems Biology Laboratory UK, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Siarhei Maslau
- Systems Biology Laboratory UK, Abingdon, Oxfordshire OX14 4SA, United Kingdom; MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | | | - Thomas Barthlott
- Paediatric Immunology, Department of Biomedicine, University of Basel and The Basel University Children's Hospital, 4058 Basel, Switzerland
| | - Ian R Humphreys
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - David A Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Georg Hollander
- Paediatric Immunology, Department of Biomedicine, University of Basel and The Basel University Children's Hospital, 4058 Basel, Switzerland; Developmental Immunology, Weatherall Institute of Molecular Medicine and Department of Paediatrics, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Michael D Fischer
- Systems Biology Laboratory UK, Abingdon, Oxfordshire OX14 4SA, United Kingdom; Department of Oncology, Division of Cellular and Molecular Medicine, St. George's, University of London, London SW17 0QT, United Kingdom
| |
Collapse
|
22
|
Gigi V, Lewis S, Shestova O, Mijušković M, Deriano L, Meng W, Luning Prak ET, Roth DB. RAG2 mutants alter DSB repair pathway choice in vivo and illuminate the nature of 'alternative NHEJ'. Nucleic Acids Res 2014; 42:6352-64. [PMID: 24753404 PMCID: PMC4041462 DOI: 10.1093/nar/gku295] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA double-stranded breaks (DSBs) can be repaired by several mechanisms, including classical NHEJ (c-NHEJ) and a poorly defined, error-prone process termed alternative NHEJ (a-NHEJ). How cells choose between these alternatives to join physiologic DSBs remains unknown. Here, we show that deletion of RAG2's C-terminus allows a-NHEJ to repair RAG-mediated DSBs in developing lymphocytes from both c-NHEJ-proficient and c-NHEJ-deficient mice, demonstrating that the V(D)J recombinase influences repair pathway choice in vivo. Analysis of V(D)J junctions revealed that, contrary to expectation, junctional characteristics alone do not reliably distinguish between a-NHEJ and c-NHEJ. These data suggest that a-NHEJ is not necessarily mutagenic, and may be more prevalent than previously appreciated. Whole genome sequencing of a lymphoma arising in a p53−/− mouse bearing a C-terminal RAG2 truncation reveals evidence of a-NHEJ and also of aberrant recognition of DNA sequences resembling RAG recognition sites.
Collapse
Affiliation(s)
- Vered Gigi
- Department of Pathology and Laboratory Medicine and Abramson Family Cancer Research Institute, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susanna Lewis
- Department of Pathology and Laboratory Medicine and Abramson Family Cancer Research Institute, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Olga Shestova
- Department of Pathology and Laboratory Medicine and Abramson Family Cancer Research Institute, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martina Mijušković
- Department of Pathology and Laboratory Medicine and Abramson Family Cancer Research Institute, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ludovic Deriano
- Departments of Immunology and Genomes & Genetics, Institut Pasteur, CNRS-URA 1961, 75015 Paris, France
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David B Roth
- Department of Pathology and Laboratory Medicine and Abramson Family Cancer Research Institute, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
23
|
Frit P, Barboule N, Yuan Y, Gomez D, Calsou P. Alternative end-joining pathway(s): bricolage at DNA breaks. DNA Repair (Amst) 2014; 17:81-97. [PMID: 24613763 DOI: 10.1016/j.dnarep.2014.02.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/01/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
To cope with DNA double strand break (DSB) genotoxicity, cells have evolved two main repair pathways: homologous recombination which uses homologous DNA sequences as repair templates, and non-homologous Ku-dependent end-joining involving direct sealing of DSB ends by DNA ligase IV (Lig4). During the last two decades a third player most commonly named alternative end-joining (A-EJ) has emerged, which is defined as any Ku- or Lig4-independent end-joining process. A-EJ increasingly appears as a highly error-prone bricolage on DSBs and despite expanding exploration, it still escapes full characterization. In the present review, we discuss the mechanism and regulation of A-EJ as well as its biological relevance under physiological and pathological situations, with a particular emphasis on chromosomal instability and cancer. Whether or not it is a genuine DSB repair pathway, A-EJ is emerging as an important cellular process and understanding A-EJ will certainly be a major challenge for the coming years.
Collapse
Affiliation(s)
- Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Nadia Barboule
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Ying Yuan
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Dennis Gomez
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France.
| |
Collapse
|
24
|
Chaumeil J, Micsinai M, Ntziachristos P, Roth DB, Aifantis I, Kluger Y, Deriano L, Skok JA. The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage. Nat Commun 2014; 4:2231. [PMID: 23900513 PMCID: PMC3903180 DOI: 10.1038/ncomms3231] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 07/02/2013] [Indexed: 01/16/2023] Open
Abstract
Tight control of antigen-receptor gene rearrangement is required to preserve genome integrity and prevent the occurrence of leukemia and lymphoma. Nonetheless, mistakes can happen, leading to the generation of aberrant rearrangements, such as Tcra/d-Igh inter-locus translocations that are a hallmark of ATM deficiency. Current evidence indicates that these translocations arise from the persistence of unrepaired breaks converging at different stages of thymocyte differentiation. Here we show that a defect in feedback control of RAG2 activity gives rise to bi-locus breaks and damage on Tcra/d and Igh in the same T cell at the same developmental stage, which provides a direct mechanism for generating these inter-locus rearrangements. Both the RAG2 C-terminus and ATM prevent bi-locus RAG-mediated cleavage through modulation of 3D conformation (higher order loops) and nuclear organization of the two loci. This limits the number of potential substrates for translocation and provides an important mechanism for protecting genome stability.
Collapse
Affiliation(s)
- Julie Chaumeil
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Coster G, Gold A, Chen D, Schatz DG, Goldberg M. A dual interaction between the DNA damage response protein MDC1 and the RAG1 subunit of the V(D)J recombinase. J Biol Chem 2012; 287:36488-98. [PMID: 22942284 DOI: 10.1074/jbc.m112.402487] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The first step in V(D)J recombination is the formation of specific DNA double-strand breaks (DSBs) by the RAG1 and RAG2 proteins, which form the RAG recombinase. DSBs activate a complex network of proteins termed the DNA damage response (DDR). A key early event in the DDR is the phosphorylation of histone H2AX around DSBs, which forms a binding site for the tandem BRCA1 C-terminal (tBRCT) domain of MDC1. This event is required for subsequent signal amplification and recruitment of additional DDR proteins to the break site. RAG1 bears a histone H2AX-like motif at its C terminus (R1Ct), making it a putative MDC1-binding protein. In this work we show that the tBRCT domain of MDC1 binds the R1Ct motif of RAG1. Surprisingly, we also observed a second binding interface between the two proteins that involves the Proline-Serine-Threonine rich (PST) repeats of MDC1 and the N-terminal non-core region of RAG1 (R1Nt). The repeats-R1Nt interaction is constitutive, whereas the tBRCT-R1Ct interaction likely requires phosphorylation of the R1Ct motif of RAG1. As the C terminus of RAG1 has been implicated in inhibition of RAG activity, we propose a model in which phosphorylation of the R1Ct motif of RAG1 functions as a self-initiated regulatory signal.
Collapse
Affiliation(s)
- Gideon Coster
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | | | | | | |
Collapse
|
26
|
Kassmeier MD, Mondal K, Palmer VL, Raval P, Kumar S, Perry GA, Anderson DK, Ciborowski P, Jackson S, Xiong Y, Swanson PC. VprBP binds full-length RAG1 and is required for B-cell development and V(D)J recombination fidelity. EMBO J 2011; 31:945-58. [PMID: 22157821 DOI: 10.1038/emboj.2011.455] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 11/11/2011] [Indexed: 11/09/2022] Open
Abstract
The N-terminus of full-length RAG1, though dispensable for RAG1/2 cleavage activity, is required for efficient V(D)J recombination. This region supports RING E3 ubiquitin ligase activity in vitro, but whether full-length RAG1 functions as a single subunit or a multi-subunit E3 ligase in vivo is unclear. We show the multi-subunit cullin RING E3 ligase complex VprBP/DDB1/Cul4A/Roc1 associates with full-length RAG1 through VprBP. This complex is assembled into RAG protein-DNA complexes, and supports in-vitro ubiquitylation activity that is insensitive to RAG1 RING domain mutations. Conditional B lineage-specific VprBP disruption arrests B-cell development at the pro-B-to-pre-B cell transition, but this block is bypassed by expressing rearranged immunoglobulin transgenes. Mice with a conditional VprBP disruption show modest reduction of D-J(H) rearrangement, whereas V(H)-DJ(H) and V(κ)-J(κ) rearrangements are severely impaired. D-J(H) coding joints from VprBP-insufficent mice show longer junctional nucleotide insertions and a higher mutation frequency in D and J segments than normal. These data suggest full-length RAG1 recruits a cullin RING E3 ligase complex to ubiquitylate an unknown protein(s) to limit error-prone repair during V(D)J recombination.
Collapse
Affiliation(s)
- Michele D Kassmeier
- Department of Medical Microbiology and Immunology, Creighton University Medical Center, Omaha, NE, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Abstract
V(D)J recombination assembles immunoglobulin and T cell receptor genes during lymphocyte development through a series of carefully orchestrated DNA breakage and rejoining events. DNA cleavage requires a series of protein-DNA complexes containing the RAG1 and RAG2 proteins and recombination signals that flank the recombining gene segments. In this review, we discuss recent advances in our understanding of the function and domain organization of the RAG proteins, the composition and structure of RAG-DNA complexes, and the pathways that lead to the formation of these complexes. We also consider the functional significance of RAG-mediated histone recognition and ubiquitin ligase activities, and the role played by RAG in ensuring proper repair of DNA breaks made during V(D)J recombination. Finally, we propose a model for the formation of RAG-DNA complexes that involves anchoring of RAG1 at the recombination signal nonamer and RAG2-dependent surveillance of adjoining DNA for suitable spacer and heptamer sequences.
Collapse
Affiliation(s)
- David G Schatz
- Department of Immunobiology and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06520-8011, USA.
| | | |
Collapse
|
28
|
Nambiar M, Raghavan SC. How does DNA break during chromosomal translocations? Nucleic Acids Res 2011; 39:5813-25. [PMID: 21498543 PMCID: PMC3152359 DOI: 10.1093/nar/gkr223] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 03/25/2011] [Accepted: 03/29/2011] [Indexed: 12/20/2022] Open
Abstract
Chromosomal translocations are one of the most common types of genetic rearrangements and are molecular signatures for many types of cancers. They are considered as primary causes for cancers, especially lymphoma and leukemia. Although many translocations have been reported in the last four decades, the mechanism by which chromosomes break during a translocation remains largely unknown. In this review, we summarize recent advances made in understanding the molecular mechanism of chromosomal translocations.
Collapse
Affiliation(s)
- Mridula Nambiar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | | |
Collapse
|
29
|
Arbuckle JL, Rahman NS, Zhao S, Rodgers W, Rodgers KK. Elucidating the domain architecture and functions of non-core RAG1: the capacity of a non-core zinc-binding domain to function in nuclear import and nucleic acid binding. BMC BIOCHEMISTRY 2011; 12:23. [PMID: 21599978 PMCID: PMC3124419 DOI: 10.1186/1471-2091-12-23] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 05/20/2011] [Indexed: 12/19/2022]
Abstract
Background The repertoire of the antigen-binding receptors originates from the rearrangement of immunoglobulin and T-cell receptor genetic loci in a process known as V(D)J recombination. The initial site-specific DNA cleavage steps of this process are catalyzed by the lymphoid specific proteins RAG1 and RAG2. The majority of studies on RAG1 and RAG2 have focused on the minimal, core regions required for catalytic activity. Though not absolutely required, non-core regions of RAG1 and RAG2 have been shown to influence the efficiency and fidelity of the recombination reaction. Results Using a partial proteolysis approach in combination with bioinformatics analyses, we identified the domain boundaries of a structural domain that is present in the 380-residue N-terminal non-core region of RAG1. We term this domain the Central Non-core Domain (CND; residues 87-217). Conclusions We show how the CND alone, and in combination with other regions of non-core RAG1, functions in nuclear localization, zinc coordination, and interactions with nucleic acid. Together, these results demonstrate the multiple roles that the non-core region can play in the function of the full length protein.
Collapse
Affiliation(s)
- Janeen L Arbuckle
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73190, USA
| | | | | | | | | |
Collapse
|
30
|
Zhang L, Reynolds TL, Shan X, Desiderio S. Coupling of V(D)J recombination to the cell cycle suppresses genomic instability and lymphoid tumorigenesis. Immunity 2011; 34:163-74. [PMID: 21349429 DOI: 10.1016/j.immuni.2011.02.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 10/06/2010] [Accepted: 12/01/2010] [Indexed: 11/30/2022]
Abstract
V(D)J gene segment recombination is linked to the cell cycle by the periodic phosphorylation and destruction of the RAG-2 protein at the G1-to-S cell cycle transition. To examine the function of this coupling, we constructed mice in which the phosphorylation site at threonine 490 of RAG-2 was mutated to alanine. The RAG-2(T490A) mutation uncoupled DNA cleavage from cell cycle and promoted aberrant recombination. Similar aberrant recombination products were observed in mice deficient in the Skp2 ubiquitin ligase subunit, which is required for periodic destruction of RAG-2. On a p53-deficient background, the RAG-2(T490A) mutation induced lymphoid malignancies characterized by clonal chromosomal translocations involving antigen receptor genes. Taken together, these observations provide a direct link between the periodic destruction of RAG-2 and lymphoid tumorigenesis. We infer that cell cycle control of the V(D)J recombinase limits the potential genomic damage that could otherwise result from RAG-mediated DNA cleavage.
Collapse
Affiliation(s)
- Li Zhang
- Department of Molecular Biology and Genetics and Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | |
Collapse
|
31
|
The RAG2 C terminus suppresses genomic instability and lymphomagenesis. Nature 2011; 471:119-23. [PMID: 21368836 PMCID: PMC3174233 DOI: 10.1038/nature09755] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 12/15/2010] [Indexed: 01/09/2023]
Abstract
Misrepair of DNA double-strand breaks (DSBs) produced by the V(D)J recombinase (the RAG1/RAG2 proteins) at immunoglobulin (Ig) and T cell receptor (Tcr) loci has been implicated in pathogenesis of lymphoid malignancies in humans1 and in mice2–7. Defects in DNA damage response factors such as ATM and combined deficiencies in classical nonhomologous end joining (NHEJ) and p53 predispose to RAG-initiated genomic rearrangements and lymphomagenesis2–11. Although we showed previously that RAG1/RAG2 shepherd the broken DNA ends to classical NHEJ for proper repair12,13, roles for the RAG proteins in preserving genomic stability remain poorly defined. Here we show that the RAG2 C-terminus, although dispensable for recombination14,15, is critical for maintaining genomic stability. Thymocytes from “core” Rag2 homozygotes (Rag2c/c mice) show dramatic disruption of Tcrα/δ locus integrity. Furthermore, all Rag2c/c p53−/− mice, unlike Rag1c/c p53−/− and p53−/− animals, rapidly develop thymic lymphomas bearing complex chromosomal translocations, amplifications, and deletions involving the Tcrα/δ and Igh loci. We also find these features in lymphomas from Atm−/− mice. We show that, like ATM-deficiency3, core RAG2 severely destabilizes the RAG post-cleavage complex. These results reveal a novel genome guardian role for RAG2 and suggest that similar “end release/end persistence” mechanisms underlie genomic instability and lymphomagenesis in Rag2c/c p53−/− and Atm−/− mice.
Collapse
|
32
|
Autoinhibition of DNA cleavage mediated by RAG1 and RAG2 is overcome by an epigenetic signal in V(D)J recombination. Proc Natl Acad Sci U S A 2010; 107:22487-92. [PMID: 21149691 DOI: 10.1073/pnas.1014958107] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Gene assembly of the variable domain of antigen receptors is initiated by DNA cleavage by the RAG1-RAG2 protein complex at sites flanking V, D, and J gene segments. Double-strand breaks are produced via a single-strand nick that is converted to a hairpin end on coding DNA and a blunt end on the neighboring recombination signal sequence. We demonstrate that the C-terminal regions of purified murine RAG1 (aa 1009-1040) and RAG2 (aa 388-520, including a plant homeodomain [PHD domain]) collaborate to inhibit the hairpinning stage of DNA cleavage. The C-terminal region of RAG2 stabilizes the RAG1/2 heterotetramer but destabilizes the RAG-DNA precleavage complex. This destabilization is reversed by binding of the PHD domain to a histone H3 peptide trimethylated on lysine 4 (H3K4me3). The addition of H3K4me3 likewise alleviates the RAG1/RAG2 C-terminus-mediated inhibition of hairpinning and the PHD-mediated inhibition of transposition activity. Thus a negative regulatory function of the noncore regions of RAG1/2 limits the RAG endonuclease activity in the absence of an activating methylated histone tail bound to the complex.
Collapse
|
33
|
Numata M, Saito S, Nagata K. RAG-dependent recombination at cryptic RSSs within TEL–AML1 t(12;21)(p13;q22) chromosomal translocation region. Biochem Biophys Res Commun 2010; 402:718-24. [DOI: 10.1016/j.bbrc.2010.10.092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022]
|
34
|
Desiderio S. Temporal and spatial regulatory functions of the V(D)J recombinase. Semin Immunol 2010; 22:362-9. [PMID: 21036059 DOI: 10.1016/j.smim.2010.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 09/09/2010] [Indexed: 12/20/2022]
Abstract
In developing lymphocytes, V(D)J recombination is subject to tight spatial and temporal regulation. An emerging body of evidence indicates that some of these constraints, particularly with respect to locus specificity and cell cycle phase, are enforced by regulatory cues that converge directly on the RAG proteins themselves. Active chromatin is bound by RAG-2 through a specific histone modification that may serve the recombinase as an allosteric activator as well as a docking site. RAG-1 possesses intrinsic histone ubiquitin ligase activity, suggesting that the recombinase not only responds to chromatin modification but is itself able to modify chromatin. The cyclin A/Cdk2 component of the cell cycle clock triggers periodic destruction of RAG-2, thereby restricting V(D)J recombination to the G0/G1 cell cycle phases. These examples illustrate that the RAG proteins, in addition to their direct actions on DNA, are able to detect and respond to intracellular signals, thereby coordinating recombinase activity with intracellular processes such as cell division and transcription.
Collapse
Affiliation(s)
- Stephen Desiderio
- Department of Molecular Biology and Genetics and Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21210, United States
| |
Collapse
|
35
|
Grazini U, Zanardi F, Citterio E, Casola S, Goding CR, McBlane F. The RING domain of RAG1 ubiquitylates histone H3: a novel activity in chromatin-mediated regulation of V(D)J joining. Mol Cell 2010; 37:282-93. [PMID: 20122409 DOI: 10.1016/j.molcel.2009.12.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2009] [Revised: 08/06/2009] [Accepted: 12/08/2009] [Indexed: 01/15/2023]
Abstract
The RAG1 and RAG2 proteins are the only lymphoid-specific factors required to perform the first step of V(D)J recombination, DNA cleavage. While the catalytic domain of RAG1, the core region, has been well characterized, the role of the noncore region in modulating chromosomal V(D)J recombination efficiency remains ill defined. Recent studies have highlighted the role of chromatin structure in regulation of V(D)J recombination. Here we show that RAG1 itself, through a RING domain within its N-terminal noncore region, preferentially interacts directly with and promotes monoubiquitylation of histone H3. Mutations affecting the RAG1 RING domain reduce histone H3 monoubiquitylation activity, decrease V(D)J recombination activity in vivo, reduce formation of both signal-joint and coding-joint products on episomal substrates, and decrease efficiency of V(D)J recombination at the endogenous IgH locus in lymphoid cells. The results reveal that RAG1-mediated histone monoubiquitylation activity plays a role in regulating the joining phase of chromosomal V(D)J recombination.
Collapse
Affiliation(s)
- Ursula Grazini
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | | | | | | | | | | |
Collapse
|
36
|
Abstract
In a recent issue of Molecular Cell, Shimazaki et al. (2009) show that an interaction between RAG2 and a methylated histone might play a critical regulatory role in V(D)J recombination by enhancing DNA binding and enzymatic activity of the V(D)J recombinase.
Collapse
Affiliation(s)
- Mark S Schlissel
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | | | | |
Collapse
|
37
|
Deriano L, Stracker TH, Baker A, Petrini JHJ, Roth DB. Roles for NBS1 in alternative nonhomologous end-joining of V(D)J recombination intermediates. Mol Cell 2009; 34:13-25. [PMID: 19362533 DOI: 10.1016/j.molcel.2009.03.009] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 01/28/2009] [Accepted: 03/20/2009] [Indexed: 11/29/2022]
Abstract
Recent work has highlighted the importance of alternative, error-prone mechanisms for joining DNA double-strand breaks (DSBs) in mammalian cells. These noncanonical, nonhomologous end-joining (NHEJ) pathways threaten genomic stability but remain poorly characterized. The RAG postcleavage complex normally prevents V(D)J recombination-associated DSBs from accessing alternative NHEJ. Because the MRE11/RAD50/NBS1 complex localizes to RAG-mediated DSBs and possesses DNA end tethering, processing, and joining activities, we asked whether it plays a role in the mechanism of alternative NHEJ or participates in regulating access of DSBs to alternative repair pathways. We find that NBS1 is required for alternative NHEJ of hairpin coding ends, suppresses alternative NHEJ of signal ends, and promotes proper resolution of inversional recombination intermediates. These data demonstrate that the MRE11 complex functions at two distinct levels, regulating repair pathway choice (likely through enhancing the stability of DNA end complexes) and participating in alternative NHEJ of coding ends.
Collapse
Affiliation(s)
- Ludovic Deriano
- Department of Pathology, The Helen L and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute for Biomolecular Medicine and , New York University School of Medicine, New York, NY 10016, USA
| | | | | | | | | |
Collapse
|
38
|
Jones JM, Simkus C. The roles of the RAG1 and RAG2 "non-core" regions in V(D)J recombination and lymphocyte development. Arch Immunol Ther Exp (Warsz) 2009; 57:105-16. [PMID: 19333736 DOI: 10.1007/s00005-009-0011-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 01/28/2009] [Indexed: 11/27/2022]
Abstract
The enormous repertoire of the vertebrate specific immune system relies on the rearrangement of discrete gene segments into intact antigen receptor genes during the early stages of B-and T-cell development. This V(D)J recombination is initiated by a lymphoid-specific recombinase comprising the RAG1 and RAG2 proteins, which introduces double-strand breaks in the DNA adjacent to the coding segments. Much of the biochemical research into V(D)J recombination has focused on truncated or "core" fragments of RAG1 and RAG2, which lack approximately one third of the amino acids from each. However, genetic analyses of SCID and Omenn syndrome patients indicate that residues outside the cores are essential to normal immune development. This is in agreement with the striking degree of conservation across all vertebrate classes in certain non-core domains. Work from multiple laboratories has shed light on activities resident within these domains, including ubiquitin ligase activity and KPNA1 binding by the RING finger domain of RAG1 and the recognition of specific chromatin modifications as well as phosphoinositide binding by the PHD module of RAG2. In addition, elements outside of the cores are necessary for regulated protein expression and turnover. Here the current state of knowledge is reviewed regarding the non-core regions of RAG1 and RAG2 and how these findings contribute to our broader understanding of recombination.
Collapse
Affiliation(s)
- Jessica M Jones
- Department of Biochemistry and Molecular and Cellular Sciences, Georgetown University Medical Center, Washington, DC 20007, USA.
| | | |
Collapse
|
39
|
Temporal and spatial regulation of V(D)J recombination: interactions of extrinsic factors with the RAG complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 650:157-65. [PMID: 19731809 DOI: 10.1007/978-1-4419-0296-2_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In the course of lymphoid development, V(D)J recombination is subject to stringent locus-specific and temporal regulation. These constraints are ultimately responsible for several features peculiar to lymphoid development, including the lineage specificity of antigen receptor assembly, allelic exclusion and receptor editing. In addition, cell cycle phase-dependent regulation of V(D)J recombinase activity ensures that DNA rearrangement is completed by the appropriate mechanism of DNA repair. Regulation of V(D)J recombination involves interactions between the V(D)J recombinase--a heteromeric complex consisting of RAG-1 and RAG-2 subunits--and macromolecular assemblies extrinsic to the recombinase. This chapter will focus on those features of the recombinase itself--and in particular the RAG-2 subunit--that interact with extrinsic factors to establish patterns of temporal control and locus specificity in developing lymphocytes.
Collapse
|
40
|
Difilippantonio S, Gapud E, Wong N, Huang CY, Mahowald G, Chen HT, Kruhlak MJ, Callen E, Livak F, Nussenzweig MC, Sleckman BP, Nussenzweig A. 53BP1 facilitates long-range DNA end-joining during V(D)J recombination. Nature 2008; 456:529-33. [PMID: 18931658 PMCID: PMC3596817 DOI: 10.1038/nature07476] [Citation(s) in RCA: 244] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 09/08/2008] [Indexed: 11/22/2022]
Abstract
V(D)J recombination and class switch recombination employ overlapping but distinct non-homologous end-joining (NHEJ) pathways to repair DNA double strand break (DSB) intermediates. 53BP1 is a DNA damage response protein that is rapidly recruited to sites of chromosomal DSBs, where it appears to function in a subset of ataxia-telangiectasia mutated (ATM) kinase, H2AX- and MDC1- dependent events1,2. A 53BP1 dependent end joining pathway has been described that is dispensable for V(D)J recombination but essential for class-switch recombination CSR3, 4. Here, we report a previously unrecognized defect in the joining phase of V(D)J recombination in 53BP1 deficient lymphocytes distinct from that found in classical NHEJ-, H2AX-, MDC1- and Atm-deficient mice. Absence of 53BP1 leads to impairment of distal V-DJ joining with extensive degradation of un-repaired coding ends and episomal signal joint reintegration at V(D)J junctions. This results in apoptosis, loss of T-cell receptor alpha locus integrity and lymphopenia. Further impairment of the apoptotic checkpoint causes propagation of lymphocytes bearing antigen receptor breaks. These data suggest a more general role for 53BP1 in maintaining genomic stability during long range joining of DNA breaks.
Collapse
Affiliation(s)
- Simone Difilippantonio
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1360, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Curry JD, Schlissel MS. RAG2's non-core domain contributes to the ordered regulation of V(D)J recombination. Nucleic Acids Res 2008; 36:5750-62. [PMID: 18776220 PMCID: PMC2566892 DOI: 10.1093/nar/gkn553] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Variable (diversity) joining [V(D)J] recombination of immune gene loci proceeds in an ordered manner with D to J portions recombining first and then an upstream V joins that recombinant. We present evidence that the non-core domain of recombination activating gene (RAG) protein 2 is involved in the regulation of recombinatorial order. In mice lacking the non-core domain of RAG2 the ordered rearrangement is disturbed and direct V to D rearrangements are 10- to 1000-times increased in tri-partite immune gene loci. Some forms of inter-chromosomal translocations between TCRβ and TCRδ D gene segments are also increased in the core RAG2 animals as compared with their wild-type (WT) counterparts. In addition, the concise use of proper recombination signal sequences (RSSs) appears to be disturbed in the core RAG2 mice as compared with WT RAG2 animals.
Collapse
Affiliation(s)
- John D Curry
- Division of Immunology, Department of Molecular and Cell Biology, University of California at Berkeley, 439 Life Sciences Addition, Berkeley, CA 94720-3200, USA
| | | |
Collapse
|
42
|
Touvrey C, Couedel C, Soulas P, Couderc R, Jasin M, de Villartay JP, Marche PN, Jouvin-Marche E, Candéias SM. Distinct effects of DNA-PKcs and Artemis inactivation on signal joint formation in vivo. Mol Immunol 2008; 45:3383-91. [PMID: 18501428 DOI: 10.1016/j.molimm.2008.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 04/09/2008] [Indexed: 12/17/2022]
Abstract
The assembly of functional immune receptor genes via V(D)J recombination in developing lymphocytes generates DNA double-stranded breaks intermediates that are repaired by non-homologous end joining (NHEJ). This repair pathway requires the sequential recruitment and activation onto coding and signal DNA ends of several proteins, including the DNA-dependent protein kinase and the nuclease Artemis. Artemis activity, triggered by the DNA-dependent protein kinase, is necessary to process the genes hairpin-sealed coding ends but appears dispensable for the ligation of the reciprocal phosphorylated, blunt-ended signal ends into a signal joint. The DNA-dependent protein kinase is however present on signal ends and could potentially recruit and activate Artemis during signal joint formation. To determine whether Artemis plays a role during the resolution of signal ends during V(D)J recombination, we analyzed the structure of signal joints generated in developing thymocytes during the rearrangement of T cell receptor genes in wild type mice and mice mutated for NHEJ factors. These joints exhibit junctional diversity resulting from N nucleotide polymerization by the terminal nucleotidyl transferase and nucleotide loss from one or both of the signal ends before they are ligated. Our results show that Artemis participates in the repair of signal ends in vivo. Furthermore, our results also show that while the DNA-dependent protein kinase complex protects signal ends from processing, including deletions, Artemis seems on the opposite to promote their accessibility to modifying enzymes. In addition, these data suggest that Artemis might be the nuclease responsible for nucleotide loss from signal ends during the repair process.
Collapse
Affiliation(s)
- Cédric Touvrey
- CEA, DSV, DRDC, Laboratoire d'Immunochimie, INSERM U548, Université Joseph Fourier, Grenoble F-38054, France
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Raval P, Kriatchko AN, Kumar S, Swanson PC. Evidence for Ku70/Ku80 association with full-length RAG1. Nucleic Acids Res 2008; 36:2060-72. [PMID: 18281312 PMCID: PMC2330247 DOI: 10.1093/nar/gkn049] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Antigen receptor genes are assembled by a site-specific DNA rearrangement process called V(D)J recombination. This process proceeds through two distinct phases: a cleavage phase in which the RAG1 and RAG2 proteins introduce DNA double-strand breaks at antigen receptor gene segments, and a joining phase in which the resulting DNA breaks are processed and repaired via the non-homologous end-joining (NHEJ) repair pathway. Genetic and biochemical evidence suggest that the RAG proteins play an active role in guiding the repair of DNA breaks introduced during V(D)J recombination to the NHEJ pathway. However, evidence for specific association between the RAG proteins and any of the factors involved in NHEJ remains elusive. Here we present evidence that two components of the NHEJ pathway, Ku70 and Ku80, interact with full-length RAG1, providing a biochemical link between the two phases of V(D)J recombination.
Collapse
Affiliation(s)
- Prafulla Raval
- Department of Medical Microbiology and Immunology, Creighton University Medical Center, Omaha, NE 68178, USA
| | | | | | | |
Collapse
|
44
|
Simkus C, Anand P, Bhattacharyya A, Jones JM. Biochemical and Folding Defects in a RAG1 Variant Associated with Omenn Syndrome. THE JOURNAL OF IMMUNOLOGY 2007; 179:8332-40. [DOI: 10.4049/jimmunol.179.12.8332] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
45
|
Corneo B, Wendland RL, Deriano L, Cui X, Klein IA, Wong SY, Arnal S, Holub AJ, Weller GR, Pancake BA, Shah S, Brandt VL, Meek K, Roth DB. Rag mutations reveal robust alternative end joining. Nature 2007; 449:483-6. [PMID: 17898768 DOI: 10.1038/nature06168] [Citation(s) in RCA: 255] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 08/17/2007] [Indexed: 12/15/2022]
Abstract
Mammalian cells repair DNA double-strand breaks (DSBs) through either homologous recombination or non-homologous end joining (NHEJ). V(D)J recombination, a cut-and-paste mechanism for generating diversity in antigen receptors, relies on NHEJ for repairing DSBs introduced by the Rag1-Rag2 protein complex. Animals lacking any of the seven known NHEJ factors are therefore immunodeficient. Nevertheless, DSB repair is not eliminated entirely in these animals: evidence of a third mechanism, 'alternative NHEJ', appears in the form of extremely rare V(D)J junctions and a higher rate of chromosomal translocations. The paucity of these V(D)J events has suggested that alternative NHEJ contributes little to a cell's overall repair capacity, being operative only (and inefficiently) when classical NHEJ fails. Here we find that removing certain portions of murine Rag proteins reveals robust alternative NHEJ activity in NHEJ-deficient cells and some alternative joining activity even in wild-type cells. We propose a two-tier model in which the Rag proteins collaborate with NHEJ factors to preserve genomic integrity during V(D)J recombination.
Collapse
Affiliation(s)
- Barbara Corneo
- The Kimmel Center for Biology and Medicine of the Skirball Institute and Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
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 2007; 27:561-71. [PMID: 17936034 DOI: 10.1016/j.immuni.2007.09.005] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Revised: 09/11/2007] [Accepted: 09/13/2007] [Indexed: 12/24/2022]
Abstract
V(D)J recombination is initiated by the recombination activating gene (RAG) proteins RAG-1 and RAG-2. The ability of antigen-receptor-gene segments to undergo V(D)J recombination is correlated with spatially- and temporally-restricted chromatin modifications. We have found that RAG-2 bound specifically to histone H3 and that this binding was absolutely dependent on dimethylation or trimethylation at lysine 4 (H3K4me2 or H3K4me3). The interaction required a noncanonical plant homeodomain (PHD) that had previously been described within the noncore region of RAG-2. Binding of the RAG-2 PHD finger to chromatin across the IgH D-J(H)-C locus showed a strong correlation with the distribution of trimethylated histone H3 K4. Mutation of a conserved tryptophan residue in the RAG-2 PHD finger abolished binding to H3K4me3 and greatly impaired recombination of extrachromosomal and endogenous immunoglobulin gene segments. Together, these findings are consistent with the interpretation that recognition of hypermethylated histone H3 K4 promotes efficient V(D)J recombination in vivo.
Collapse
Affiliation(s)
- Yun Liu
- Department of Molecular Biology and Genetics, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | | |
Collapse
|
47
|
Sobacchi C, Marrella V, Rucci F, Vezzoni P, Villa A. RAG-dependent primary immunodeficiencies. Hum Mutat 2006; 27:1174-84. [PMID: 16960852 DOI: 10.1002/humu.20408] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mutations in recombination activating genes 1 and 2 (RAG1 and RAG2) cause a spectrum of severe immunodeficiencies ranging from classical T cell-B cell-severe combined immunodeficiency (T(-)B(-)SCID) and Omenn syndrome (OS) to an increasing number of peculiar cases. While it is well established from biochemical data that the specific genetic defect in either of the RAG genes is the first determinant of the clinical presentation, there is also increasing evidence that environmental factors play an important role and can lead to a different phenotypic expression of a given genotype. However, a better understanding of the mechanisms by which the molecular defect impinges on the cellular phenotype of OS is still lacking. Ongoing studies in knock-in mice could better clarify this aspect.
Collapse
|
48
|
Touvrey C, Cowell LG, Lieberman AE, Marche PN, Jouvin-Marche E, Candéias SM. Reassignment of the murine 3'TRDD1 recombination signal sequence. Immunogenetics 2006; 58:895-903. [PMID: 17021860 PMCID: PMC1876511 DOI: 10.1007/s00251-006-0150-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Accepted: 08/03/2006] [Indexed: 11/30/2022]
Abstract
T cell receptor genes are assembled in developing T lymphocytes from discrete V, D, and J genes by a site-specific somatic rearrangement mechanism. A flanking recombination signal, composed of a conserved heptamer and a semiconserved nonamer separated by 12 or 23 variable nucleotides, targets the activity of the rearrangement machinery to the adjoining V, D, and J genes. Following the rearrangement of V, D, or J genes, their respective recombination signals are ligated together. Although these signal joints are allegedly invariant, created by the head-to-head abuttal of the heptamers, some do exhibit junctional diversity. Recombination signals were initially identified by comparison and alignment of germ-line sequences with the sequence of rearranged genes. However, their overall low level of sequence conservation makes their characterization solely from sequence data difficult. Recently, computational analysis unraveled correlations between nucleotides at several positions scattered within the spacer and recombination activity, so that it is now possible to identify putative recombination signals and determine and predict their recombination efficiency. In this paper, we analyzed the variability introduced in signal joints generated after rearrangement of the TRDD1 and TRDD2 genes in murine thymocytes. The recurrent presence of identical nucleotides inserted in these signal joints led us to reconsider the location and sequence of the TRDD1 recombination signal. By combining molecular characterization and computational analysis, we show that the functional TRDD1 recombination signal is shifted inside the putative coding sequence of the TRDD1 gene and, consequently, that this gene is shorter than indicated in the databases.
Collapse
Affiliation(s)
- Cédric Touvrey
- Laboratoire d'immunochimie
INSERM : U548 CEA-DSV-DRDCUniversité Joseph-Fourier - Grenoble I17, Rue Des Martyrs
38054 Grenoble Cedex 9, FR
| | - Lindsay G. Cowell
- Departments of Biostatistics & Bioinformatics and Immunology
Duke UniversityDurham, NC, US
| | - Ann E. Lieberman
- Departments of Biostatistics & Bioinformatics and Immunology
Duke UniversityDurham, NC, US
| | - Patrice N. Marche
- Laboratoire d'immunochimie
INSERM : U548 CEA-DSV-DRDCUniversité Joseph-Fourier - Grenoble I17, Rue Des Martyrs
38054 Grenoble Cedex 9, FR
| | - Evelyne Jouvin-Marche
- Laboratoire d'immunochimie
INSERM : U548 CEA-DSV-DRDCUniversité Joseph-Fourier - Grenoble I17, Rue Des Martyrs
38054 Grenoble Cedex 9, FR
| | - Serge M. Candéias
- Laboratoire d'immunochimie
INSERM : U548 CEA-DSV-DRDCUniversité Joseph-Fourier - Grenoble I17, Rue Des Martyrs
38054 Grenoble Cedex 9, FR
- * Correspondence should be adressed to: Serge M. Candéias
| |
Collapse
|
49
|
Sen R, Oltz E. Genetic and epigenetic regulation of IgH gene assembly. Curr Opin Immunol 2006; 18:237-42. [PMID: 16616470 DOI: 10.1016/j.coi.2006.03.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Accepted: 03/27/2006] [Indexed: 12/19/2022]
Abstract
Precursor B cells assemble a diverse repertoire of immunoglobulin (Ig) genes by the process of V(D)J recombination. Assembly of IgH genes is regulated in a tissue- and stage-specific manner via the activation and then the inactivation of distinct regions within the one megabase IgH locus. Recent studies have shown that regional control is achieved using a combination of genetic and epigenetic strategies, which modulate chromatin accessibility to V(D)J recombinase, relocate IgH loci within the nucleus, and promote changes in locus conformation that alter the spatial proximity of target gene segments. Orchestration of these regulatory processes is crucial for the generation of a functional B cell repertoire.
Collapse
Affiliation(s)
- Ranjan Sen
- Laboratory of Cellular and Molecular Biology, National Institute on Aging/National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
| | | |
Collapse
|
50
|
Chatterji M, Tsai CL, Schatz DG. Mobilization of RAG-generated signal ends by transposition and insertion in vivo. Mol Cell Biol 2006; 26:1558-68. [PMID: 16449665 PMCID: PMC1367191 DOI: 10.1128/mcb.26.4.1558-1568.2006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In addition to their essential roles in V(D)J recombination, the RAG proteins have been found to catalyze transposition in vitro, but it has been difficult to demonstrate transposition by the RAG proteins in vivo in vertebrate cells. As genomic instability and chromosomal translocations are common outcomes of transposition in other species, it is critical to understand if the RAG proteins behave as a transposase in vertebrate cells. To facilitate this, we have developed an episome-based assay to detect products of RAG-mediated transposition in the human embryonic kidney cell line 293T. Transposition events into the target episome, accompanied by characteristic target site duplications, were detected at a low frequency using RAG1 and either truncated "core" RAG2 or full-length RAG2. More frequently, insertion of the RAG-generated signal end fragment into the target was accompanied by deletions or more complex rearrangements, and our data indicate that these events occur by a mechanism that is distinct from transposition. An assay to detect transposition from an episome into the human genome failed to detect bona fide transposition events but instead yielded chromosome deletion and translocation events involving the signal end fragment mobilized by the RAG proteins. These assays provide a means of assessing RAG-mediated transposition in vivo, and our findings provide insight into the potential for the products of RAG-mediated DNA cleavage to cause genome instability.
Collapse
Affiliation(s)
- Monalisa Chatterji
- Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | | | | |
Collapse
|