Genomic instability due to V(D)J recombination-associated transposition

Reddy, Yeturu V. R.; Perkins, Eric J.; Ramsden, Dale A.

doi:10.1101/gad.1432706

Cited by 67 publications

(66 citation statements)

References 24 publications

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“…Thus, because V(D)J recombination occurs in the context of inversion within certain Ig and TCR loci, defects in SJ formation during inversional V(D)J recombination could result in chromosomal breaks that would be highly detrimental to developing B and T cells. Likewise, unjoined SEs could be mutagenic after insertion into a chromosome (22)(23)(24) or might trigger DSB responses (25).…”

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confidence: 99%

Ataxia telangiectasia-mutated protein and DNA-dependent protein kinase have complementary V(D)J recombination functions

Zha

Jiang

Fujiwara

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Antigen receptor variable region exons are assembled during lymphocyte development from variable (V), diversity (D), and joining (J) gene segments. Each germ-line gene segment is flanked by recombination signal sequences (RSs). Recombination-activating gene endonuclease initiates V(D)J recombination by cleaving a pair of gene segments at their junction with flanking RSs to generate covalently sealed (hairpinned) coding ends (CEs) and blunt 5′-phosphorylated RS ends (SEs). Subsequently, nonhomologous end joining (NHEJ) opens, processes, and fuses CEs to form coding joins (CJs) and precisely joins SEs to form signal joins (SJs). DNA-dependent protein kinase catalytic subunit (DNA-PKcs) activates Artemis endonuclease to open and process hairpinned CEs before their fusion into CJs by other NHEJ factors. Although DNA-PKcs is absolutely required for CJs, SJs are formed to variable degrees and with variable fidelity in different DNA-PKcs-deficient cell types. Thus, other factors may compensate for DNA-PKcs function in SJ formation. DNA-PKcs and the ataxia telangiectasia-mutated (ATM) kinase are members of the same family, and they share common substrates in the DNA damage response. Although ATM deficiency compromises chromosomal V(D)J CJ formation, it has no reported role in SJ formation in normal cells. Here, we report that DNA-PKcs and ATM have redundant functions in SJ formation. Thus, combined DNA-PKcs and ATM deficiency during V(D)J recombination leads to accumulation of unjoined SEs and lack of SJ fidelity. Moreover, treatment of DNA-PKcs-or ATM-deficient cells, respectively, with specific kinase inhibitors for ATM or DNA-PKcs recapitulates SJ defects, indicating that the overlapping V(D)J recombination functions of ATM and DNA-PKcs are mediated through their kinase activities.DNA repair | DNA double-strand break repair I g and T-cell receptor (TCR) variable region exons are assembled during early lymphocyte development from variable (V), diversity (D), and joining (J) gene segments (1). This V(D)J recombination reaction is initiated by recombination-activating gene (RAG) endonuclease (1). RAG recognizes short recombination signal sequences (RSs) that flank each germ-line V, D, and J segment; in the context of an appropriate pair of V, D, or J segments, RAG introduces DNA double-strand breaks (DSBs) between V, D, or J coding sequences and flanking RSs. The RAG cleavage reaction generates two kinds of ends. Coding ends (CEs) are generated as covalently sealed hairpins, whereas the RS ends (SEs) are generated as blunt 5′-phosphorylated broken ends (1

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Ataxia telangiectasia-mutated protein and DNA-dependent protein kinase have complementary V(D)J recombination functions

Zha

Jiang

Fujiwara

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…Although the aberrant resolution of RAG DSBs occurs extremely rarely in wild-type lymphocytes, these lesions are generated at higher frequencies in lymphocytes with DNA repair defects (14)(15)(16). In this regard, deficiency in the ataxia telangiectasia mutated (ATM) serine threonine kinase in both mice and humans leads to an increased incidence of lymphoid tumors with RAG-dependent translocations involving antigen receptor loci (17)(18)(19)(20)(21).…”

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Aberrantly resolved RAG-mediated DNA breaks in Atm-deficient lymphocytes target chromosomal breakpoints incis

Mahowald

Baron

Mahowald

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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Canonical chromosomal translocations juxtaposing antigen receptor genes and oncogenes are a hallmark of many lymphoid malignancies. These translocations frequently form through the joining of DNA ends from double-strand breaks (DSBs) generated by the recombinase activating gene (RAG)-1 and -2 proteins at lymphocyte antigen receptor loci and breakpoint targets near oncogenes. Our understanding of chromosomal breakpoint target selection comes primarily from the analyses of these lesions, which are selected based on their transforming properties. RAG DSBs are rarely resolved aberrantly in wild-type developing lymphocytes. However, in ataxia telangiectasia mutated (ATM)-deficient lymphocytes, RAG breaks are frequently joined aberrantly, forming chromosomal lesions such as translocations that predispose (ATM)-deficient mice and humans to the development of lymphoid malignancies. Here, an approach that minimizes selection biases is used to isolate a large cohort of breakpoint targets of aberrantly resolved RAG DSBs in Atm-deficient lymphocytes. Analyses of this cohort revealed that frequently, the breakpoint targets for aberrantly resolved RAG breaks are other DSBs. Moreover, these nonselected lesions exhibit a bias for using breakpoints in cis, forming small chromosomal deletions, rather than breakpoints in trans, forming chromosomal translocations.ataxia telangiectasia mutated ͉ chromosomal translocation ͉ DNA double-strand break repair ͉ V(D)J recombination D ouble-strand breaks (DSBs) in DNA are generated by genotoxic agents and cellular endonucleases as intermediates in several important physiologic processes including V(D)J recombination, Ig class switch recombination (CSR), DNA replication, gene transcription, and meiosis. DNA DSBs activate a highly conserved cellular response that prevents cell cycle progression, initiates repair of the broken DNA ends, and promotes apoptosis of cells with persistent un-repaired DSBs (1, 2). Broken DNA ends from a single DSB are usually rejoined; however, in some processes, such as V(D)J recombination and CSR, DNA ends arising from two DSBs are joined in a regulated fashion, generating a new gene product (1-4). Broken DNA ends from distinct DSBs can also be joined aberrantly, leading to the formation of potentially dangerous chromosomal lesions such as translocations, deletions, and inversions.All developing lymphocytes generate programmed DNA DSBs during V(D)J recombination, a process that joins variable (V), joining (J), and in some cases, diversity (D) gene segments to generate the second exon of antigen receptor genes (4). The V(D)J recombination reaction is initiated by the recombinase activating gene (RAG)-1 and -2 proteins, which together form the RAG endonuclease (5). RAG introduces DNA DSBs at the border of two recombining gene segments and their flanking RAG recognition sequences, termed recombination signals (RSs) (5). DNA cleavage by RAG occurs after an appropriate RS pair (12/23 compatible) forms a synaptic complex, generating

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“…This may occur by any of several mechanisms, including mistakenly binding and cleaving a DNA sequence that resembles an authentic RSS by a standard nick-hairpin mechanism, by targeting non-B form DNA structures and cleaving them through the introduction of staggered nicks (6), by mobilizing signal ends or episomal signal joints generated after initial RSS cleavage and promoting their integration elsewhere in the genome (either by direct transposition, end donation, or trans-V(D)J recombination) (7)(8)(9)(10), or through repair failures that allow DNA breaks to become illegitimately joined to DNA ends produced by RAG-mediated cleavage at antigen receptor loci (5).…”

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V(D)J Recombinase Binding and Cleavage of Cryptic Recombination Signal Sequences Identified from Lymphoid Malignancies

Zhang

Swanson

2008

Journal of Biological Chemistry

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To understand the molecular basis for these large differences, we investigated the binding and cleavage of these cRSSs by the RAG1/2 proteins that initiate V(D)J recombination. We find that the RAG proteins comparably bind all cRSSs tested, albeit more poorly than a consensus RSS. We show that four cRSSs that support levels of V(D)J recombination above background levels in cell culture (LMO2, TAL1, Ttg-1, and SIL) are also cleaved by the RAG proteins in vitro with efficiencies ranging from 18 to 70% of a consensus RSS. Cleavage of LMO2 and Ttg-1 by the RAG proteins can also be detected in cell culture using ligation-mediated PCR. In contrast, Hox11 and SCL are nicked but not cleaved efficiently in vitro, and cleavage at other adventitious sites in plasmid substrates may also limit the ability to detect recombination activity at these cRSSs in cell culture.The antigen binding domains of immunoglobulins and T cell receptors are encoded in germ line arrays of V, D, and J gene segments that are assembled into functional variable exons by V(D)J recombination during lymphocyte development (1). The site of recombination is directed by a recombination signal sequence (RSS) 2 that flanks each receptor gene segment and consists of a conserved heptamer (consensus 5Ј-CACAGTG-3Ј) and nonamer (consensus 5Ј-ACAAAAACC-3Ј) separated by either 12 or 23 Ϯ 1 nucleotides of more highly varied sequence. V(D)J recombination can be conceptually divided into two phases, a cleavage phase and a joining phase (2). In the cleavage phase, the lymphoid cell-specific RAG1 and RAG2 (recombination activating gene-1 and -2, respectively) proteins assemble a multiprotein synaptic complex with two RSSs (generally one 12-RSS and one 23-RSS) and introduce a DNA double strand break at each RSS between the heptamer and adjacent coding segment via a nick-hairpin mechanism to yield a blunt 5Ј-phosphorylated signal end and a coding end terminating in a covalently sealed DNA hairpin structure. In the joining phase, the signal ends are generally joined precisely to form signal joints, and the coding ends are processed and joined to form coding joints that typically contain nucleotide additions or deletions at the junction. These processes are normally mediated by components of the nonhomologous end-joining DNA repair pathway.

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Genomic instability due to V(D)J recombination-associated transposition

Cited by 67 publications

References 24 publications

Ataxia telangiectasia-mutated protein and DNA-dependent protein kinase have complementary V(D)J recombination functions

Ataxia telangiectasia-mutated protein and DNA-dependent protein kinase have complementary V(D)J recombination functions

Aberrantly resolved RAG-mediated DNA breaks in Atm-deficient lymphocytes target chromosomal breakpoints incis

V(D)J Recombinase Binding and Cleavage of Cryptic Recombination Signal Sequences Identified from Lymphoid Malignancies

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