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Abstract
Immunoglobulin heavy chain (IgH) translocations are common and early oncogenic events in B cell and plasma cell malignancies including B cell non-Hodgkin's lymphoma (NHL) and multiple myeloma (MM). IgH translocations bring oncogenes into close proximity with potent enhancer elements within the IgH locus, leading to oncogene up-regulation. As IgH enhancer activity is tightly controlled by B cell lineage-specific signaling and transcriptional networks, we hypothesized that IgH enhancers are potentially druggable targets/elements. To test this, we developed a molecular imaging-based high-throughput screening platform for discovering inhibitors of IgH enhancer-driven transcriptional activity. As proof of concept, we identified a low micromolar potency molecule (compound 30666) that inhibited immunoglobulin production by MM cells and blocked expression of an array of IgH translocation-induced oncogenes (CCND1, FGFR3/MMSET, and MYC) in MM and NHL cell lines. Prolonged exposure to 30666 significantly reduced the viability of IgH translocation-positive NHL and MM cells, but was less effective against cells lacking IgH translocations. Compound 30666 exhibited suitable pharmacological properties, including metabolic stability in liver microsomes and oral bioavailability in mice, and demonstrated preclinical anti-MM activity in a plasmacytoma mouse model. Our work suggests that IgH enhancers are attractive and potentially druggable targets for IgH translocation driven malignancies.
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Affiliation(s)
- Nathan G Dolloff
- a Department of Cellular and Molecular Pharmacology & Experimental Therapeutics , Medical University of South Carolina , Charleston , SC , USA
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52
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Delgado-Benito V, Rosen DB, Wang Q, Gazumyan A, Pai JA, Oliveira TY, Sundaravinayagam D, Zhang W, Andreani M, Keller L, Kieffer-Kwon KR, Pękowska A, Jung S, Driesner M, Subbotin RI, Casellas R, Chait BT, Nussenzweig MC, Di Virgilio M. The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination. Mol Cell 2018; 72:636-649.e8. [PMID: 30293785 PMCID: PMC6242708 DOI: 10.1016/j.molcel.2018.08.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 07/01/2018] [Accepted: 08/25/2018] [Indexed: 01/18/2023]
Abstract
Class switch recombination (CSR) is a DNA recombination reaction that diversifies the effector component of antibody responses. CSR is initiated by activation-induced cytidine deaminase (AID), which targets transcriptionally active immunoglobulin heavy chain (Igh) switch donor and acceptor DNA. The 3′ Igh super-enhancer, 3′ regulatory region (3′RR), is essential for acceptor region transcription, but how this function is regulated is unknown. Here, we identify the chromatin reader ZMYND8 as an essential regulator of the 3′RR. In B cells, ZMYND8 binds promoters and super-enhancers, including the Igh enhancers. ZMYND8 controls the 3′RR activity by modulating the enhancer transcriptional status. In its absence, there is increased 3′RR polymerase loading and decreased acceptor region transcription and CSR. In addition to CSR, ZMYND8 deficiency impairs somatic hypermutation (SHM) of Igh, which is also dependent on the 3′RR. Thus, ZMYND8 controls Igh diversification in mature B lymphocytes by regulating the activity of the 3′ Igh super-enhancer. ZMYND8 is required for GLT of acceptor S regions and Class Switch Recombination ZMYND8 supports efficient somatic hypermutation of the Igh variable regions ZMYND8 binds B cell super-enhancers, including the 3′ Igh enhancer ZMYND8 modulates the transcriptional status and activity of the 3′ Igh enhancer
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Affiliation(s)
- Verónica Delgado-Benito
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Daniel B Rosen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Qiao Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Joy A Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Devakumar Sundaravinayagam
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Matteo Andreani
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Lisa Keller
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | | | | | - Seolkyoung Jung
- Lymphocyte Nuclear Biology, NIAMS, NCI, NIH, Bethesda, MD 20892, USA
| | - Madlen Driesner
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Roman I Subbotin
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NCI, NIH, Bethesda, MD 20892, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Michela Di Virgilio
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
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53
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Kinase-dependent structural role of DNA-PKcs during immunoglobulin class switch recombination. Proc Natl Acad Sci U S A 2018; 115:8615-8620. [PMID: 30072430 DOI: 10.1073/pnas.1808490115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is a classical nonhomologous end-joining (cNHEJ) factor. Loss of DNA-PKcs diminished mature B cell class switch recombination (CSR) to other isotypes, but not IgG1. Here, we show that expression of the kinase-dead DNA-PKcs (DNA-PKcsKD/KD ) severely compromises CSR to IgG1. High-throughput sequencing analyses of CSR junctions reveal frequent accumulation of nonproductive interchromosomal translocations, inversions, and extensive end resection in DNA-PKcsKD/KD , but not DNA-PKcs-/- , B cells. Meanwhile, the residual joints from DNA-PKcsKD/KD cells and the efficient Sµ-Sγ1 junctions from DNA-PKcs-/- B cells both display similar preferences for small (2-6 nt) microhomologies (MH). In DNA-PKcs-/- cells, Sµ-Sγ1 joints are more resistant to inversions and extensive resection than Sµ-Sε and Sµ-Sµ joints, providing a mechanism for the isotype-specific CSR defects. Together, our findings identify a kinase-dependent role of DNA-PKcs in suppressing MH-mediated end joining and a structural role of DNA-PKcs protein in the orientation of CSR.
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54
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Nicolas L, Cols M, Choi JE, Chaudhuri J, Vuong B. Generating and repairing genetically programmed DNA breaks during immunoglobulin class switch recombination. F1000Res 2018; 7:458. [PMID: 29744038 PMCID: PMC5904731 DOI: 10.12688/f1000research.13247.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/09/2018] [Indexed: 01/03/2023] Open
Abstract
Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig locus, DNA repair pathways are diverted from their canonical role in maintaining genomic integrity to permit AID-directed mutation and deletion of gene coding segments. Recently identified proteins, genes, and regulatory networks have provided new insights into the temporally and spatially coordinated molecular interactions that control the formation and repair of DSBs within the Ig locus. Unravelling the genetic program that allows B cells to selectively alter the Ig coding regions while protecting non-Ig genes from DNA damage advances our understanding of the molecular processes that maintain genomic integrity as well as humoral immunity.
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Affiliation(s)
- Laura Nicolas
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Montserrat Cols
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jee Eun Choi
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, NY, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bao Vuong
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, NY, USA
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55
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Qiu X, Kumari G, Gerasimova T, Du H, Labaran L, Singh A, De S, Wood WH, Becker KG, Zhou W, Ji H, Sen R. Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus. Mol Cell 2018; 70:21-33.e6. [PMID: 29576529 DOI: 10.1016/j.molcel.2018.02.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 12/19/2017] [Accepted: 02/13/2018] [Indexed: 12/22/2022]
Abstract
Immunoglobulin heavy-chain (IgH) genes are assembled by DNA rearrangements that juxtapose a variable (VH), a diversity (DH), and a joining (JH) gene segment. Here, we report that in the absence of intergenic control region 1 (IGCR1), the intronic enhancer (Eμ) associates with the next available CTCF binding site located close to VH81X via putative heterotypic interactions involving YY1 and CTCF. The alternate Eμ/VH81X loop leads to formation of a distorted recombination center and altered DH rearrangements and disrupts chromosome conformation that favors distal VH recombination. Cumulatively, these features drive highly skewed, Eμ-dependent recombination of VH81X. Sequential deletion of CTCF binding regions on IGCR1-deleted alleles suggests that they influence recombination of single proximal VH gene segments. Our observations demonstrate that Eμ interacts differently with IGCR1- or VH-associated CTCF binding sites and thereby identify distinct roles for insulator-like elements in directing enhancer activity.
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Affiliation(s)
- Xiang Qiu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Gita Kumari
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Tatiana Gerasimova
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Hansen Du
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Lawal Labaran
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - William H Wood
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Kevin G Becker
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA.
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56
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The IgH 3' regulatory region and c-myc-induced B-cell lymphomagenesis. Oncotarget 2018; 8:7059-7067. [PMID: 27729620 PMCID: PMC5351691 DOI: 10.18632/oncotarget.12535] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/05/2016] [Indexed: 01/18/2023] Open
Abstract
Deregulation and mutations of c-myc have been reported in multiple mature B-cell malignancies such as Burkitt lymphoma, myeloma and plasma cell lymphoma. After translocation into the immunoglobulin heavy chain (IgH) locus, c-myc is constitutively expressed under the control of active IgH cis-regulatory enhancers. Those located in the IgH 3 regulatory region (3RR) are master control elements of transcription. Over the past decade numerous convincing demonstrations of 3RRs contribution to mature c-myc-induced lymphomagenesis have been made using transgenic models with various types of IgH-c-myc translocations and transgenes. This review highlights how IgH 3RR physiological functions play a critical role in c-myc deregulation during lymphomagenesis.
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57
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DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner. Cell Rep 2017; 17:2927-2942. [PMID: 27974207 DOI: 10.1016/j.celrep.2016.11.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/07/2016] [Accepted: 11/11/2016] [Indexed: 11/22/2022] Open
Abstract
Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division.
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58
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Laffleur B, Debeaupuis O, Dalloul Z, Cogné M. B Cell Intrinsic Mechanisms Constraining IgE Memory. Front Immunol 2017; 8:1277. [PMID: 29180995 PMCID: PMC5694035 DOI: 10.3389/fimmu.2017.01277] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022] Open
Abstract
Memory B cells and long-lived plasma cells are key elements of adaptive humoral immunity. Regardless of the immunoglobulin class produced, these cells can ensure long-lasting protection but also long-lasting immunopathology, thus requiring tight regulation of their generation and survival. Among all antibody classes, this is especially true for IgE, which stands as the most potent, and can trigger dramatic inflammatory reactions even when present in minute amounts. IgE responses and memory crucially protect against parasites and toxic components of venoms, conferring selective advantages and explaining their conservation in all mammalian species despite a parallel broad spectrum of IgE-mediated immunopathology. Long-term memory of sensitization and anaphylactic responses to allergens constitute the dark side of IgE responses, which can trigger multiple acute or chronic pathologic manifestations, some punctuated with life-threatening events. This Janus face of the IgE response and memory, both necessary and potentially dangerous, thus obviously deserves the most elaborated self-control schemes.
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Affiliation(s)
- Brice Laffleur
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | | | - Zeinab Dalloul
- UMR 7276 Centre National de la Recherche Scientifique: Contrôle de la Réponse Immune B et des Lymphoproliférations, Université de Limoges, Limoges, France
| | - Michel Cogné
- UMR 7276 Centre National de la Recherche Scientifique: Contrôle de la Réponse Immune B et des Lymphoproliférations, Université de Limoges, Limoges, France.,Institut Universitaire de France, Paris, France
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59
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Le Noir S, Laffleur B, Carrion C, Garot A, Lecardeur S, Pinaud E, Denizot Y, Skok J, Cogné M. The IgH locus 3' cis-regulatory super-enhancer co-opts AID for allelic transvection. Oncotarget 2017; 8:12929-12940. [PMID: 28088785 PMCID: PMC5355067 DOI: 10.18632/oncotarget.14585] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/01/2017] [Indexed: 11/25/2022] Open
Abstract
Immunoglobulin heavy chain (IgH) alleles have ambivalent relationships: they feature both allelic exclusion, ensuring monoallelic expression of a single immunoglobulin (Ig) allele, and frequent inter-allelic class-switch recombination (CSR) reassembling genes from both alleles. The IgH locus 3' regulatory region (3'RR) includes several transcriptional cis-enhancers promoting activation-induced cytidine deaminase (AID)-dependent somatic hypermutation (SHM) and CSR, and altogether behaves as a strong super-enhancer. It can also promote deregulated expression of translocated oncogenes during lymphomagenesis. Besides these rare, illegitimate and pathogenic interactions, we now show that under physiological conditions, the 3'RR super-enhancer supports not only legitimate cis- , but also trans-recruitment of AID, contributing to IgH inter-allelic proximity and enabling the super-enhancer on one allele to stimulate biallelic SHM and CSR. Such inter-allelic activating interactions define transvection, a phenomenon well-known in drosophila but rarely observed in mammalian cells, now appearing as a unique feature of the IgH 3'RR super-enhancer.
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Affiliation(s)
- Sandrine Le Noir
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Brice Laffleur
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Claire Carrion
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Armand Garot
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Sandrine Lecardeur
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Eric Pinaud
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Yves Denizot
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Jane Skok
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Michel Cogné
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
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60
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Marina-Zárate E, Pérez-García A, Ramiro AR. CCCTC-Binding Factor Locks Premature IgH Germline Transcription and Restrains Class Switch Recombination. Front Immunol 2017; 8:1076. [PMID: 28928744 PMCID: PMC5591319 DOI: 10.3389/fimmu.2017.01076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/18/2017] [Indexed: 01/02/2023] Open
Abstract
In response to antigenic stimulation B cells undergo class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) to replace the primary IgM/IgD isotypes by IgG, IgE, or IgA. CSR is initiated by activation-induced cytidine deaminase (AID) through the deamination of cytosine residues at the switch (S) regions of IgH. B cell stimulation promotes germline transcription (GLT) of specific S regions, a necessary event prior to CSR because it facilitates AID access to S regions. Here, we show that CCCTC-binding factor (CTCF)-deficient mice are severely impaired in the generation of germinal center B cells and plasma cells after immunization in vivo, most likely due to impaired cell survival. Importantly, we find that CTCF-deficient B cells have an increased rate of CSR under various stimulation conditions in vitro. This effect is not secondary to altered cell proliferation or AID expression in CTCF-deficient cells. Instead, we find that CTCF-deficient B cells harbor an increased mutation frequency at switch regions, probably reflecting an increased accessibility of AID to IgH in the absence of CTCF. Moreover, CTCF deficiency triggers premature GLT of S regions in naïve B cells. Our results indicate that CTCF restricts CSR by enforcing GLT silencing and limiting AID access to IgH.
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Affiliation(s)
- Ester Marina-Zárate
- B Lymphocyte Biology Laboratory, Fundacion Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Arantxa Pérez-García
- B Lymphocyte Biology Laboratory, Fundacion Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Almudena R Ramiro
- B Lymphocyte Biology Laboratory, Fundacion Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
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61
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Bahjat M, Guikema JEJ. The Complex Interplay between DNA Injury and Repair in Enzymatically Induced Mutagenesis and DNA Damage in B Lymphocytes. Int J Mol Sci 2017; 18:ijms18091876. [PMID: 28867784 PMCID: PMC5618525 DOI: 10.3390/ijms18091876] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 08/24/2017] [Accepted: 08/29/2017] [Indexed: 11/25/2022] Open
Abstract
Lymphocytes are endowed with unique and specialized enzymatic mutagenic properties that allow them to diversify their antigen receptors, which are crucial sensors for pathogens and mediators of adaptive immunity. During lymphocyte development, the antigen receptors expressed by B and T lymphocytes are assembled in an antigen-independent fashion by ordered variable gene segment recombinations (V(D)J recombination), which is a highly ordered and regulated process that requires the recombination activating gene products 1 & 2 (RAG1, RAG2). Upon activation by antigen, B lymphocytes undergo additional diversifications of their immunoglobulin B-cell receptors. Enzymatically induced somatic hypermutation (SHM) and immunoglobulin class switch recombination (CSR) improves the affinity for antigen and shape the effector function of the humoral immune response, respectively. The activation-induced cytidine deaminase (AID) enzyme is crucial for both SHM and CSR. These processes have evolved to both utilize as well as evade different DNA repair and DNA damage response pathways. The delicate balance between enzymatic mutagenesis and DNA repair is crucial for effective immune responses and the maintenance of genomic integrity. Not surprisingly, disturbances in this balance are at the basis of lymphoid malignancies by provoking the formation of oncogenic mutations and chromosomal aberrations. In this review, we discuss recent mechanistic insight into the regulation of RAG1/2 and AID expression and activity in lymphocytes and the complex interplay between these mutagenic enzymes and DNA repair and DNA damage response pathways, focusing on the base excision repair and mismatch repair pathways. We discuss how disturbances of this interplay induce genomic instability and contribute to oncogenesis.
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Affiliation(s)
- Mahnoush Bahjat
- Department of Pathology, Academic Medical Center, University of Amsterdam; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam 1105 AZ, The Netherlands.
| | - Jeroen E J Guikema
- Department of Pathology, Academic Medical Center, University of Amsterdam; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam 1105 AZ, The Netherlands.
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62
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Oettgen HC. Fifty years later: Emerging functions of IgE antibodies in host defense, immune regulation, and allergic diseases. J Allergy Clin Immunol 2017; 137:1631-1645. [PMID: 27263999 DOI: 10.1016/j.jaci.2016.04.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 01/15/2023]
Abstract
Fifty years ago, after a long search, IgE emerged as the circulating factor responsible for triggering allergic reactions. Its extremely low concentration in plasma created significant hurdles for scientists working to reveal its identity. We now know that IgE levels are invariably increased in patients affected by atopic conditions and that IgE provides the critical link between the antigen recognition role of the adaptive immune system and the effector functions of mast cells and basophils at mucosal and cutaneous sites of environmental exposure. This review discusses the established mechanisms of action of IgE in pathologic immediate hypersensitivity, as well as its multifaceted roles in protective immunity, control of mast cell homeostasis, and its more recently revealed immunomodulatory functions.
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Affiliation(s)
- Hans C Oettgen
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass.
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63
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Inducible CTCF insulator delays the IgH 3' regulatory region-mediated activation of germline promoters and alters class switching. Proc Natl Acad Sci U S A 2017; 114:6092-6097. [PMID: 28533409 DOI: 10.1073/pnas.1701631114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Class switch recombination (CSR) plays an important role in adaptive immune response by enabling mature B cells to switch from IgM expression to the expression of downstream isotypes. CSR is preceded by inducible germline (GL) transcription of the constant genes and is controlled by the 3' regulatory region (3'RR) in a stimulus-dependent manner. Why the 3'RR-mediated up-regulation of GL transcription is delayed to the mature B-cell stage is presently unknown. Here we show that mice devoid of an inducible CTCF binding element, located in the α constant gene, display a marked isotype-specific increase of GL transcription in developing and resting splenic B cells and altered CSR in activated B cells. Moreover, insertion of a GL promoter downstream of the CTCF insulator led to premature activation of the ectopic promoter. This study provides functional evidence that the 3'RR has a developmentally controlled potential to constitutively activate GL promoters but that this activity is delayed, at least in part, by the CTCF insulator, which borders a transcriptionally active domain established by the 3'RR in developing B cells.
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64
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Saintamand A, Vincent-Fabert C, Marquet M, Ghazzaui N, Magnone V, Pinaud E, Cogné M, Denizot Y. E μ and 3'RR IgH enhancers show hierarchic unilateral dependence in mature B-cells. Sci Rep 2017; 7:442. [PMID: 28348365 PMCID: PMC5428668 DOI: 10.1038/s41598-017-00575-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/03/2017] [Indexed: 01/18/2023] Open
Abstract
Enhancer and super-enhancers are master regulators of cell fate. While they act at long-distances on adjacent genes, it is unclear whether they also act on one another. The immunoglobulin heavy chain (IgH) locus is unique in carrying two super-enhancers at both ends of the constant gene cluster: the 5'Eμ super-enhancer promotes VDJ recombination during the earliest steps of B-cell ontogeny while the 3' regulatory region (3'RR) is essential for late differentiation. Since they carry functional synergies in mature B-cells and physically interact during IgH locus DNA looping, we investigated if they were independent engines of locus remodelling or if their function was more intimately intermingled, their optimal activation then requiring physical contact with each other. Analysis of chromatin marks, enhancer RNA transcription and accessibility in Eμ- and 3'RR-deficient mice show, in mature activated B-cells, an unilateral dependence of this pair of enhancers: while the 3'RR acts in autonomy, Eμ in contrast likely falls under control of the 3'RR.
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Affiliation(s)
- A Saintamand
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France. .,INSERM U1236, Université Rennes 1, Rennes, France.
| | | | - M Marquet
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | - N Ghazzaui
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | - V Magnone
- CNRS et Université de Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Sophia, Antipolis, France
| | - E Pinaud
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | - M Cogné
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | - Y Denizot
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France.
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Feldman S, Wuerffel R, Achour I, Wang L, Carpenter PB, Kenter AL. 53BP1 Contributes to Igh Locus Chromatin Topology during Class Switch Recombination. THE JOURNAL OF IMMUNOLOGY 2017; 198:2434-2444. [PMID: 28159901 DOI: 10.4049/jimmunol.1601947] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/05/2017] [Indexed: 01/01/2023]
Abstract
In B lymphocytes, Ig class switch recombination (CSR) is induced by activation-induced cytidine deaminase, which initiates a cascade of events leading to DNA double-strand break formation in switch (S) regions. Resolution of DNA double-strand breaks proceeds through formation of S-S synaptic complexes. S-S synapsis is mediated by a chromatin loop that spans the C region domain of the Igh locus. S-S junctions are joined via a nonhomologous end joining DNA repair process. CSR occurs via an intrachromosomal looping out and deletion mechanism that is 53BP1 dependent. However, the mechanism by which 53BP1 facilitates deletional CSR and inhibits inversional switching events remains unknown. We report a novel architectural role for 53BP1 in Igh chromatin looping in mouse B cells. Long-range interactions between the Eμ and 3'Eα enhancers are significantly diminished in the absence of 53BP1. In contrast, germline transcript promoter:3'Eα looping interactions are unaffected by 53BP1 deficiency. Furthermore, 53BP1 chromatin occupancy at sites in the Igh locus is B cell specific, is correlated with histone H4 lysine 20 marks, and is subject to chromatin spreading. Thus, 53BP1 is required for three-dimensional organization of the Igh locus and provides a plausible explanation for the link with 53BP1 enforcement of deletional CSR.
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Affiliation(s)
- Scott Feldman
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344; and
| | - Robert Wuerffel
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344; and
| | - Ikbel Achour
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344; and
| | - Lili Wang
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344; and
| | - Phillip B Carpenter
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, TX 77030
| | - Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344; and
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66
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Laffleur B, Basu U, Lim J. RNA Exosome and Non-coding RNA-Coupled Mechanisms in AID-Mediated Genomic Alterations. J Mol Biol 2017; 429:3230-3241. [PMID: 28069372 DOI: 10.1016/j.jmb.2016.12.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/21/2016] [Accepted: 12/27/2016] [Indexed: 12/31/2022]
Abstract
The eukaryotic RNA exosome is a well-conserved protein complex with ribonuclease activity implicated in RNA metabolism. Various families of non-coding RNAs have been identified as substrates of the complex, underscoring its role as a non-coding RNA processing/degradation unit. However, the role of RNA exosome and its RNA processing activity on DNA mutagenesis/alteration events have not been investigated until recently. B lymphocytes use two DNA alteration mechanisms, class switch recombination (CSR) and somatic hypermutation (SHM), to re-engineer their antibody gene expressing loci until a tailored antibody gene for a specific antigen is satisfactorily generated. CSR and SHM require the essential activity of the DNA activation-induced cytidine deaminase (AID). Causing collateral damage to the B-cell genome during CSR and SHM, AID induces unwanted (and sometimes oncogenic) mutations at numerous non-immunoglobulin gene sequences. Recent studies have revealed that AID's DNA mutator activity is regulated by the RNA exosome complex, thus providing an example of a mechanism that relates DNA mutagenesis to RNA processing. Here, we review the emergent functions of RNA exosome during CSR, SHM, and other chromosomal alterations in B cells, and discuss implications relevant to mechanisms that maintain B-cell genomic integrity.
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Affiliation(s)
- Brice Laffleur
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Uttiya Basu
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Junghyun Lim
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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67
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MBD4 Facilitates Immunoglobulin Class Switch Recombination. Mol Cell Biol 2017; 37:MCB.00316-16. [PMID: 27777312 DOI: 10.1128/mcb.00316-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/30/2016] [Indexed: 01/02/2023] Open
Abstract
Immunoglobulin heavy chain class switch recombination (CSR) requires targeted formation of DNA double-strand breaks (DSBs) in repetitive switch region elements followed by ligation between distal breaks. The introduction of DSBs is initiated by activation-induced cytidine deaminase (AID) and requires base excision repair (BER) and mismatch repair (MMR). The BER enzyme methyl-CpG binding domain protein 4 (MBD4) has been linked to the MMR pathway through its interaction with MutL homologue 1 (MLH1). We find that when Mbd4 exons 6 to 8 are deleted in a switching B cell line, DSB formation is severely reduced and CSR frequency is impaired. Impaired CSR can be rescued by ectopic expression of Mbd4 Mbd4 deficiency yields a deficit in DNA end processing similar to that found in MutS homologue 2 (Msh2)- and Mlh1-deficient B cells. We demonstrate that microhomology-rich S-S junctions are enriched in cells in which Mbd4 is deleted. Our studies suggest that Mbd4 is a component of MMR-directed DNA end processing.
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68
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Methot S, Di Noia J. Molecular Mechanisms of Somatic Hypermutation and Class Switch Recombination. Adv Immunol 2017; 133:37-87. [DOI: 10.1016/bs.ai.2016.11.002] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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69
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YY1 controls Eμ-3'RR DNA loop formation and immunoglobulin heavy chain class switch recombination. Blood Adv 2016; 1:15-20. [PMID: 29167838 DOI: 10.1182/bloodadvances.2016000372] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Key Points
Transcription factor YY1 regulates the IgH Eμ-3′RR long-distance DNA loop without the YY1 transcriptional activation domain. YY1 constructs that rescue the Eμ-3′RR DNA loop also restore CSR strongly arguing for the necessity of this long-distance DNA loop for CSR.
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70
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Rocha PP, Raviram R, Fu Y, Kim J, Luo VM, Aljoufi A, Swanzey E, Pasquarella A, Balestrini A, Miraldi ER, Bonneau R, Petrini J, Schotta G, Skok JA. A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination. Cell Rep 2016; 16:48-55. [PMID: 27320916 PMCID: PMC4927351 DOI: 10.1016/j.celrep.2016.05.073] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/27/2016] [Accepted: 05/17/2016] [Indexed: 01/03/2023] Open
Abstract
During class switch recombination (CSR), B cells replace the Igh Cμ or δ exons with another down-stream constant region exon (CH), altering the anti-body isotype. CSR occurs through the introduction of AID-mediated double-strand breaks (DSBs) in switch regions and subsequent ligation of broken ends. Here, we developed an assay to investigate the dynamics of DSB formation in individual cells. We demonstrate that the upstream switch region Sμ is first targeted during recombination and that the mechanism underlying this control relies on 53BP1. Surprisingly, regulation of break order occurs through residual binding of 53BP1 to chromatin before the introduction of damage and independent of its established role in DNA repair. Using chromosome conformation capture, we show that 53BP1 mediates changes in chromatin architecture that affect break order. Finally, our results explain how changes in Igh architecture in the absence of 53BP1 could promote inversional rearrangements that compromise CSR.
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Affiliation(s)
- Pedro P Rocha
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| | - Ramya Raviram
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Department of Biology, New York University, New York, NY 10003, USA
| | - Yi Fu
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - JungHyun Kim
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Vincent M Luo
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Arafat Aljoufi
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Emily Swanzey
- Department of Developmental Genetics, New York University School of Medicine, New York, NY 10016, USA
| | - Alessandra Pasquarella
- Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPSM), Biomedical Center, Planegg-Martinsried 80336, Germany
| | - Alessia Balestrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10003, USA; Department of Computer Science, Courant Institute of Mathematical Sciences, New York, NY 10012, USA; Simons Center for Data Analysis, New York, NY 10010, USA
| | - John Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gunnar Schotta
- Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPSM), Biomedical Center, Planegg-Martinsried 80336, Germany
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
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71
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Related Mechanisms of Antibody Somatic Hypermutation and Class Switch Recombination. Microbiol Spectr 2016; 3:MDNA3-0037-2014. [PMID: 26104555 DOI: 10.1128/microbiolspec.mdna3-0037-2014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The primary antibody repertoire is generated by mechanisms involving the assembly of the exons that encode the antigen-binding variable regions of immunoglobulin heavy (IgH) and light (IgL) chains during the early development of B lymphocytes. After antigen-dependent activation, mature B lymphocytes can further alter their IgH and IgL variable region exons by the process of somatic hypermutation (SHM), which allows the selection of B cells in which SHMs resulted in the production of antibodies with increased antigen affinity. In addition, during antigen-dependent activation, B cells can also change the constant region of their IgH chain through a DNA double-strand-break (DSB) dependent process referred to as IgH class switch recombination (CSR), which generates B cell progeny that produce antibodies with different IgH constant region effector functions that are best suited for a elimination of a particular pathogen or in a particular setting. Both the mutations that underlie SHM and the DSBs that underlie CSR are initiated in target genes by activation-induced cytidine deaminase (AID). This review describes in depth the processes of SHM and CSR with a focus on mechanisms that direct AID cytidine deamination in activated B cells and mechanisms that promote the differential outcomes of such cytidine deamination.
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72
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Functional requirements of AID's higher order structures and their interaction with RNA-binding proteins. Proc Natl Acad Sci U S A 2016; 113:E1545-54. [PMID: 26929374 DOI: 10.1073/pnas.1601678113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential for the somatic hypermutation (SHM) and class-switch recombination (CSR) of Ig genes. Although both the N and C termini of AID have unique functions in DNA cleavage and recombination, respectively, during SHM and CSR, their molecular mechanisms are poorly understood. Using a bimolecular fluorescence complementation (BiFC) assay combined with glycerol gradient fractionation, we revealed that the AID C terminus is required for a stable dimer formation. Furthermore, AID monomers and dimers form complexes with distinct heterogeneous nuclear ribonucleoproteins (hnRNPs). AID monomers associate with DNA cleavage cofactor hnRNP K whereas AID dimers associate with recombination cofactors hnRNP L, hnRNP U, and Serpine mRNA-binding protein 1. All of these AID/ribonucleoprotein associations are RNA-dependent. We propose that AID's structure-specific cofactor complex formations differentially contribute to its DNA-cleavage and recombination functions.
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73
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DiMenna LJ, Chaudhuri J. Regulating infidelity: RNA-mediated recruitment of AID to DNA during class switch recombination. Eur J Immunol 2016; 46:523-30. [PMID: 26799454 DOI: 10.1002/eji.201545809] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/24/2015] [Accepted: 01/19/2016] [Indexed: 01/03/2023]
Abstract
The mechanism by which the DNA deaminase activation-induced cytidine deaminase (AID) is specifically recruited to repetitive switch region DNA during class switch recombination is still poorly understood. Work over the past decade has revealed a strong link between transcription and RNA polymerase-associated factors in AID recruitment, yet none of these processes satisfactorily explain how AID specificity is affected. Here, we review a recent finding wherein AID is guided to switch regions not by a protein factor but by an RNA moiety, and especially one associated with a noncoding RNA that has been long thought of as being inert. This work explains the long-standing requirement of splicing of noncoding transcripts during class switching, and has implications in both B cell-mediated immunity as well as the underlying pathological syndromes associated with the recombination reaction.
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Affiliation(s)
- Lauren J DiMenna
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jayanta Chaudhuri
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
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74
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Thomas-Claudepierre AS, Robert I, Rocha PP, Raviram R, Schiavo E, Heyer V, Bonneau R, Luo VM, Reddy JK, Borggrefe T, Skok JA, Reina-San-Martin B. Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination. J Exp Med 2016; 213:303-12. [PMID: 26903242 PMCID: PMC4813673 DOI: 10.1084/jem.20141967] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/15/2016] [Indexed: 12/21/2022] Open
Abstract
Thomas-Claudepierre et al. report that mediator facilitates the long-range contacts between acceptor switch regions and the IgH locus enhancers during class switch recombination and their transcriptional activation. Immunoglobulin (Ig) class switch recombination (CSR) is initiated by the transcription-coupled recruitment of activation-induced cytidine deaminase (AID) to Ig switch regions (S regions). During CSR, the IgH locus undergoes dynamic three-dimensional structural changes in which promoters, enhancers, and S regions are brought to close proximity. Nevertheless, little is known about the underlying mechanisms. In this study, we show that Med1 and Med12, two subunits of the mediator complex implicated in transcription initiation and long-range enhancer/promoter loop formation, are dynamically recruited to the IgH locus enhancers and the acceptor regions during CSR and that their knockdown in CH12 cells results in impaired CSR. Furthermore, we show that conditional inactivation of Med1 in B cells results in defective CSR and reduced acceptor S region transcription. Finally, we show that in B cells undergoing CSR, the dynamic long-range contacts between the IgH enhancers and the acceptor regions correlate with Med1 and Med12 binding and that they happen at a reduced frequency in Med1-deficient B cells. Our results implicate the mediator complex in the mechanism of CSR and are consistent with a model in which mediator facilitates the long-range contacts between S regions and the IgH locus enhancers during CSR and their transcriptional activation.
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Affiliation(s)
- Anne-Sophie Thomas-Claudepierre
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France Institut National de la Santé et de la Recherche Médicale, Unité 964, 67404 Illkirch, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, 67404 Illkirch, France Université de Strasbourg, 67400 Illkirch, France
| | - Isabelle Robert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France Institut National de la Santé et de la Recherche Médicale, Unité 964, 67404 Illkirch, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, 67404 Illkirch, France Université de Strasbourg, 67400 Illkirch, France
| | - Pedro P Rocha
- Department of Pathology, School of Medicine, New York University, New York, NY 10003
| | - Ramya Raviram
- Department of Pathology, School of Medicine, New York University, New York, NY 10003 Department of Biology, New York University, New York, NY 10003
| | - Ebe Schiavo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France Institut National de la Santé et de la Recherche Médicale, Unité 964, 67404 Illkirch, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, 67404 Illkirch, France Université de Strasbourg, 67400 Illkirch, France
| | - Vincent Heyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France Institut National de la Santé et de la Recherche Médicale, Unité 964, 67404 Illkirch, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, 67404 Illkirch, France Université de Strasbourg, 67400 Illkirch, France
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10003 Department of Computer Science, Courant Institute of Mathematical Sciences, New York, NY 10003 Simons Center for Data Analysis, New York, NY 10010
| | - Vincent M Luo
- Department of Pathology, School of Medicine, New York University, New York, NY 10003 Department of Biology, New York University, New York, NY 10003
| | - Janardan K Reddy
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60208
| | | | - Jane A Skok
- Department of Pathology, School of Medicine, New York University, New York, NY 10003 New York University Cancer Institute, New York University, New York, NY 10003
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France Institut National de la Santé et de la Recherche Médicale, Unité 964, 67404 Illkirch, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, 67404 Illkirch, France Université de Strasbourg, 67400 Illkirch, France
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75
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AID hits the jackpot when missing the target. Curr Opin Immunol 2016; 39:96-102. [PMID: 26845615 DOI: 10.1016/j.coi.2016.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/07/2023]
Abstract
Activation induced deaminase is the single B cell specific factor mediating class switch recombination and somatic hypermutation. Numerous studies have shown that AID preferentially targets Ig substrates and also attacks non-Ig substrates to create DNA damage that contributes to lymphomagenesis. AID targeting to Ig loci is linked to transcription but the mechanism governing this process has been obscure. Here we discuss research that illustrates the connection between AID targeting to DNA substrates and transcription processes to reveal rules governing the specificity of AID attack. These observations are woven together to provide a integrated view of AID function and a surprising linkage with global regulation of gene expression.
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76
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Looney TJ, Lee JY, Roskin KM, Hoh RA, King J, Glanville J, Liu Y, Pham TD, Dekker CL, Davis MM, Boyd SD. Human B-cell isotype switching origins of IgE. J Allergy Clin Immunol 2016; 137:579-586.e7. [PMID: 26309181 PMCID: PMC4747810 DOI: 10.1016/j.jaci.2015.07.014] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 01/13/2023]
Abstract
BACKGROUND B cells expressing IgE contribute to immunity against parasites and venoms and are the source of antigen specificity in allergic patients, yet the developmental pathways producing these B cells in human subjects remain a subject of debate. Much of our knowledge of IgE lineage development derives from model studies in mice rather than from human subjects. OBJECTIVE We evaluate models for isotype switching to IgE in human subjects using immunoglobulin heavy chain (IGH) mutational lineage data. METHODS We analyzed IGH repertoires in 9 allergic and 24 healthy adults using high-throughput DNA sequencing of 15,843,270 IGH rearrangements to identify clonal lineages of B cells containing members expressing IgE. Somatic mutations in IGH inherited from common ancestors within the clonal lineage are used to infer the relationships between B cells. RESULTS Data from 613,641 multi-isotype B-cell clonal lineages, of which 592 include an IgE member, are consistent with indirect switching to IgE from IgG- or IgA-expressing lineage members in human subjects. We also find that these inferred isotype switching frequencies are similar in healthy and allergic subjects. CONCLUSIONS We found evidence that secondary isotype switching of mutated IgG1-expressing B cells is the primary source of IgE in human subjects, with lesser contributions from precursors expressing other switched isotypes and rarely IgM or IgD, suggesting that IgE is derived from previously antigen-experienced B cells rather than naive B cells that typically express low-affinity unmutated antibodies. These data provide a basis from which to evaluate allergen-specific human antibody repertoires in healthy and diseased subjects.
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Affiliation(s)
- Timothy J Looney
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Ji-Yeun Lee
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Krishna M Roskin
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Ramona A Hoh
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Jasmine King
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif; Department of Biology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Jacob Glanville
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif; Program in Immunology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Yi Liu
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif; Biomedical Informatics Training Program, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Tho D Pham
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Cornelia L Dekker
- Department of Pediatrics, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Mark M Davis
- Department of Microbiology & Immunology, Transplantation and Infection, Stanford University, Stanford, Calif; Howard Hughes Medical Institute, Transplantation and Infection, Stanford University, Stanford, Calif; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Scott D Boyd
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif.
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77
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Sander S, Chu VT, Yasuda T, Franklin A, Graf R, Calado DP, Li S, Imami K, Selbach M, Di Virgilio M, Bullinger L, Rajewsky K. PI3 Kinase and FOXO1 Transcription Factor Activity Differentially Control B Cells in the Germinal Center Light and Dark Zones. Immunity 2015; 43:1075-86. [PMID: 26620760 DOI: 10.1016/j.immuni.2015.10.021] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/28/2015] [Accepted: 10/28/2015] [Indexed: 12/17/2022]
Abstract
Phosphatidylinositol 3' OH kinase (PI3K) signaling and FOXO transcription factors play opposing roles at several B cell developmental stages. We show here abundant nuclear FOXO1 expression in the proliferative compartment of the germinal center (GC), its dark zone (DZ), and PI3K activity, downregulating FOXO1, in the light zone (LZ), where cells are selected for further differentiation. In the LZ, however, FOXO1 was expressed in a fraction of cells destined for DZ reentry. Upon FOXO1 ablation or induction of PI3K activity, GCs lost their DZ, owing at least partly to downregulation of the chemokine receptor CXCR4. Although this prevented proper cyclic selection of cells in GCs, somatic hypermutation and proliferation were maintained. Class switch recombination was partly lost due to a failure of switch region targeting by activation-induced deaminase (AID).
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Affiliation(s)
- Sandrine Sander
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany.
| | - Van Trung Chu
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Tomoharu Yasuda
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Andrew Franklin
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Robin Graf
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Dinis Pedro Calado
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany; Cancer Research UK, London Research Institute, London WC2A 3LY, UK; Peter Gorer Department of Immunobiology, Kings College London, London SE1 9RT, UK
| | - Shuang Li
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Koshi Imami
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Michela Di Virgilio
- DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Lars Bullinger
- Department of Internal Medicine III, University Hospital Ulm, Ulm 89081, Germany
| | - Klaus Rajewsky
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany.
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78
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Abstract
Gerasimova et al. describe a three-step pathway that establishes the structure of the 2.8-Mb immunoglobulin heavy chain gene (IgH) locus in pro-B cells. Each step uses a different transcription factor and leads to increasing levels of structural organization. Conformation of antigen receptor gene loci spatially juxtaposes rearranging gene segments in the appropriate cell lineage and developmental stage. We describe a three-step pathway that establishes the structure of the 2.8-Mb immunoglobulin heavy chain gene (IgH) locus in pro-B cells. Each step uses a different transcription factor and leads to increasing levels of structural organization. CTCF mediates one level of compaction that folds the locus into several 250- to 400-kb subdomains, and Pax5 further compacts the 2-Mb region that encodes variable (VH) gene segments. The 5′ and 3′ domains are brought together by the transcription factor YY1 to establish the configuration within which gene recombination initiates. Such stepwise mechanisms may apply more generally to establish regulatory fine structure within megabase-sized topologically associated domains.
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79
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Saad F, Saintamand A, Cogné M, Denizot Y. The IgH 3' regulatory region influences lymphomagenesis in Igλ-Myc mice. Oncotarget 2015; 6:20302-11. [PMID: 25980500 PMCID: PMC4653006 DOI: 10.18632/oncotarget.3963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/10/2015] [Indexed: 01/11/2023] Open
Abstract
The IgH 3′regulatory region (3′RR), encompassing the four transcriptional enhancers hs3a-hs1,2-hs3b-hs4, has a key role on class switch recombination, somatic hypermutation, IgH transcription and B-cell fate. In plasma cells, transcribed IgH and IgL loci often colocalized in transcription factories and an IgL transcription defect might translate into lowered IgH transcription. We explored whether the 3′RR would affect lymphomagenesis in Igλ-Myc transgenic mice prone to lymphoproliferations. Breeding Igλ-Myc transgenics in a background deficient for the 3′RR influences lymphomagenesis toward less mature lymphomas (16% vs 54%, p = 0.01, Z test for two population proportions). In a 3′RR-deficient background mature tumors less often expressed the CD43 antigen (54% vs 0%, p = 0.02), a membrane glycoprotein expressed on activated mature B-cells. In contrast, in a 3′RR-deficient background tumors more often expressed the CD5 antigen (32% vs 12%, p = 0.05) that may serve to control autoimmunity and that is suspected to play a role in leukemic transformation. Lymphoma myc transcript levels, the Ki67 index of proliferation, the clonality, the usage of V(D)J segments, and their somatic hypermutation status were not affected in the 3′RR-deficient background. In conclusion, most probably through its action during the maturation process, the 3′RR can influence lymphomagenesis even when not linked with an oncogene.
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Affiliation(s)
- Faten Saad
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | | | - Michel Cogné
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | - Yves Denizot
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
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80
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Bonaud A, Lechouane F, Le Noir S, Monestier O, Cogné M, Sirac C. Efficient AID targeting of switch regions is not sufficient for optimal class switch recombination. Nat Commun 2015; 6:7613. [PMID: 26146363 DOI: 10.1038/ncomms8613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 05/26/2015] [Indexed: 02/07/2023] Open
Abstract
Antibody affinity maturation relies on activation-induced cytidine deaminase (AID)-dependent somatic hypermutation (SHM) of immunoglobulin (Ig) loci. Class switch recombination (CSR) can in parallel occur between AID-targeted, transcribed, spliced and repetitive switch (S) regions. AID thus initiates not only mutations but also double-strand breaks (DSBs). What governs the choice between those two outcomes remains uncertain. Here we explore whether insertion of transcribed intronic S regions in a locus (Igκ) strongly recruiting AID is sufficient for efficient CSR. Although strongly targeted by AID and carrying internal deletions, the knocked-in S regions only undergo rare CSR-like events. This model confirms S regions as exquisite SHM targets, extending AID activity far from transcription initiation sites, and shows that such spliced and repetitive AID targets are not sufficient by themselves for CSR. Beyond transcription and AID recruitment, additional IgH elements are thus needed for CSR, restricting this hazardous gene remodelling to IgH loci.
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Affiliation(s)
- Amélie Bonaud
- Immunology, CNRS UMR 7276, Centre Nationale de la Recherche Scientifique, Université de Limoges, Limoges 87025, France
| | - Fabien Lechouane
- Immunology, CNRS UMR 7276, Centre Nationale de la Recherche Scientifique, Université de Limoges, Limoges 87025, France
| | - Sandrine Le Noir
- Immunology, CNRS UMR 7276, Centre Nationale de la Recherche Scientifique, Université de Limoges, Limoges 87025, France
| | - Olivier Monestier
- Immunology, CNRS UMR 7276, Centre Nationale de la Recherche Scientifique, Université de Limoges, Limoges 87025, France
| | - Michel Cogné
- 1] Immunology, CNRS UMR 7276, Centre Nationale de la Recherche Scientifique, Université de Limoges, Limoges 87025, France. [2] Institut Universitaire de France, Paris 75000, France
| | - Christophe Sirac
- Immunology, CNRS UMR 7276, Centre Nationale de la Recherche Scientifique, Université de Limoges, Limoges 87025, France
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81
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Saintamand A, Rouaud P, Saad F, Rios G, Cogné M, Denizot Y. Elucidation of IgH 3′ region regulatory role during class switch recombination via germline deletion. Nat Commun 2015; 6:7084. [DOI: 10.1038/ncomms8084] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/01/2015] [Indexed: 02/06/2023] Open
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82
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Stavnezer J, Schrader CE. IgH chain class switch recombination: mechanism and regulation. THE JOURNAL OF IMMUNOLOGY 2015; 193:5370-8. [PMID: 25411432 DOI: 10.4049/jimmunol.1401849] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
IgH class switching occurs rapidly after activation of mature naive B cells, resulting in a switch from expression of IgM and IgD to expression of IgG, IgE, or IgA; this switch improves the ability of Abs to remove the pathogen that induces the humoral immune response. Class switching occurs by a deletional recombination between two switch regions, each of which is associated with a H chain constant region gene. Class switch recombination (CSR) is instigated by activation-induced cytidine deaminase, which converts cytosines in switch regions to uracils. The uracils are subsequently removed by two DNA-repair pathways, resulting in mutations, single-strand DNA breaks, and the double-strand breaks required for CSR. We discuss several aspects of CSR, including how CSR is induced, CSR in B cell progenitors, the roles of transcription and chromosomal looping in CSR, and the roles of certain DNA-repair enzymes in CSR.
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Affiliation(s)
- Janet Stavnezer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Carol E Schrader
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
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83
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Kracker S, Di Virgilio M, Schwartzentruber J, Cuenin C, Forveille M, Deau MC, McBride KM, Majewski J, Gazumyan A, Seneviratne S, Grimbacher B, Kutukculer N, Herceg Z, Cavazzana M, Jabado N, Nussenzweig MC, Fischer A, Durandy A. An inherited immunoglobulin class-switch recombination deficiency associated with a defect in the INO80 chromatin remodeling complex. J Allergy Clin Immunol 2015; 135:998-1007.e6. [PMID: 25312759 PMCID: PMC4382329 DOI: 10.1016/j.jaci.2014.08.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/31/2014] [Accepted: 08/05/2014] [Indexed: 11/29/2022]
Abstract
BACKGROUND Immunoglobulin class-switch recombination defects (CSR-D) are rare primary immunodeficiencies characterized by impaired production of switched immunoglobulin isotypes and normal or elevated IgM levels. They are caused by impaired T:B cooperation or intrinsic B cell defects. However, many immunoglobulin CSR-Ds are still undefined at the molecular level. OBJECTIVE This study's objective was to delineate new causes of immunoglobulin CSR-Ds and thus gain further insights into the process of immunoglobulin class-switch recombination (CSR). METHODS Exome sequencing in 2 immunoglobulin CSR-D patients identified variations in the INO80 gene. Functional experiments were performed to assess the function of INO80 on immunoglobulin CSR. RESULTS We identified recessive, nonsynonymous coding variations in the INO80 gene in 2 patients affected by defective immunoglobulin CSR. Expression of wild-type INO80 in patients' fibroblastic cells corrected their hypersensitivity to high doses of γ-irradiation. In murine CH12-F3 cells, the INO80 complex accumulates at Sα and Eμ regions of the IgH locus, and downregulation of INO80 as well as its partners Reptin and Pontin impaired CSR. In addition, Reptin and Pontin were shown to interact with activation-induced cytidine deaminase. Finally, an abnormal separation of sister chromatids was observed upon INO80 downregulation in CH12-F3 cells, pinpointing its role in cohesin activity. CONCLUSION INO80 deficiency appears to be associated with defective immunoglobulin CSR. We propose that the INO80 complex modulates cohesin function that may be required during immunoglobulin switch region synapsis.
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Affiliation(s)
- Sven Kracker
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Imagine Institute, Paris, France; Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Michela Di Virgilio
- Laboratory of Molecular Immunology, Howard Hughes Medical Institute, the Rockefeller University, New York, NY
| | - Jeremy Schwartzentruber
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Cyrille Cuenin
- International Agency for Research on Cancer, F-69008 Lyon, Lyon, France
| | - Monique Forveille
- Center for Primary Immunodeficiencies, Hôpital Necker Enfants Malades, F-75015 Paris, Paris, France
| | - Marie-Céline Deau
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Imagine Institute, Paris, France; Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Kevin M McBride
- Laboratory of Molecular Immunology, Howard Hughes Medical Institute, the Rockefeller University, New York, NY
| | - Jacek Majewski
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, Howard Hughes Medical Institute, the Rockefeller University, New York, NY
| | - Suranjith Seneviratne
- UCL Institute of Immunity and Transplantation, Royal Free London NHS Foundation Tust, London, United Kingdom
| | - Bodo Grimbacher
- UCL Institute of Immunity and Transplantation, Royal Free London NHS Foundation Tust, London, United Kingdom; Centre of Chronic Immunodeficiency, University Medical Center Freiburg and University of Freiburg, D-79106 Freiburg, Freiburg, Germany
| | - Necil Kutukculer
- Ege University Faculty of Medicine, Department of Pediatric Immunology, 35100 Bornova, Izmir, Turkey
| | - Zdenko Herceg
- International Agency for Research on Cancer, F-69008 Lyon, Lyon, France
| | - Marina Cavazzana
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Imagine Institute, Paris, France; Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France; Department of Biotherapy, AP-HP Hôpital Necker Enfants Malades, F-75015 Paris, Paris, France; Clinical Investigation Center (CIC)-Biotherapy GHU Ouest, INSERM-APHP (Assistance Publique des Hôpitaux de Paris), Paris, France
| | - Nada Jabado
- Department of Pediatrics, McGill University and McGill University Health Center, Montreal, Quebec, Canada
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, Howard Hughes Medical Institute, the Rockefeller University, New York, NY
| | - Alain Fischer
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Imagine Institute, Paris, France; Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France; Department of Immunology and Hematology, Hôpital Necker Enfants Malades, F-75015 Paris, Paris, France; Collège de France, Paris, France
| | - Anne Durandy
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Imagine Institute, Paris, France; Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France; Department of Immunology and Hematology, Hôpital Necker Enfants Malades, F-75015 Paris, Paris, France.
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84
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Bailey SD, Zhang X, Desai K, Aid M, Corradin O, Cowper-Sal Lari R, Akhtar-Zaidi B, Scacheri PC, Haibe-Kains B, Lupien M. ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. Nat Commun 2015; 2:6186. [PMID: 25645053 PMCID: PMC4431651 DOI: 10.1038/ncomms7186] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/30/2014] [Indexed: 12/21/2022] Open
Abstract
Chromatin interactions connect distal regulatory elements to target gene promoters
guiding stimulus- and lineage-specific transcription. Few factors securing chromatin
interactions have so far been identified. Here, by integrating chromatin interaction
maps with the large collection of transcription factor-binding profiles provided by
the ENCODE project, we demonstrate that the zinc-finger protein ZNF143 preferentially occupies anchors of
chromatin interactions connecting promoters with distal regulatory elements. It
binds directly to promoters and associates with lineage-specific chromatin
interactions and gene expression. Silencing ZNF143 or modulating its DNA-binding affinity using
single-nucleotide polymorphisms (SNPs) as a surrogate of site-directed mutagenesis
reveals the sequence dependency of chromatin interactions at gene promoters. We also
find that chromatin interactions alone do not regulate gene expression. Together,
our results identify ZNF143 as a
novel chromatin-looping factor that contributes to the architectural foundation of
the genome by providing sequence specificity at promoters connected with distal
regulatory elements. Chromatin interactions can connect distal regulatory elements to
promoters via protein factors, but few such factors have been identified. Here, the
authors show that zinc-finger protein ZNF143 is a sequence-specific chromatin-looping
factor that connects promoters with distal regulatory elements.
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Affiliation(s)
- Swneke D Bailey
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada
| | - Xiaoyang Zhang
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, 03755, New Hampshire, USA.,Present address: Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Kinjal Desai
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, 03755, New Hampshire, USA
| | - Malika Aid
- Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, H2W 1R7, Quebec, Canada
| | - Olivia Corradin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Richard Cowper-Sal Lari
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Present address: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Batool Akhtar-Zaidi
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Present address: Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02142, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Benjamin Haibe-Kains
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada.,Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, H2W 1R7, Quebec, Canada
| | - Mathieu Lupien
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada. .,Ontario Institute for Cancer Research, Toronto, M5G 1L7, Ontario, Canada.
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85
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Laffleur B, Denis-Lagache N, Péron S, Sirac C, Moreau J, Cogné M. AID-induced remodeling of immunoglobulin genes and B cell fate. Oncotarget 2015; 5:1118-31. [PMID: 24851241 PMCID: PMC4012742 DOI: 10.18632/oncotarget.1546] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Survival and phenotype of normal and malignant B lymphocytes are critically dependent on constitutive signals by the B cell receptor (BCR) for antigen. In addition, either antigen ligation of the BCR or various mitogenic stimuli result in B cell activation and induction of activation-induced deaminase (AID). AID activity can in turn mediate somatic hypermutation (SHM) of immunoglobulin (Ig) V regions and also deeply remodel the Ig heavy chain locus through class switch recombination (CSR) or locus suicide recombination (LSR). In addition to changes linked to affinity for antigen, modifying the class/isotype (i.e. the structure and function) of the BCR or suddenly deleting BCR expression also modulates the fate of antigen-experienced B cells.
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86
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Feldman S, Achour I, Wuerffel R, Kumar S, Gerasimova T, Sen R, Kenter AL. Constraints contributed by chromatin looping limit recombination targeting during Ig class switch recombination. THE JOURNAL OF IMMUNOLOGY 2015; 194:2380-9. [PMID: 25624452 DOI: 10.4049/jimmunol.1401170] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Engagement of promoters with distal elements in long-range looping interactions has been implicated in regulation of Ig class switch recombination (CSR). The principles determining the spatial and regulatory relationships among Igh transcriptional elements remain poorly defined. We examined the chromosome conformation of C region (CH) loci that are targeted for CSR in a cytokine-dependent fashion in mature B lymphocytes. Germline transcription (GLT) of the γ1 and ε CH loci is controlled by two transcription factors, IL-4-inducible STAT6 and LPS-activated NF-κB. We showed that although STAT6 deficiency triggered loss of GLT, deletion of NF-κB p50 abolished both GLT and γ1 locus:enhancer looping. Thus, chromatin looping between CH loci and Igh enhancers is independent of GLT production and STAT6, whereas the establishment and maintenance of these chromatin contacts requires NF-κB p50. Comparative analysis of the endogenous γ1 locus and a knock-in heterologous promoter in mice identified the promoter per se as the interactive looping element and showed that transcription elongation is dispensable for promoter/enhancer interactions. Interposition of the LPS-responsive heterologous promoter between the LPS-inducible γ3 and γ2b loci altered GLT expression and essentially abolished direct IgG2b switching while maintaining a sequential μ→γ3→γ2b format. Our study provides evidence that promoter/enhancer looping interactions can introduce negative constraints on distal promoters and affect their ability to engage in germline transcription and determine CSR targeting.
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Affiliation(s)
- Scott Feldman
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612; and
| | - Ikbel Achour
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612; and
| | - Robert Wuerffel
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612; and
| | - Satyendra Kumar
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612; and
| | - Tatiana Gerasimova
- Gene Regulation Section, Laboratory of Cellular and Molecular Biology, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224
| | - Ranjan Sen
- Gene Regulation Section, Laboratory of Cellular and Molecular Biology, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224
| | - Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612; and
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87
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Günal-Sadık G, Paszkowski-Rogacz M, Singaravelu K, Beyer A, Buchholz F, Jessberger R. Stage-specific binding profiles of cohesin in resting and activated B lymphocytes suggest a role for cohesin in immunoglobulin class switching and maturation. PLoS One 2014; 9:e111748. [PMID: 25375358 PMCID: PMC4222939 DOI: 10.1371/journal.pone.0111748] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/30/2014] [Indexed: 11/19/2022] Open
Abstract
The immunoglobulin heavy chain locus (Igh) features higher-order chromosomal interactions to facilitate stage-specific assembly of the Ig molecule. Cohesin, a ring-like protein complex required for sister chromatid cohesion, shapes chromosome architecture and chromatin interactions important for transcriptional regulation and often acts together with CTCF. Cohesin is likely involved in B cell activation and Ig class switch recombination. Hence, binding profiles of cohesin in resting mature murine splenic B lymphocytes and at two stages after cell activation were elucidated by chromatin immunoprecipitation and deep sequencing. Comparative genomic analysis revealed cohesin extensively changes its binding to transcriptional control elements after 48 h of stimulation with LPS/IL-4. Cohesin was clearly underrepresented at switch regions regardless of their activation status, suggesting that switch regions need to be cohesin-poor. Specific binding changes of cohesin at B-cell specific gene loci Pax5 and Blimp-1 indicate new cohesin-dependent regulatory pathways. Together with conserved cohesin/CTCF sites at the Igh 3'RR, a prominent cohesin/CTCF binding site was revealed near the 3' end of Cα where PolII localizes to 3' enhancers. Our study shows that cohesin likely regulates B cell activation and maturation, including Ig class switching.
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Affiliation(s)
- Gamze Günal-Sadık
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Department of Medical Systems Biology, University Hospital and Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Kalaimathy Singaravelu
- Cellular Networks and Systems Biology, Biotechnology Center, Dresden University of Technology, Dresden, Germany
| | - Andreas Beyer
- Cellular Networks and Systems Biology, Biotechnology Center, Dresden University of Technology, Dresden, Germany
- CECAD, Universität zu Köln, Köln, Germany
| | - Frank Buchholz
- Department of Medical Systems Biology, University Hospital and Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
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88
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Immunoglobulin genes undergo legitimate repair in human B cells not only after cis- but also frequent trans-class switch recombination. Genes Immun 2014; 15:341-6. [PMID: 24848929 DOI: 10.1038/gene.2014.25] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 03/26/2014] [Accepted: 04/14/2014] [Indexed: 12/23/2022]
Abstract
Immunoglobulin (Ig) genes specifically recruit activation-induced deaminase (AID) for 'on-target' DNA deamination, initiating either variable (V) region somatic hypermutation, or double-strand break intermediates of class switch recombination (CSR). Such breaks overwhelmingly undergo legitimate intra-Ig repair rather than rare illegitimate and potentially oncogenic junctions outside of Ig loci. We show that in human B cells, legitimate synapsis and repair efficiently join Ig genes whether physically linked on one chromosome or located apart on both alleles. This indicates mechanisms faithfully recognizing and/or pairing loci with homology in structure and accessibility, thus licensing interchromosomal trans-CSR junctions while usually preventing illegitimate interchromosomal recombination with AID off-target genes. Physical linkage of IgH genes in cis on the same allele just increases the likelihood of legitimate repair by another fourfold. The strongest force driving CSR might thus be recognition of legitimate target genes. Formation of IgH intra-allelic loops along this process would then constitute a consequence rather than a pre-requisite of this gene-pairing process.
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89
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Khair L, Guikema JE, Linehan EK, Ucher AJ, Leus NG, Ogilvie C, Lou Z, Schrader CE, Stavnezer J. ATM increases activation-induced cytidine deaminase activity at downstream S regions during class-switch recombination. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 192:4887-96. [PMID: 24729610 PMCID: PMC4049217 DOI: 10.4049/jimmunol.1303481] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Activation-induced cytidine deaminase (AID) initiates Ab class-switch recombination (CSR) in activated B cells resulting in exchanging the IgH C region and improved Ab effector function. During CSR, AID instigates DNA double-strand break (DSB) formation in switch (S) regions located upstream of C region genes. DSBs are necessary for CSR, but improper regulation of DSBs can lead to chromosomal translocations that can result in B cell lymphoma. The protein kinase ataxia telangiectasia mutated (ATM) is an important proximal regulator of the DNA damage response (DDR), and translocations involving S regions are increased in its absence. ATM phosphorylates H2AX, which recruits other DNA damage response (DDR) proteins, including mediator of DNA damage checkpoint 1 (Mdc1) and p53 binding protein 1 (53BP1), to sites of DNA damage. As these DDR proteins all function to promote repair and recombination of DSBs during CSR, we examined whether mouse splenic B cells deficient in these proteins would show alterations in S region DSBs when undergoing CSR. We find that in atm(-/-) cells Sμ DSBs are increased, whereas DSBs in downstream Sγ regions are decreased. We also find that mutations in the unrearranged Sγ3 segment are reduced in atm(-/-) cells. Our data suggest that ATM increases AID targeting and activity at downstream acceptor S regions during CSR and that in atm(-/-) cells Sμ DSBs accumulate as they lack a recombination partner.
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Affiliation(s)
- Lyne Khair
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Jeroen E.J. Guikema
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Erin K. Linehan
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Anna J. Ucher
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Niek G.J. Leus
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Colin Ogilvie
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Zhenkun Lou
- Division of Oncology Research, Mayo Clinic, Rochester, MN
| | - Carol E. Schrader
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Janet Stavnezer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
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90
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Birshtein BK. Epigenetic Regulation of Individual Modules of the immunoglobulin heavy chain locus 3' Regulatory Region. Front Immunol 2014; 5:163. [PMID: 24795714 PMCID: PMC4000994 DOI: 10.3389/fimmu.2014.00163] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/27/2014] [Indexed: 11/18/2022] Open
Abstract
The Igh locus undergoes an amazing array of DNA rearrangements and modifications during B cell development. During early stages, the variable region gene is constructed from constituent variable (V), diversity (D), and joining (J) segments (VDJ joining). B cells that successfully express an antibody can be activated, leading to somatic hypermutation (SHM) focused on the variable region, and class switch recombination (CSR), which substitutes downstream constant region genes for the originally used Cμ constant region gene. Many investigators, ourselves included, have sought to understand how these processes specifically target the Igh locus and avoid other loci and potential deleterious consequences of malignant transformation. Our laboratory has concentrated on a complex regulatory region (RR) that is located downstream of Cα, the most 3′ of the Igh constant region genes. The ~40 kb 3′ RR, which is predicted to serve as a downstream major regulator of the Igh locus, contains two distinct segments: an ~28 kb region comprising four enhancers, and an adjacent ~12 kb region containing multiple CTCF and Pax5 binding sites. Analysis of targeted mutations in mice by a number of investigators has concluded that the entire 3′ RR enhancer region is essential for SHM and CSR (but not for VDJ joining) and for high levels of expression of multiple isotypes. The CTCF/Pax5 binding region is a candidate for influencing VDJ joining early in B cell development and serving as a potential insulator of the Igh locus. Components of the 3′ RR are subject to a variety of epigenetic changes during B cell development, i.e., DNAse I hypersensitivity, histone modifications, and DNA methylation, in association with transcription factor binding. I propose that these changes provide a foundation by which regulatory elements in modules of the 3′ RR function by interacting with each other and with target sequences of the Igh locus.
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Affiliation(s)
- Barbara K Birshtein
- Department of Cell Biology, Albert Einstein College of Medicine , Bronx, NY , USA
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91
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Fear DJ. Mechanisms regulating the targeting and activity of activation induced cytidine deaminase. Curr Opin Immunol 2014; 25:619-28. [PMID: 24209594 DOI: 10.1016/j.coi.2013.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 05/23/2013] [Indexed: 01/03/2023]
Abstract
Activation induced cytidine deaminase (AID) plays a central role in the vertebrate adaptive immune response, initiating immunoglobulin (Ig) somatic hypermutation (SHM) and class-switch recombination (CSR). AID converts deoxycytosine (dC) in the DNA to deoxyuridine (dU), causing a DNA base-pairing mismatch. How this mismatch is recognised and resolved determines whether the site will undergo mutation, recombination or high-fidelity repair. Although AID action is essential for antibody diversification it is also known to act upon many non-Ig genes where it can cause tumourigenic mutations and translocations. Although much is known about the pathways of Ig diversification, there is still very little known about the mechanisms that target AID to its sites of action and regulate the different repair processes that can participate at these sites.
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92
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Vaidyanathan B, Yen WF, Pucella JN, Chaudhuri J. AIDing Chromatin and Transcription-Coupled Orchestration of Immunoglobulin Class-Switch Recombination. Front Immunol 2014; 5:120. [PMID: 24734031 PMCID: PMC3975107 DOI: 10.3389/fimmu.2014.00120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/07/2014] [Indexed: 12/29/2022] Open
Abstract
Secondary diversification of the antibody repertoire upon antigenic challenge, in the form of immunoglobulin heavy chain (IgH) class-switch recombination (CSR) endows mature, naïve B cells in peripheral lymphoid organs with a limitless ability to mount an optimal humoral immune response, thus expediting pathogen elimination. CSR replaces the default constant (CH) region exons (Cμ) of IgH with any of the downstream CH exons (Cγ, Cε, or Cα), thereby altering effector functions of the antibody molecule. This process depends on, and is orchestrated by, activation-induced deaminase (AID), a DNA cytidine deaminase that acts on single-stranded DNA exposed during transcription of switch (S) region sequences at the IgH locus. DNA lesions thus generated are processed by components of several general DNA repair pathways to drive CSR. Given that AID can instigate DNA lesions and genomic instability, stringent checks are imposed that constrain and restrict its mutagenic potential. In this review, we will discuss how AID expression and substrate specificity and activity is rigorously enforced at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and how the DNA-damage response is choreographed with precision to permit targeted activity while limiting bystander catastrophe.
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Affiliation(s)
- Bharat Vaidyanathan
- Weill Cornell Graduate School of Medical Sciences , New York, NY , USA ; Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
| | - Wei-Feng Yen
- Weill Cornell Graduate School of Medical Sciences , New York, NY , USA ; Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
| | - Joseph N Pucella
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
| | - Jayanta Chaudhuri
- Weill Cornell Graduate School of Medical Sciences , New York, NY , USA ; Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
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93
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Activation induced deaminase C-terminal domain links DNA breaks to end protection and repair during class switch recombination. Proc Natl Acad Sci U S A 2014; 111:E988-97. [PMID: 24591601 DOI: 10.1073/pnas.1320486111] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Activation-induced deaminase (AID) triggers antibody class switch recombination (CSR) in B cells by initiating DNA double strand breaks that are repaired by nonhomologous end-joining pathways. A role for AID at the repair step is unclear. We show that specific inactivation of the C-terminal AID domain encoded by exon 5 (E5) allows very efficient deamination of the AID target regions but greatly impacts the efficiency and quality of subsequent DNA repair. Specifically eliminating E5 not only precludes CSR but also, causes an atypical, enzymatic activity-dependent dominant-negative effect on CSR. Moreover, the E5 domain is required for the formation of AID-dependent Igh-cMyc chromosomal translocations. DNA breaks at the Igh switch regions induced by AID lacking E5 display defective end joining, failing to recruit DNA damage response factors and undergoing extensive end resection. These defects lead to nonproductive resolutions, such as rearrangements and homologous recombination that can antagonize CSR. Our results can explain the autosomal dominant inheritance of AID variants with truncated E5 in patients with hyper-IgM syndrome 2 and establish that AID, through the E5 domain, provides a link between DNA damage and repair during CSR.
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94
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Differential regulation of S-region hypermutation and class-switch recombination by noncanonical functions of uracil DNA glycosylase. Proc Natl Acad Sci U S A 2014; 111:E1016-24. [PMID: 24591630 DOI: 10.1073/pnas.1402391111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential to class-switch recombination (CSR) and somatic hypermutation (SHM) in both V region SHM and S region SHM (s-SHM). Uracil DNA glycosylase (UNG), a member of the base excision repair (BER) complex, is required for CSR. Strikingly, however, UNG deficiency causes augmentation of SHM, suggesting involvement of distinct functions of UNG in SHM and CSR. Here, we show that noncanonical scaffold functions of UNG regulate s-SHM negatively and CSR positively. The s-SHM suppressive function of UNG is attributed to the recruitment of faithful BER components at the cleaved DNA locus, with competition against error-prone polymerases. By contrast, the CSR-promoting function of UNG enhances AID-dependent S-S synapse formation by recruiting p53-binding protein 1 and DNA-dependent protein kinase, catalytic subunit. Several loss-of-catalysis mutants of UNG discriminated CSR-promoting activity from s-SHM suppressive activity. Taken together, the noncanonical function of UNG regulates the steps after AID-induced DNA cleavage: error-prone repair suppression in s-SHM and end-joining promotion in CSR.
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95
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Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 2014; 155:1507-20. [PMID: 24360274 DOI: 10.1016/j.cell.2013.11.039] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/01/2013] [Accepted: 11/25/2013] [Indexed: 12/31/2022]
Abstract
A key finding of the ENCODE project is that the enhancer landscape of mammalian cells undergoes marked alterations during ontogeny. However, the nature and extent of these changes are unclear. As part of the NIH Mouse Regulome Project, we here combined DNaseI hypersensitivity, ChIP-seq, and ChIA-PET technologies to map the promoter-enhancer interactomes of pluripotent ES cells and differentiated B lymphocytes. We confirm that enhancer usage varies widely across tissues. Unexpectedly, we find that this feature extends to broadly transcribed genes, including Myc and Pim1 cell-cycle regulators, which associate with an entirely different set of enhancers in ES and B cells. By means of high-resolution CpG methylomes, genome editing, and digital footprinting, we show that these enhancers recruit lineage-determining factors. Furthermore, we demonstrate that the turning on and off of enhancers during development correlates with promoter activity. We propose that organisms rely on a dynamic enhancer landscape to control basic cellular functions in a tissue-specific manner.
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Affiliation(s)
| | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Ewy Mathe
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Qian
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guoliang Li
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Wolfgang Resch
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nathanael Pruett
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lars Grøntved
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Vian
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steevenson Nelson
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hossein Zare
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ofir Hakim
- Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
| | - Arito Yamane
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hirotaka Nakahashi
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander L Kovalchuk
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jizhong Zou
- Laboratory of Stem Cell Biology, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chia-Lin Wei
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Xiaoan Ruan
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA.
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96
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Atchison ML. Function of YY1 in Long-Distance DNA Interactions. Front Immunol 2014; 5:45. [PMID: 24575094 PMCID: PMC3918653 DOI: 10.3389/fimmu.2014.00045] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 01/27/2014] [Indexed: 11/13/2022] Open
Abstract
During B cell development, long-distance DNA interactions are needed for V(D)J somatic rearrangement of the immunoglobulin (Ig) loci to produce functional Ig genes, and for class switch recombination (CSR) needed for antibody maturation. The tissue-specificity and developmental timing of these mechanisms is a subject of active investigation. A small number of factors are implicated in controlling Ig locus long-distance interactions including Pax5, Yin Yang 1 (YY1), EZH2, IKAROS, CTCF, cohesin, and condensin proteins. Here we will focus on the role of YY1 in controlling these mechanisms. YY1 is a multifunctional transcription factor involved in transcriptional activation and repression, X chromosome inactivation, Polycomb Group (PcG) protein DNA recruitment, and recruitment of proteins required for epigenetic modifications (acetylation, deacetylation, methylation, ubiquitination, sumoylation, etc.). YY1 conditional knock-out indicated that YY1 is required for B cell development, at least in part, by controlling long-distance DNA interactions at the immunoglobulin heavy chain and Igκ loci. Our recent data show that YY1 is also required for CSR. The mechanisms implicated in YY1 control of long-distance DNA interactions include controlling non-coding antisense RNA transcripts, recruitment of PcG proteins to DNA, and interaction with complexes involved in long-distance DNA interactions including the cohesin and condensin complexes. Though common rearrangement mechanisms operate at all Ig loci, their distinct temporal activation along with the ubiquitous nature of YY1 poses challenges for determining the specific mechanisms of YY1 function in these processes, and their regulation at the tissue-specific and B cell stage-specific level. The large numbers of post-translational modifications that control YY1 functions are possible candidates for regulation.
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Affiliation(s)
- Michael L Atchison
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, PA , USA
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97
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C-terminal region of activation-induced cytidine deaminase (AID) is required for efficient class switch recombination and gene conversion. Proc Natl Acad Sci U S A 2014; 111:2253-8. [PMID: 24469810 DOI: 10.1073/pnas.1324057111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) introduces single-strand breaks (SSBs) to initiate class switch recombination (CSR), gene conversion (GC), and somatic hypermutation (SHM). CSR is mediated by double-strand breaks (DSBs) at donor and acceptor switch (S) regions, followed by pairing of DSB ends in two S regions and their joining. Because AID mutations at its C-terminal region drastically impair CSR but retain its DNA cleavage and SHM activity, the C-terminal region of AID likely is required for the recombination step after the DNA cleavage. To test this hypothesis, we analyzed the recombination junctions generated by AID C-terminal mutants and found that 0- to 3-bp microhomology junctions are relatively less abundant, possibly reflecting the defects of the classical nonhomologous end joining (C-NHEJ). Consistently, the accumulation of C-NHEJ factors such as Ku80 and XRCC4 was decreased at the cleaved S region. In contrast, an SSB-binding protein, poly (ADP)-ribose polymerase1, was recruited more abundantly, suggesting a defect in conversion from SSB to DSB. In addition, recruitment of critical DNA synapse factors such as 53BP1, DNA PKcs, and UNG at the S region was reduced during CSR. Furthermore, the chromosome conformation capture assay revealed that DNA synapse formation is impaired drastically in the AID C-terminal mutants. Interestingly, these mutants showed relative reduction in GC compared with SHM in chicken DT40 cells. Collectively, our data indicate that the C-terminal region of AID is required for efficient generation of DSB in CSR and GC and thus for the subsequent pairing of cleaved DNA ends during recombination in CSR.
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98
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Kumar S, Wuerffel R, Achour I, Lajoie B, Sen R, Dekker J, Feeney AJ, Kenter AL. Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny. Genes Dev 2014; 27:2439-44. [PMID: 24240234 PMCID: PMC3841733 DOI: 10.1101/gad.227165.113] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Omenn syndrome is a severe immunodeficiency disease commonly arising from hypomorphic RAG recombinase gene mutations. RAG recombinase mediates V(D)J joining during early B-lymphocyte development in the bone marrow (BM). V(D)J recombination and class switch recombination are thought to partition between the BM and secondary lymphoid organs. Kenter and colleagues show that V(D)J joining and switching are interchangeably inducible in the BM. This study has important implications for the development of Omenn syndrome, autoimmune diseases, and leukemia. V(D)J joining is mediated by RAG recombinase during early B-lymphocyte development in the bone marrow (BM). Activation-induced deaminase initiates isotype switching in mature B cells of secondary lymphoid structures. Previous studies questioned the strict ontological partitioning of these processes. We show that pro-B cells undergo robust switching to a subset of immunoglobulin H (IgH) isotypes. Chromatin studies reveal that in pro-B cells, the spatial organization of the Igh locus may restrict switching to this subset of isotypes. We demonstrate that in the BM, V(D)J joining and switching are interchangeably inducible, providing an explanation for the hyper-IgE phenotype of Omenn syndrome.
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Affiliation(s)
- Satyendra Kumar
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, Illinois 60612, USA
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99
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Matthews AJ, Zheng S, DiMenna LJ, Chaudhuri J. Regulation of immunoglobulin class-switch recombination: choreography of noncoding transcription, targeted DNA deamination, and long-range DNA repair. Adv Immunol 2014; 122:1-57. [PMID: 24507154 PMCID: PMC4150736 DOI: 10.1016/b978-0-12-800267-4.00001-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default Cμ constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as "Ch genes", e.g., Cγ, Cɛ, or Cα). The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction. CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor Sμ and acceptor S regions. CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining. In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs. Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations. Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming.
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Affiliation(s)
- Allysia J Matthews
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Simin Zheng
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Lauren J DiMenna
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA.
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100
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Kenter AL, Wuerffel R, Kumar S, Grigera F. Genomic Architecture may Influence Recurrent Chromosomal Translocation Frequency in the Igh Locus. Front Immunol 2013; 4:500. [PMID: 24416036 PMCID: PMC3874557 DOI: 10.3389/fimmu.2013.00500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 12/18/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine , Chicago, IL , USA
| | - Robert Wuerffel
- Department of Microbiology and Immunology, University of Illinois College of Medicine , Chicago, IL , USA
| | - Satyendra Kumar
- Department of Microbiology and Immunology, University of Illinois College of Medicine , Chicago, IL , USA
| | - Fernando Grigera
- Department of Microbiology and Immunology, University of Illinois College of Medicine , Chicago, IL , USA
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