1
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Kasprzyk ME, Sura W, Dzikiewicz-Krawczyk A. Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer. Cancers (Basel) 2021; 13:3270. [PMID: 34210001 PMCID: PMC8269369 DOI: 10.3390/cancers13133270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 01/19/2023] Open
Abstract
B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.
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2
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Bruzeau C, Moreau J, Le Noir S, Pinaud E. Panorama of stepwise involvement of the IgH 3' regulatory region in murine B cells. Adv Immunol 2021; 149:95-114. [PMID: 33993921 DOI: 10.1016/bs.ai.2021.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Among the multiple events leading to immunoglobulin (Ig) expression in B cells, stepwise activation of the Ig heavy chain locus (IgH) is of critical importance. Transcription regulation of the complex IgH locus has always been an interesting viewpoint to unravel the multiple and complex events required for IgH expression. First, regulatory germline transcripts (GLT) assist DNA remodeling events such as VDJ recombination, class switch recombination (CSR) and somatic hypermutation (SHM). Second, productive spliced transcripts restrict heavy chain protein expression associated either with the surface receptor of developing B cells or secreted in large amounts in plasma cells. One main transcriptional regulator for IgH lies at its 3' extremity and includes both a set of enhancers grouped in a large 3' regulatory region (3'RR) and a cluster of 3'CTCF-binding elements (3'CBEs). In this focused review, we will preferentially refer to evidence reported for the murine endogenous IgH locus, whether it is wt or carries deletions or insertions within the IgH 3' boundary and associated regulatory region.
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Affiliation(s)
- Charlotte Bruzeau
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France
| | - Jeanne Moreau
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France
| | - Sandrine Le Noir
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France
| | - Eric Pinaud
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France.
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3
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Laffleur B, Lim J, Zhang W, Chen Y, Pefanis E, Bizarro J, Batista CR, Wu L, Economides AN, Wang J, Basu U. Noncoding RNA processing by DIS3 regulates chromosomal architecture and somatic hypermutation in B cells. Nat Genet 2021; 53:230-242. [PMID: 33526923 PMCID: PMC8011275 DOI: 10.1038/s41588-020-00772-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Noncoding RNAs are exquisitely titrated by the cellular RNA surveillance machinery for regulating diverse biological processes. The RNA exosome, the predominant 3' RNA exoribonuclease in mammalian cells, is composed of nine core and two catalytic subunits. Here, we developed a mouse model with a conditional allele to study the RNA exosome catalytic subunit DIS3. In DIS3-deficient B cells, integrity of the immunoglobulin heavy chain (Igh) locus in its topologically associating domain is affected, with accumulation of DNA-associated RNAs flanking CTCF-binding elements, decreased CTCF binding to CTCF-binding elements and disorganized cohesin localization. DIS3-deficient B cells also accumulate activation-induced cytidine deaminase-mediated asymmetric nicks, altering somatic hypermutation patterns and increasing microhomology-mediated end-joining DNA repair. Altered mutation patterns and Igh architectural defects in DIS3-deficient B cells lead to decreased class-switch recombination but increased chromosomal translocations. Our observations of DIS3-mediated architectural regulation at the Igh locus are reflected genome wide, thus providing evidence that noncoding RNA processing is an important mechanism for controlling genome organization.
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Affiliation(s)
- Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pharmacy, School of Pharmacy, Jeonbuk National University, Jeonju, South Korea
| | - Wanwei Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Yiyun Chen
- Division of Life Science, Department of Chemical and Biological Engineering, Center for Systems Biology and Human Health, and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Evangelos Pefanis
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Jonathan Bizarro
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Carolina R Batista
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lijing Wu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | | | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, Center for Systems Biology and Human Health, and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
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4
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Ros F, Offner S, Klostermann S, Thorey I, Niersbach H, Breuer S, Zarnt G, Lorenz S, Puels J, Siewe B, Schueler N, Dragicevic T, Ostler D, Hansen-Wester I, Lifke V, Kaluza B, Kaluza K, van Schooten W, Buelow R, Tissot AC, Platzer J. Rabbits transgenic for human IgG genes recapitulating rabbit B-cell biology to generate human antibodies of high specificity and affinity. MAbs 2020; 12:1846900. [PMID: 33228444 PMCID: PMC7780963 DOI: 10.1080/19420862.2020.1846900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Transgenic animals incorporating human antibody genes are extremely attractive for drug development because they obviate subsequent antibody humanization procedures required for therapeutic translation. Transgenic platforms have previously been established using mice, but also more recently rats, chickens, and cows and are now in abundant use for drug development. However, rabbit-based antibody generation, with a strong track record for specificity and affinity, is able to include gene conversion mediated sequence diversification, thereby enhancing binder maturation and improving the variance/selection of output antibodies in a different way than in rodents. Since it additionally frequently permits good binder generation against antigens that are only weakly immunogenic in other organisms, it is a highly interesting species for therapeutic antibody generation. We report here on the generation, utilization, and analysis of the first transgenic rabbit strain for human antibody production. Through the knockout of endogenous IgM genes and the introduction of human immunoglobulin sequences, this rabbit strain has been engineered to generate a highly diverse human IgG antibody repertoire. We further incorporated human CD79a/b and Bcl2 (B-cell lymphoma 2) genes, which enhance B-cell receptor expression and B-cell survival. Following immunization against the angiogenic factor BMP9 (Bone Morphogenetic Proteins 9), we were able to isolate a set of exquisitely affine and specific neutralizing antibodies from these rabbits. Sequence analysis of these binders revealed that both somatic hypermutation and gene conversion are fully operational in this strain, without compromising the very high degree of humanness. This powerful new transgenic strategy will allow further expansion of the use of endogenous immune mechanisms in drug development.
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Affiliation(s)
- Francesca Ros
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | - Sonja Offner
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | - Stefan Klostermann
- Roche Pharmaceutical Research and Early Development, Informatics, Roche Innovation Center Munich , Penzberg, Germany
| | - Irmgard Thorey
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | - Helmut Niersbach
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Munich , Penzberg, Germany
| | - Sebastian Breuer
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | - Grit Zarnt
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | - Stefan Lorenz
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | | | - Basile Siewe
- THE JACKSON LABORATORY JMCRS, Sacramento, CA, USA
| | - Nicole Schueler
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | - Tajana Dragicevic
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | - Dominique Ostler
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | - Imke Hansen-Wester
- Supplier Quality Management, Global External Quality Roche Diagnostics GmbH , Penzberg, Germany
| | - Valeria Lifke
- Personalized Healthcare Solution, Immunoassay Development and System Integration, Roche Diagnostics GmbH , Penzberg, Germany
| | - Brigitte Kaluza
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | - Klaus Kaluza
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | | | | | - Alain C Tissot
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
| | - Josef Platzer
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg, Germany
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5
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Dinesh RK, Barnhill B, Ilanges A, Wu L, Michelson DA, Senigl F, Alinikula J, Shabanowitz J, Hunt DF, Schatz DG. Transcription factor binding at Ig enhancers is linked to somatic hypermutation targeting. Eur J Immunol 2019; 50:380-395. [PMID: 31821534 DOI: 10.1002/eji.201948357] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/05/2019] [Accepted: 12/02/2019] [Indexed: 01/15/2023]
Abstract
Secondary diversification of the Ig repertoire occurs through somatic hypermutation (SHM), gene conversion (GCV), and class switch recombination (CSR)-three processes that are initiated by activation-induced cytidine deaminase (AID). AID targets Ig genes at orders of magnitude higher than the rest of the genome, but the basis for this specificity is poorly understood. We have previously demonstrated that enhancers and enhancer-like sequences from Ig genes are capable of stimulating SHM of neighboring genes in a capacity distinct from their roles in increasing transcription. Here, we use an in vitro proteomics approach to identify E-box, MEF2, Ets, and Ikaros transcription factor family members as potential binders of these enhancers. ChIP assays in the hypermutating Ramos B cell line confirmed that many of these factors bound the endogenous Igλ enhancer and/or the IgH intronic enhancer (Eμ) in vivo. Further investigation using SHM reporter assays identified binding sites for E2A and MEF2B in Eμ and demonstrated an association between loss of factor binding and decreases in the SHM stimulating activity of Eμ mutants. Our results provide novel insights into trans-acting factors that dictate SHM targeting and link their activity to specific DNA binding sites within Ig enhancers.
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Affiliation(s)
- Ravi K Dinesh
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Benjamin Barnhill
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Anoj Ilanges
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Lizhen Wu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel A Michelson
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Filip Senigl
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, CZ-14220, Prague 4, Czech Republic
| | - Jukka Alinikula
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.,Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
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6
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Mediator contributes to IgH locus VDJ rearrangements by promoting usage of most distal V segments. Cell Mol Immunol 2018; 17:407-409. [PMID: 30405149 DOI: 10.1038/s41423-018-0175-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 11/08/2022] Open
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7
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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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8
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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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9
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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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10
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Saintamand A, Vincent-Fabert C, Garot A, Rouaud P, Oruc Z, Magnone V, Cogné M, Denizot Y. Deciphering the importance of the palindromic architecture of the immunoglobulin heavy-chain 3' regulatory region. Nat Commun 2016; 7:10730. [PMID: 26883548 PMCID: PMC4757795 DOI: 10.1038/ncomms10730] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/15/2016] [Indexed: 01/16/2023] Open
Abstract
The IgH 3' regulatory region (3'RR) controls class switch recombination (CSR) and somatic hypermutation (SHM) in B cells. The mouse 3'RR contains four enhancer elements with hs1,2 flanked by inverted repeated sequences and the centre of a 25-kb palindrome bounded by two hs3 enhancer inverted copies (hs3a and hs3b). hs4 lies downstream of the palindrome. In mammals, evolution maintained this unique palindromic arrangement, suggesting that it is functionally significant. Here we report that deconstructing the palindromic IgH 3'RR strongly affects its function even when enhancers are preserved. CSR and IgH transcription appear to be poorly dependent on the 3'RR architecture and it is more or less preserved, provided 3'RR enhancers are present. By contrast, a ‘palindromic effect' significantly lowers VH germline transcription, AID recruitment and SHM. In conclusion, this work indicates that the IgH 3'RR does not simply pile up enhancer units but also optimally exposes them into a functional architecture of crucial importance. The IgH 3' regulatory region contains an evolutionarily conserved palindromic sequence flanking important enhancer elements. Here the authors show that the palindrome is required for generating antibody diversity.
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Affiliation(s)
| | | | - Armand Garot
- Université de Limoges, CRIBL, UMR CNRS 7276, Limoges 87025, France
| | - Pauline Rouaud
- Université de Limoges, CRIBL, UMR CNRS 7276, Limoges 87025, France
| | - Zeliha Oruc
- Université de Limoges, CRIBL, UMR CNRS 7276, Limoges 87025, France
| | - Virginie Magnone
- CNRS et Université de Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Sophia Antipolis 06560, France
| | - Michel Cogné
- Université de Limoges, CRIBL, UMR CNRS 7276, Limoges 87025, France.,Institut Universitaire de France, Paris 75231, France
| | - Yves Denizot
- Université de Limoges, CRIBL, UMR CNRS 7276, Limoges 87025, France
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11
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Sequential activation and distinct functions for distal and proximal modules within the IgH 3' regulatory region. Proc Natl Acad Sci U S A 2016; 113:1618-23. [PMID: 26831080 DOI: 10.1073/pnas.1514090113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
As a master regulator of functional Ig heavy chain (IgH) expression, the IgH 3' regulatory region (3'RR) controls multiple transcription events at various stages of B-cell ontogeny, from newly formed B cells until the ultimate plasma cell stage. The IgH 3'RR plays a pivotal role in early B-cell receptor expression, germ-line transcription preceding class switch recombination, interactions between targeted switch (S) regions, variable region transcription before somatic hypermutation, and antibody heavy chain production, but the functional ranking of its different elements is still inaccurate, especially that of its evolutionarily conserved quasi-palindromic structure. By comparing relevant previous knockout (KO) mouse models (3'RR KO and hs3b-4 KO) to a novel mutant devoid of the 3'RR quasi-palindromic region (3'PAL KO), we pinpointed common features and differences that specify two distinct regulatory entities acting sequentially during B-cell ontogeny. Independently of exogenous antigens, the 3'RR distal part, including hs4, fine-tuned B-cell receptor expression in newly formed and naïve B-cell subsets. At mature stages, the 3'RR portion including the quasi-palindrome dictated antigen-dependent locus remodeling (global somatic hypermutation and class switch recombination to major isotypes) in activated B cells and antibody production in plasma cells.
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12
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Amin R, Marfak A, Pangault C, Oblet C, Chanut A, Tarte K, Denizot Y, Cogné M. The class-specific BCR tonic signal modulates lymphomagenesis in a c-myc deregulation transgenic model. Oncotarget 2015; 5:8995-9006. [PMID: 25229630 PMCID: PMC4253413 DOI: 10.18632/oncotarget.2297] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Deregulation of c-myc by translocation onto immunoglobulin (Ig) loci can promote B cell malignant proliferations with phenotypes as diverse as acute lymphoid leukemia, Burkitt lymphoma, diffuse large B cell lymphoma, myeloma… The B cell receptor (BCR) normally providing tonic signals for cell survival and mitogenic responses to antigens, can also contribute to lymphomagenesis upon sustained ligand binding or activating mutations. BCR signaling varies among cell compartments and BCR classes. For unknown reasons, some malignancies associate with expression of either IgM or class-switched Ig. We explored whether an IgA BCR, with strong tonic signaling, would affect lymphomagenesis in c-myc IgH 3′RR transgenic mice prone to lymphoproliferations. Breeding c-myc transgenics in a background where IgM expression was replaced with IgA delayed lymphomagenesis. By comparison to single c-myc transgenics, lymphomas from double mutant animals were more differentiated and less aggressive, with an altered transcriptional program. Larger tumor cells more often expressed CD43 and CD138, which culminated in a plasma cell phenotype in 10% of cases. BCR class-specific signals thus appear to modulate lymphomagenesis and may partly explain the observed association of specific Ig classes with human B cell malignancies of differential phenotype, progression and prognosis.
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Affiliation(s)
- Rada Amin
- Centre National de la Recherche Scientifique, Limoges, France. Université de Limoges, Limoges, France. INSERM UMR U917, Rennes, France
| | | | | | - Christelle Oblet
- Centre National de la Recherche Scientifique, Limoges, France. Université de Limoges, Limoges, France
| | - Aurélie Chanut
- Centre National de la Recherche Scientifique, Limoges, France. Université de Limoges, Limoges, France
| | | | - Yves Denizot
- Centre National de la Recherche Scientifique, Limoges, France. Université de Limoges, Limoges, France
| | - Michel Cogné
- Centre National de la Recherche Scientifique, Limoges, France. Université de Limoges, Limoges, France
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13
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14
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Marquet M, Garot A, Bender S, Carrion C, Rouaud P, Lecardeur S, Denizot Y, Cogné M, Pinaud E. The Eμ enhancer region influences H chain expression and B cell fate without impacting IgVH repertoire and immune response in vivo. THE JOURNAL OF IMMUNOLOGY 2014; 193:1171-83. [PMID: 24965776 DOI: 10.4049/jimmunol.1302868] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The IgH intronic enhancer region Eμ is a combination of both a 220-bp core enhancer element and two 310-350-bp flanking scaffold/matrix attachment regions named MARsEμ. In the mouse, deletion of the core-enhancer Eμ element mainly affects VDJ recombination with minor effects on class switch recombination. We carried out endogenous deletion of the full-length Eμ region (core plus MARsEμ) in the mouse genome to study VH gene repertoire and IgH expression in developing B-lineage cells. Despite a severe defect in VDJ recombination with partial blockade at the pro-B cell stage, Eμ deletion (core or full length) did not affect VH gene usage. Deletion of this regulatory region induced both a decrease of pre-B cell and newly formed B cell compartments and a strong orientation toward the marginal zone B cell subset. Because Igμ H chain expression was decreased in Eμ-deficient pre-B cells, we propose that modification of B cell homeostasis in deficient animals was caused by "weak" pre-B cell and BCR expression. Besides imbalances in B cell compartments, Ag-specific Ab responses were not impaired in animals carrying the Eμ deletion. In addition to its role in VDJ recombination, our study points out that the full-length Eμ region does not influence VH segment usage but ensures efficient Igμ-chain expression required for strong signaling through pre-B cells and newly formed BCRs and thus participates in B cell inflow and fate.
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Affiliation(s)
- Marie Marquet
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7276, Université de Limoges, 87025 Limoges, France
| | - Armand Garot
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7276, Université de Limoges, 87025 Limoges, France
| | - Sébastien Bender
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7276, Université de Limoges, 87025 Limoges, France; Centre Hospitalier Universitaire Dupuytren, Centre de Référence des Amyloses, 87042 Limoges, France; and
| | - Claire Carrion
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7276, Université de Limoges, 87025 Limoges, France
| | - Pauline Rouaud
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7276, Université de Limoges, 87025 Limoges, France
| | - Sandrine Lecardeur
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7276, Université de Limoges, 87025 Limoges, France
| | - Yves Denizot
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7276, Université de Limoges, 87025 Limoges, France
| | - Michel Cogné
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7276, Université de Limoges, 87025 Limoges, France; Institut Universitaire de France, 75005 Paris, France
| | - Eric Pinaud
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7276, Université de Limoges, 87025 Limoges, France;
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15
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Chen Z, Wang JH. Generation and repair of AID-initiated DNA lesions in B lymphocytes. Front Med 2014; 8:201-16. [PMID: 24748462 PMCID: PMC4039616 DOI: 10.1007/s11684-014-0324-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/30/2013] [Indexed: 01/12/2023]
Abstract
Activation-induced deaminase (AID) initiates the secondary antibody diversification process in B lymphocytes. In mammalian B cells, this process includes somatic hypermutation (SHM) and class switch recombination (CSR), both of which require AID. AID induces U:G mismatch lesions in DNA that are subsequently converted into point mutations or DNA double stranded breaks during SHM/CSR. In a physiological context, AID targets immunoglobulin (Ig) loci to mediate SHM/CSR. However, recent studies reveal genome-wide access of AID to numerous non-Ig loci. Thus, AID poses a threat to the genome of B cells if AID-initiated DNA lesions cannot be properly repaired. In this review, we focus on the molecular mechanisms that regulate the specificity of AID targeting and the repair pathways responsible for processing AID-initiated DNA lesions.
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Affiliation(s)
- Zhangguo Chen
- Integrated Department of Immunology, University of Colorado Anschutz Medical Campus and National Jewish Health, Denver, CO 80206
| | - Jing H. Wang
- Integrated Department of Immunology, University of Colorado Anschutz Medical Campus and National Jewish Health, Denver, CO 80206
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16
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Rouaud P, Vincent-Fabert C, Saintamand A, Fiancette R, Marquet M, Robert I, Reina-San-Martin B, Pinaud E, Cogné M, Denizot Y. The IgH 3' regulatory region controls somatic hypermutation in germinal center B cells. ACTA ACUST UNITED AC 2013; 210:1501-7. [PMID: 23825188 PMCID: PMC3727322 DOI: 10.1084/jem.20130072] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Somatic hypermutation in variable heavy chain rearranged regions is abrogated in the absence of the 3′ regulatory region enhancer, whereas transcription rate in the Ig heavy chain is only partially reduced. Interactions with cognate antigens recruit activated B cells into germinal centers where they undergo somatic hypermutation (SHM) in V(D)J exons for the generation of high-affinity antibodies. The contribution of IgH transcriptional enhancers in SHM is unclear. The Eμ enhancer upstream of Cμ has a marginal role, whereas the influence of the IgH 3′ regulatory region (3′RR) enhancers (hs3a, hs1,2, hs3b, and hs4) is controversial. To clarify the latter issue, we analyzed mice lacking the whole 30-kb extent of the IgH 3′RR. We show that SHM in VH rearranged regions is almost totally abrogated in 3′RR-deficient mice, whereas the simultaneous Ig heavy chain transcription rate is only partially reduced. In contrast, SHM in κ light chain genes remains unaltered, acquitting for any global SHM defect in our model. Beyond class switch recombination, the IgH 3′RR is a central element that controls heavy chain accessibility to activation-induced deaminase modifications including SHM.
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Affiliation(s)
- Pauline Rouaud
- Centre National de la Recherche Scientifique (CNRS) UMR 7276, Université de Limoges, 87025 Limoges, France
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17
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Jaszczur M, Bertram JG, Pham P, Scharff MD, Goodman MF. AID and Apobec3G haphazard deamination and mutational diversity. Cell Mol Life Sci 2012. [PMID: 23178850 DOI: 10.1007/s00018-012-1212-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Activation-induced deoxycytidine deaminase (AID) and Apobec 3G (Apo3G) cause mutational diversity by initiating mutations on regions of single-stranded (ss) DNA. Expressed in B cells, AID deaminates C → U in actively transcribed immunoglobulin (Ig) variable and switch regions to initiate the somatic hypermutation (SHM) and class switch recombination (CSR) that are essential for antibody diversity. Apo3G expressed in T cells catalyzes C deaminations on reverse transcribed cDNA causing HIV-1 retroviral inactivation. When operating properly, AID- and Apo3G-initiated mutations boost human fitness. Yet, both enzymes are potentially powerful somatic cell "mutators". Loss of regulated expression and proper genome targeting can cause human cancer. Here, we review well-established biological roles of AID and Apo3G. We provide a synopsis of AID partnering proteins during SHM and CSR, and describe how an Apo2 crystal structure provides "surrogate" insight for AID and Apo3G biochemical behavior. However, large gaps remain in our understanding of how dC deaminases search ssDNA to identify trinucleotide motifs to deaminate. We discuss two recent methods to analyze ssDNA scanning and deamination. Apo3G scanning and deamination is visualized in real-time using single-molecule FRET, and AID deamination efficiencies are determined with a random walk analysis. AID and Apo3G encounter many candidate deamination sites while scanning ssDNA. Generating mutational diversity is a principal aim of AID and an important ancillary property of Apo3G. Success seems likely to involve hit and miss deamination motif targeting, biased strongly toward miss.
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Affiliation(s)
- Malgorzata Jaszczur
- Departments of Biological Sciences and Chemistry, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089-2910, USA
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18
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Rouaud P, Vincent-Fabert C, Fiancette R, Cogné M, Pinaud E, Denizot Y. Enhancers located in heavy chain regulatory region (hs3a, hs1,2, hs3b, and hs4) are dispensable for diversity of VDJ recombination. J Biol Chem 2012; 287:8356-60. [PMID: 22270371 DOI: 10.1074/jbc.m112.341024] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
V(D)J recombination occurs during the antigen-independent early steps of B-cell ontogeny. Multiple IgH cis-regulatory elements control B-cell ontogeny. IGCR1 (intergenic control region 1), the DQ52 promoter/enhancer, and the intronic Emu enhancer, all three located upstream of Cmu, have important roles during V(D)J recombination, whereas there is no clue about a role of the IgH regulatory region (RR) encompassing the four transcriptional enhancers hs3a, hs1,2, hs3b, and hs4 during these early stages. To clarify the role of the RR in V(D)J recombination, we totally deleted it in the mouse genome. Here, we show that V(D)J recombination is unaffected by the complete absence of the IgH RR, highlighting that this region only orchestrates IgH locus activity during the late stages of B-cell differentiation. In contrast, the earliest antigen-independent steps of B-cell ontogeny would be under the control of only the upstream Cmu elements of the locus.
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Affiliation(s)
- Pauline Rouaud
- UMR CNRS 7276, Centre National de la Recherche Scientifique, Université de Limoges, 87025 Limoges Cedex, France
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19
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Abstract
Antibody maturation requires class switch recombination (CSR) and somatic hypermutation (SHM), both of which are initiated by activation-induced cytidine deaminase (AID). AID deaminates cytosine residues resulting in mismatches that are differentially processed to produce double-strand breaks in Ig switch (S) regions that lead to CSR, or to point mutations in variable (V) exons resulting in SHM. Although AID was first thought to be Ig-specific, recent work indicates that it also targets a diverse group of non-Ig loci, including genes such as Bcl6 and c-myc, whose modification by AID results in lymphoma-associated mutations and translocations. Here, we review the recent literature on AID targeting and the role for transcriptional stalling in recruitment of this enzyme to Ig and non-Ig loci. We propose a model for AID recruitment based on transcriptional stalling, which reconciles several of the key features of SHM, CSR, and lymphoma-associated translocation.
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Affiliation(s)
- Rushad Pavri
- Laboratory of Molecular Immunology, The Rockefeller University, New York, USA
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20
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Degner SC, Verma-Gaur J, Wong TP, Bossen C, Iverson GM, Torkamani A, Vettermann C, Lin YC, Ju Z, Schulz D, Murre CS, Birshtein BK, Schork NJ, Schlissel MS, Riblet R, Murre C, Feeney AJ. CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells. Proc Natl Acad Sci U S A 2011; 108:9566-71. [PMID: 21606361 PMCID: PMC3111298 DOI: 10.1073/pnas.1019391108] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Compaction and looping of the ~2.5-Mb Igh locus during V(D)J rearrangement is essential to allow all V(H) genes to be brought in proximity with D(H)-J(H) segments to create a diverse antibody repertoire, but the proteins directly responsible for this are unknown. Because CCCTC-binding factor (CTCF) has been demonstrated to be involved in long-range chromosomal interactions, we hypothesized that CTCF may promote the contraction of the Igh locus. ChIP sequencing was performed on pro-B cells, revealing colocalization of CTCF and Rad21 binding at ~60 sites throughout the V(H) region and 2 other sites within the Igh locus. These numerous CTCF/cohesin sites potentially form the bases of the multiloop rosette structures at the Igh locus that compact during Ig heavy chain rearrangement. To test whether CTCF was involved in locus compaction, we used 3D-FISH to measure compaction in pro-B cells transduced with CTCF shRNA retroviruses. Reduction of CTCF binding resulted in a decrease in Igh locus compaction. Long-range interactions within the Igh locus were measured with the chromosomal conformation capture assay, revealing direct interactions between CTCF sites 5' of DFL16 and the 3' regulatory region, and also the intronic enhancer (Eμ), creating a D(H)-J(H)-Eμ-C(H) domain. Knockdown of CTCF also resulted in the increase of antisense transcription throughout the D(H) region and parts of the V(H) locus, suggesting a widespread regulatory role for CTCF. Together, our findings demonstrate that CTCF plays an important role in the 3D structure of the Igh locus and in the regulation of antisense germline transcription and that it contributes to the compaction of the Igh locus.
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MESH Headings
- Animals
- Binding Sites/genetics
- Blotting, Western
- CCCTC-Binding Factor
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line
- Cells, Cultured
- Chromatin Immunoprecipitation
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA, Antisense/genetics
- DNA-Binding Proteins
- Enhancer Elements, Genetic/genetics
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Heavy Chains/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Precursor Cells, B-Lymphoid/metabolism
- Protein Binding
- RNA Interference
- RNA, Antisense/genetics
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Transcription, Genetic
- Cohesins
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Affiliation(s)
- Stephanie C. Degner
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Jiyoti Verma-Gaur
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Timothy P. Wong
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Claudia Bossen
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
| | | | - Ali Torkamani
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, and The Scripps Translational Science Institute, La Jolla, CA 92037
| | - Christian Vettermann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and
| | - Yin C. Lin
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
| | - Zhongliang Ju
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Danae Schulz
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and
| | - Caroline S. Murre
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
| | - Barbara K. Birshtein
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Nicholas J. Schork
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, and The Scripps Translational Science Institute, La Jolla, CA 92037
| | - Mark S. Schlissel
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and
| | - Roy Riblet
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121
| | - Cornelis Murre
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
| | - Ann J. Feeney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
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21
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Pinaud E, Marquet M, Fiancette R, Péron S, Vincent-Fabert C, Denizot Y, Cogné M. The IgH locus 3' regulatory region: pulling the strings from behind. Adv Immunol 2011; 110:27-70. [PMID: 21762815 DOI: 10.1016/b978-0-12-387663-8.00002-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antigen receptor gene loci are among the most complex in mammals. The IgH locus, encoding the immunoglobulin heavy chain (IgH) in B-lineage cells, undergoes major transcription-dependent DNA remodeling events, namely V(D)J recombination, Ig class-switch recombination (CSR), and somatic hypermutation (SHM). Various cis-regulatory elements (encompassing promoters, enhancers, and chromatin insulators) recruit multiple nuclear factors in order to ensure IgH locus regulation by tightly orchestrated physical and/or functional interactions. Among major IgH cis-acting regions, the large 3' regulatory region (3'RR) located at the 3' boundary of the locus includes several enhancers and harbors an intriguing quasi-palindromic structure. In this review, we report progress insights made over the past decade in order to describe in more details the structure and functions of IgH 3'RRs in mouse and human. Generation of multiple cellular, transgenic and knock-out models helped out to decipher the function of the IgH 3' regulatory elements in the context of normal and pathologic B cells. Beside its interest in physiology, the challenge of elucidating the locus-wide cross talk between distant cis-regulatory elements might provide useful insights into the mechanisms that mediate oncogene deregulation after chromosomal translocations onto the IgH locus.
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Affiliation(s)
- Eric Pinaud
- UMR CNRS 6101, Centre National de la Recherche Scientifique, Université de Limoges, Limoges, France
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22
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Li F, Yan Y, Pieretti J, Feldman DA, Eckhardt LA. Comparison of identical and functional Igh alleles reveals a nonessential role for Eμ in somatic hypermutation and class-switch recombination. THE JOURNAL OF IMMUNOLOGY 2010; 185:6049-57. [PMID: 20937850 DOI: 10.4049/jimmunol.0902992] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Somatic hypermutation (SHM), coupled with Ag selection, provides a mechanism for generating Abs with high affinity for invading pathogens. Class-switch recombination (CSR) ensures that these Abs attain pathogen-appropriate effector functions. Although the enzyme critical to both processes, activation-induced cytidine deaminase, has been identified, it remains unclear which cis-elements within the Ig loci are responsible for recruiting activation-induced cytidine deaminase and promoting its activity. Studies showed that Ig gene-transcription levels are positively correlated with the frequency of SHM and CSR, making the intronic, transcriptional enhancer Eμ a likely contributor to both processes. Tests of this hypothesis yielded mixed results arising, in part, from the difficulty in studying B cell function in mice devoid of Eμ. In Eμ's absence, V(H) gene assembly is dramatically impaired, arresting B cell development. The current study circumvented this problem by modifying the murine Igh locus through simultaneous insertion of a fully assembled V(H) gene and deletion of Eμ. The behavior of this allele was compared with that of a matched allele carrying the same V(H) gene but with Eμ intact. Although IgH transcription was as great or greater on the Eμ-deficient allele, CSR and SHM were consistently, but modestly, reduced relative to the allele in which Eμ remained intact. We conclude that Eμ contributes to, but is not essential for, these complex processes and that its contribution is not as a transcriptional enhancer but, rather, is at the level of recruitment and/or activation of the SHM/CSR machinery.
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Affiliation(s)
- Fubin Li
- Department of Biological Sciences, Hunter College and Graduate Center, City University of New York, New York, NY 10065, USA
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23
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Abstract
In response to an assault by foreign organisms, peripheral B cells can change their antibody affinity and isotype by somatically mutating their genomic DNA. The ability of a cell to modify its DNA is exceptional in light of the potential consequences of genetic alterations to cause human disease and cancer. Thus, as expected, this mechanism of antibody diversity is tightly regulated and coordinated through one protein, activation-induced deaminase (AID). AID produces diversity by converting cytosine to uracil within the immunoglobulin loci. The deoxyuracil residue is mutagenic when paired with deoxyguanosine, since it mimics thymidine during DNA replication. Additionally, B cells can manipulate the DNA repair pathways so that deoxyuracils are not faithfully repaired. Therefore, an intricate balance exists which is regulated at multiple stages to promote mutation of immunoglobulin genes, while retaining integrity of the rest of the genome. Here we discuss and summarize the current understanding of how AID functions to cause somatic hypermutation.
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Affiliation(s)
- Robert W Maul
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
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24
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Genomic deletion of the whole IgH 3' regulatory region (hs3a, hs1,2, hs3b, and hs4) dramatically affects class switch recombination and Ig secretion to all isotypes. Blood 2010; 116:1895-8. [PMID: 20538806 DOI: 10.1182/blood-2010-01-264689] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The immunoglobulin heavy chain locus (IgH) undergoes multiple changes along B-cell differentiation. In progenitor B cells, V(D)J assembly allows expression of μ heavy chains. In mature B cells, class switch recombination may replace the expressed constant (C)μ gene with a downstream C(H) gene. Finally, plasma cell differentiation strongly boosts IgH transcription. How the multiple IgH transcriptional enhancers tune these changes is unclear. Here we demonstrate that deletion of the whole IgH 3' regulatory region (3'RR) allows normal maturation until the stage of IgM/IgD expressing lymphocytes, but nearly abrogates class switch recombination to all C(H) genes. Although plasma cell numbers are unaffected, we reveal the role of the 3'RR into the transcriptional burst normally associated with plasma cell differentiation. Our study shows that transcriptional changes and recombinations occurring after antigen-encounter appear mainly controlled by the 3'RR working as a single functional unit.
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25
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Bébin AG, Carrion C, Marquet M, Cogné N, Lecardeur S, Cogné M, Pinaud E. In vivo redundant function of the 3' IgH regulatory element HS3b in the mouse. THE JOURNAL OF IMMUNOLOGY 2010; 184:3710-7. [PMID: 20176739 DOI: 10.4049/jimmunol.0901978] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In the mouse, the regulatory region located at the 3' end of the IgH locus includes four transcriptional enhancers: HS3a, HS1-2, HS3b, and HS4; the first three lie in a quasi-palindromic structure. Although the upstream elements HS3a and HS1-2 proved dispensable for Ig expression and class switch recombination (CSR), the joint deletion of HS3b and HS4 led to a consistent decrease in IgH expression in resting B cells and to a major CSR defect. Within this pair of distal enhancers, it was questionable whether HS3b and HS4 could be considered individually as elements critical for IgH expression and/or CSR. Studies in HS4-deficient mice recently revealed the role of HS4 as restricted to Igmicro-chain expression from the pre-B to the mature B cell stage and left HS3b as the last candidate for CSR regulation. Our present study finally invalidates the hypothesis that CSR could mostly rely on HS3b itself. B cells from HS3b-deficient animals undergo normal proliferation, germline transcription, and CSR upon in vitro stimulation with LPS; in vivo Ag-specific responses are not affected. In conclusion, our study highlights a major effect of the global ambiance of the IgH locus; enhancers demonstrated as being strongly synergistic in transgenes turn out to be redundant in their endogenous context.
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Affiliation(s)
- Anne-Gaëlle Bébin
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche, Université de Limoges, Limoges, France
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26
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Dunnick WA, Collins JT, Shi J, Westfield G, Fontaine C, Hakimpour P, Papavasiliou FN. Switch recombination and somatic hypermutation are controlled by the heavy chain 3' enhancer region. ACTA ACUST UNITED AC 2009; 206:2613-23. [PMID: 19887393 PMCID: PMC2806627 DOI: 10.1084/jem.20091280] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Both class switch recombination (CSR) and somatic hypermutation (SHM) require transcription and the trans-acting factor activation-induced cytidine deaminase (AID), and must be up-regulated during antigen-dependent differentiation of B lymphocytes. To test the role of the heavy chain 3′ enhancers in both CSR and SHM, we used a BAC transgene of the entire heavy chain constant region locus. Using Cre-loxP recombination to delete a 28-kb region that contains the four known 3′ heavy chain enhancers, we isolated lines of BAC transgenic mice with an intact heavy chain locus and paired lines in the same chromosomal insertion site lacking the 3′ enhancers. Intact heavy chain transgenes undergo CSR to all heavy chain genes and mutate their transgenic VDJ exon. In paired transgenes lacking the 3′ enhancer region, CSR to most heavy chain genes is reduced to ∼1% of the levels for intact heavy chain loci; SHM is also reduced. Finally, we find that in B cells with a transgene lacking the 3′ enhancers, interchromosomal recombination between the transgenic VDJ exon and the endogenous heavy chain C genes is more easily detected than CSR within the transgene.
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Affiliation(s)
- Wesley A Dunnick
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48103, USA
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27
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Perlot T, Alt FW. Cis-regulatory elements and epigenetic changes control genomic rearrangements of the IgH locus. Adv Immunol 2009; 99:1-32. [PMID: 19117530 DOI: 10.1016/s0065-2776(08)00601-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Immunoglobulin variable region exons are assembled from discontinuous variable (V), diversity (D), and joining (J) segments by the process of V(D)J recombination. V(D)J rearrangements of the immunoglobulin heavy chain (IgH) locus are tightly controlled in a tissue-specific, ordered and allele-specific manner by regulating accessibility of V, D, and J segments to the recombination activating gene proteins which are the specific components of the V(D)J recombinase. In this review we discuss recent advances and established models brought forward to explain the mechanisms underlying accessibility control of V(D)J recombination, including research on germline transcripts, spatial organization, and chromatin modifications of the immunoglobulin heavy chain (IgH) locus. Furthermore, we review the functions of well-described and potential new cis-regulatory elements with regard to processes such as V(D)J recombination, allelic exclusion, and IgH class switch recombination.
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Affiliation(s)
- Thomas Perlot
- The Howard Hughes Medical Institute, The Children's Hospital, Immune Disease Institute, Harvard Medical School, Boston, Massachusetts, USA
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28
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Kim Y, Tian M. NF-kappaB family of transcription factor facilitates gene conversion in chicken B cells. Mol Immunol 2009; 46:3283-91. [PMID: 19699530 DOI: 10.1016/j.molimm.2009.07.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 07/26/2009] [Indexed: 12/21/2022]
Abstract
Activation-induced cytidine deaminase (AID) is critical for immunoglobulin (Ig) diversification in B cells. The majority of evidence supports the model that AID modifies Ig genes at the DNA level by deaminating cytosines into uracils. The mutagenic activity is largely restricted to Ig genes to avoid genomic damage in general, but the underlying mechanism is not understood. We addressed this question in chicken B cell line DT40. We characterized a regulatory region within the Iglambda locus. This regulatory region is important for AID-mediated gene conversion at the Iglambda locus, and is capable of targeting AID activity to ectopic loci. This regulatory region contains binding sites for transcription factors NF-kappaB, Mef2 and octamer binding proteins. Mutation of these binding sites or ablation of NF-kappaB family member, p50 or c-Rel, impairs the AID targeting function of this regulatory region. These results suggest that NF-kappaB family of transcription factors contribute to AID-mediated gene conversion.
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Affiliation(s)
- Yonghwan Kim
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station, Austin, TX 78712, USA
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Vincent-Fabert C, Truffinet V, Fiancette R, Cogné N, Cogné M, Denizot Y. Ig synthesis and class switching do not require the presence of the hs4 enhancer in the 3' IgH regulatory region. THE JOURNAL OF IMMUNOLOGY 2009; 182:6926-32. [PMID: 19454689 DOI: 10.4049/jimmunol.0900214] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Several studies have reported that regulatory elements located 3' of the IgH locus (namely hs3a, hs1,2, hs3b, and hs4) might play a role during class switch recombination (CSR) and Ig synthesis. While individual deletion of hs3a or hs1,2 had no effect, pairwise deletion of hs3b (an inverted copy of hs3a) and hs4 markedly affected CSR and Ig expression. Among these two elements, hs4 was tentatively presented with the master role due to its unique status within the 3' regulatory region: distal position outside repeated regions, early activation in pre-B cells, strong activity throughout B cell ontogeny. To clarify its role, we generated mice with a clean deletion of the hs4 after replacement with a floxed neo(R) cassette. Surprisingly, and as for previous deletion of hs3a or hs1,2, deletion of hs4 did not affect either in vivo CSR or the secretion level of any Ig isotype. In vitro CSR and Ig secretion in response to LPS and cytokines was not affected either. The only noticeable effects of the hs4 deletion were a decrease in the number of B splenocytes and a decreased membrane IgM expression. In conclusion, while dispensable for CSR and Ig transcription in plasma cells, hs4 mostly appears to contribute to Ig transcription in resting B lymphocytes.
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Affiliation(s)
- Christelle Vincent-Fabert
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 6101, Université de Limoges, France
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30
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Peled JU, Kuang FL, Iglesias-Ussel MD, Roa S, Kalis SL, Goodman MF, Scharff MD. The biochemistry of somatic hypermutation. Annu Rev Immunol 2008; 26:481-511. [PMID: 18304001 DOI: 10.1146/annurev.immunol.26.021607.090236] [Citation(s) in RCA: 368] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Affinity maturation of the humoral response is mediated by somatic hypermutation of the immunoglobulin (Ig) genes and selection of higher-affinity B cell clones. Activation-induced cytidine deaminase (AID) is the first of a complex series of proteins that introduce these point mutations into variable regions of the Ig genes. AID deaminates deoxycytidine residues in single-stranded DNA to deoxyuridines, which are then processed by DNA replication, base excision repair (BER), or mismatch repair (MMR). In germinal center B cells, MMR, BER, and other factors are diverted from their normal roles in preserving genomic integrity to increase diversity within the Ig locus. Both AID and these components of an emerging error-prone mutasome are regulated on many levels by complex mechanisms that are only beginning to be elucidated.
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Affiliation(s)
- Jonathan U Peled
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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31
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Truffinet V, Pinaud E, Cogné N, Petit B, Guglielmi L, Cogné M, Denizot Y. The 3' IgH locus control region is sufficient to deregulate a c-myc transgene and promote mature B cell malignancies with a predominant Burkitt-like phenotype. THE JOURNAL OF IMMUNOLOGY 2007; 179:6033-42. [PMID: 17947677 DOI: 10.4049/jimmunol.179.9.6033] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Burkitt lymphoma (BL) features translocations linking c-myc to an Ig locus. Breakpoints in the H chain locus (IgH) stand either close to J(H) or within switch regions and always link c-myc to the 3' IgH locus control region (3' LCR). To test the hypothesis that the 3' LCR alone was sufficient to deregulate c-myc, we generated mice carrying a 3' LCR-driven c-myc transgene and specifically up-regulating c-myc in B cells. Splenic B cells from mice proliferated exaggeratedly in response to various signals had an elevated apoptosis rate but normal B220/IgM/IgD expression. Although all Ig levels were lowered in vivo, class switching and Ig secretion proved normal in vitro. Beginning at the age of 12 wk, transgenic mice developed clonal lymphoblastic lymphomas or diffuse anaplastic plasmacytomas with an overall incidence of 80% by 40 wk. Lymphoblastic lymphomas were B220(+)IgM(+)IgD(+) with the BL "starry sky" appearance. Gene expression profiles revealed broad alterations in the proliferation program and the Ras-p21 pathway. Our study demonstrates that 3' IgH enhancers alone can deregulate c-myc and initiate the development of BL-like lymphomas. The rapid and constant occurrence of lymphoma in this model makes it valuable for the understanding and the potential therapeutic manipulation of c-myc oncogenicity in vivo.
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Affiliation(s)
- Véronique Truffinet
- Unité Mixte de Recherche, Centre National de la Recherche Scientifique 6101, Université de Limoges, Limoges, France
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32
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Yan Y, Park SS, Janz S, Eckhardt LA. In a model of immunoglobulin heavy-chain (IGH)/MYC translocation, the Igh 3' regulatory region induces MYC expression at the immature stage of B cell development. Genes Chromosomes Cancer 2007; 46:950-9. [PMID: 17639584 PMCID: PMC2742353 DOI: 10.1002/gcc.20480] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Reciprocal translocations involving the immunoglobulin loci and the cellular oncogene MYC are hallmark mutations of the human postgerminal center B cell neoplasm, Burkitt's lymphoma. They are occasionally found in other B cell lymphomas, as well. Translocations involving the heavy chain locus (IGH) place the MYC gene either in cis with both the intronic enhancer Emu and the IGH 3' regulatory region (3'RR) or in cis with only the 3'RR. The result is deregulated MYC expression. Recent studies have led to some controversy as to when, during B lymphocyte development, IGH/MYC chromosome translocations take place. A related issue, relevant not only to lymphoma development but also to normal controls on IGH gene expression, is the stage, during B lymphocyte development, at which the 3'RR is capable of activating MYC expression. We have developed mice transgenic for a human MYC (hMYC) gene under control of the four core enhancers from the mouse Igh 3'RR. Unlike other transgenic mouse models where premature and inappropriate MYC expression disrupts normal B cell development, the hMYC transgene in these studies carries a mutation that prohibits MYC protein synthesis. As a result, hMYC expression can be analyzed in all of the normal B cell compartments. Our data show that hMYC is expressed almost exclusively in B-lineage cells and is induced to high levels as soon as bone marrow cells reach the immature B cell stage.
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Affiliation(s)
- Yi Yan
- Department of Biological Sciences, Hunter College and Graduate Center of the City University of New York, New York, NY, USA
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33
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Ohm-Laursen L, Barington T. Analysis of 6912 unselected somatic hypermutations in human VDJ rearrangements reveals lack of strand specificity and correlation between phase II substitution rates and distance to the nearest 3' activation-induced cytidine deaminase target. THE JOURNAL OF IMMUNOLOGY 2007; 178:4322-34. [PMID: 17371989 DOI: 10.4049/jimmunol.178.7.4322] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The initial event of somatic hypermutation (SHM) is the deamination of cytidine residues by activation-induced cytidine deaminase (AID). Deamination is followed by the replication over uracil and/or different error-prone repair events. We sequenced 659 nonproductive human IgH rearrangements (IGHV3-23*01) from blood B lymphocytes enriched for CD27-positive memory cells. Analyses of 6,912 unique, unselected substitutions showed that in vivo hot and cold spots for the SHM of C and G residues corresponded closely to the target preferences reported for AID in vitro. A detailed analysis of all possible four-nucleotide motifs present on both strands of the V(H) gene showed significant correlations between the substitution frequencies in reverse complementary motifs, suggesting that the SHM machinery targets both strands equally well. An analysis of individual J(H) and D gene segments showed that the substitution frequencies in the individual motifs were comparable to the frequencies found in the V(H) gene. Interestingly, J(H)6-carrying sequences were less likely to undergo SHM (average 15.2 substitutions per V(H) region) than sequences using J(H)4 (18.1 substitutions, p = 0.03). We also found that the substitution rates in G and T residues correlated inversely with the distance to the nearest 3' WRC AID hot spot motif on both the nontranscribed and transcribed strands. This suggests that phase II SHM takes place 5' of the initial AID deamination target and primarily targets T and G residues or, alternatively, the corresponding A and C residues on the opposite strand.
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Affiliation(s)
- Line Ohm-Laursen
- Department of Clinical Immunology, Odense University Hospital, 5000 Odense C, Denmark
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34
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Li Z, Luo Z, Ronai D, Kuang FL, Peled JU, Iglesias-Ussel MD, Scharff MD. Targeting AID to the Ig genes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 596:93-109. [PMID: 17338179 DOI: 10.1007/0-387-46530-8_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ziqiang Li
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York 10461, USA
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35
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Laurencikiene J, Tamosiunas V, Severinson E. Regulation of epsilon germline transcription and switch region mutations by IgH locus 3' enhancers in transgenic mice. Blood 2006; 109:159-67. [PMID: 16968901 DOI: 10.1182/blood-2006-02-005355] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Germline (GL) transcription is regulated by specific promoters and immunoglobulin heavy chain (IgH) 3' locus enhancers and is necessary for Ig class-switch recombination (CSR). We have generated different transgenic lines containing the GL epsilon promoter, switch (S) epsilon region, and constant (C) epsilon region with or without the DNase I-sensitive regions (HS) 3A-HS1,2 or HS3B-HS4 3' IgH enhancer pairs. The enhancerless construct was expressed in B cells activated by interleukin (IL)-4 and CD40, thus resembling regulation of the endogenous gene. Both enhancer-containing transgenes efficiently increased expression in B cells and were strongly up-regulated by stimuli. In addition, Sepsilon regions of the transgene containing HS3B-HS4 were mutated in activated, sorted B cells. Such mutations are known to precede CSR and are dependent on activation-induced cytidine deaminase (AID). Our findings show that all elements necessary for recruitment of the recombination machinery are present in the transgene containing HS3 and HS4. These enhancers probably provide something more specific than mere increased accessibility of switch regions. We propose that transcription factors binding the enhancers help to target the recombination machinery to the switch regions.
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Affiliation(s)
- Jurga Laurencikiene
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
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36
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Abstract
Somatic hypermutation (SHM) introduces mutations in the variable region of immunoglobulin genes at a rate of approximately 10(-3) mutations per base pair per cell division, which is 10(6)-fold higher than the spontaneous mutation rate in somatic cells. To ensure genomic integrity, SHM needs to be targeted specifically to immunoglobulin genes. The rare mistargeting of SHM can result in mutations and translocations in oncogenes, and is thought to contribute to the development of B-cell malignancies. Despite years of intensive investigation, the mechanism of SHM targeting is still unclear. We review and attempt to reconcile the numerous and sometimes conflicting studies on the targeting of SHM to immunoglobulin loci, and highlight areas that hold promise for further investigation.
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Affiliation(s)
- Valerie H Odegard
- VaxInnate Corporation, 300 George Street, Suite 311, New Haven, Connecticut 06511, USA
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37
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Bransteitter R, Sneeden JL, Allen S, Pham P, Goodman MF. First AID (activation-induced cytidine deaminase) is needed to produce high affinity isotype-switched antibodies. J Biol Chem 2006; 281:16833-16836. [PMID: 16624806 DOI: 10.1074/jbc.r600006200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Ronda Bransteitter
- Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089-2910
| | - Jessica L Sneeden
- Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089-2910
| | - Sariah Allen
- Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089-2910
| | - Phuong Pham
- Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089-2910
| | - Myron F Goodman
- Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089-2910.
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Franklin A. Hypothesis: a biological role for germline transcription in the mechanism of V(D)J recombination--implications for initiation of allelic exclusion. Immunol Cell Biol 2006; 84:396-403. [PMID: 16594898 DOI: 10.1111/j.1440-1711.2006.01437.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sequences that encode the antigen-binding sites of IgH and IgL chains - variable (V), diversity (D, H chain loci only) and joining (J) sequences - are configured as separate DNA segments at the germline level. Expression of an Ig molecule requires V(D)J assembly. Productive V(D)J recombination is monoallelic. How rearrangement is initiated differentially at maternal and paternal alleles is unclear. The products of recombination activating gene (RAG)1 and RAG2 mediate rearrangement by cleaving the DNA between an unrearranged gene segment and adjacent recombination signal sequences (RSS). It is proposed that supercoiling generated during germline transcription at Ig loci (which occurs concomitantly with rearrangement) is required at RSS for RAG1/2 recognition. Rearrangement might hence initiate sequentially at maternal and paternal alleles where deregulated germline transcription causes RAG1/2 recognition of RSS to become stochastic.
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Affiliation(s)
- Andrew Franklin
- Biocontrol Group, School of Botany and Zoology, Australian National University, Canberra, Australian Capital Territory, Australia.
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39
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Komori A, Xu Z, Wu X, Zan H, Casali P. Biased dA/dT somatic hypermutation as regulated by the heavy chain intronic iEmu enhancer and 3'Ealpha enhancers in human lymphoblastoid B cells. Mol Immunol 2006; 43:1817-26. [PMID: 16412510 PMCID: PMC4621958 DOI: 10.1016/j.molimm.2005.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Accepted: 10/28/2005] [Indexed: 12/18/2022]
Abstract
Somatic hypermutation (SHM) in immunoglobulin gene (Ig) variable (V) regions is critical for the maturation of the antibody response. It is dependent on the expression of activation-induced cytidine deaminase (AID) and translesion DNA polymerases in germinal center B cells as well as Ig V transcription, as regulated by the Ig heavy chain (H) intronic enhancer (iEmu) and the 3' enhancer (3'Ealpha) region. We analyzed the role of these cis elements in SHM by stably transfecting Ramos human lymphoblastoid B cells with a rearranged human IgH chain VD (diversity) J (joining) DNA construct containing a V(H) promoter at the 5' end and C(H)1 and C(H)2 exons of Cgamma1 at the 3' end. In this construct, mutations preferentially targeted dA/dT basepairs in the RGYW/WRCY hotspot. Most of the dA/dT mutations and accompanying dC/dG mutations were transitions. Deletion of iEmu resulted in decreased SHM which could be partially restored by insertion of the IgH hs1,2 enhancer. Other two 3'Ealpha enhancers, hs3-hs4, did not significantly increase the mutation frequency, but further strengthened the dA/dT bias. The frequency and spectrum of the mutations were independent of the genomic integration of the transgene or V gene transcription level. Thus, we have established a novel in vitro system to analyze SHM and identify the role of multiple cis-regulatory elements in regulating dA/dT biased SHM. This model system will be useful to further address the role of other cis-regulating elements and recruited trans-acting factors in expressing the modalities of SHM.
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Affiliation(s)
| | | | | | | | - Paolo Casali
- Corresponding author. Tel.: +1 949 824 4456; fax: +1 949 824 2305. (P. Casali)
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40
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Perlot T, Alt FW, Bassing CH, Suh H, Pinaud E. Elucidation of IgH intronic enhancer functions via germ-line deletion. Proc Natl Acad Sci U S A 2005; 102:14362-7. [PMID: 16186486 PMCID: PMC1242331 DOI: 10.1073/pnas.0507090102] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Studies of chimeric mice demonstrated that the core Ig heavy chain (IgH) intronic enhancer (iEmu) functions in V(D)J and class switch recombination at the IgH locus. To more fully evaluate the role of this element in these and other processes, we generated mice homozygous for germ-line mutations in which the core sequences of iEmu (cEmu) were either deleted (cEmu(Delta/Delta) mice) or replaced with a pgk-Neo(R) cassette (cEmu(N/N) mice). The cEmu(Delta/Delta) mice had reduced B cell numbers, in association with impaired D to J(H) and V(H) to DJ(H) rearrangement, whereas cEmu(N/N) mice had a complete block in IgH V(D)J(H) recombination, confirming that additional cis elements cooperate with iEmu to enforce D to J(H) recombination. In addition, developing cEmu(Delta/Delta) and cEmu(N/N) B lineage cells had correspondingly decreased levels of germ-line transcripts from the J(H) region of the IgH locus (mu0 and Imu transcripts); although both had normal levels of germ-line V(H) transcripts, suggesting that cEmu may influence IgH locus V(D)J recombination by influencing accessibility of J(H) proximal regions of the locus. Consistent with chimera studies, peripheral cEmu(Delta/Delta) B cells had normal surface Ig and relatively normal class switch recombination. However, cEmu(Delta/Delta) B cells also had relatively normal somatic hypermutation of their IgH variable region genes, showing unexpectedly that the cEmu is not required for this process. The availability of mice with the iEmu mutation in their germ line will facilitate future studies to elucidate the roles of iEmu in V(H)(D)J(H) recombination in the context of IgH chromatin structure and germ-line transcription.
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Affiliation(s)
- Thomas Perlot
- The CBR Institute for Biomedical Research, Inc., and Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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41
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Ronai D, Iglesias-Ussel MD, Fan M, Shulman MJ, Scharff MD. Complex regulation of somatic hypermutation by cis-acting sequences in the endogenous IgH gene in hybridoma cells. Proc Natl Acad Sci U S A 2005; 102:11829-34. [PMID: 16087866 PMCID: PMC1188009 DOI: 10.1073/pnas.0505449102] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To create high-affinity antibodies, B cells target a high rate of somatic hypermutation (SHM) to the Ig variable-region genes that encode the antigen-binding site. This mutational process requires transcription and is triggered by activation-induced cytidine deaminase (AID), which converts deoxycytidine to deoxyuridine. Mistargeting of AID to non-Ig genes is thought to result in the malignant transformation of B cells, but the mechanism responsible for targeting SHM to certain DNA regions and not to others is largely unknown. Cis-acting elements have been proposed to play a role in directing the hypermutation machinery, but the motifs required for targeting SHM have been difficult to identify because many of the candidate elements, such as promoters or enhancers, are also required for transcription of Ig genes. Here we describe a system in cultured hybridoma cells in which transcription of the endogenous heavy-chain Ig gene continues in the absence of the core intronic enhancer (Emu) and its flanking matrix attachment regions (MARs). When AID is expressed in these cells, SHM occurred at the WT frequency even when Emu and the MARs were absent together. Interestingly, SHM occurred at less than the WT frequency when Emu or the MARs were individually absent. Our results suggest that these intronic regulatory elements can exert a complex influence on SHM that is separable from their role in regulating transcription.
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Affiliation(s)
- Diana Ronai
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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Kim EC, Edmonston CR, Wu X, Schaffer A, Casali P. The HoxC4 homeodomain protein mediates activation of the immunoglobulin heavy chain 3' hs1,2 enhancer in human B cells. Relevance to class switch DNA recombination. J Biol Chem 2004; 279:42258-69. [PMID: 15252056 PMCID: PMC4631311 DOI: 10.1074/jbc.m407496200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The immunoglobulin heavy chain (IgH) 3' regulatory region modulates IgH locus transcription, upon induction by specific trans-acting factors, and plays a significant role in class switch DNA recombination (CSR) and, perhaps, somatic hypermutation (SHM). CSR and SHM are central to the maturation of the antibody response. In contrast to the single 5'-hs3a-hs1,2-hs3b-hs4-3 ' mouse IgH 3 ' regulatory region, the human IgH 3 ' regulatory region exists as a 5'-hs3-hs1,2-hs4-3' cluster duplicated 3 ' of Calpha1 and Calpha2. We show here that the human hs1,2 element is the strongest enhancer of transcription, as directed by a V(H)1 or the ECS-Igamma3 promoter, thereby suggesting a dominant role for hs1,2 over hs3 and hs4 in the overall activity of the 3 ' regulatory region. Within hs1,2, we identified three regions (1, 2, and 3) that are all necessary, but individually not sufficient, for enhancement of transcription. In region 2, a HoxC4 site and a HoxC4/embedded octamer (HoxC4/Oct) site are conserved across human, mouse, rat, and rabbit. These two sites recruit HoxC4 and Oct-1/Oct-2, which act synergistically with the Oca-B coactivator to effect the full hs1,2-enhancing activity. HoxC4, Oct-1/Oct-2, and Oca-B recruitment is negligible in pro-B cells, moderate in pre-B cells, and maximal in germinal center B cells and plasma cells, where HoxC4, Oct-2, and Oca-B expression correlates with hs1,2 activation and ongoing CSR. The hs1,2mediated enhancement of V(H) and C(H) promoter-driven transcription as induced by HoxC4 and Oct-1/Oct-2 suggests an important role of these homeodomain proteins in the overall regulation of the IgH locus expression.
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Affiliation(s)
| | | | | | | | - Paolo Casali
- To whom correspondence should be addressed: Center for Immunology, 3028 Hewitt Hall, University of California, Irvine, CA 92697-4120. Tel.: 949-824-9648;
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43
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Li Z, Woo CJ, Iglesias-Ussel MD, Ronai D, Scharff MD. The generation of antibody diversity through somatic hypermutation and class switch recombination. Genes Dev 2004; 18:1-11. [PMID: 14724175 DOI: 10.1101/gad.1161904] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ziqiang Li
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York 10461, USA
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44
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Sepulveda MA, Emelyanov AV, Birshtein BK. NF-κB and Oct-2 Synergize to Activate the Human 3′ Igh hs4 Enhancer in B Cells. THE JOURNAL OF IMMUNOLOGY 2004; 172:1054-64. [PMID: 14707079 DOI: 10.4049/jimmunol.172.2.1054] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In B cells, the Igh gene locus contains several DNase I-hypersensitive (hs) sites with enhancer activity. These include the 3' Igh enhancers, which are located downstream of the Calpha gene(s) in both mouse and human. In vivo experiments have implicated murine 3' enhancers, hs3B and/or hs4, in class switching and somatic hypermutation. We previously reported that murine hs4 was regulated by NF-kappaB, octamer binding proteins, and Pax5 (B cell-specific activator protein). In this study we report that human hs4 is regulated differently. EMSAs and Western analysis of normal B cells before and after stimulation with anti-IgM plus anti-CD40 showed the same complex binding pattern formed by NF-kappaB, Oct-1, and Oct-2 (but not by Pax5). A similar EMSA pattern was detected in mature human B cell lines (BL-2, Ramos, and HS-Sultan) and in diffuse large B cell lymphoma cell lines, although yin yang 1 protein (YY1) binding was also observed. We have confirmed the in vivo association of these transcription factors with hs4 in B cells by chromatin immunoprecipitation assays. The diffuse large B cell lymphoma cell lines had a distinctive slow-migrating complex containing YY1 associated with Rel-B. We have confirmed by endogenous coimmunoprecipitation an association of YY1 with Rel-B, but not with other NF-kappaB family members. Transient transfection assays showed robust hs4 enhancer activity in the mature B cell lines, which was dependent on synergistic interactions between NF-kappaB and octamer binding proteins. In addition, human hs4 enhancer activity required Oct-2 and correlated with expression of Oct coactivator from B cells (OCA-B).
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Affiliation(s)
- Manuel A Sepulveda
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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