1
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Miglierina E, Ordanoska D, Le Noir S, Laffleur B. RNA processing mechanisms contribute to genome organization and stability in B cells. Oncogene 2024; 43:615-623. [PMID: 38287115 PMCID: PMC10890934 DOI: 10.1038/s41388-024-02952-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
RNA processing includes post-transcriptional mechanisms controlling RNA quality and quantity to ensure cellular homeostasis. Noncoding (nc) RNAs that are regulated by these dynamic processes may themselves fulfill effector and/or regulatory functions, and recent studies demonstrated the critical role of RNAs in organizing both chromatin and genome architectures. Furthermore, RNAs can threaten genome integrity when accumulating as DNA:RNA hybrids, but could also facilitate DNA repair depending on the molecular context. Therefore, by qualitatively and quantitatively fine-tuning RNAs, RNA processing contributes directly or indirectly to chromatin states, genome organization, and genome stability. B lymphocytes represent a unique model to study these interconnected mechanisms as they express ncRNAs transcribed from key specific sequences before undergoing physiological genetic remodeling processes, including V(D)J recombination, somatic hypermutation, and class switch recombination. RNA processing actors ensure the regulation and degradation of these ncRNAs for efficient DNA repair and immunoglobulin gene remodeling while failure leads to B cell development alterations, aberrant DNA repair, and pathological translocations. This review highlights how RNA processing mechanisms contribute to genome architecture and stability, with emphasis on their critical roles during B cell development, enabling physiological DNA remodeling while preventing lymphomagenesis.
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Affiliation(s)
- Emma Miglierina
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Delfina Ordanoska
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Sandrine Le Noir
- UMR CNRS 7276, Inserm 1262, Université de Limoges: Contrôle de la Réponse Immune B et des Lymphoproliférations, Team 2, B-NATION: B cell Nuclear Architecture, Immunoglobulin genes and Oncogenes, Limoges, France
| | - Brice Laffleur
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France.
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2
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Bello A, Hirth G, Voigt S, Tepper S, Jungnickel B. Mechanism and regulation of secondary immunoglobulin diversification. Cell Cycle 2023; 22:2070-2087. [PMID: 37909747 PMCID: PMC10761156 DOI: 10.1080/15384101.2023.2275397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Secondary immunoglobulin diversification by somatic hypermutation and class switch recombination in B cells is instrumental for an adequate adaptive humoral immune response. These genetic events may, however, also introduce aberrations into other cellular genes and thereby cause B cell malignancies. While the basic mechanism of somatic hypermutation and class switch recombination is now well understood, their regulation and in particular the mechanism of their specific targeting to immunoglobulin genes is still rather mysterious. In this review, we summarize the current knowledge on the mechanism and regulation of secondary immunoglobulin diversification and discuss known mechanisms of physiological targeting to immunoglobulin genes and mistargeting to other cellular genes. We summarize open questions in the field and provide an outlook on future research.
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Affiliation(s)
- Amanda Bello
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Gianna Hirth
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Stefanie Voigt
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Sandra Tepper
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Berit Jungnickel
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
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3
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Shen HM, Wuerffel R, Cantillo JF, Priyadarshi S, Lei X, Liang J, Wu YL, Kenter AL. Loop extrusion promotes an alternate pathway for isotype switching. Cell Rep 2021; 37:110059. [PMID: 34818547 PMCID: PMC8979556 DOI: 10.1016/j.celrep.2021.110059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/22/2021] [Accepted: 11/03/2021] [Indexed: 01/02/2023] Open
Abstract
Class-switch recombination (CSR) involves replacement of the Cμ
constant region with another downstream CH region. CSR is initiated
by activation-induced cytidine deaminase (AID)-mediated DNA breaks that are
targeted to transcriptionally active switch (S) regions. S region promoters
(Prs) direct synapsis by associating with the Eμ and 3′Eα
enhancers that jointly anchor a chromatin loop. We report that asymmetric loop
extrusion allows 3′Eα to track along the locus and form Pr-Pr-E
interactions that mediate CSR between downstream S regions, followed by
switching to donor Sμ. This alternative pathway bypasses sequential
switching and creates immunoglobulin (Ig)E+ B cells in the absence of
IgG1 expression. Based on the analysis of diagnostic CSR products in B cell
subsets, we identify a BCR-negative cell intermediate that is pivotal to
efficient CSR. Shen et al. report that 3′Eα tracks along the Igh locus via
unidirectional loop extrusion to form germline transcript promoter (Pr)-Pr-E
interactions that mediate an alternative CSR pathway. B cell intermediates of
CSR are identified, which are AID-dependent, surface BCR-negative, and in the
G1 phase of the cell cycle.
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Affiliation(s)
- Hong Ming Shen
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Robert Wuerffel
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Jose F Cantillo
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Saurabh Priyadarshi
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Xue Lei
- Department of Bioengineering, University of Illinois Colleges of Engineering and Medicine, Chicago, IL 60612-7344, USA
| | - Jie Liang
- Department of Bioengineering, University of Illinois Colleges of Engineering and Medicine, Chicago, IL 60612-7344, USA
| | - Yee Ling Wu
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA.
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4
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Dalloul I, Laffleur B, Dalloul Z, Wehbi B, Jouan F, Brauge B, Derouault P, Moreau J, Kracker S, Fischer A, Durandy A, Le Noir S, Cogné M. UnAIDed Class Switching in Activated B-Cells Reveals Intrinsic Features of a Self-Cleaving IgH Locus. Front Immunol 2021; 12:737427. [PMID: 34777346 PMCID: PMC8581400 DOI: 10.3389/fimmu.2021.737427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Activation-induced deaminase (AID) is the major actor of immunoglobulin (Ig) gene diversification in germinal center B-cells. From its first description, it was considered as mandatory for class switch recombination (CSR), and this discovery initiated a long quest for all of the AID-interacting factors controlling its activity. The mechanisms focusing AID-mediated DNA lesions to given target sequences remain incompletely understood with regards the detailed characterization of optimal substrates in which cytidine deamination will lead to double strand breaks (DSBs) and chromosomal cleavage. In an effort to reconsider whether such CSR breaks absolutely require AID, we herein provide evidence, based on deep-sequencing approaches, showing that this dogma is not absolute in both human and mouse B lymphocytes. In activated B-cells from either AID-deficient mice or human AID-deficient patients, we report an intrinsic ability of the IgH locus to undergo "on-target" cleavage and subsequent synapsis of broken regions in conditions able to yield low-level CSR. DNA breaks occur in such conditions within the same repetitive S regions usually targeted by AID, but their repair follows a specific pathway with increased usage of microhomology-mediated repair. These data further demonstrate the role of AID machinery as not initiating de novo chromosomal cleavage but rather catalyzing a process which spontaneously initiates at low levels in an appropriately conformed IgH locus.
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Affiliation(s)
- Iman Dalloul
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Brice Laffleur
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
| | - Zeinab Dalloul
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Batoul Wehbi
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Florence Jouan
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
| | - Baptiste Brauge
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
| | - Paco Derouault
- Centre Hospitalier Universitaire (CHU) Dupuytren, Limoges, France
| | - Jeanne Moreau
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Sven Kracker
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1163, Laboratory of Human Lympho-hematopoiesis, Imagine Institute, Université de Paris, Paris, France
| | - Alain Fischer
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1163, Laboratory of Human Lympho-hematopoiesis, Imagine Institute, Université de Paris, Paris, France
| | - Anne Durandy
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1163, Laboratory of Human Lympho-hematopoiesis, Imagine Institute, Université de Paris, Paris, France
| | - Sandrine Le Noir
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Michel Cogné
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
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5
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Oudinet C, Braikia FZ, Dauba A, Khamlichi AA. Mechanism and regulation of class switch recombination by IgH transcriptional control elements. Adv Immunol 2020; 147:89-137. [PMID: 32981636 DOI: 10.1016/bs.ai.2020.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Class switch recombination (CSR) plays an important role in humoral immunity by generating antibodies with different effector functions. CSR to a particular antibody isotype is induced by external stimuli, and occurs between highly repetitive switch (S) sequences. CSR requires transcription across S regions, which generates long non-coding RNAs and secondary structures that promote accessibility of S sequences to activation-induced cytidine deaminase (AID). AID initiates DNA double-strand breaks (DSBs) intermediates that are repaired by general DNA repair pathways. Switch transcription is controlled by various regulatory elements, including enhancers and insulators. The current paradigm posits that transcriptional control of CSR involves long-range chromatin interactions between regulatory elements and chromatin loops-stabilizing factors, which promote alignment of partner S regions in a CSR centre (CSRC) and initiation of CSR. In this review, we focus on the role of IgH transcriptional control elements in CSR and the chromatin-based mechanisms underlying this control.
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Affiliation(s)
- Chloé Oudinet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France
| | - Fatima-Zohra Braikia
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France
| | - Audrey Dauba
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France.
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6
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Marchalot A, Ashi MO, Lambert JM, Carrion C, Lecardeur S, Srour N, Delpy L, Le Pennec S. Uncoupling Splicing From Transcription Using Antisense Oligonucleotides Reveals a Dual Role for I Exon Donor Splice Sites in Antibody Class Switching. Front Immunol 2020; 11:780. [PMID: 32477332 PMCID: PMC7233311 DOI: 10.3389/fimmu.2020.00780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/06/2020] [Indexed: 01/08/2023] Open
Abstract
Class switch recombination (CSR) changes antibody isotype by replacing Cμ constant exons with different constant exons located downstream on the immunoglobulin heavy (IgH) locus. During CSR, transcription through specific switch (S) regions and processing of non-coding germline transcripts (GLTs) are essential for the targeting of activation-induced cytidine deaminase (AID). While CSR to IgG1 is abolished in mice lacking an Iγ1 exon donor splice site (dss), many questions remain regarding the importance of I exon dss recognition in CSR. To further clarify the role of I exon dss in CSR, we first evaluated RNA polymerase II (RNA pol II) loading and chromatin accessibility in S regions after activation of mouse B cells lacking Iγ1 dss. We found that deletion of Iγ1 dss markedly reduced RNA pol II pausing and active chromatin marks in the Sγ1 region. We then challenged the post-transcriptional function of I exon dss in CSR by using antisense oligonucleotides (ASOs) masking I exon dss on GLTs. Treatment of stimulated B cells with an ASO targeting Iγ1 dss, in the acceptor Sγ1 region, or Iμ dss, in the donor Sμ region, did not decrease germline transcription but strongly inhibited constitutive splicing and CSR to IgG1. Supporting a global effect on CSR, we also observed that the targeting of Iμ dss reduced CSR to IgG3 and, to a lesser extent, IgG2b isotypes. Altogether, this study reveals that the recognition of I exon dss first supports RNA pol II pausing and the opening of chromatin in targeted S regions and that GLT splicing events using constitutive I exon dss appear mandatory for the later steps of CSR, most likely by guiding AID to S regions.
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Affiliation(s)
- Anne Marchalot
- Unité Mixte de Recherche CNRS 7276, INSERM 1262, Université de Limoges, Limoges, France
| | - Mohamad Omar Ashi
- Unité Mixte de Recherche CNRS 7276, INSERM 1262, Université de Limoges, Limoges, France
| | - Jean-Marie Lambert
- Unité Mixte de Recherche CNRS 7276, INSERM 1262, Université de Limoges, Limoges, France
| | - Claire Carrion
- Unité Mixte de Recherche CNRS 7276, INSERM 1262, Université de Limoges, Limoges, France
| | - Sandrine Lecardeur
- Unité Mixte de Recherche CNRS 7276, INSERM 1262, Université de Limoges, Limoges, France
| | - Nivine Srour
- Unité Mixte de Recherche CNRS 7276, INSERM 1262, Université de Limoges, Limoges, France
- Segal Cancer Center, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montréal, QC, Canada
| | - Laurent Delpy
- Unité Mixte de Recherche CNRS 7276, INSERM 1262, Université de Limoges, Limoges, France
| | - Soazig Le Pennec
- Unité Mixte de Recherche CNRS 7276, INSERM 1262, Université de Limoges, Limoges, France
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7
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Jones BG, Sealy RE, Penkert RR, Surman SL, Birshtein BK, Xu B, Neale G, Maul RW, Gearhart PJ, Hurwitz JL. From Influenza Virus Infections to Lupus: Synchronous Estrogen Receptor α and RNA Polymerase II Binding Within the Immunoglobulin Heavy Chain Locus. Viral Immunol 2020; 33:307-315. [PMID: 32105583 DOI: 10.1089/vim.2019.0144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Males and females respond to pathogens differently and exhibit significantly different frequencies of autoimmune disease. For example, vaccinated adult females control influenza virus better than males, but females suffer systemic lupus erythematosus at a 9:1 frequency compared to males. Numerous explanations have been offered for these sex differences, but most have involved indirect mechanisms by which estrogen, a nuclear hormone, modifies cell barriers or immunity. In search of a direct mechanism, we examined the binding of estrogen receptor α (ERα), a class I nuclear hormone receptor, to the immunoglobulin heavy chain locus. Here, we show that in purified murine B cells, ERα and RNA polymerase II (RNA Pol II) exhibit extraordinarily similar DNA binding patterns. We further demonstrate that ERα preferentially binds adenosine-cytidine (AC)-repeats in the immunoglobulin heavy chain locus when supplemental estrogen is added to purified, lipopolysaccharide-activated B cells. Based on these and previous data, we hypothesize that (i) estrogen guides the binding of ERα and its RNA Pol II partner within the locus, which in turn instructs sterile transcription and class switch recombination (CSR), (ii) ERα binding to AC-repeats modifies the DNA architecture and loops associated with CSR, and (iii) by these mechanisms, estrogen instructs antibody expression. By targeting ERα-DNA interactions in the immunoglobulin heavy chain locus, clinicians may ultimately enhance antibody responses in the context of infectious diseases and reduce antibody responses in the context of allergic or autoimmune reactions.
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Affiliation(s)
- Bart G Jones
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Robert E Sealy
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rhiannon R Penkert
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sherri L Surman
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Barbara K Birshtein
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Robert W Maul
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Patricia J Gearhart
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Julia L Hurwitz
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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8
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Jones BG, Sealy RE, Penkert RR, Surman SL, Maul RW, Neale G, Xu B, Gearhart PJ, Hurwitz JL. Complex sex-biased antibody responses: estrogen receptors bind estrogen response elements centered within immunoglobulin heavy chain gene enhancers. Int Immunol 2020; 31:141-156. [PMID: 30407507 DOI: 10.1093/intimm/dxy074] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 11/02/2018] [Indexed: 01/10/2023] Open
Abstract
Nuclear hormone receptors including the estrogen receptor (ERα) and the retinoic acid receptor regulate a plethora of biological functions including reproduction, circulation and immunity. To understand how estrogen and other nuclear hormones influence antibody production, we characterized total serum antibody isotypes in female and male mice of C57BL/6J, BALB/cJ and C3H/HeJ mouse strains. Antibody levels were higher in females compared to males in all strains and there was a female preference for IgG2b production. Sex-biased patterns were influenced by vitamin levels, and by antigen specificity toward influenza virus or pneumococcus antigens. To help explain sex biases, we examined the direct effects of estrogen on immunoglobulin heavy chain sterile transcript production among purified, lipopolysaccharide-stimulated B cells. Supplemental estrogen in B-cell cultures significantly increased immunoglobulin heavy chain sterile transcripts. Chromatin immunoprecipitation analyses of activated B cells identified significant ERα binding to estrogen response elements (EREs) centered within enhancer elements of the immunoglobulin heavy chain locus, including the Eµ enhancer and hypersensitive site 1,2 (HS1,2) in the 3' regulatory region. The ERE in HS1,2 was conserved across animal species, and in humans marked a site of polymorphism associated with the estrogen-augmented autoimmune disease, lupus. Taken together, the results highlight: (i) the important targets of ERα in regulatory regions of the immunoglobulin heavy chain locus that influence antibody production, and (ii) the complexity of mechanisms by which estrogen instructs sex-biased antibody production profiles.
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Affiliation(s)
- Bart G Jones
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Danny Thomas Place, Memphis, USA
| | - Robert E Sealy
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Danny Thomas Place, Memphis, USA
| | - Rhiannon R Penkert
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Danny Thomas Place, Memphis, USA
| | - Sherri L Surman
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Danny Thomas Place, Memphis, USA
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Geoff Neale
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children's Research Hospital, Memphis, USA
| | - Beisi Xu
- Computational Biology, St. Jude Children's Research Hospital, Memphis, USA
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Julia L Hurwitz
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Danny Thomas Place, Memphis, USA.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, USA
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9
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Sheppard EC, Morrish RB, Dillon MJ, Leyland R, Chahwan R. Epigenomic Modifications Mediating Antibody Maturation. Front Immunol 2018. [PMID: 29535729 PMCID: PMC5834911 DOI: 10.3389/fimmu.2018.00355] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications, such as histone modifications, DNA methylation status, and non-coding RNAs (ncRNA), all contribute to antibody maturation during somatic hypermutation (SHM) and class-switch recombination (CSR). Histone modifications alter the chromatin landscape and, together with DNA primary and tertiary structures, they help recruit Activation-Induced Cytidine Deaminase (AID) to the immunoglobulin (Ig) locus. AID is a potent DNA mutator, which catalyzes cytosine-to-uracil deamination on single-stranded DNA to create U:G mismatches. It has been shown that alternate chromatin modifications, in concert with ncRNAs and potentially DNA methylation, regulate AID recruitment and stabilize DNA repair factors. We, hereby, assess the combination of these distinct modifications and discuss how they contribute to initiating differential DNA repair pathways at the Ig locus, which ultimately leads to enhanced antibody–antigen binding affinity (SHM) or antibody isotype switching (CSR). We will also highlight how misregulation of epigenomic regulation during DNA repair can compromise antibody development and lead to a number of immunological syndromes and cancer.
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Affiliation(s)
- Emily C Sheppard
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - Michael J Dillon
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - Richard Chahwan
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
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10
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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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11
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Jones BG, Penkert RR, Xu B, Fan Y, Neale G, Gearhart PJ, Hurwitz JL. Binding of estrogen receptors to switch sites and regulatory elements in the immunoglobulin heavy chain locus of activated B cells suggests a direct influence of estrogen on antibody expression. Mol Immunol 2016; 77:97-102. [PMID: 27494228 DOI: 10.1016/j.molimm.2016.07.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 07/17/2016] [Accepted: 07/21/2016] [Indexed: 12/31/2022]
Abstract
Females and males differ in antibody isotype expression patterns and in immune responses to foreign- and self-antigens. For example, systemic lupus erythematosus is a condition that associates with the production of isotype-skewed anti-self antibodies, and exhibits a 9:1 female:male disease ratio. To explain differences between B cell responses in males and females, we sought to identify direct interactions of the estrogen receptor (ER) with the immunoglobulin heavy chain locus. This effort was encouraged by our previous identification of estrogen response elements (ERE) in heavy chain switch (S) regions. We conducted a full-genome chromatin immunoprecipitation analysis (ChIP-seq) using DNA from LPS-activated B cells and an ERα-specific antibody. Results revealed ER binding to a wide region of DNA, spanning sequences from the JH cluster to Cδ, with peaks in Eμ and Sμ sites. Additional peaks of ERα binding were coincident with hs1,2 and hs4 sites in the 3' regulatory region (3'RR) of the heavy chain locus. This first demonstration of direct binding of ER to key regulatory elements in the immunoglobulin locus supports our hypothesis that estrogen and other nuclear hormone receptors and ligands may directly influence antibody expression and class switch recombination (CSR). Our hypothesis encourages the conduct of new experiments to evaluate the consequences of ER binding. A better understanding of ER:DNA interactions in the immunoglobulin heavy chain locus, and respective mechanisms, may ultimately translate to better control of antibody expression, better protection against pathogens, and prevention of pathologies caused by auto-immune disease.
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Affiliation(s)
- Bart G Jones
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Rhiannon R Penkert
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Geoff Neale
- Hartwell Center, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Julia L Hurwitz
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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12
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Romanello M, Schiavone D, Frey A, Sale JE. Histone H3.3 promotes IgV gene diversification by enhancing formation of AID-accessible single-stranded DNA. EMBO J 2016; 35:1452-64. [PMID: 27220848 PMCID: PMC4883027 DOI: 10.15252/embj.201693958] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/25/2016] [Indexed: 11/30/2022] Open
Abstract
Immunoglobulin diversification is driven by activation‐induced deaminase (AID), which converts cytidine to uracil within the Ig variable (IgV) regions. Central to the recruitment of AID to the IgV genes are factors that regulate the generation of single‐stranded DNA (ssDNA), the enzymatic substrate of AID. Here, we report that chicken DT40 cells lacking variant histone H3.3 exhibit reduced IgV sequence diversification. We show that this results from impairment of the ability of AID to access the IgV genes due to reduced formation of ssDNA during IgV transcription. Loss of H3.3 also diminishes IgV R‐loop formation. However, reducing IgV R‐loops by RNase HI overexpression in wild‐type cells does not affect IgV diversification, showing that these structures are not necessary intermediates for AID access. Importantly, the reduction in the formation of AID‐accessible ssDNA in cells lacking H3.3 is independent of any effect on the level of transcription or the kinetics of RNAPII elongation, suggesting the presence of H3.3 in the nucleosomes of the IgV genes increases the chances of the IgV DNA becoming single‐stranded, thereby creating an effective AID substrate.
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Affiliation(s)
- Marina Romanello
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Davide Schiavone
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Alexander Frey
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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13
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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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14
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Starnes LM, Su D, Pikkupeura LM, Weinert BT, Santos MA, Mund A, Soria R, Cho YW, Pozdnyakova I, Kubec Højfeldt M, Vala A, Yang W, López-Méndez B, Lee JE, Peng W, Yuan J, Ge K, Montoya G, Nussenzweig A, Choudhary C, Daniel JA. A PTIP-PA1 subcomplex promotes transcription for IgH class switching independently from the associated MLL3/MLL4 methyltransferase complex. Genes Dev 2016; 30:149-63. [PMID: 26744420 PMCID: PMC4719306 DOI: 10.1101/gad.268797.115] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/04/2015] [Indexed: 01/13/2023]
Abstract
Transcription at the immunoglobulin heavy chain (Igh) locus targets class switch recombination (CSR)-associated DNA damage and is promoted by the BRCT domain-containing PTIP protein. Starnes et al. found that PTIP functions in transcription and CSR separately from its association with the MLL3/MLL4 complex and from its localization to sites of DNA damage. Class switch recombination (CSR) diversifies antibodies for productive immune responses while maintaining stability of the B-cell genome. Transcription at the immunoglobulin heavy chain (Igh) locus targets CSR-associated DNA damage and is promoted by the BRCT domain-containing PTIP (Pax transactivation domain-interacting protein). Although PTIP is a unique component of the mixed-lineage leukemia 3 (MLL3)/MLL4 chromatin-modifying complex, the mechanisms for how PTIP promotes transcription remain unclear. Here we dissected the minimal structural requirements of PTIP and its different protein complexes using quantitative proteomics in primary lymphocytes. We found that PTIP functions in transcription and CSR separately from its association with the MLL3/MLL4 complex and from its localization to sites of DNA damage. We identified a tandem BRCT domain of PTIP that is sufficient for CSR and identified PA1 as its main functional protein partner. Collectively, we provide genetic and biochemical evidence that a PTIP–PA1 subcomplex functions independently from the MLL3/MLL4 complex to mediate transcription during CSR. These results further our understanding of how multifunctional chromatin-modifying complexes are organized by subcomplexes that harbor unique and distinct activities.
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Affiliation(s)
- Linda M Starnes
- Chromatin Structure and Function Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Dan Su
- Chromatin Structure and Function Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Laura M Pikkupeura
- Chromatin Structure and Function Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Brian T Weinert
- Proteomics and Cell Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Margarida A Santos
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Andreas Mund
- Chromatin Structure and Function Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Rebeca Soria
- Chromatin Structure and Function Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Young-Wook Cho
- Adipocyte Biology and Gene Regulation Section, Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Irina Pozdnyakova
- Protein Production and Characterization Platform, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Martina Kubec Højfeldt
- Chromatin Structure and Function Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Andrea Vala
- Protein Production and Characterization Platform, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Wenjing Yang
- Department of Physics, The George Washington University, Washington, DC 20052, USA
| | - Blanca López-Méndez
- Protein Production and Characterization Platform, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Ji-Eun Lee
- Adipocyte Biology and Gene Regulation Section, Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC 20052, USA
| | - Joan Yuan
- Developmental Immunology Group, Division of Molecular Hematology, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund 22184, Sweden
| | - Kai Ge
- Adipocyte Biology and Gene Regulation Section, Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Guillermo Montoya
- Protein Production and Characterization Platform, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Macromolecular Crystallography Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chunaram Choudhary
- Proteomics and Cell Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jeremy A Daniel
- Chromatin Structure and Function Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
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15
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Zan H, Casali P. Epigenetics of Peripheral B-Cell Differentiation and the Antibody Response. Front Immunol 2015; 6:631. [PMID: 26697022 PMCID: PMC4677338 DOI: 10.3389/fimmu.2015.00631] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications, such as histone post-translational modifications, DNA methylation, and alteration of gene expression by non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are heritable changes that are independent from the genomic DNA sequence. These regulate gene activities and, therefore, cellular functions. Epigenetic modifications act in concert with transcription factors and play critical roles in B cell development and differentiation, thereby modulating antibody responses to foreign- and self-antigens. Upon antigen encounter by mature B cells in the periphery, alterations of these lymphocytes epigenetic landscape are induced by the same stimuli that drive the antibody response. Such alterations instruct B cells to undergo immunoglobulin (Ig) class switch DNA recombination (CSR) and somatic hypermutation (SHM), as well as differentiation to memory B cells or long-lived plasma cells for the immune memory. Inducible histone modifications, together with DNA methylation and miRNAs modulate the transcriptome, particularly the expression of activation-induced cytidine deaminase, which is essential for CSR and SHM, and factors central to plasma cell differentiation, such as B lymphocyte-induced maturation protein-1. These inducible B cell-intrinsic epigenetic marks guide the maturation of antibody responses. Combinatorial histone modifications also function as histone codes to target CSR and, possibly, SHM machinery to the Ig loci by recruiting specific adaptors that can stabilize CSR/SHM factors. In addition, lncRNAs, such as recently reported lncRNA-CSR and an lncRNA generated through transcription of the S region that form G-quadruplex structures, are also important for CSR targeting. Epigenetic dysregulation in B cells, including the aberrant expression of non-coding RNAs and alterations of histone modifications and DNA methylation, can result in aberrant antibody responses to foreign antigens, such as those on microbial pathogens, and generation of pathogenic autoantibodies, IgE in allergic reactions, as well as B cell neoplasia. Epigenetic marks would be attractive targets for new therapeutics for autoimmune and allergic diseases, and B cell malignancies.
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Affiliation(s)
- Hong Zan
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
| | - Paolo Casali
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
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16
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Abstract
The immunoglobulin diversification processes of somatic hypermutation and class switch recombination critically rely on transcription-coupled targeting of activation-induced cytidine deaminase (AID) to Ig loci in activated B lymphocytes. AID catalyzes deamination of cytidine deoxynucleotides on exposed single-stranded DNA. In addition to driving immunoglobulin diversity, promiscuous targeting of AID mutagenic activity poses a deleterious threat to genomic stability. Recent genome-wide studies have uncovered pervasive AID activity throughout the B cell genome. It is increasingly apparent that AID activity is frequently targeted to genomic loci undergoing early transcription termination where RNA exosome promotes the resolution of stalled transcription complexes via cotranscriptional RNA degradation mechanisms. Here, we review aspects and consequences of eukaryotic transcription that lead to early termination, RNA exosome recruitment, and ultimately targeting of AID mutagenic activity.
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Affiliation(s)
- Evangelos Pefanis
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, USA.
| | - Uttiya Basu
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, USA.
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17
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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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18
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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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19
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Taylor BJM, Wu YL, Rada C. Active RNAP pre-initiation sites are highly mutated by cytidine deaminases in yeast, with AID targeting small RNA genes. eLife 2014; 3:e03553. [PMID: 25237741 PMCID: PMC4359381 DOI: 10.7554/elife.03553] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/17/2014] [Indexed: 12/21/2022] Open
Abstract
Cytidine deaminases are single stranded DNA mutators diversifying antibodies and restricting viral infection. Improper access to the genome leads to translocations and mutations in B cells and contributes to the mutation landscape in cancer, such as kataegis. It remains unclear how deaminases access double stranded genomes and whether off-target mutations favor certain loci, although transcription and opportunistic access during DNA repair are thought to play a role. In yeast, AID and the catalytic domain of APOBEC3G preferentially mutate transcriptionally active genes within narrow regions, 110 base pairs in width, fixed at RNA polymerase initiation sites. Unlike APOBEC3G, AID shows enhanced mutational preference for small RNA genes (tRNAs, snoRNAs and snRNAs) suggesting a putative role for RNA in its recruitment. We uncover the high affinity of the deaminases for the single stranded DNA exposed by initiating RNA polymerases (a DNA configuration reproduced at stalled polymerases) without a requirement for specific cofactors.
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Affiliation(s)
- Benjamin J M Taylor
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Yee Ling Wu
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Cristina Rada
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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20
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A source of the single-stranded DNA substrate for activation-induced deaminase during somatic hypermutation. Nat Commun 2014; 5:4137. [PMID: 24923561 PMCID: PMC4154566 DOI: 10.1038/ncomms5137] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 05/16/2014] [Indexed: 11/08/2022] Open
Abstract
During somatic hypermutation (SHM), activation-induced deaminase (AID) mutates deoxycytidine on single-stranded DNA (ssDNA) generated by the transcription machinery, but the detailed mechanism remains unclear. Here we report a higher abundance of RNA polymerase II (Pol II) at the immunoglobulin heavy-chain variable (Igh-V) region compared with the constant region and partially transcribed Igh RNAs, suggesting a slower Pol II progression at Igh-V that could result in some early/premature transcription termination after prolonged pausing/stalling of Pol II. Knocking down RNA-exosome complexes, which could decrease premature transcription termination, leads to decreased SHM. Knocking down Spt5, which can augment premature transcription termination, leads to increase in both, SHM and the abundance of ssDNA substrates. Collectively, our data support the model that, following the reduction of Pol II progression (pausing or stalling) at the Igh-V, additional steps such as premature transcription termination are involved in providing ssDNA substrates for AID during SHM.
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21
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Abstract
microRNAs are a class of regulators of gene expression that have been shown critical for a great number of biological processes; however, little is known of their role in germinal center (GC) B cells. Although the GC reaction is crucial to ensure a competent immune response, GC B cells are also the origin of most human lymphomas, presumably due to bystander effects of the immunoglobulin gene remodeling that takes place at these sites. Here we report that miR-217 is specifically upregulated in GC B cells. Gain- and loss-of-function mouse models reveal that miR-217 is a positive modulator of the GC response that increases the generation of class-switched antibodies and the frequency of somatic hypermutation. We find that miR-217 down-regulates the expression of a DNA damage response and repair gene network and in turn stabilizes Bcl-6 expression in GC B cells. Importantly, miR-217 overexpression also promotes mature B-cell lymphomagenesis; this is physiologically relevant as we find that miR-217 is overexpressed in aggressive human B-cell lymphomas. Therefore, miR-217 provides a novel molecular link between the normal GC response and B-cell transformation.
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22
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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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23
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Chao J, Rothschild G, Basu U. Ubiquitination events that regulate recombination of immunoglobulin Loci gene segments. Front Immunol 2014; 5:100. [PMID: 24653725 PMCID: PMC3949197 DOI: 10.3389/fimmu.2014.00100] [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: 12/22/2013] [Accepted: 02/25/2014] [Indexed: 11/13/2022] Open
Abstract
Programed DNA mutagenesis events in the immunoglobulin (Ig) loci of developing B cells utilize the common and conserved mechanism of protein ubiquitination for subsequent proteasomal degradation to generate the required antigen-receptor diversity. Recombinase proteins RAG1 and RAG2, necessary for V(D)J recombination, and activation-induced cytidine deaminase, an essential mutator protein for catalyzing class switch recombination and somatic hypermutation, are regulated by various ubiquitination events that affect protein stability and activity. Programed DNA breaks in the Ig loci can be identified by various components of DNA repair pathways, also regulated by protein ubiquitination. Errors in the ubiquitination pathways for any of the DNA double-strand break repair proteins can lead to inefficient recombination and repair events, resulting in a compromised adaptive immune system or development of cancer.
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Affiliation(s)
- Jaime Chao
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University , New York, NY , USA
| | - Gerson Rothschild
- 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
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24
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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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25
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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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26
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Lam T, Thomas LM, White CA, Li G, Pone EJ, Xu Z, Casali P. Scaffold functions of 14-3-3 adaptors in B cell immunoglobulin class switch DNA recombination. PLoS One 2013; 8:e80414. [PMID: 24282540 PMCID: PMC3840166 DOI: 10.1371/journal.pone.0080414] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 10/02/2013] [Indexed: 12/22/2022] Open
Abstract
Class switch DNA recombination (CSR) of the immunoglobulin heavy chain (IgH) locus crucially diversifies antibody biological effector functions. CSR involves the induction of activation-induced cytidine deaminase (AID) expression and AID targeting to switch (S) regions by 14-3-3 adaptors. 14-3-3 adaptors specifically bind to 5'-AGCT-3' repeats, which make up for the core of all IgH locus S regions. They selectively target the upstream and downstream S regions that are set to undergo S-S DNA recombination. We hypothesized that 14-3-3 adaptors function as scaffolds to stabilize CSR enzymatic elements on S regions. Here we demonstrate that all seven 14-3-3β, 14-3-3ε, 14-3-3γ, 14-3-3η, 14-3-3σ, 14-3-3τ and 14-3-3ζ adaptors directly interacted with AID, PKA-Cα (catalytic subunit) and PKA-RIα (regulatory inhibitory subunit) and uracil DNA glycosylase (Ung). 14-3-3 adaptors, however, did not interact with AID C-terminal truncation mutant AIDΔ(180-198) or AIDF193A and AIDL196A point-mutants (which have been shown not to bind to S region DNA and fail to mediate CSR). 14-3-3 adaptors colocalized with AID and replication protein A (RPA) in B cells undergoing CSR. 14-3-3 and AID binding to S region DNA was disrupted by viral protein R (Vpr), an accessory protein of human immunodeficiency virus type-1 (HIV-1), which inhibited CSR without altering AID expression or germline IH-CH transcription. Accordingly, we demonstrated that 14-3-3 directly interact with Vpr, which in turn, also interact with AID, PKA-Cα and Ung. Altogether, our findings suggest that 14-3-3 adaptors play important scaffold functions and nucleate the assembly of multiple CSR factors on S regions. They also show that such assembly can be disrupted by a viral protein, thereby allowing us to hypothesize that small molecule compounds that specifically block 14-3-3 interactions with AID, PKA and/or Ung can be used to inhibit unwanted CSR.
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Affiliation(s)
- Tonika Lam
- Institute for Immunology, School of Medicine and School of Biological Sciences, University of California Irvine, Irvine, California, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Lisa M. Thomas
- Institute for Immunology, School of Medicine and School of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Clayton A. White
- Institute for Immunology, School of Medicine and School of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Guideng Li
- Institute for Immunology, School of Medicine and School of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Egest J. Pone
- Institute for Immunology, School of Medicine and School of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Zhenming Xu
- Institute for Immunology, School of Medicine and School of Biological Sciences, University of California Irvine, Irvine, California, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Paolo Casali
- Institute for Immunology, School of Medicine and School of Biological Sciences, University of California Irvine, Irvine, California, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
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Grigera F, Bellacosa A, Kenter AL. Complex relationship between mismatch repair proteins and MBD4 during immunoglobulin class switch recombination. PLoS One 2013; 8:e78370. [PMID: 24205214 PMCID: PMC3812156 DOI: 10.1371/journal.pone.0078370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/19/2013] [Indexed: 11/19/2022] Open
Abstract
Mismatch repair (MMR) safeguards against genomic instability and is required for efficient Ig class switch recombination (CSR). Methyl CpG binding domain protein 4 (MBD4) binds to MutL homologue 1 (MLH1) and controls the post-transcriptional level of several MMR proteins, including MutS homologue 2 (MSH2). We show that in WT B cells activated for CSR, MBD4 is induced and interacts with MMR proteins, thereby implying a role for MBD4 in CSR. However, CSR is in the normal range in Mbd4 deficient mice deleted for exons 2–5 despite concomitant reduction of MSH2. We show by comparison in Msh2+/− B cells that a two-fold reduction of MSH2 and MBD4 proteins is correlated with impaired CSR. It is therefore surprising that CSR occurs at normal frequencies in the Mbd4 deficient B cells where MSH2 is reduced. We find that a variant Mbd4 transcript spanning exons 1,6–8 is expressed in Mbd4 deficient B cells. This transcript can be ectopically expressed and produces a truncated MBD4 peptide. Thus, the 3′ end of the Mbd4 locus is not silent in Mbd4 deficient B cells and may contribute to CSR. Our findings highlight a complex relationship between MBD4 and MMR proteins in B cells and a potential reconsideration of their role in CSR.
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Affiliation(s)
- Fernando Grigera
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, Illinois, United States of America
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Sun J, Keim CD, Wang J, Kazadi D, Oliver PM, Rabadan R, Basu U. E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells. Genes Dev 2013; 27:1821-33. [PMID: 23964096 PMCID: PMC3759698 DOI: 10.1101/gad.210211.112] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Programmed mutagenesis of the immunoglobulin locus of B lymphocytes during class switch recombination (CSR) and somatic hypermutation requires RNA polymerase II (polII) transcription complex-dependent targeting of the DNA mutator activation-induced cytidine deaminase (AID). AID deaminates cytidine residues on substrate sequences in the immunoglobulin (Ig) locus via a transcription-dependent mechanism, and this activity is stimulated by the RNA polII stalling cofactor Spt5 and the 11-subunit cellular noncoding RNA 3'-5' exonucleolytic processing complex RNA exosome. The mechanism by which the RNA exosome recognizes immunoglobulin locus RNA substrates to stimulate AID DNA deamination activity on its in vivo substrate sequences is an important question. Here we report that E3-ubiquitin ligase Nedd4 destabilizes AID-associated RNA polII by a ubiquitination event, leading to generation of 3' end free RNA exosome RNA substrates at the Ig locus and other AID target sequences genome-wide. We found that lack of Nedd4 activity in B cells leads to accumulation of RNA exosome substrates at AID target genes and defective CSR. Taken together, our study links noncoding RNA processing following RNA polII pausing with regulation of the mutator AID protein. Our study also identifies Nedd4 as a regulator of noncoding RNAs that are generated by stalled RNA polII genome-wide.
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Affiliation(s)
- Jianbo Sun
- Department of Microbiology and Immunology, Columbia University, New York, New York 10032, USA
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29
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Schrader CE, Linehan EK, Ucher AJ, Bertocci B, Stavnezer J. DNA polymerases β and λ do not directly affect Ig variable region somatic hypermutation although their absence reduces the frequency of mutations. DNA Repair (Amst) 2013; 12:1087-93. [PMID: 24084171 DOI: 10.1016/j.dnarep.2013.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/02/2013] [Accepted: 09/09/2013] [Indexed: 11/28/2022]
Abstract
During somatic hypermutation (SHM) of antibody variable (V) region genes, activation-induced cytidine deaminase (AID) converts dC to dU, and dUs can either be excised by uracil DNA glycosylase (UNG), by mismatch repair, or replicated over. If UNG excises the dU, the abasic site could be cleaved by AP-endonuclease (APE), introducing the single-strand DNA breaks (SSBs) required for generating mutations at A:T bp, which are known to depend upon mismatch repair and DNA Pol η. DNA Pol β or λ could instead repair the lesion correctly. To assess the involvement of Pols β and λ in SHM of antibody genes, we analyzed mutations in the VDJh4 3' flanking region in Peyer's patch germinal center (GC) B cells from polβ(-/-)polλ(-/-), polλ(-/-), and polβ(-/-) mice. We find that deficiency of either or both polymerases results in a modest but significant decrease in V region SHM, with Pol β having a greater effect, but there is no effect on mutation specificity, suggesting they have no direct role in SHM. Instead, the effect on SHM appears to be due to a role for these enzymes in GC B cell proliferation or viability. The results suggest that the BER pathway is not important during V region SHM for generating mutations at A:T bp. Furthermore, this implies that most of the SSBs required for Pol η to enter and create A:T mutations are likely generated during replication instead. These results contrast with the inhibitory effect of Pol β on mutations at the Ig Sμ locus, Sμ DSBs and class switch recombination (CSR) reported previously. We show here that B cells deficient in Pol λ or both Pol β and λ proliferate normally in culture and undergo slightly elevated CSR, as shown previously for Pol β-deficient B cells.
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Affiliation(s)
- Carol E Schrader
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, United States
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30
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Li G, Zan H, Xu Z, Casali P. Epigenetics of the antibody response. Trends Immunol 2013; 34:460-70. [PMID: 23643790 PMCID: PMC3744588 DOI: 10.1016/j.it.2013.03.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 12/19/2022]
Abstract
Epigenetic marks, such as DNA methylation, histone post-translational modifications and miRNAs, are induced in B cells by the same stimuli that drive the antibody response. They play major roles in regulating somatic hypermutation (SHM), class switch DNA recombination (CSR), and differentiation to plasma cells or long-lived memory B cells. Histone modifications target the CSR and, possibly, SHM machinery to the immunoglobulin locus; they together with DNA methylation and miRNAs modulate the expression of critical elements of that machinery, such as activation-induced cytidine deaminase (AID), as well as factors central to plasma cell differentiation, such as B lymphocyte-induced maturation protein-1 (Blimp-1). These inducible B cell-intrinsic epigenetic marks instruct the maturation of antibody responses. Their dysregulation plays an important role in aberrant antibody responses to foreign antigens, such as those of microbial pathogens, and self-antigens, such as those targeted in autoimmunity, and B cell neoplasia.
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Affiliation(s)
- Guideng Li
- Institute for Immunology and School of Medicine, University of California, Irvine, CA 92697-4120, USA
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31
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Mai T, Pone EJ, Li G, Lam TS, Moehlman J, Xu Z, Casali P. Induction of activation-induced cytidine deaminase-targeting adaptor 14-3-3γ is mediated by NF-κB-dependent recruitment of CFP1 to the 5'-CpG-3'-rich 14-3-3γ promoter and is sustained by E2A. THE JOURNAL OF IMMUNOLOGY 2013; 191:1895-906. [PMID: 23851690 DOI: 10.4049/jimmunol.1300922] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Class switch DNA recombination (CSR) crucially diversifies Ab biologic effector functions. 14-3-3γ specifically binds to the 5'-AGCT-3' repeats in the IgH locus switch (S) regions. By interacting directly with the C-terminal region of activation-induced cytidine deaminase (AID), 14-3-3γ targets this enzyme to S regions to mediate CSR. In this study, we showed that 14-3-3γ was expressed in germinal center B cells in vivo and induced in B cells by T-dependent and T-independent primary CSR-inducing stimuli in vitro in humans and mice. Induction of 14-3-3γ was rapid, peaking within 3 h of stimulation by LPSs, and sustained over the course of AID and CSR induction. It was dependent on recruitment of NF-κB to the 14-3-3γ gene promoter. The NF-κB recruitment enhanced the occupancy of the CpG island within the 14-3-3γ promoter by CFP1, a component of the COMPASS histone methyltransferase complex, and promoter-specific enrichment of histone 3 lysine 4 trimethylation (H3K4me3), which is indicative of open chromatin state and marks transcription-competent promoters. NF-κB also potentiated the binding of B cell lineage-specific factor E2A to an E-box motif located immediately downstream of the two closely-spaced transcription start sites for sustained 14-3-3γ expression and CSR induction. Thus, 14-3-3γ induction in CSR is enabled by the CFP1-mediated H3K4me3 enrichment in the promoter, dependent on NF-κB and sustained by E2A.
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Affiliation(s)
- Thach Mai
- Institute for Immunology, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
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32
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Panyukov VV, Ozoline ON. Promoters of Escherichia coli versus promoter islands: function and structure comparison. PLoS One 2013; 8:e62601. [PMID: 23717391 PMCID: PMC3661553 DOI: 10.1371/journal.pone.0062601] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 03/23/2013] [Indexed: 12/21/2022] Open
Abstract
Expression of bacterial genes takes place under the control of RNA polymerase with exchangeable σ-subunits and multiple transcription factors. A typical promoter region contains one or several overlapping promoters. In the latter case promoters have the same or different σ-specificity and are often subjected to different regulatory stimuli. Genes, transcribed from multiple promoters, have on average higher expression levels. However, recently in the genome of Escherichia coli we found 78 regions with an extremely large number of potential transcription start points (promoter islands, PIs). It was shown that all PIs interact with RNA polymerase in vivo and are able to form transcriptionally competent open complexes both in vitro and in vivo but their transcriptional activity measured by oligonucleotide microarrays was very low, if any. Here we confirmed transcriptional defectiveness of PIs by analyzing the 5'-end specific RNA-seq data, but showed their ability to produce short oligos (9-14 bases). This combination of functional properties indicated a deliberate suppression of transcriptional activity within PIs. According to our data this suppression may be due to a specific conformation of the DNA double helix, which provides an ideal platform for interaction with both RNA polymerase and the histone-like nucleoid protein H-NS. The genomic DNA of E.coli contains therefore several dozen sites optimized by evolution for staying in a heterochromatin-like state. Since almost all promoter islands are associated with horizontally acquired genes, we offer them as specific components of bacterial evolution involved in acquisition of foreign genetic material by turning off the expression of toxic or useless aliens or by providing optimal promoter for beneficial genes. The putative molecular mechanism underlying the appearance of promoter islands within recipient genomes is discussed.
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Affiliation(s)
- Valeriy V. Panyukov
- Department of Bioinformatics, Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Olga N. Ozoline
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
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