1
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Heltzel JHM, Maul RW, Yang W, Gearhart PJ. Promoter Proximity Defines Mutation Window for V H and V Κ Genes Rearranged to Different J Genes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2220-2226. [PMID: 35418469 PMCID: PMC9050841 DOI: 10.4049/jimmunol.2101002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/21/2022] [Indexed: 05/03/2023]
Abstract
Somatic hypermutation induced by activation-induced deaminase (AID) occurs at high densities between the Ig V gene promoter and intronic enhancer, which encompasses DNA encoding the rearranged V gene exon and J intron. It has been proposed that proximity between the promoter and enhancer defines the boundaries of mutation in V regions. However, depending on the J gene used, the distance between the promoter and enhancer is quite variable and may result in differential targeting around the V gene. To examine the effect of distance in mutation accumulation, we sequenced 320 clones containing different endogenous rearranged V genes in the IgH and Igκ loci from Peyer's patch B cells of mice. Clones were grouped by their use of different J genes. Distances between the V gene and enhancer ranged from ∼2.3 kb of intron DNA for rearrangements using J1, ∼2.0 kb for rearrangements using J2, ∼1.6 kb for rearrangements using J3 (H) or 4 (κ), and 1.1 kb for rearrangements using J4 (H) or 5 (κ). Strikingly, >90% of intron mutations occurred within 1 kb downstream of the J gene for both H and κ clones, regardless of which J gene was used. Thus, there is no evidence that the intron sequence or enhancer plays a role in determining the extent of mutation. The results indicate that V region intron mutations are targeted by their proximity to the promoter, suggesting they result from AID interactions with RNA polymerase II over a 1-kb region.
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Affiliation(s)
- Justin H M Heltzel
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD
| | - William Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD
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2
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Tarsalainen A, Maman Y, Meng FL, Kyläniemi MK, Soikkeli A, Budzynska P, McDonald JJ, Šenigl F, Alt FW, Schatz DG, Alinikula J. Ig Enhancers Increase RNA Polymerase II Stalling at Somatic Hypermutation Target Sequences. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:143-154. [PMID: 34862258 PMCID: PMC8702490 DOI: 10.4049/jimmunol.2100923] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/20/2021] [Indexed: 01/03/2023]
Abstract
Somatic hypermutation (SHM) drives the genetic diversity of Ig genes in activated B cells and supports the generation of Abs with increased affinity for Ag. SHM is targeted to Ig genes by their enhancers (diversification activators [DIVACs]), but how the enhancers mediate this activity is unknown. We show using chicken DT40 B cells that highly active DIVACs increase the phosphorylation of RNA polymerase II (Pol II) and Pol II occupancy in the mutating gene with little or no accompanying increase in elongation-competent Pol II or production of full-length transcripts, indicating accumulation of stalled Pol II. DIVAC has similar effect also in human Ramos Burkitt lymphoma cells. The DIVAC-induced stalling is weakly associated with an increase in the detection of ssDNA bubbles in the mutating target gene. We did not find evidence for antisense transcription, or that DIVAC functions by altering levels of H3K27ac or the histone variant H3.3 in the mutating gene. These findings argue for a connection between Pol II stalling and cis-acting targeting elements in the context of SHM and thus define a mechanistic basis for locus-specific targeting of SHM in the genome. Our results suggest that DIVAC elements render the target gene a suitable platform for AID-mediated mutation without a requirement for increasing transcriptional output.
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Affiliation(s)
- Alina Tarsalainen
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Yaakov Maman
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, 1311502, Israel
| | - Fei-Long Meng
- Department of Genetics, Harvard Medical School and Program in Cellular and Molecular Medicine, HHMI, Boston Children’s Hospital, Boston, MA 02115, USA.,Current address: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Minna K. Kyläniemi
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland,Current address: Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Anni Soikkeli
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Paulina Budzynska
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Jessica J. McDonald
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA,Current address: The Annenberg Public Policy Center, Philadelphia, PA 19104-3806, USA
| | - Filip Šenigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Praha 4, Czech Republic
| | - Frederic W. Alt
- Department of Genetics, Harvard Medical School and Program in Cellular and Molecular Medicine, HHMI, Boston Children’s Hospital, Boston, MA 02115, USA
| | - David G. Schatz
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA,Correspondence should be addressed to and
| | - Jukka Alinikula
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland,Correspondence should be addressed to and
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3
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Senigl F, Maman Y, Dinesh RK, Alinikula J, Seth RB, Pecnova L, Omer AD, Rao SSP, Weisz D, Buerstedde JM, Aiden EL, Casellas R, Hejnar J, Schatz DG. Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation. Cell Rep 2020; 29:3902-3915.e8. [PMID: 31851922 PMCID: PMC6980758 DOI: 10.1016/j.celrep.2019.11.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/26/2019] [Accepted: 11/08/2019] [Indexed: 12/26/2022] Open
Abstract
Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (Ig) genes but also causes mutations in other parts of the genome. We have used lentiviral SHM reporter vectors to identify regions of the genome that are susceptible (“hot”) and resistant (“cold”) to SHM, revealing that SHM susceptibility and resistance are often properties of entire topologically associated domains (TADs). Comparison of hot and cold TADs reveals that while levels of transcription are equivalent, hot TADs are enriched for the cohesin loader NIPBL, super-enhancers, markers of paused/stalled RNA polymerase 2, and multiple important B cell transcription factors. We demonstrate that at least some hot TADs contain enhancers that possess SHM targeting activity and that insertion of a strong Ig SHM-targeting element into a cold TAD renders it hot. Our findings lead to a model for SHM susceptibility involving the cooperative action of cis-acting SHM targeting elements and the dynamic and architectural properties of TADs. Senigl et al. show that genome susceptibility to somatic hypermutation (SHM) is confined within topologically associated domains (TADs) and is linked to markers of strong enhancers and stalled transcription and high levels of the cohesin loader NIPBL. Insertion of an ectopic SHM targeting element renders an entire TAD susceptible to SHM.
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Affiliation(s)
- Filip Senigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic.
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ravi K Dinesh
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Jukka Alinikula
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Rashu B Seth
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Lubomira Pecnova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Arina D Omer
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Erez Lieberman Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jiri Hejnar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA.
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4
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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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5
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Caldwell RB, Braselmann H, Heuer S, Schötz U, Zitzelsberger H. Gain-of-function analysis of cis-acting diversification elements in DT40 cells. Immunol Cell Biol 2018; 96:948-957. [PMID: 29665088 DOI: 10.1111/imcb.12158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 02/02/2023]
Abstract
Activation-induced cytidine deaminase (AID) is required for the immunoglobulin diversification processes of somatic hypermutation, gene conversion and class-switch recombination. The targeting of AID's deamination activity is thought to be a combination of cis- and trans-acting elements, but has not been fully elucidated. Deletion analysis of putative proximal cis-regulatory motifs, while helpful, fails to identify additive versus cumulative effects, redundancy, and may create new motifs where none previously existed. In contrast, gain-of-function analysis can be more insightful with fewer of the same drawbacks and the output is a positive result. Here, we show five defined DNA regions of the avian Igλ locus that are sufficient to confer events of hypermutation to a target gene. In our analysis, the essential cis-targeting elements fully reconstituted diversification of a transgene under heterologous promotion in the avian B-cell line DT40. Furthermore, to the best of our knowledge two of the five regions we report on here have not previously been described as individually having an influence on somatic hypermutation.
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Affiliation(s)
- Randolph B Caldwell
- Department of Radiation Sciences - Research Unit Radiation Cytogenetics, Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Neuherberg, 85764, Germany
| | - Herbert Braselmann
- Department of Radiation Sciences - Research Unit Radiation Cytogenetics, Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Neuherberg, 85764, Germany
| | - Steffen Heuer
- Department of Radiation Sciences - Research Unit Radiation Cytogenetics, Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Neuherberg, 85764, Germany
| | - Ulrike Schötz
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, University Hospital Gießen and Marburg, Marburg, 35043, Germany
| | - Horst Zitzelsberger
- Department of Radiation Sciences - Research Unit Radiation Cytogenetics, Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Neuherberg, 85764, Germany.,Helmholtz Center Munich, Clinical Cooperation Group 'Personalized Radiotherapy of Head and Neck Cancer', Neuherberg, 85764, Germany.,Department of Radiotherapy and Radiation Oncology, Ludwig-Maximilians-Universitaet, University Hospital Munich, Munich, 81377, Germany
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6
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Castiblanco DP, Norton DD, Maul RW, Gearhart PJ. J H6 downstream intronic sequence is dispensable for RNA polymerase II accumulation and somatic hypermutation of the variable gene in Ramos cells. Mol Immunol 2018; 97:101-108. [PMID: 29625296 DOI: 10.1016/j.molimm.2018.03.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/09/2018] [Accepted: 03/30/2018] [Indexed: 02/03/2023]
Abstract
Activation-induced deaminase (AID) introduces nucleotide substitutions within the variable region of immunoglobulin genes to promote antibody diversity. This activity, which is limited to 1.5 kb downstream of the variable gene promoter, mutates both the coding exon and downstream intronic sequences. We recently reported that RNA polymerase II accumulates in these regions during transcription in mice. This build-up directly correlates with the area that is accessible to AID, and manipulation of RNA polymerase II levels alters the mutation frequency. To address whether the intronic DNA sequence by itself can regulate RNA polymerase II accumulation and promote mutagenesis, we deleted 613 bp of DNA downstream of the JH6 intron in the human Ramos B cell line. The loss of this sequence did not alter polymerase abundance or mutagenesis in the variable gene, suggesting that most of the intronic sequence is dispensable for somatic hypermutation.
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Affiliation(s)
- Diana P Castiblanco
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Darrell D Norton
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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7
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Abstract
Chromosomal translocations are a hallmark of cancer. Unraveling the molecular mechanism of these rare genetic events requires a clear distinction between correlative and causative risk-determinants, where technical and analytical issues can be excluded. To meet this goal, we performed in-depth analyses of publicly available genome-wide datasets. In contrast to several recent reports, we demonstrate that chromosomal translocation risk is causally unrelated to promoter stalling (Spt5), transcriptional activity, or off-targeting activity of the activation-induced cytidine deaminase. Rather, an open chromatin configuration, which is not promoter-specific, explained the elevated translocation risk of promoter regions. Furthermore, the fact that gene size directly correlates with the translocation risk in mice and human cancers further demonstrated the general irrelevance of promoter-specific activities. Interestingly, a subset of translocations observed in cancer patients likely initiates from double-strand breaks induced by an access-independent process. Together, these unexpected and novel insights are fundamental in understanding the origin of chromosome translocations and, consequently, cancer.
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8
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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9
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Maul RW, Saribasak H, Cao Z, Gearhart PJ. Topoisomerase I deficiency causes RNA polymerase II accumulation and increases AID abundance in immunoglobulin variable genes. DNA Repair (Amst) 2015; 30:46-52. [PMID: 25869824 DOI: 10.1016/j.dnarep.2015.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/03/2015] [Accepted: 03/09/2015] [Indexed: 10/23/2022]
Abstract
Activation-induced deaminase (AID) is a DNA cytosine deaminase that diversifies immunoglobulin genes in B cells. Recent work has shown that RNA polymerase II (Pol II) accumulation correlates with AID recruitment. However, a direct link between Pol II and AID abundance has not been tested. We used the DT40 B-cell line to manipulate levels of Pol II by decreasing topoisomerase I (Top1), which relaxes DNA supercoiling in front of the transcription complex. Top1 was decreased by stable transfection of a short hairpin RNA against Top1, which produced an accumulation of Pol II in transcribed genes, compared to cells transfected with sh-control RNA. The increased Pol II density enhanced AID recruitment to variable genes in the λ light chain locus, and resulted in higher levels of somatic hypermutation and gene conversion. It has been proposed by another lab that AID itself might directly suppress Top1 to increase somatic hypermutation. However, we found that in both AID(+/+) and AID(-/-) B cells from DT40 and mice, Top1 protein levels were identical, indicating that the presence or absence of AID did not decrease Top1 expression. Rather, our results suggest that the mechanism for increased diversity when Top1 is reduced is that Pol II accumulates and recruits AID to variable genes.
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Affiliation(s)
- Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Huseyin Saribasak
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Zheng Cao
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States.
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10
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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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11
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Abstract
In this review, I discuss the currently available experimental evidence concerning the molecular interactions of the activation-induced cytidine deaminase (AID) with transcription of its target genes. The basic question that underlies the transcription relationship is how the process of somatic hypermutation of Ig genes can be restricted to their variable (V) regions. This hallmark of SHM assures that high affinity antibodies can be created while the biological functions of their constant (C) region are undisturbed. I present a revised model of AID function in somatic hypermutation (SHM): In a B cell that produces AID protein and undergoes mutation of the V regions of the expressed Ig heavy and light chain genes, only some of the transcription complexes initiating at the active V-region promoters are associated with AID. When AID travels with the elongating RNA polymerase (pol), it attracts proteins that cause the pausing/stalling of pol and termination of transcription, followed by termination of SHM. This differential AID loading model would allow the mutating B cell to continue producing full-length Ig proteins that are required to avoid apoptosis by permitting the cell to assemble functional B cell receptors.
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Affiliation(s)
- Ursula Storb
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA.
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12
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McDonald JJ, Alinikula J, Buerstedde JM, Schatz DG. A critical context-dependent role for E boxes in the targeting of somatic hypermutation. THE JOURNAL OF IMMUNOLOGY 2013; 191:1556-66. [PMID: 23836058 PMCID: PMC3735716 DOI: 10.4049/jimmunol.1300969] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Secondary B cell repertoire diversification occurs by somatic hypermutation (SHM) in germinal centers following Ag stimulation. In SHM, activation-induced cytidine deaminase mutates the V region of the Ig genes to increase the affinity of Abs. Although SHM acts primarily at Ig loci, low levels of off-target mutation can result in oncogenic DNA damage, illustrating the importance of understanding SHM targeting mechanisms. A candidate targeting motif is the E box, a short DNA sequence (CANNTG) found abundantly in the genome and in many SHM target genes. Using a reporter assay in chicken DT40 B cells, we previously identified a 1928-bp portion of the chicken IgL locus capable of supporting robust SHM. In this article, we demonstrate that mutation of all 20 E boxes in this fragment reduces SHM targeting activity by 90%, and that mutation of subsets of E boxes reveals a functional hierarchy in which E boxes within "core" targeting regions are of greatest importance. Strikingly, when the sequence and spacing of the 20 E boxes are preserved but surrounding sequences are altered, SHM targeting activity is eliminated. Hence, although E boxes are vital SHM targeting elements, their function is completely dependent on their surrounding sequence context. These results suggest an intimate cooperation between E boxes and other sequence motifs in SHM targeting to Ig loci and perhaps also in restricting mistargeting to certain non-Ig loci.
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Affiliation(s)
- Jessica J McDonald
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
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13
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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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Duke JL, Liu M, Yaari G, Khalil AM, Tomayko MM, Shlomchik MJ, Schatz DG, Kleinstein SH. Multiple transcription factor binding sites predict AID targeting in non-Ig genes. THE JOURNAL OF IMMUNOLOGY 2013; 190:3878-88. [PMID: 23514741 DOI: 10.4049/jimmunol.1202547] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Aberrant targeting of the enzyme activation-induced cytidine deaminase (AID) results in the accumulation of somatic mutations in ≈ 25% of expressed genes in germinal center B cells. Observations in Ung(-/-) Msh2(-/-) mice suggest that many other genes efficiently repair AID-induced lesions, so that up to 45% of genes may actually be targeted by AID. It is important to understand the mechanisms that recruit AID to certain genes, because this mistargeting represents an important risk for genome instability. We hypothesize that several mechanisms combine to target AID to each locus. To resolve which mechanisms affect AID targeting, we analyzed 7.3 Mb of sequence data, along with the regulatory context, from 83 genes in Ung(-/-) Msh2(-/-) mice to identify common properties of AID targets. This analysis identifies three transcription factor binding sites (E-box motifs, along with YY1 and C/EBP-β binding sites) that may work together to recruit AID. Based on previous knowledge and these newly discovered features, a classification tree model was built to predict genome-wide AID targeting. Using this predictive model, we were able to identify a set of 101 high-interest genes that are likely targets of AID.
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Affiliation(s)
- Jamie L Duke
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
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15
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Kohler KM, McDonald JJ, Duke JL, Arakawa H, Tan S, Kleinstein SH, Buerstedde JM, Schatz DG. Identification of core DNA elements that target somatic hypermutation. THE JOURNAL OF IMMUNOLOGY 2012; 189:5314-26. [PMID: 23087403 PMCID: PMC3664039 DOI: 10.4049/jimmunol.1202082] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Somatic hypermutation (SHM) diversifies the V region of Ig genes and underlies the process of affinity maturation, in which B lymphocytes producing high-affinity Abs are generated and selected. SHM is triggered in activated B cells by deamination of deoxycytosine residues mediated by activation-induced deaminase (AID). Whereas mistargeting of SHM and AID results in mutations and DNA damage in many non-Ig genes, they act preferentially at Ig loci. The mechanisms responsible for preferential targeting of SHM and AID activity to Ig loci are poorly understood. Using an assay involving an SHM reporter cassette inserted into the Ig L chain locus (IgL) of chicken DT40 B cells, we have identified a 1.9-kb DIVAC (diversification activator) element derived from chicken IgL that supports high levels of AID-dependent mutation activity. Systematic deletion analysis reveals that targeting activity is spread throughout much of the sequence and identifies two core regions that are particularly critical for function: a 200-bp region within the IgL enhancer, and a 350-bp 3' element. Chromatin immunoprecipitation experiments demonstrate that whereas DIVAC does not alter levels of several epigenetic marks in the mutation cassette, it does increase levels of serine-5 phosphorylated RNA polymerase II in the mutation target region, consistent with an effect on transcriptional elongation/pausing. We propose that multiple, dispersed DNA elements collaborate to recruit and activate the mutational machinery at Ig gene variable regions during SHM.
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Affiliation(s)
- Kristin M Kohler
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
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Saribasak H, Gearhart PJ. Does DNA repair occur during somatic hypermutation? Semin Immunol 2012; 24:287-92. [PMID: 22728014 DOI: 10.1016/j.smim.2012.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 05/18/2012] [Indexed: 11/25/2022]
Abstract
Activation-induced deaminase (AID) initiates a flood of DNA damage in the immunoglobulin loci, leading to abasic sites, single-strand breaks and mismatches. It is compelling that some proteins in the canonical base excision and mismatch repair pathways have been hijacked to increase mutagenesis during somatic hypermutation. Thus, the AID-induced mutagenic pathways involve a mix of DNA repair proteins and low fidelity DNA polymerases to create antibody diversity. In this review, we analyze the roles of base excision repair, mismatch repair, and mutagenesis during somatic hypermutation of rearranged variable genes. The emerging view is that faithful base excision repair occurs simultaneously with mutagenesis, whereas faithful mismatch repair is mostly absent.
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Affiliation(s)
- Huseyin Saribasak
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
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Zhu C, Lee V, Finn A, Senger K, Zarrin AA, Du Pasquier L, Hsu E. Origin of immunoglobulin isotype switching. Curr Biol 2012; 22:872-80. [PMID: 22542103 DOI: 10.1016/j.cub.2012.03.060] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/02/2012] [Accepted: 03/19/2012] [Indexed: 12/11/2022]
Abstract
BACKGROUND From humans to frogs, immunoglobulin class switching introduces different effector functions to antibodies through an intrachromosomal DNA recombination process at the heavy-chain locus. Although there are two conventional antibody classes (IgM, IgW) in sharks, their heavy chains are encoded by 20 to >100 miniloci. These representatives of the earliest jawed vertebrates possess a primordial immunoglobulin gene organization where each gene cluster is autonomous and contains a few rearranging gene segments (VH-D1-D2-JH) with one constant region, μ or ω. RESULTS V(D)J rearrangement always takes place within the μ cluster, but here we show that the VDJ can be expressed with constant regions from different clusters, although IgH genes are spatially distant, at >120 kb. Moreover, reciprocal exchanges take place between Igω and Igμ genes. Switching is augmented with deliberate immunization and is concomitant with somatic hypermutation activity. Because switching occurs independently of the partners' linkage position, some events involve transchromosomal recombination. The switch sites consist of direct joins between two genes in the 3' intron flanking JH. CONCLUSIONS Our data are consistent with a mechanism of cutting or joining of distal DNA lesions initiated by activation-induced cytidine deaminase (AID), in the absence of mammalian-type switch regions. We suggest that, in shark, with its many autonomous IgH targeted by programmed DNA breakage, factors predisposing broken DNA ends to translocate configured the earliest version of class switch recombination.
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Affiliation(s)
- Catherine Zhu
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203, USA
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