1
|
Hirokawa S, Chure G, Belliveau NM, Lovely GA, Anaya M, Schatz DG, Baltimore D, Phillips R. Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination. Nucleic Acids Res 2020; 48:6726-6739. [PMID: 32449932 PMCID: PMC7337519 DOI: 10.1093/nar/gkaa418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/20/2020] [Accepted: 05/07/2020] [Indexed: 12/25/2022] Open
Abstract
Developing lymphocytes of jawed vertebrates cleave and combine distinct gene segments to assemble antigen-receptor genes. This process called V(D)J recombination that involves the RAG recombinase binding and cutting recombination signal sequences (RSSs) composed of conserved heptamer and nonamer sequences flanking less well-conserved 12- or 23-bp spacers. Little quantitative information is known about the contributions of individual RSS positions over the course of the RAG-RSS interaction. We employ a single-molecule method known as tethered particle motion to track the formation, lifetime and cleavage of individual RAG-12RSS-23RSS paired complexes (PCs) for numerous synthetic and endogenous 12RSSs. We reveal that single-bp changes, including in the 12RSS spacer, can significantly and selectively alter PC formation or the probability of RAG-mediated cleavage in the PC. We find that some rarely used endogenous gene segments can be mapped directly to poor RAG binding on their adjacent 12RSSs. Finally, we find that while abrogating RSS nicking with Ca2+ leads to substantially shorter PC lifetimes, analysis of the complete lifetime distributions of any 12RSS even on this reduced system reveals that the process of exiting the PC involves unidentified molecular details whose involvement in RAG-RSS dynamics are crucial to quantitatively capture kinetics in V(D)J recombination.
Collapse
Affiliation(s)
- Soichi Hirokawa
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Griffin Chure
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nathan M Belliveau
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Geoffrey A Lovely
- National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Michael Anaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
2
|
Patil P, Cieslak A, Bernhart SH, Toprak UH, Wagener R, López C, Wiehle L, Bens S, Altmüller J, Franitza M, Scholz I, Jayne S, Ahearne MJ, Scheffold A, Jebaraj BMC, Schneider C, Costa D, Braun T, Schrader A, Campo E, Dyer MJS, Nürnberg P, Dürig J, Johansson P, Böttcher S, Schlesner M, Herling M, Stilgenbauer S, Macintyre E, Siebert R. Reconstruction of rearranged T-cell receptor loci by whole genome and transcriptome sequencing gives insights into the initial steps of T-cell prolymphocytic leukemia. Genes Chromosomes Cancer 2019; 59:261-267. [PMID: 31677197 DOI: 10.1002/gcc.22821] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022] Open
Abstract
T-cell prolymphocytic leukemia (T-PLL) is an aggressive tumor with leukemic presentation of mature T-lymphocytes. Here, we aimed at characterizing the initial events in the molecular pathogenesis of T-PLL and particularly, at determining the point in T-cell differentiation when the hallmark oncogenic events, that is, inv(14)(q11q32)/t(14;14)(q11;q32) and t(X;14)(q28;q11) occur. To this end, we mined whole genome and transcriptome sequencing data of 17 and 11 T-PLL cases, respectively. Mapping of the 14q32.1 locus breakpoints identified only TCL1A, which was moreover significantly overexpressed in T-PLL as compared to benign CD4+ and CD8+ T-cells, as the only common oncogenic target of aberrations. In cases with t(14;14), the breakpoints mapped telomeric and in cases with inv(14) centromeric or in the 3'-untranslated region of TCL1A. Regarding the T-cell receptor alpha (TRA) locus-TCL1A breakpoint junctions, all 17 breakpoints involved recombination signal sequences and 15 junctions contained nontemplated (N-) nucleotides. All T-PLL cases studied carried in-frame TRA rearrangements on the intact allele, which skewed significantly toward usage of distal/central TRAV/TRAJ gene segments as compared to the illegitimate TRA rearrangements. Our findings suggest that the oncogenic TRA-TCL1A/MTCP1 rearrangements in T-PLL occur during opening of the TRA locus, that is, during the progression from CD4+ immature single positive to early double positive thymocyte stage, just before physiologic TCL1A expression is silenced. The cell carrying such an oncogenic event continues maturation and rearranges the second TRA allele to achieve a functional T-cell receptor. Thereafter, it switches off RAG and DNTT expression in line with the mature T-cell phenotype at presentation of T-PLL.
Collapse
Affiliation(s)
- Paurnima Patil
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Agata Cieslak
- Diagnostic Haematology, Necker-Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris, Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM), Paris, France
| | - Stephan H Bernhart
- Interdisciplinary Center for Bioinformatics, Transcriptome Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Umut H Toprak
- Bioinformatics and Omics Data Analytics, German Cancer Research Center, Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Division Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Rabea Wagener
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany.,Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Cristina López
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany.,Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Laura Wiehle
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Susanne Bens
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany.,Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Marek Franitza
- Cologne Center for Genomics, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Ingrid Scholz
- Omics IT and Data Management Core Facility, German Cancer Research Center, Heidelberg, Germany
| | - Sandrine Jayne
- Ernest and Helen Scott Haematological Research Institute, Department of Cancer Studies, University of Leicester, Leicester, UK
| | - Matthew J Ahearne
- Ernest and Helen Scott Haematological Research Institute, Department of Cancer Studies, University of Leicester, Leicester, UK
| | - Annika Scheffold
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Billy M C Jebaraj
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | | | - Dolors Costa
- Haematopathology Section, Hospital Clínic, Institut d'Investigaciones Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Till Braun
- Department I of Internal Medicine, Center for Integrated Oncology Köln Bonn, Deutsche CLL Studiengruppe (DCLLSG), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Alexandra Schrader
- Department I of Internal Medicine, Center for Integrated Oncology Köln Bonn, Deutsche CLL Studiengruppe (DCLLSG), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Elias Campo
- Haematopathology Section, Hospital Clínic, Institut d'Investigaciones Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Martin J S Dyer
- Ernest and Helen Scott Haematological Research Institute, Department of Cancer Studies, University of Leicester, Leicester, UK
| | - Peter Nürnberg
- Cologne Center for Genomics, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Jan Dürig
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Patricia Johansson
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sebastian Böttcher
- Department III of Internal Medicine, University Hospital Rostock, Rostock, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center, Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Marco Herling
- Department I of Internal Medicine, Center for Integrated Oncology Köln Bonn, Deutsche CLL Studiengruppe (DCLLSG), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | - Elizabeth Macintyre
- Diagnostic Haematology, Necker-Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris, Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM), Paris, France
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany.,Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| |
Collapse
|
3
|
Cut-and-Run: A Distinct Mechanism by which V(D)J Recombination Causes Genome Instability. Mol Cell 2019; 74:584-597.e9. [PMID: 30905508 PMCID: PMC6509286 DOI: 10.1016/j.molcel.2019.02.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/20/2018] [Accepted: 02/14/2019] [Indexed: 12/28/2022]
Abstract
V(D)J recombination is essential to generate antigen receptor diversity but is also a potent cause of genome instability. Many chromosome alterations that result from aberrant V(D)J recombination involve breaks at single recombination signal sequences (RSSs). A long-standing question, however, is how such breaks occur. Here, we show that the genomic DNA that is excised during recombination, the excised signal circle (ESC), forms a complex with the recombinase proteins to efficiently catalyze breaks at single RSSs both in vitro and in vivo. Following cutting, the RSS is released while the ESC-recombinase complex remains intact to potentially trigger breaks at further RSSs. Consistent with this, chromosome breaks at RSSs increase markedly in the presence of the ESC. Notably, these breaks co-localize with those found in acute lymphoblastic leukemia patients and occur at key cancer driver genes. We have named this reaction “cut-and-run” and suggest that it could be a significant cause of lymphocyte genome instability. A complex between the recombination by-product and RAGs triggers multiple DNA breaks The breaks co-localize with chromosome breakpoints in acute lymphoblastic leukemias The breaks occur at many frequently mutated genes in acute lymphoblastic leukemia Cut-and-run may underpin the most common types of lymphocyte chromosome instabilities
Collapse
|
4
|
On being the right size: antibody repertoire formation in the mouse and human. Immunogenetics 2017; 70:143-158. [DOI: 10.1007/s00251-017-1049-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/04/2017] [Indexed: 01/01/2023]
|
5
|
Kidd MJ, Jackson KJL, Boyd SD, Collins AM. DJ Pairing during VDJ Recombination Shows Positional Biases That Vary among Individuals with Differing IGHD Locus Immunogenotypes. THE JOURNAL OF IMMUNOLOGY 2015; 196:1158-64. [PMID: 26700767 DOI: 10.4049/jimmunol.1501401] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/20/2015] [Indexed: 11/19/2022]
Abstract
Human IgH diversity is influenced by biases in the pairing of IGHD and IGHJ genes, but these biases have not been described in detail. We used high-throughput sequencing of VDJ rearrangements to explore DJ pairing biases in 29 individuals. It was possible to infer three contrasting IGHD-IGHJ haplotypes in nine of these individuals, and two of these haplotypes include deletion polymorphisms involving multiple contiguous IGHD genes. Therefore, we were able to explore how the underlying genetic makeup of the H chain locus influences the formation of particular DJ pairs. Analysis of nonproductive rearrangements demonstrates that 3' IGHD genes tend to pair preferentially with 5' IGHJ genes, whereas 5' IGHD genes pair preferentially with 3' IGHJ genes; the relationship between IGHD gene pairing frequencies and IGHD gene position is a near linear one for each IGHJ gene. However, striking differences are seen in individuals who carry deletion polymorphisms in the D locus. The absence of different blocks of IGHD genes leads to increases in the utilization frequencies of just a handful of genes, and these genes have no clear positional relationships to the deleted genes. This suggests that pairing frequencies may be influenced by additional complex positional relationships that perhaps arise from chromatin structure. In contrast to IGHD gene usage, IGHJ gene usage is unaffected by the IGHD gene-deletion polymorphisms. Such an outcome would be expected if the recombinase complex associates with an IGHJ gene before associating with an IGHD gene partner.
Collapse
Affiliation(s)
- Marie J Kidd
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia; and
| | - Katherine J L Jackson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia; and Department of Pathology, Stanford University, Stanford, CA 94305
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia; and
| |
Collapse
|
6
|
Outters P, Jaeger S, Zaarour N, Ferrier P. Long-Range Control of V(D)J Recombination & Allelic Exclusion: Modeling Views. Adv Immunol 2015; 128:363-413. [PMID: 26477371 DOI: 10.1016/bs.ai.2015.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Allelic exclusion of immunoglobulin (Ig) and T-cell receptor (TCR) genes ensures the development of B and T lymphocytes operating under the mode of clonal selection. This phenomenon associates asynchronous V(D)J recombination events at Ig or TCR alleles and inhibitory feedback control. Despite years of intense research, however, the mechanisms that sustain asymmetric choice in random Ig/TCR dual allele usage and the production of Ig/TCR monoallelic expressing B and T lymphocytes remain unclear and open for debate. In this chapter, we first recapitulate the biological evidence that almost from the start appeared to link V(D)J recombination and allelic exclusion. We review the theoretical models previously proposed to explain this connection. Finally, we introduce our own mathematical modeling views based on how the developmental dynamics of individual lymphoid cells combine to sustain allelic exclusion.
Collapse
Affiliation(s)
- Pernelle Outters
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Sébastien Jaeger
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Nancy Zaarour
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Pierre Ferrier
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France.
| |
Collapse
|
7
|
The proximal J kappa germline-transcript promoter facilitates receptor editing through control of ordered recombination. PLoS One 2015; 10:e0113824. [PMID: 25559567 PMCID: PMC4283955 DOI: 10.1371/journal.pone.0113824] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 10/31/2014] [Indexed: 12/31/2022] Open
Abstract
V(D)J recombination creates antibody light chain diversity by joining a Vκ gene segment with one of four Jκ segments. Two Jκ germline-transcript (GT) promoters control Vκ-Jκ joining, but the mechanisms that govern Jκ choice are unclear. Here, we show in gene-targeted mice that the proximal GT promoter helps targeting rearrangements to Jκ1 by preventing premature DNA breaks at Jκ2. Consequently, cells lacking the proximal GT promoter show a biased utilization of downstream Jκ segments, resulting in a diminished potential for receptor editing. Surprisingly, the proximal—in contrast to the distal—GT promoter is transcriptionally inactive prior to Igκ recombination, indicating that its role in Jκ choice is independent of classical promoter function. Removal of the proximal GT promoter increases H3K4me3 levels at Jκ segments, suggesting that this promoter could act as a suppressor of recombination by limiting chromatin accessibility to RAG. Our findings identify the first cis-element critical for Jκ choice and demonstrate that ordered Igκ recombination facilitates receptor editing.
Collapse
|
8
|
Illegitimate V(D)J recombination-mediated deletions in Notch1 and Bcl11b are not sufficient for extensive clonal expansion and show minimal age or sex bias in frequency or junctional processing. Mutat Res 2014; 761:34-48. [PMID: 24530429 DOI: 10.1016/j.mrfmmm.2014.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 12/23/2013] [Accepted: 01/28/2014] [Indexed: 01/22/2023]
Abstract
Illegitimate V(D)J recombination at oncogenes and tumor suppressor genes is implicated in formation of several T cell malignancies. Notch1 and Bcl11b, genes involved in developing T cell specification, selection, proliferation, and survival, were previously shown to contain hotspots for deletional illegitimate V(D)J recombination associated with radiation-induced thymic lymphoma. Interestingly, these deletions were also observed in wild-type animals. In this study, we conducted frequency, clonality, and junctional processing analyses of Notch1 and Bcl11b deletions during mouse development and compared results to published analyses of authentic V(D)J rearrangements at the T cell receptor beta (TCRβ) locus and illegitimate V(D)J deletions observed at the human, nonimmune HPRT1 locus not involved in T cell malignancies. We detect deletions in Notch1 and Bcl11b in thymic and splenic T cell populations, consistent with cells bearing deletions in the circulating lymphocyte pool. Deletions in thymus can occur in utero, increase in frequency between fetal and postnatal stages, are detected at all ages examined between fetal and 7 months, exhibit only limited clonality (contrasting with previous results in radiation-sensitive mouse strains), and consistent with previous reports are more frequent in Bcl11b, partially explained by relatively high Recombination Signal Information Content (RIC) scores. Deletion junctions in Bcl11b exhibit greater germline nucleotide loss, while in Notch1 palindromic (P) nucleotides are more abundant, although average P nucleotide length is similar for both genes and consistent with results at the TCRβ locus. Non-templated (N) nucleotide insertions appear to increase between fetal and postnatal stages for Notch1, consistent with normal terminal deoxynucleotidyl transferase (TdT) activity; however, neonatal Bcl11b junctions contain elevated levels of N insertions. Finally, contrasting with results at the HPRT1 locus, we find no obvious age or gender bias in junctional processing, and inverted repeats at recessed coding ends (Pr nucleotides) correspond mostly to single-base additions consistent with normal TdT activity.
Collapse
|
9
|
An automated algorithm for extracting functional immunologic V-genes from genomes in jawed vertebrates. Immunogenetics 2013; 65:691-702. [DOI: 10.1007/s00251-013-0715-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/06/2013] [Indexed: 10/26/2022]
|
10
|
Trancoso I, Bonnet M, Gardner R, Carneiro J, Barreto VM, Demengeot J, Sarmento LM. A Novel Quantitative Fluorescent Reporter Assay for RAG Targets and RAG Activity. Front Immunol 2013; 4:110. [PMID: 23720659 PMCID: PMC3655321 DOI: 10.3389/fimmu.2013.00110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 04/27/2013] [Indexed: 12/11/2022] Open
Abstract
Recombination-Activating Genes (RAG) 1 and 2 form the site specific recombinase that mediates V(D)J recombination, a process of DNA editing required for lymphocyte development and responsible for their diverse repertoire of antigen receptors. Mistargeted RAG activity associates with genome alteration and is responsible for various lymphoid tumors. Moreover several non-lymphoid tumors express RAG ectopically. A practical and powerful tool to perform quantitative assessment of RAG activity and to score putative RAG-Recognition signal sequences (RSS) is required in the fields of immunology, oncology, gene therapy, and development. Here we report the detailed characterization of a novel fluorescence-based reporter of RAG activity, named GFPi, a tool that allows measuring recombination efficiency (RE) by simple flow cytometry analysis. GFPi can be produced both as a plasmid for transient transfection experiments in cell lines or as a retrovirus for stable integration in the genome, thus supporting ex vivo and in vivo studies. The GFPi assay faithfully quantified endogenous and ectopic RAG activity as tested in genetically modified fibroblasts, tumor derived cell lines, developing pre-B cells, and hematopoietic cells. The GFPi assay also successfully ranked the RE of various RSS pairs, including bona fide RSS associated with V(D)J segments, artificial consensus sequences modified or not at specific nucleotides known to affect their efficiencies, or cryptic RSS involved in RAG-dependent activation of oncogenes. Our work validates the GFPi reporter as a practical quantitative tool for the study of RAG activity and RSS efficiencies. It should turn useful for the study of RAG-mediated V(D)J and aberrant rearrangements, lineage commitment, and vertebrate evolution.
Collapse
|
11
|
Stone JL, McMillan RE, Skaar DA, Bradshaw JM, Jirtle RL, Sikes ML. DNA double-strand breaks relieve USF-mediated repression of Dβ2 germline transcription in developing thymocytes. THE JOURNAL OF IMMUNOLOGY 2012; 188:2266-75. [PMID: 22287717 DOI: 10.4049/jimmunol.1002931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Activation of germline promoters is central to V(D)J recombinational accessibility, driving chromatin remodeling, nucleosome repositioning, and transcriptional read-through of associated DNA. We have previously shown that of the two TCRβ locus (Tcrb) D segments, Dβ1 is flanked by an upstream promoter that directs its transcription and recombinational accessibility. In contrast, transcription within the DJβ2 segment cluster is initially restricted to the J segments and only redirected upstream of Dβ2 after D-to-J joining. The repression of upstream promoter activity prior to Tcrb assembly correlates with evidence that suggests DJβ2 recombination is less efficient than that of DJβ1. Because inefficient DJβ2 assembly offers the potential for V-to-DJβ2 recombination to rescue frameshifted V-to-DJβ1 joints, we wished to determine how Dβ2 promoter activity is modulated upon Tcrb recombination. In this study, we show that repression of the otherwise transcriptionally primed 5'Dβ2 promoter requires binding of upstream stimulatory factor (USF)-1 to a noncanonical E-box within the Dβ2 12-recombination signal sequence spacer prior to Tcrb recombination. USF binding is lost from both rearranged and germline Dβ2 sites in DNA-dependent protein kinase, catalytic subunit-competent thymocytes. Finally, genotoxic dsDNA breaks lead to rapid loss of USF binding and gain of transcriptionally primed 5'Dβ2 promoter activity in a DNA-dependent protein kinase, catalytic subunit-dependent manner. Together, these data suggest a mechanism by which V(D)J recombination may feed back to regulate local Dβ2 recombinational accessibility during thymocyte development.
Collapse
Affiliation(s)
- Jennifer L Stone
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | | | | | | |
Collapse
|
12
|
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
|
13
|
Merelli I, Guffanti A, Fabbri M, Cocito A, Furia L, Grazini U, Bonnal RJ, Milanesi L, McBlane F. RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes. Nucleic Acids Res 2010; 38:W262-7. [PMID: 20478831 PMCID: PMC2896083 DOI: 10.1093/nar/gkq391] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recombination signal sequences (RSSs) flanking V, D and J gene segments are recognized and cut by the VDJ recombinase during development of B and T lymphocytes. All RSSs are composed of seven conserved nucleotides, followed by a spacer (containing either 12 ± 1 or 23 ± 1 poorly conserved nucleotides) and a conserved nonamer. Errors in V(D)J recombination, including cleavage of cryptic RSS outside the immunoglobulin and T cell receptor loci, are associated with oncogenic translocations observed in some lymphoid malignancies. We present in this paper the RSSsite web server, which is available from the address http://www.itb.cnr.it/rss. RSSsite consists of a web-accessible database, RSSdb, for the identification of pre-computed potential RSSs, and of the related search tool, DnaGrab, which allows the scoring of potential RSSs in user-supplied sequences. This latter algorithm makes use of probability models, which can be recasted to Bayesian network, taking into account correlations between groups of positions of a sequence, developed starting from specific reference sets of RSSs. In validation laboratory experiments, we selected 33 predicted cryptic RSSs (cRSSs) from 11 chromosomal regions outside the immunoglobulin and TCR loci for functional testing.
Collapse
Affiliation(s)
- Ivan Merelli
- Institute for Biomedical Technologies, National Research Council, via Fratelli Cervi 93, 20090 Segrate, Milano, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Fugmann SD. The origins of the Rag genes--from transposition to V(D)J recombination. Semin Immunol 2009; 22:10-6. [PMID: 20004590 DOI: 10.1016/j.smim.2009.11.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Accepted: 11/11/2009] [Indexed: 01/06/2023]
Abstract
The recombination activating genes 1 and 2 (Rag1 and Rag2) encode the key enzyme that is required for the generation of the highly diversified antigen receptor repertoire central to adaptive immunity. The longstanding model proposed that this gene pair was acquired by horizontal gene transfer to explain its abrupt appearance in the vertebrate lineage. The analyses of the enormous amount of sequence data created by many genome sequencing projects now provide the basis for a more refined model as to how this unique gene pair evolved from a selfish DNA transposon into a sophisticated DNA recombinase essential for immunity.
Collapse
Affiliation(s)
- Sebastian D Fugmann
- Laboratory of Cellular and Molecular Biology, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd., Suite 100, Baltimore, MD 21224, USA.
| |
Collapse
|
15
|
Affiliation(s)
- Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America.
| |
Collapse
|
16
|
Fitzsimmons SP, Bernstein RM, Max EE, Skok JA, Shapiro MA. Dynamic changes in accessibility, nuclear positioning, recombination, and transcription at the Ig kappa locus. THE JOURNAL OF IMMUNOLOGY 2007; 179:5264-73. [PMID: 17911612 DOI: 10.4049/jimmunol.179.8.5264] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The 3-megabase Igkappa locus undergoes differentially controlled nuclear positioning events and chromatin structural changes during the course of B cell development. The temporal association of chromatin structural changes, transcription, and recombination at the Igkappa locus was determined in a murine pre-B cell line that can be induced to recombine at the Igkappa locus and in ex vivo-cultured murine pre-B cells. Additionally, the timing of nuclear positioning relative to the temporal order of chromatin structural changes and recombination and transcription was determined. We demonstrate that before induction, the Igkappa locus was poised for recombination; both alleles were in a contracted state, and the enrichment of histone modifications and germline transcripts of specific Vkappa genes were observed. Histone modifications of the Vkappa genes did not vary upon induction but the levels of modifications correlated with the levels of germline Vkappa gene transcripts and recombination. Upon induction, but before VkappaJkappa recombination, centromeric recruitment of single Igkappa alleles occurred. DNase I sensitivity of the entire locus increased gradually over the course of differentiation while the enrichment of histone modifications downstream of the Vkappa genes was increased in the silencer regions upstream of Jkappa1, within the Igkappa sterile transcript, the kappa constant region, the Ekappai and Ekappa3' enhancers, and the recombining sequence. The ex vivo pre-B cells showed similar patterns of histone modifications across the locus except at the Vkappa genes. In this study, H3 acetylation correlated with levels of germline transcripts while H3 methylation correlated with levels of recombination.
Collapse
Affiliation(s)
- Sean P Fitzsimmons
- Division of Monoclonal Antibodies, Food and Drug Administration, Center for Drug Evaluation and Research, Rockville, MD 20852, USA
| | | | | | | | | |
Collapse
|
17
|
Drejer-Teel AH, Fugmann SD, Schatz DG. The beyond 12/23 restriction is imposed at the nicking and pairing steps of DNA cleavage during V(D)J recombination. Mol Cell Biol 2007; 27:6288-99. [PMID: 17636023 PMCID: PMC2099602 DOI: 10.1128/mcb.00835-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The beyond 12/23 (B12/23) rule ensures inclusion of a Dbeta gene segment in the assembled T-cell receptor (TCR) beta variable region exon and is manifest by a failure of direct Vbeta-to-Jbeta gene segment joining. The restriction is enforced during the DNA cleavage step of V(D)J recombination by the recombination-activating gene 1 and 2 (RAG1/2) proteins and the recombination signal sequences (RSSs) flanking the TCRbeta gene segments. Nothing is known about the step(s) at which DNA cleavage is defective or how TCRbeta locus sequences contribute to these defects. To address this, we examined the steps of DNA cleavage by the RAG proteins using TCRbeta locus V, D, and J RSS oligonucleotide substrates. The results demonstrate that the B12/23 rule is enforced through slow nicking of Jbeta substrates and to some extent through poor synapsis of Vbeta and Jbeta substrates. Nicking is controlled largely by the coding flank and, unexpectedly, the RSS spacer, while synapsis is controlled primarily by the RSS nonamer. The results demonstrate that different Jbeta substrates are crippled at different steps of cleavage by distinct combinations of defects in the various DNA elements and strongly suggest that the DNA nicking step of V(D)J recombination can be rate limiting in vivo.
Collapse
Affiliation(s)
- Anna H Drejer-Teel
- Department of Genetics, Yale University School of Medicine, 330 Cedar St., New Haven, Connecticut 06510, USA
| | | | | |
Collapse
|
18
|
Dik WA, Nadel B, Przybylski GK, Asnafi V, Grabarczyk P, Navarro JM, Verhaaf B, Schmidt CA, Macintyre EA, van Dongen JJM, Langerak AW. Different chromosomal breakpoints impact the level of LMO2 expression in T-ALL. Blood 2007; 110:388-92. [PMID: 17360939 DOI: 10.1182/blood-2006-12-064816] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The t(11;14)(p13;q11) is presumed to arise from an erroneous T-cell receptor delta TCRD V(D)J recombination and to result in LMO2 activation. However, the mechanisms underlying this translocation and the resulting LMO2 activation are poorly defined. We performed combined in vivo, ex vivo, and in silico analyses on 9 new t(11;14)(p13;q11)-positive T-cell acute lymphoblastic leukemia (T-ALL) as well as normal thymocytes. Our data support the involvement of 2 distinct t(11;14)(p13;q11) V(D)J-related translocation mechanisms. We provide compelling evidence that removal of a negative regulatory element from the LMO2 locus, rather than juxtaposition to the TCRD enhancer, is the main determinant for LMO2 activation in the majority of t(11;14)(p13;q11) translocations. Furthermore, the position of the LMO2 breakpoints in T-ALL in the light of the occurrence of TCRD-LMO2 translocations in normal thymocytes points to a critical role for the exact breakpoint location in determining LMO2 activation levels and the consequent pressure for T-ALL development.
Collapse
Affiliation(s)
- Willem A Dik
- Department of Immunology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
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
|
20
|
Finette BA. Analysis of mutagenic V(D)J recombinase mediated mutations at the HPRT locus as an in vivo model for studying rearrangements with leukemogenic potential in children. DNA Repair (Amst) 2006; 5:1049-64. [PMID: 16807138 DOI: 10.1016/j.dnarep.2006.05.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Pediatric acute lymphocytic leukemia (ALL) is a multifactorial malignancy with many distinctive developmentally specific features that include age specific acquisition of deletions, insertions and chromosomal translocations. The analysis of breakpoint regions involved in these leukemogenic genomic rearrangements has provided evidence that many are the consequence of V(D)J recombinase mediated events at both immune and non-immune loci. Hence, the direct investigation of in vivo genetic and epigenetic features in human peripheral lymphocytes is necessary to fully understand the mechanisms responsible for the specificity and frequency of these leukemogenic non-immune V(D)J recombinase events. In this review, I will present the utility of analyzing mutagenic V(D)J recombinase mediated genomic rearrangements at the HPRT locus in humans as an in vivo model system for understanding the mechanisms responsible for leukemogenic genetic alterations observed in children with leukemia.
Collapse
Affiliation(s)
- Barry A Finette
- Department of Pediatrics, Microbiology and Molecular Genetics, University of Vermont College of Medicine, E203 Given Building, 89 Beaumont Ave., Burlington, VT 05405, USA.
| |
Collapse
|
21
|
Abstract
Antigen receptor genes exist in the germline in a "split" configuration and are assembled in developing B and T lymphocytes by V(D)J recombination. This site-specific recombination reaction is initiated by a complex containing the RAG1 and RAG2 proteins and completed by general DNA repair factors. RAG1 and RAG2, like the adaptive immune system itself, are found exclusively in jawed vertebrates, and are thought to have entered the vertebrate genome by horizontal transmission as components of a transposable element. This review discusses the structure of antigen receptor genes and the mechanisms by which they are assembled and diversified, and then goes on to consider the evolutionary implications of the arrival of the hypothetical "RAG transposon".
Collapse
Affiliation(s)
- David G Schatz
- Section of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA.
| |
Collapse
|