1
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Feng J, Pucella JN, Jang G, Alcántara-Hernández M, Upadhaya S, Adams NM, Khodadadi-Jamayran A, Lau CM, Stoeckius M, Hao S, Smibert P, Tsirigos A, Idoyaga J, Reizis B. Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells. Immunity 2022; 55:405-422.e11. [PMID: 35180378 PMCID: PMC9344860 DOI: 10.1016/j.immuni.2022.01.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/23/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022]
Abstract
Developmental origins of dendritic cells (DCs) including conventional DCs (cDCs, comprising cDC1 and cDC2 subsets) and plasmacytoid DCs (pDCs) remain unclear. We studied DC development in unmanipulated adult mice using inducible lineage tracing combined with clonal DNA "barcoding" and single-cell transcriptome and phenotype analysis (CITE-seq). Inducible tracing of Cx3cr1+ hematopoietic progenitors in the bone marrow showed that they simultaneously produce all DC subsets including pDCs, cDC1s, and cDC2s. Clonal tracing of hematopoietic stem cells (HSCs) and of Cx3cr1+ progenitors revealed clone sharing between cDC1s and pDCs, but not between the two cDC subsets or between pDCs and B cells. Accordingly, CITE-seq analyses of differentiating HSCs and Cx3cr1+ progenitors identified progressive stages of pDC development including Cx3cr1+ Ly-6D+ pro-pDCs that were distinct from lymphoid progenitors. These results reveal the shared origin of pDCs and cDCs and suggest a revised scheme of DC development whereby pDCs share clonal relationship with cDC1s.
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Affiliation(s)
- Jue Feng
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Joseph N Pucella
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Geunhyo Jang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Marcela Alcántara-Hernández
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samik Upadhaya
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Nicholas M Adams
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alireza Khodadadi-Jamayran
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Colleen M Lau
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Marlon Stoeckius
- Technology Innovation Laboratory, New York Genome Center, New York, NY 10013, USA
| | - Stephanie Hao
- Technology Innovation Laboratory, New York Genome Center, New York, NY 10013, USA
| | - Peter Smibert
- Technology Innovation Laboratory, New York Genome Center, New York, NY 10013, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Juliana Idoyaga
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA.
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2
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Yen WF, Sharma R, Cols M, Lau CM, Chaudhry A, Chowdhury P, Yewdell WT, Vaidyanathan B, Sun A, Coffre M, Pucella JN, Chen CC, Jasin M, Sun JC, Rudensky AY, Koralov SB, Chaudhuri J. Distinct Requirements of CHD4 during B Cell Development and Antibody Response. Cell Rep 2020; 27:1472-1486.e5. [PMID: 31042474 PMCID: PMC6527137 DOI: 10.1016/j.celrep.2019.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/15/2019] [Accepted: 04/01/2019] [Indexed: 11/21/2022] Open
Abstract
The immunoglobulin heavy chain (Igh) locus features a dynamic chromatin landscape to promote class switch recombination (CSR), yet the mechanisms that regulate this landscape remain poorly understood. CHD4, a component of the chromatin remodeling NuRD complex, directly binds H3K9me3, an epigenetic mark present at the Igh locus during CSR. We find that CHD4 is essential for early B cell development but is dispensable for the homeostatic maintenance of mature, naive B cells. However, loss of CHD4 in mature B cells impairs CSR because of suboptimal targeting of AID to the Igh locus. Additionally, we find that CHD4 represses p53 expression to promote B cell proliferation. This work reveals distinct roles for CHD4 in B cell development and CSR and links the H3K9me3 epigenetic mark with AID recruitment to the Igh locus. Yen et al. demonstrate that CHD4, a component of the NuRD remodeling complex, is essential for early B cell development, represses p53 expression in mature B cells, and influences the recruitment of AID to DNA during class switch recombination.
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Affiliation(s)
- Wei-Feng Yen
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Biochemistry, Cellular and Molecular Biology Program, Weill Graduate School of Medical Sciences, New York, NY, USA
| | - Rahul Sharma
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Montserrat Cols
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Colleen M Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashutosh Chaudhry
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Priyanka Chowdhury
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - William T Yewdell
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bharat Vaidyanathan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Amy Sun
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Maryaline Coffre
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Joseph N Pucella
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA
| | - Chun-Chin Chen
- Biochemistry, Cellular and Molecular Biology Program, Weill Graduate School of Medical Sciences, New York, NY, USA; Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Jasin
- Biochemistry, Cellular and Molecular Biology Program, Weill Graduate School of Medical Sciences, New York, NY, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA; Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA
| | - Alexander Y Rudensky
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA.
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3
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Abstract
The generation of all blood cell lineages (hematopoiesis) is sustained throughout the entire life span of adult mammals. Studies using cell transplantation identified the self-renewing, multipotent hematopoietic stem cells (HSCs) as the source of hematopoiesis in adoptive hosts and delineated a hierarchy of HSC-derived progenitors that ultimately yield mature blood cells. However, much less is known about adult hematopoiesis as it occurs in native hosts, i.e., without transplantation. Here we review recent advances in our understanding of native hematopoiesis, focusing in particular on the application of genetic lineage tracing in mice. The emerging evidence has established HSCs as the major source of native hematopoiesis, helped to define the kinetics of HSC differentiation, and begun exploring native hematopoiesis in stress conditions such as aging and inflammation. Major outstanding questions about native hematopoiesis still remain, such as its clonal composition, the nature of lineage commitment, and the dynamics of the process in humans.
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Affiliation(s)
- Joseph N Pucella
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; , ,
| | - Samik Upadhaya
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; , ,
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; , ,
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Soni C, Perez OA, Voss WN, Pucella JN, Serpas L, Mehl J, Ching KL, Goike J, Georgiou G, Ippolito GC, Sisirak V, Reizis B. Plasmacytoid Dendritic Cells and Type I Interferon Promote Extrafollicular B Cell Responses to Extracellular Self-DNA. Immunity 2020; 52:1022-1038.e7. [PMID: 32454024 PMCID: PMC7306002 DOI: 10.1016/j.immuni.2020.04.015] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 03/13/2020] [Accepted: 04/23/2020] [Indexed: 01/06/2023]
Abstract
Class-switched antibodies to double-stranded DNA (dsDNA) are prevalent and pathogenic in systemic lupus erythematosus (SLE), yet mechanisms of their development remain poorly understood. Humans and mice lacking secreted DNase DNASE1L3 develop rapid anti-dsDNA antibody responses and SLE-like disease. We report that anti-DNA responses in Dnase1l3-/- mice require CD40L-mediated T cell help, but proceed independently of germinal center formation via short-lived antibody-forming cells (AFCs) localized to extrafollicular regions. Type I interferon (IFN-I) signaling and IFN-I-producing plasmacytoid dendritic cells (pDCs) facilitate the differentiation of DNA-reactive AFCs in vivo and in vitro and are required for downstream manifestations of autoimmunity. Moreover, the endosomal DNA sensor TLR9 promotes anti-dsDNA responses and SLE-like disease in Dnase1l3-/- mice redundantly with another nucleic acid-sensing receptor, TLR7. These results establish extrafollicular B cell differentiation into short-lived AFCs as a key mechanism of anti-DNA autoreactivity and reveal a major contribution of pDCs, endosomal Toll-like receptors (TLRs), and IFN-I to this pathway.
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Affiliation(s)
- Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Oriana A Perez
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - William N Voss
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Joseph N Pucella
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Justin Mehl
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Krystal L Ching
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jule Goike
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - George Georgiou
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA
| | - Vanja Sisirak
- CNRS-UMR 5164, ImmunoConcEpt, Université de Bordeaux, 33076 Bordeaux, France.
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA.
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5
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Pucella JN, Cols M, Yen WF, Xu S, Chaudhuri J. The B Cell Activation-Induced miR-183 Cluster Plays a Minimal Role in Canonical Primary Humoral Responses. J Immunol 2019; 202:1383-1396. [PMID: 30683701 DOI: 10.4049/jimmunol.1800071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022]
Abstract
Although primary humoral responses are vital to durable immunity, fine-tuning is critical to preventing catastrophes such as autoimmunity, chronic inflammation, and lymphomagenesis. MicroRNA (miRNA)-mediated regulation is particularly well suited for fine-tuning roles in physiology. Expression of clustered paralogous miR-182, miR-96, and miR-183 (collectively, 183c) is robustly induced upon B cell activation, entry into the germinal center, and plasmablast differentiation. 183cGT/GT mice lacking 183c miRNA expression exhibit largely normal primary humoral responses, encompassing class switch recombination, affinity maturation, and germinal center reaction, as well as plasmablast differentiation. Our rigorous analysis included ex vivo class switch recombination and plasmablast differentiation models as well as in vivo immunization with thymus-dependent and thymus-independent Ags. Our work sways the debate concerning the role of miR-182 in plasmablast differentiation, strongly suggesting that 183c miRNAs are dispensable. In the process, we present a valuable framework for systematic evaluation of primary humoral responses. Finally, our work bolsters the notion of robustness in miRNA:target interaction networks and advocates a paradigm shift in miRNA studies.
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Affiliation(s)
- Joseph N Pucella
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School, New York, NY 10065; and
| | - Montserrat Cols
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School, New York, NY 10065; and
| | - Wei-Feng Yen
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School, New York, NY 10065; and
| | - Shunbin Xu
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI 48201
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School, New York, NY 10065; and
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6
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Pucella JN, Yen WF, Kim MV, van der Veeken J, Socci ND, Naito Y, Li MO, Iwai N, Chaudhuri J. Correction: miR-182 Is Largely Dispensable for Adaptive Immunity: Lack of Correlation between Expression and Function. J Immunol 2015; 195:1903. [PMID: 26254268 DOI: 10.4049/jimmunol.1501331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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7
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Pucella JN, Yen WF, Kim MV, van der Veeken J, Luo CT, Socci ND, Naito Y, Li MO, Iwai N, Chaudhuri J. miR-182 is largely dispensable for adaptive immunity: lack of correlation between expression and function. J Immunol 2015; 194:2635-42. [PMID: 25672759 DOI: 10.4049/jimmunol.1402261] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
MicroRNA (miR)-mediated regulation of protein abundance is a pervasive mechanism of directing cellular processes. The well-studied and abundant miR-182 has previously been implicated in many aspects of T cell function, DNA repair, and cancer. In this study, we show that miR-182 is the most highly induced miR in B cells undergoing class-switch recombination. To elucidate the requirement of miR-182 in lymphocyte function, we extensively characterized mice with a targeted deletion of Mir182. We show that despite its dramatic induction, loss of miR-182 has minimal impact on B cell development, the ability of B cells to undergo class-switch recombination ex vivo and to undergo Ag-driven affinity maturation in vivo. Furthermore, in striking contrast to knockdown studies that demonstrated the requirement of miR-182 in T cell function, miR-182-deficient mice display no defect in T cell development and activation. Finally, we show that T cell-dependent immune response to experimental Listeria monocytogenes infection is intact in miR-182-deficient mice. We conclude that, contrary to previous studies, miR-182 does not play a significant role in all measured aspects of mouse adaptive immunity. This striking absence of a phenotype highlights the lack of correlation between expression pattern and functional requirement, underscores the limitations of using knockdown approaches to assess miR requirements, and suggests that miR networks may compensate for the chronic loss of specific miRs.
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Affiliation(s)
- Joseph N Pucella
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School, New York, NY 10065
| | - Wei-Feng Yen
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School, New York, NY 10065; Immunology and Microbial Pathogenesis Program, Weill-Cornell Graduate School of Medical Sciences, New York, NY 10065
| | - Myoungjoo V Kim
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School, New York, NY 10065; Immunology and Microbial Pathogenesis Program, Weill-Cornell Graduate School of Medical Sciences, New York, NY 10065
| | - Joris van der Veeken
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School, New York, NY 10065; Immunology and Microbial Pathogenesis Program, Weill-Cornell Graduate School of Medical Sciences, New York, NY 10065
| | | | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065; and
| | - Yukiko Naito
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center, Suita, Osaka 565-8565, Japan
| | - Ming O Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School, New York, NY 10065; Immunology and Microbial Pathogenesis Program, Weill-Cornell Graduate School of Medical Sciences, New York, NY 10065
| | - Naoharu Iwai
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center, Suita, Osaka 565-8565, Japan
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School, New York, NY 10065; Immunology and Microbial Pathogenesis Program, Weill-Cornell Graduate School of Medical Sciences, New York, NY 10065;
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8
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Vaidyanathan B, Yen WF, Pucella JN, Chaudhuri J. AIDing Chromatin and Transcription-Coupled Orchestration of Immunoglobulin Class-Switch Recombination. Front Immunol 2014; 5:120. [PMID: 24734031 PMCID: PMC3975107 DOI: 10.3389/fimmu.2014.00120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/07/2014] [Indexed: 12/29/2022] Open
Abstract
Secondary diversification of the antibody repertoire upon antigenic challenge, in the form of immunoglobulin heavy chain (IgH) class-switch recombination (CSR) endows mature, naïve B cells in peripheral lymphoid organs with a limitless ability to mount an optimal humoral immune response, thus expediting pathogen elimination. CSR replaces the default constant (CH) region exons (Cμ) of IgH with any of the downstream CH exons (Cγ, Cε, or Cα), thereby altering effector functions of the antibody molecule. This process depends on, and is orchestrated by, activation-induced deaminase (AID), a DNA cytidine deaminase that acts on single-stranded DNA exposed during transcription of switch (S) region sequences at the IgH locus. DNA lesions thus generated are processed by components of several general DNA repair pathways to drive CSR. Given that AID can instigate DNA lesions and genomic instability, stringent checks are imposed that constrain and restrict its mutagenic potential. In this review, we will discuss how AID expression and substrate specificity and activity is rigorously enforced at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and how the DNA-damage response is choreographed with precision to permit targeted activity while limiting bystander catastrophe.
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Affiliation(s)
- Bharat Vaidyanathan
- Weill Cornell Graduate School of Medical Sciences , New York, NY , USA ; Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
| | - Wei-Feng Yen
- Weill Cornell Graduate School of Medical Sciences , New York, NY , USA ; Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
| | - Joseph N Pucella
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
| | - Jayanta Chaudhuri
- Weill Cornell Graduate School of Medical Sciences , New York, NY , USA ; Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
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