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Alberca CD, Georgieff EI, Berardino BG, Ferroni NM, Fesser EA, Cantarelli VI, Ponzio MF, Cánepa ET, Chertoff M. Perinatal protein malnutrition alters maternal behavior and leads to maladaptive stress response, neurodevelopmental delay and disruption on DNA methylation machinery in female mice offspring. Horm Behav 2024; 164:105603. [PMID: 39029339 DOI: 10.1016/j.yhbeh.2024.105603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 07/21/2024]
Abstract
Deficiencies in maternal nutrition have long-term consequences affecting brain development of the progeny and its behavior. In the present work, female mice were exposed to a normal-protein or a low-protein diet during gestation and lactation. We analyzed behavioral and molecular consequences of malnutrition in dams and how it affects female offspring at weaning. We have observed that a low-protein diet during pregnancy and lactation leads to anxiety-like behavior and anhedonia in dams. Protein malnutrition during the perinatal period delays physical and neurological development of female pups. Glucocorticoid levels increased in the plasma of malnourished female offspring but not in dams when compared to the control group. Interestingly, the expression of glucocorticoid receptor (GR) was reduced in hippocampus and amygdala on both malnourished dams and female pups. In addition, malnourished pups exhibited a significant increase in the expression of Dnmt3b, Gadd45b, and Fkbp5 and a reduction in Bdnf VI variant mRNA in hippocampus. In contrast, a reduction on Dnmt3b has been observed on the amygdala of weaned mice. No changes have been observed on global methylation levels (5-methylcytosine) in hippocampal genomic DNA neither in dams nor female offspring. In conclusion, deregulated behaviors observed in malnourished dams might be mediated by a low expression of GR in brain regions associated with emotive behaviors. Additionally, low-protein diet differentially deregulates the expression of genes involved in DNA methylation/demethylation machinery in female offspring but not in dams, providing an insight into regional- and age-specific mechanisms due to protein malnutrition.
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Affiliation(s)
- Carolina D Alberca
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Erika I Georgieff
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Bruno G Berardino
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nadina M Ferroni
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Estefanía A Fesser
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Verónica I Cantarelli
- Instituto de Fisiología, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, e Instituto de Investigaciones en Ciencias de la Salud (INICSA; CONICET-UNC), Santa Rosa 1085, X5000ESU Córdoba, Argentina
| | - Marina F Ponzio
- Instituto de Fisiología, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, e Instituto de Investigaciones en Ciencias de la Salud (INICSA; CONICET-UNC), Santa Rosa 1085, X5000ESU Córdoba, Argentina
| | - Eduardo T Cánepa
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariela Chertoff
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina.
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2
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Aburajab R, Pospiech M, Alachkar H. Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data. Nat Methods 2023; 20:477-481. [PMID: 36522502 PMCID: PMC11058354 DOI: 10.1038/s41592-022-01723-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High-resolution sequencing methods that capture the epigenetic landscape within the T cell receptor (TCR) gene loci are pivotal for a fundamental understanding of the epigenetic regulatory mechanisms of the TCR repertoire. In our opinion, filling the gaps in our understanding of the epigenetic mechanisms regulating the TCR repertoire will benefit the development of strategies that can modulate the TCR repertoire composition by leveraging the dynamic nature of epigenetic modifications.
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Affiliation(s)
- Rayyan Aburajab
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Mateusz Pospiech
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Houda Alachkar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
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3
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Renna V, Surova E, Khadour A, Datta M, Amendt T, Hobeika E, Jumaa H. Defective Allelic Exclusion by IgD in the Absence of Autoantigen. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:293-302. [PMID: 34930782 DOI: 10.4049/jimmunol.2100726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022]
Abstract
A considerable proportion of peripheral B cells is autoreactive, and it is unclear how the activation of such potentially harmful cells is regulated. In this study, we show that the different activation thresholds or IgM and IgD BCRs adjust B cell activation to the diverse requirements during development. We rely on the autoreactive 3-83 model BCR to generate and analyze mice expressing exclusively autoreactive IgD BCRs on two different backgrounds that determine two stages of autoreactivity, depending on the presence or absence of the cognate Ag. By comparing these models with IgM-expressing control mice, we found that, compared with IgM, IgD has a higher activation threshold in vivo, as it requires autoantigen to enable normal B cell development, including allelic exclusion. Our data indicate that IgM provides the high sensitivity required during early developmental stages to trigger editing of any autoreactive specificities, including those enabling weak interaction with autoantigen. In contrast, IgD has the unique ability to neglect weakly interacting autoantigens while retaining reactivity to higher-affinity Ag. This IgD function enables mature B cells to ignore autoantigens while remaining able to efficiently respond to foreign threats.
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Affiliation(s)
- Valerio Renna
- Institute of Immunology, Ulm University Medical Center, Ulm, Germany
| | - Elena Surova
- Spemann Graduate School of Biology and Medicine, Albert Ludwig University of Freiburg, Freiburg, Germany; and.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ahmad Khadour
- Institute of Immunology, Ulm University Medical Center, Ulm, Germany
| | - Moumita Datta
- Institute of Immunology, Ulm University Medical Center, Ulm, Germany
| | - Timm Amendt
- Institute of Immunology, Ulm University Medical Center, Ulm, Germany
| | - Elias Hobeika
- Institute of Immunology, Ulm University Medical Center, Ulm, Germany
| | - Hassan Jumaa
- Institute of Immunology, Ulm University Medical Center, Ulm, Germany;
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4
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Bergman Y, Simon I, Cedar H. Asynchronous Replication Timing: A Mechanism for Monoallelic Choice During Development. Front Cell Dev Biol 2021; 9:737681. [PMID: 34660595 PMCID: PMC8517340 DOI: 10.3389/fcell.2021.737681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
Developmental programming is carried out by a sequence of molecular choices that epigenetically mark the genome to generate the stable cell types which make up the total organism. A number of important processes, such as genomic imprinting, selection of immune or olfactory receptors, and X-chromosome inactivation in females are dependent on the ability to stably choose one single allele in each cell. In this perspective, we propose that asynchronous replication timing (ASRT) serves as the basis for a sophisticated universal mechanism for mediating and maintaining these decisions.
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Affiliation(s)
- Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, Hebrew University Hadassah Medical School, The Institute for Medical Research Israel-Canada (IMRIC), Jerusalem, Israel
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Hebrew University Hadassah Medical School, Jerusalem, Israel
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Abstract
DNA damage occurs on exposure to genotoxic agents and during physiological DNA transactions. DNA double-strand breaks (DSBs) are particularly dangerous lesions that activate DNA damage response (DDR) kinases, leading to initiation of a canonical DDR (cDDR). This response includes activation of cell cycle checkpoints and engagement of pathways that repair the DNA DSBs to maintain genomic integrity. In adaptive immune cells, programmed DNA DSBs are generated at precise genomic locations during the assembly and diversification of lymphocyte antigen receptor genes. In innate immune cells, the production of genotoxic agents, such as reactive nitrogen molecules, in response to pathogens can also cause genomic DNA DSBs. These DSBs in adaptive and innate immune cells activate the cDDR. However, recent studies have demonstrated that they also activate non-canonical DDRs (ncDDRs) that regulate cell type-specific processes that are important for innate and adaptive immune responses. Here, we review these ncDDRs and discuss how they integrate with other signals during immune system development and function.
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Heritable, Allele-Specific Chromosomal Looping between Tandem Promoters Specifies Promoter Usage of SHC1. Mol Cell Biol 2018; 38:MCB.00658-17. [PMID: 29440311 DOI: 10.1128/mcb.00658-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/08/2018] [Indexed: 11/20/2022] Open
Abstract
One-half of the genes in the human genome contain alternative promoters, some of which generate products with opposing functions. Aberrant silencing or activation of such alternative promoters is associated with multiple diseases, including cancer, but little is known regarding the molecular mechanisms that control alternative promoter choice. The SHC1 gene encodes p46Shc/p52Shc and p66Shc, proteins oppositely regulating anchorage-independent growth that are produced by transcription initiated from the upstream and downstream tandem promoters of SHC1, respectively. Here we demonstrate that activation of these promoters is mutually exclusive on separate alleles in single primary endothelial cells in a heritable fashion, ensuring expression of both transcripts by the cell. Peripheral blood lymphocytes that do not transcribe p66Shc transcribed p52Shc biallelically. This distinct monoallelic transcription pattern is established by allele-specific chromosomal looping between tandem promoters, which silences the upstream promoter. Our results reveal a new mechanism to control alternative promoter usage through higher-order chromatin structure.
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7
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Programming asynchronous replication in stem cells. Nat Struct Mol Biol 2017; 24:1132-1138. [PMID: 29131141 DOI: 10.1038/nsmb.3503] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 10/12/2017] [Indexed: 01/12/2023]
Abstract
Many regions of the genome replicate asynchronously and are expressed monoallelically. It is thought that asynchronous replication may be involved in choosing one allele over the other, but little is known about how these patterns are established during development. We show that, unlike somatic cells, which replicate in a clonal manner, embryonic and adult stem cells are programmed to undergo switching, such that daughter cells with an early-replicating paternal allele are derived from mother cells that have a late-replicating paternal allele. Furthermore, using ground-state embryonic stem (ES) cells, we demonstrate that in the initial transition to asynchronous replication, it is always the paternal allele that is chosen to replicate early, suggesting that primary allelic choice is directed by preset gametic DNA markers. Taken together, these studies help define a basic general strategy for establishing allelic discrimination and generating allelic diversity throughout the organism.
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Wu C, Dong Y, Zhao X, Zhang P, Zheng M, Zhang H, Li S, Jin Y, Ma Y, Ren H, Ji Y. RAG2 involves the Igκ locus demethylation during B cell development. Mol Immunol 2017. [PMID: 28641141 DOI: 10.1016/j.molimm.2017.06.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The genes encoding the immunoglobulin κ light chain are assembled during B cell development by V(D)J recombination. For efficient rearrangement, the Igκ locus must undergo a series of epigenetic changes. One such epigenetic mark is DNA methylation. The mechanism that the Igκ locus is selectively demethylated at the pre-B cell stage has not previously been characterized. Here, we employed bisulfite DNA-modification assays to analyze the methylation status of the Igκ locus in primary pre-B cells from RAG-deficient mice with pre-rearranged Igh knock-in allele. We observed that the Igκ locus was hypermethylated in RAG2-deficient pre-B cells but hypomethylated in RAG1-deficient pre-B cells, indicating that wild-type (WT) RAG2 involves the Igκ locus demethylation in a RAG1-independent manner prior to rearrangement. We generated a series of RAG2 mutants between residue 350 and 383. We showed that these mutants mediated the Igκ rearrangement but failed to regulate the Igκ gene demethylation. We further analyzed that these mutants could increase RAG recombinase activity in vivo. We conclude that residues 350-383 region are responsible for endogenous Igκ locus demethylation at pre-B cells. We propose that WT RAG2 has an intrinsic function to regulate the Igκ locus demethylation.
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Affiliation(s)
- Caijun Wu
- Department of Pathogenic Biology and Immunology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi,710061, China
| | - Yanying Dong
- Department of Pathogenic Biology and Immunology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi,710061, China
| | - Xiaohui Zhao
- Department of Pathogenic Biology and Immunology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi,710061, China
| | - Ping Zhang
- Department of Pathogenic Biology and Immunology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi,710061, China
| | - Mingzhe Zheng
- Department of Pathogenic Biology and Immunology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi,710061, China
| | - Hua Zhang
- Department of Pathogenic Biology and Immunology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi,710061, China
| | - Shichang Li
- Department of Pathogenic Biology and Immunology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi,710061, China
| | - Yaofeng Jin
- Department of Pathology, the 2nd Affiliated hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, China
| | - Yunfeng Ma
- Department of Pathogenic Biology and Immunology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi,710061, China
| | - Huixun Ren
- Department of Pathogenic Biology and Immunology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi,710061, China
| | - Yanhong Ji
- Department of Pathogenic Biology and Immunology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi,710061, China.
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9
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Clonally stable Vκ allelic choice instructs Igκ repertoire. Nat Commun 2017; 8:15575. [PMID: 28555639 PMCID: PMC5459994 DOI: 10.1038/ncomms15575] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 04/07/2017] [Indexed: 12/30/2022] Open
Abstract
Although much has been done to understand how rearrangement of the Igκ locus is regulated during B-cell development, little is known about the way the variable (V) segments themselves are selected. Here we show, using B6/Cast hybrid pre-B-cell clones, that a limited number of V segments on each allele is stochastically activated as characterized by the appearance of non-coding RNA and histone modifications. The activation states are clonally distinct, stable across cell division and developmentally important in directing the Ig repertoire upon differentiation. Using a new approach of allelic ATAC-seq, we demonstrate that the Igκ V alleles have differential chromatin accessibility, which may serve as the underlying basis of clonal maintenance at this locus, as well as other instances of monoallelic expression throughout the genome. These findings highlight a new level of immune system regulation that optimizes gene diversity. B cell development involves sequential rearrangement of the immunoglobulin chains, but fine control over the selection process remains a mystery. Here the authors show that individual alleles in pre-B cells are clonally unique and result from stochastic activation of V gene segments to induce optimal generation of a diverse repertoire.
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10
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Gebert C, Correia L, Li Z, Petrie HT, Love PE, Pfeifer K. Chromosome choice for initiation of V-(D)-J recombination is not governed by genomic imprinting. Immunol Cell Biol 2017; 95:473-477. [PMID: 28244489 PMCID: PMC5788196 DOI: 10.1038/icb.2017.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/16/2016] [Accepted: 12/18/2016] [Indexed: 01/04/2023]
Abstract
V-(D)-J recombination generates the antigen receptor diversity necessary for immune cell function, while allelic exclusion ensures that each cell expresses a single antigen receptor. V-(D)-J recombination of the Ig, Tcrb, Tcrg and Tcrd antigen receptor genes is ordered and sequential so that only one allele generates a productive rearrangement. The mechanism controlling sequential rearrangement of antigen receptor genes, in particular how only one allele is selected to initiate recombination while at least temporarily leaving the other intact, remains unresolved. Genomic imprinting, a widespread phenomenon wherein maternal or paternal allele inheritance determines allele activity, could represent a regulatory mechanism for controlling sequential V-(D)-J rearrangement. We used strain-specific single-nucleotide polymorphisms within antigen receptor genes to determine if maternal vs paternal inheritance could underlie chromosomal choice for the initiation of recombination. We found no parental chromosomal bias in the initiation of V-(D)-J recombination in T or B cells, eliminating genomic imprinting as a potential regulator for this tightly regulated process.
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Affiliation(s)
- Claudia Gebert
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | - Lauren Correia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | - Zhenhu Li
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | | | - Paul E Love
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | - Karl Pfeifer
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
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11
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Tissue-specific DNA demethylation is required for proper B-cell differentiation and function. Proc Natl Acad Sci U S A 2016; 113:5018-23. [PMID: 27091986 DOI: 10.1073/pnas.1604365113] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is ample evidence that somatic cell differentiation during development is accompanied by extensive DNA demethylation of specific sites that vary between cell types. Although the mechanism of this process has not yet been elucidated, it is likely to involve the conversion of 5mC to 5hmC by Tet enzymes. We show that a Tet2/Tet3 conditional knockout at early stages of B-cell development largely prevents lineage-specific programmed demethylation events. This lack of demethylation affects the expression of nearby B-cell lineage genes by impairing enhancer activity, thus causing defects in B-cell differentiation and function. Thus, tissue-specific DNA demethylation appears to be necessary for proper somatic cell development in vivo.
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12
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Ebert A, Hill L, Busslinger M. Spatial Regulation of V-(D)J Recombination at Antigen Receptor Loci. Adv Immunol 2015; 128:93-121. [PMID: 26477366 DOI: 10.1016/bs.ai.2015.07.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Lymphocytes express a diverse repertoire of antigen receptors, which are able to recognize a large variety of foreign pathogens. Functional antigen receptor genes are assembled by V(D)J recombination in immature B cells (Igh and Igk) and T cells (Tcr b and Tcra/d). V(D)J recombination takes place in the 3' proximal domain containing the D, J, and C gene segments, whereas 31 (Tcrb) to 200 (Igh) V genes are spread over a large region of 0.67 (Tcrb) to 3 (Igk) megabase pairs. The spatial regulation of V(D)J recombination has been best studied for the Igh locus, which undergoes reversible contraction by long-range looping in pro-B cells. This large-scale contraction brings distantly located VH genes into close proximity of the DJH-rearranged gene segment, which facilitates VH-DJH recombination. The B-cell-specific Pax5, ubiquitous YY1, and architectural CTCF/cohesin proteins regulate Igh locus contraction in pro-B cells by binding to multiple sites in the VH gene cluster. These regulators also control the pro-B-cell-specific activity of the distally located PAIR elements, which may be involved in the regulation of VH-DJH recombination by promoting locus contraction. Moreover, the large VH gene cluster of the Igh locus undergoes flexible long-range looping, which guarantees similar participation of all VH genes in VH-DJH recombination to generate a diverse antibody repertoire. Importantly, long-range looping is a more general regulatory principle, as other antigen receptor loci also undergo reversible contraction at the developmental stage, where they engage in V-(D)J recombination.
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Affiliation(s)
- Anja Ebert
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Louisa Hill
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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13
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de Almeida CR, Hendriks RW, Stadhouders R. Dynamic Control of Long-Range Genomic Interactions at the Immunoglobulin κ Light-Chain Locus. Adv Immunol 2015; 128:183-271. [DOI: 10.1016/bs.ai.2015.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Levin-Klein R, Bergman Y. Epigenetic regulation of monoallelic rearrangement (allelic exclusion) of antigen receptor genes. Front Immunol 2014; 5:625. [PMID: 25538709 PMCID: PMC4257082 DOI: 10.3389/fimmu.2014.00625] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 11/22/2014] [Indexed: 12/31/2022] Open
Abstract
While most genes in the mammalian genome are transcribed from both parental chromosomes in cells where they are expressed, approximately 10% of genes are expressed monoallelically, so that any given cell will express either the paternal or maternal allele, but not both. The antigen receptor genes in B and T cells are well-studied examples of a gene family, which is expressed in a monoallelic manner, in a process coined "allelic exclusion." During lymphocyte development, only one allele of each antigen receptor undergoes V(D)J rearrangement at a time, and once productive rearrangement is sensed, rearrangement of the second allele is prevented. In this mini review, we discuss the epigenetic processes, including asynchronous replication, nuclear localization, chromatin condensation, histone modifications, and DNA methylation, which appear to regulate the primary rearrangement of a single allele, while blocking the rearrangement of the second allele.
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Affiliation(s)
- Rena Levin-Klein
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel Canada, Hebrew University Medical School , Jerusalem , Israel
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel Canada, Hebrew University Medical School , Jerusalem , Israel
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15
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Steinel NC, Fisher MR, Yang-Iott KS, Bassing CH. The ataxia telangiectasia mutated and cyclin D3 proteins cooperate to help enforce TCRβ and IgH allelic exclusion. THE JOURNAL OF IMMUNOLOGY 2014; 193:2881-90. [PMID: 25127855 DOI: 10.4049/jimmunol.1302201] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Coordination of V rearrangements between loci on homologous chromosomes is critical for Ig and TCR allelic exclusion. The Ataxia Telangietasia mutated (ATM) protein kinase promotes DNA repair and activates checkpoints to suppress aberrant Ig and TCR rearrangements. In response to RAG cleavage of Igκ loci, ATM inhibits RAG expression and suppresses further Vκ-to-Jκ rearrangements to enforce Igκ allelic exclusion. Because V recombination between alleles is more strictly regulated for TCRβ and IgH loci, we evaluated the ability of ATM to restrict biallelic expression and V-to-DJ recombination of TCRβ and IgH genes. We detected greater frequencies of lymphocytes with biallelic expression or aberrant V-to-DJ rearrangement of TCRβ or IgH loci in mice lacking ATM. A preassembled DJβ complex that decreases the number of TCRβ rearrangements needed for a productive TCRβ gene further increased frequencies of ATM-deficient cells with biallelic TCRβ expression. IgH and TCRβ proteins drive proliferation of prolymphocytes through cyclin D3 (Ccnd3), which also inhibits VH transcription. We show that inactivation of Ccnd3 leads to increased frequencies of lymphocytes with biallelic expression of IgH or TCRβ genes. We also show that Ccnd3 inactivation cooperates with ATM deficiency to increase the frequencies of cells with biallelic TCRβ or IgH expression while decreasing the frequency of ATM-deficient lymphocytes with aberrant V-to-DJ recombination. Our data demonstrate that core components of the DNA damage response and cell cycle machinery cooperate to help enforce IgH and TCRβ allelic exclusion and indicate that control of V-to-DJ rearrangements between alleles is important to maintain genomic stability.
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Affiliation(s)
- Natalie C Steinel
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Abramson Family Cancer Research Institute, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Megan R Fisher
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Abramson Family Cancer Research Institute, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Katherine S Yang-Iott
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Abramson Family Cancer Research Institute, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Craig H Bassing
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Abramson Family Cancer Research Institute, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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16
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Levin-Klein R, Kirillov A, Rosenbluh C, Cedar H, Bergman Y. A novel pax5-binding regulatory element in the igκ locus. Front Immunol 2014; 5:240. [PMID: 24904588 PMCID: PMC4033077 DOI: 10.3389/fimmu.2014.00240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/08/2014] [Indexed: 12/31/2022] Open
Abstract
The Igκ locus undergoes a variety of different molecular processes during B cell development, including V(D)J rearrangement and somatic hypermutations (SHM), which are influenced by cis regulatory regions (RRs) within the locus. The Igκ locus includes three characterized RRs termed the intronic (iEκ), 3′Eκ, and Ed enhancers. We had previously noted that a region of DNA upstream of the iEκ and matrix attachment region (MAR) was necessary for demethylation of the locus in cell culture. In this study, we further characterized this region, which we have termed Dm, for demethylation element. Pre-rearranged Igκ transgenes containing a deletion of the entire Dm region, or of a Pax5-binding site within the region, fail to undergo efficient CpG demethylation in mature B cells in vivo. Furthermore, we generated mice with a deletion of the full Dm region at the endogenous Igκ locus. The most prominent phenotype of these mice is reduced SHM in germinal center B cells in Peyer’s patches. In conclusion, we propose the Dm element as a novel Pax5-binding cis regulatory element, which works in concert with the known enhancers, and plays a role in Igκ demethylation and SHM.
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Affiliation(s)
- Rena Levin-Klein
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School , Jerusalem , Israel
| | - Andrei Kirillov
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School , Jerusalem , Israel
| | - Chaggai Rosenbluh
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School , Jerusalem , Israel
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School , Jerusalem , Israel
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School , Jerusalem , Israel
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17
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Selimyan R, Gerstein RM, Ivanova I, Precht P, Subrahmanyam R, Perlot T, Alt FW, Sen R. Localized DNA demethylation at recombination intermediates during immunoglobulin heavy chain gene assembly. PLoS Biol 2013; 11:e1001475. [PMID: 23382652 PMCID: PMC3558432 DOI: 10.1371/journal.pbio.1001475] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 12/14/2012] [Indexed: 12/23/2022] Open
Abstract
The dynamics of DNA methylation during the complex genomic rearrangement of antigen receptor genes in developing B lymphocytes reveal localized demethylation of the first recombination product that may serve as a mark necessary for the second step of rearrangement. Multiple epigenetic marks have been proposed to contribute to the regulation of antigen receptor gene assembly via V(D)J recombination. Here we provide a comprehensive view of DNA methylation at the immunoglobulin heavy chain (IgH) gene locus prior to and during V(D)J recombination. DNA methylation did not correlate with the histone modification state on unrearranged alleles, indicating that these epigenetic marks were regulated independently. Instead, pockets of tissue-specific demethylation were restricted to DNase I hypersensitive sites within this locus. Though unrearranged diversity (DH) and joining (JH) gene segments were methylated, DJH junctions created after the first recombination step were largely demethylated in pro-, pre-, and mature B cells. Junctional demethylation was highly localized, B-lineage-specific, and required an intact tissue-specific enhancer, Eμ. We propose that demethylation occurs after the first recombination step and may mark the junction for secondary recombination. DNA methylation at CpG dinucleotides is implicated in the regulation of gene expression in mammals. However, the regulation of DNA methylation itself is less clear despite recent advances in identifying enzymes that add or remove methyl groups. We have investigated the dynamics of DNA methylation during genome rearrangements that assemble antigen receptor genes in developing B lymphocytes to determine whether methylation status correlates with rearrangement potential. Two recombination events generate immunoglobulin heavy chain (IgH) genes. The first step brings together diversity (DH) and joining (JH) gene segments to produce DJH junctions. We show that both gene segments are methylated prior to rearrangement, whereas the DJH product is demethylated. DJH junctional demethylation is tissue-specific and requires an enhancer, Eμ, located within the IgH locus. The latter observations indicate that localized demethylation of the DJH junction occurs after the first recombination step and thus does not guide this first step of IgH gene assembly. Our working hypothesis is that recombination induces demethylation of recombinant product and may mark the junction for the second step of IgH rearrangement, juxtaposition of variable (VH) gene segments to rearranged DJH products to produce fully recombined V(D)J alleles.
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Affiliation(s)
- Roza Selimyan
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Rachel M. Gerstein
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Irina Ivanova
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Patricia Precht
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Ramesh Subrahmanyam
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Thomas Perlot
- The Howard Hughes Medical Institute, The Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Frederick W. Alt
- The Howard Hughes Medical Institute, The Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
- * E-mail:
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18
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Berkowska MA, van der Burg M, van Dongen JJM, van Zelm MC. Checkpoints of B cell differentiation: visualizing Ig-centric processes. Ann N Y Acad Sci 2012; 1246:11-25. [PMID: 22236426 DOI: 10.1111/j.1749-6632.2011.06278.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The generation of antibody responses and B cell memory can only take place following multiple steps of differentiation. Key molecular processes during precursor B cell differentiation in bone marrow generate unique antibodies. These antibodies are further optimized via molecular modifications during immune responses in peripheral lymphoid organs. Multiple checkpoints ensure proper differentiation of precursor and mature B lymphocytes. Many of these checkpoints have been found disrupted in patients with a primary immunodeficiency. Based on studies in these patients and in mouse models, new insights have been generated in B cell differentiation and antibody responses. Still, in many patients with impaired antibody formation, it remains unclear how B cells are affected. In this perspective, we present 11 critical processes in B cell differentiation. We discuss how defects in these processes can result in impaired checkpoint selection and how they can be visualized in healthy subjects and patients with immunodeficiency or other immunological disease.
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Affiliation(s)
- Magdalena A Berkowska
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
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19
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Sleckman BP, Oltz EM. Preparing targets for V(D)J recombinase: transcription paves the way. THE JOURNAL OF IMMUNOLOGY 2012; 188:7-9. [PMID: 22187481 DOI: 10.4049/jimmunol.1103195] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Barry P Sleckman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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20
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Bossen C, Mansson R, Murre C. Chromatin topology and the regulation of antigen receptor assembly. Annu Rev Immunol 2012; 30:337-56. [PMID: 22224771 DOI: 10.1146/annurev-immunol-020711-075003] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During an organism's ontogeny and in the adult, each B and T lymphocyte generates a unique antigen receptor, thereby creating the organism's ability to respond to a vast number of different antigens. The antigen receptor loci are organized into distinct regions that contain multiple variable (V), diversity (D), and/or joining (J) and constant (C) coding elements that are scattered across large genomic regions. In this review, we discuss the epigenetic modifications that take place in the different antigen receptor loci, the chromatin structure adopted by the antigen receptor loci to allow recombination of elements separated by large genomic distances, and the relationship between epigenetics and chromatin structure and how they relate to the generation of antigen receptor diversity.
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Affiliation(s)
- Claudia Bossen
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093-0377, USA
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21
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Abstract
Cells of the immune system are generated through a developmental cascade that begins in haematopoietic stem cells. During this process, gene expression patterns are programmed in a series of stages that bring about the restriction of cell potential, ultimately leading to the formation of specialized innate immune cells and mature lymphocytes that express antigen receptors. These events involve the regulation of both gene expression and DNA recombination, mainly through the control of chromatin accessibility. In this Review, we describe the epigenetic changes that mediate this complex differentiation process and try to understand the logic of the programming mechanism.
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22
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Matheson LS, Corcoran AE. Local and global epigenetic regulation of V(D)J recombination. Curr Top Microbiol Immunol 2011; 356:65-89. [PMID: 21695632 DOI: 10.1007/82_2011_137] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite using the same Rag recombinase machinery expressed in both lymphocyte lineages, V(D)J recombination of immunoglobulins only occurs in B cells and T cell receptor recombination is confined to T cells. This vital segregation of recombination targets is governed by the coordinated efforts of several epigenetic mechanisms that control both the general chromatin accessibility of these loci to the Rag recombinase, and the movement and synapsis of distal gene segments in these enormous multigene AgR loci, in a lineage and developmental stage-specific manner. These mechanisms operate both locally at individual gene segments and AgR domains, and globally over large distances in the nucleus. Here we will discuss the roles of several epigenetic components that regulate V(D)J recombination of the immunoglobulin heavy chain locus in B cells, both in the context of the locus itself, and of its 3D nuclear organization, focusing in particular on non-coding RNA transcription. We will also speculate about how several newly described epigenetic mechanisms might impact on AgR regulation.
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Affiliation(s)
- Louise S Matheson
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
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23
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Zhou X, Xiang Y, Garrard WT. The Igκ gene enhancers, E3' and Ed, are essential for triggering transcription. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2010; 185:7544-52. [PMID: 21076060 PMCID: PMC3059262 DOI: 10.4049/jimmunol.1002665] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mouse Igκ gene locus has three known transcriptional enhancers: an intronic enhancer (Ei), a 3' enhancer (E3'), and a further downstream enhancer (Ed). Previous studies on B lymphocytes derived from mutant embryonic stem cells have shown that deletion of either Ei or E3' significantly reduces Igκ gene rearrangement, whereas the combined deletion of both Ei and E3' eliminates such recombination. Furthermore, deletion of either E3' or Ed significantly reduces rearranged Igκ gene transcription. To determine whether the combined presence of both E3' and Ed are essential for Igκ gene expression, we generated homozygous double knockout (DKO) mice with targeted deletions in both elements. Significantly, homozygous DKO mice were unable to generate κ(+) B cells both in bone marrow and the periphery and exhibited surface expression almost exclusively of Igλ-chains, despite the fact that they possessed potentially functional rearranged Igκ genes. Compared with their single-enhancer-deleted counterparts, Igκ loci in homozygous DKO mice exhibited dramatically reduced germline and rearranged gene transcription, lower levels of gene rearrangement and histone H3 acetylation, and markedly increased DNA methylation. This contributed to a partial developmental block at the pre-B cell stage of development. We conclude that the two downstream enhancers are essential in Igκ gene expression and that Ei in homozygous DKO mice is incapable of triggering Igκ gene transcription. Furthermore, these results reveal unexpected compensatory roles for Ed in E3' knockout mice in triggering germline transcription and Vκ gene rearrangements to both Jκ and RS elements.
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Affiliation(s)
- Xiaorong Zhou
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148
- Department of Microbiology and Immunology, Medical School of Nantong University, 19 Qixiu Road, Nantong, Jiangsu 226001, PR China
| | - Yougui Xiang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148
| | - William T. Garrard
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9148
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24
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Abstract
Immune receptor gene expression is regulated by a series of developmental events that modify their accessibility in a locus, cell type, stage and allele-specific manner. This is carried out by a programmed combination of many different molecular mechanisms, including region-wide replication timing, changes in nuclear localization, chromatin contraction, histone modification, nucleosome positioning and DNA methylation. These modalities ultimately work by controlling steric interactions between receptor loci and the recombination machinery.
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Affiliation(s)
- Yehudit Bergman
- Department of Developmental Biology and Cancer Research, The Hebrew University, Hadassah Medical School, Jerusalem 91120, Israel.
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25
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Wang J, Valo Z, Bowers CW, Smith DD, Liu Z, Singer-Sam J. Dual DNA methylation patterns in the CNS reveal developmentally poised chromatin and monoallelic expression of critical genes. PLoS One 2010; 5:e13843. [PMID: 21079792 PMCID: PMC2973945 DOI: 10.1371/journal.pone.0013843] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 10/15/2010] [Indexed: 11/30/2022] Open
Abstract
As a first step towards discovery of genes expressed from only one allele in the CNS, we used a tiling array assay for DNA sequences that are both methylated and unmethylated (the MAUD assay). We analyzed regulatory regions of the entire mouse brain transcriptome, and found that approximately 10% of the genes assayed showed dual DNA methylation patterns. They include a large subset of genes that display marks of both active and silent, i.e., poised, chromatin during development, consistent with a link between differential DNA methylation and lineage-specific differentiation within the CNS. Sixty-five of the MAUD hits and 57 other genes whose function is of relevance to CNS development and/or disorders were tested for allele-specific expression in F1 hybrid clonal neural stem cell (NSC) lines. Eight MAUD hits and one additional gene showed such expression. They include Lgi1, which causes a subtype of inherited epilepsy that displays autosomal dominance with incomplete penetrance; Gfra2, a receptor for glial cell line-derived neurotrophic factor GDNF that has been linked to kindling epilepsy; Unc5a, a netrin-1 receptor important in neurodevelopment; and Cspg4, a membrane chondroitin sulfate proteoglycan associated with malignant melanoma and astrocytoma in human. Three of the genes, Camk2a, Kcnc4, and Unc5a, show preferential expression of the same allele in all clonal NSC lines tested. The other six genes show a stochastic pattern of monoallelic expression in some NSC lines and bi-allelic expression in others. These results support the estimate that 1–2% of genes expressed in the CNS may be subject to allelic exclusion, and demonstrate that the group includes genes implicated in major disorders of the CNS as well as neurodevelopment.
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Affiliation(s)
- Jinhui Wang
- Division of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
| | - Zuzana Valo
- Division of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
| | - Chauncey W. Bowers
- Division of Computational Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
| | - David D. Smith
- Division of Biostatistics, City of Hope National Medical Center, Duarte, California, United States of America
| | - Zheng Liu
- Bioinformatics Core Facility, Department of Molecular Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
| | - Judith Singer-Sam
- Division of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
- * E-mail:
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26
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Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, Li JR, Clark D, Kaur M, Tatsuro K, Kline AD, Chang C, Vega H, Jackson LG, Spinner NB, Shirahige K, Krantz ID. Genome-wide DNA methylation analysis in cohesin mutant human cell lines. Nucleic Acids Res 2010; 38:5657-71. [PMID: 20448023 PMCID: PMC2943628 DOI: 10.1093/nar/gkq346] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Revised: 04/19/2010] [Accepted: 04/21/2010] [Indexed: 12/17/2022] Open
Abstract
The cohesin complex has recently been shown to be a key regulator of eukaryotic gene expression, although the mechanisms by which it exerts its effects are poorly understood. We have undertaken a genome-wide analysis of DNA methylation in cohesin-deficient cell lines from probands with Cornelia de Lange syndrome (CdLS). Heterozygous mutations in NIPBL, SMC1A and SMC3 genes account for ∼65% of individuals with CdLS. SMC1A and SMC3 are subunits of the cohesin complex that controls sister chromatid cohesion, whereas NIPBL facilitates cohesin loading and unloading. We have examined the methylation status of 27 578 CpG dinucleotides in 72 CdLS and control samples. We have documented the DNA methylation pattern in human lymphoblastoid cell lines (LCLs) as well as identified specific differential DNA methylation in CdLS. Subgroups of CdLS probands and controls can be classified using selected CpG loci. The X chromosome was also found to have a unique DNA methylation pattern in CdLS. Cohesin preferentially binds to hypo-methylated DNA in control LCLs, whereas the differential DNA methylation alters cohesin binding in CdLS. Our results suggest that in addition to DNA methylation multiple mechanisms may be involved in transcriptional regulation in human cells and in the resultant gene misexpression in CdLS.
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Affiliation(s)
- Jinglan Liu
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Masashige Bando
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Takehiko Itoh
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Matthew A. Deardorff
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Jennifer R. Li
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Dinah Clark
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Maninder Kaur
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Kondo Tatsuro
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Antonie D. Kline
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Celia Chang
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Hugo Vega
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Laird G. Jackson
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Nancy B. Spinner
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Katsuhiko Shirahige
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Ian D. Krantz
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
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27
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Abstract
The allelic exclusion of immunoglobulin (Ig) genes is one of the most evolutionarily conserved features of the adaptive immune system and underlies the monospecificity of B cells. While much has been learned about how Ig allelic exclusion is established during B-cell development, the relevance of monospecificity to B-cell function remains enigmatic. Here, we review the theoretical models that have been proposed to explain the establishment of Ig allelic exclusion and focus on the molecular mechanisms utilized by developing B cells to ensure the monoallelic expression of Ig kappa and Ig lambda light chain genes. We also discuss the physiological consequences of Ig allelic exclusion and speculate on the importance of monospecificity of B cells for immune recognition.
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Affiliation(s)
- Christian Vettermann
- Division of Immunology & Pathogenesis, Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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28
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Brady BL, Oropallo MA, Yang-Iott KS, Serwold T, Hochedlinger K, Jaenisch R, Weissman IL, Bassing CH. Position-dependent silencing of germline Vß segments on TCRß alleles containing preassembled VßDJßCß1 genes. THE JOURNAL OF IMMUNOLOGY 2010; 185:3564-73. [PMID: 20709953 DOI: 10.4049/jimmunol.0903098] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The genomic organization of TCRbeta loci enables Vbeta-to-DJbeta2 rearrangements on alleles with assembled VbetaDJbetaCbeta1 genes, which could have deleterious physiologic consequences. To determine whether such Vbeta rearrangements occur and, if so, how they might be regulated, we analyzed mice with TCRbeta alleles containing preassembled functional VbetaDJbetaCbeta1 genes. Vbeta10 segments were transcribed, rearranged, and expressed in thymocytes when located immediately upstream of a Vbeta1DJbetaCbeta1 gene, but not on alleles with a Vbeta14DJbetaCbeta1 gene. Germline Vbeta10 transcription was silenced in mature alphabeta T cells. This allele-dependent and developmental stage-specific silencing of Vbeta10 correlated with increased CpG methylation and decreased histone acetylation over the Vbeta10 promoter and coding region. Transcription, rearrangement, and expression of the Vbeta4 and Vbeta16 segments located upstream of Vbeta10 were silenced on alleles containing either VbetaDJbetaCbeta1 gene; sequences within Vbeta4, Vbeta16, and the Vbeta4/Vbeta16-Vbeta10 intergenic region exhibited constitutive high CpG methylation and low histone acetylation. Collectively, our data indicate that the position of Vbeta segments relative to assembled VbetaDJbetaCbeta1 genes influences their rearrangement and suggest that DNA sequences between Vbeta segments may form boundaries between active and inactive Vbeta chromatin domains upstream of VbetaDJbetaCbeta genes.
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Affiliation(s)
- Brenna L Brady
- Immunology Graduate Group, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA
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29
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Farcot E, Bonnet M, Jaeger S, Spicuglia S, Fernandez B, Ferrier P. TCR beta allelic exclusion in dynamical models of V(D)J recombination based on allele independence. THE JOURNAL OF IMMUNOLOGY 2010; 185:1622-32. [PMID: 20585038 DOI: 10.4049/jimmunol.0904182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Allelic exclusion represents a major aspect of TCRbeta gene assembly by V(D)J recombination in developing T lymphocytes. Despite recent progress, its comprehension remains problematic when confronted with experimental data. Existing models fall short in terms of incorporating into a unique distribution all the cell subsets emerging from the TCRbeta assembly process. To revise this issue, we propose dynamical, continuous-time Markov chain-based modeling whereby essential steps in the biological procedure (D-J and V-DJ rearrangements and feedback inhibition) evolve independently on the two TCRbeta alleles in every single cell while displaying random modes of initiation and duration. By selecting parameters via fitting procedures, we demonstrate the capacity of the model to offer accurate fractions of all distinct TCRbeta genotypes observed in studies using developing and mature T cells from wild-type or mutant mice. Selected parameters in turn afford relative duration for each given step, hence updating TCRbeta recombination distinctive timings. Overall, our dynamical modeling integrating allele independence and noise in recombination and feedback-inhibition events illustrates how the combination of these ingredients alone may enforce allelic exclusion at the TCRbeta locus.
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Affiliation(s)
- Etienne Farcot
- Centre de Physique Théorique, Centre National de la Recherche Scientifique Unité Mixte de Recherche 6207, Université de la Méditerranée-Université de Provence-Université Sud Toulon Var, Centre National de la Recherche Scientifique Luminy Case 907, France
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30
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Yang-Iott KS, Carpenter AC, Rowh MAW, Steinel N, Brady BL, Hochedlinger K, Jaenisch R, Bassing CH. TCR beta feedback signals inhibit the coupling of recombinationally accessible V beta 14 segments with DJ beta complexes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2010; 184:1369-78. [PMID: 20042591 PMCID: PMC2873682 DOI: 10.4049/jimmunol.0900723] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ag receptor allelic exclusion is thought to occur through monoallelic initiation and subsequent feedback inhibition of recombinational accessibility. However, our previous analysis of mice containing a V(D)J recombination reporter inserted into Vbeta14 (Vbeta14(Rep)) indicated that Vbeta14 chromatin accessibility is biallelic. To determine whether Vbeta14 recombinational accessibility is subject to feedback inhibition, we analyzed TCRbeta rearrangements in Vbeta14(Rep) mice containing a preassembled in-frame transgenic Vbeta8.2Dbeta1Jbeta1.1 or an endogenous Vbeta14Dbeta1Jbeta1.4 rearrangement on the homologous chromosome. Expression of either preassembled VbetaDJbetaC beta-chain accelerated thymocyte development because of enhanced cellular selection, demonstrating that the rate-limiting step in early alphabeta T cell development is the assembly of an in-frame VbetaDJbeta rearrangement. Expression of these preassembled VbetaDJbeta rearrangements inhibited endogenous Vbeta14-to-DJbeta rearrangements as expected. However, in contrast to results predicted by the accepted model of TCRbeta feedback inhibition, we found that expression of these preassembled TCR beta-chains did not downregulate recombinational accessibility of Vbeta14 chromatin. Our findings suggest that TCRbeta-mediated feedback inhibition of Vbeta14 rearrangements depends on inherent properties of Vbeta14, Dbeta, and Jbeta recombination signal sequences.
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MESH Headings
- Animals
- Antibody Diversity/genetics
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Chromatin/physiology
- Feedback, Physiological/physiology
- Gene Expression Regulation, Developmental/immunology
- Gene Rearrangement, T-Lymphocyte/immunology
- Genes, Reporter/immunology
- Germ-Line Mutation/immunology
- Immunoglobulin Joining Region/genetics
- Immunoglobulin Variable Region/genetics
- Loss of Heterozygosity/immunology
- Mice
- Mice, Transgenic
- Receptors, Antigen, T-Cell, alpha-beta/antagonists & inhibitors
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Signal Transduction/genetics
- Signal Transduction/immunology
- T-Lymphocyte Subsets/cytology
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
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Affiliation(s)
- Katherine S. Yang-Iott
- Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Abramson Family Cancer Research Institute, Philadelphia, PA 19104
| | - Andrea C. Carpenter
- Immunology Graduate Group, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Abramson Family Cancer Research Institute, Philadelphia, PA 19104
| | - Marta A. W. Rowh
- Immunology Graduate Group, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Abramson Family Cancer Research Institute, Philadelphia, PA 19104
| | - Natalie Steinel
- Immunology Graduate Group, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Abramson Family Cancer Research Institute, Philadelphia, PA 19104
| | - Brenna L. Brady
- Immunology Graduate Group, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Abramson Family Cancer Research Institute, Philadelphia, PA 19104
| | - Konrad Hochedlinger
- Department of Medicine, Harvard Medical School, Massachusetts General Hospital, Cancer Center and Center for Regenerative Medicine, Boston, MA 02114
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Craig H. Bassing
- Immunology Graduate Group, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Abramson Family Cancer Research Institute, Philadelphia, PA 19104
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31
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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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32
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Abstract
The adaptive immune system of jawed vertebrates is based on a vast, anticipatory repertoire of specific antigen receptors, immunoglobulins (Ig) in B-lymphocytes and T-cell receptors (TCR) in T-lymphocytes. The Ig and TCRdiversity is generated by a process called V(D)J recombination, which is initiated by the RAG recombinase. Although RAG activity is very well conserved, the regulated accessibility of the antigen receptor genes to RAG has evolved with the species' organizational structure, which differs most significantly between fishes and tetrapods. V(D)J recombination was primarily characterized in developing lymphocytes of mice and human beings and is often described as an ordered, two-stage program. Studies in rabbit, chicken and shark show that this process does not have to be ordered, nor does it need to take place in two stages to generate a diverse repertoire and enable the expression of a single species of antigen receptor per cell, a restriction called allelic exclusion.
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33
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Bolland DJ, Wood AL, Corcoran AE. Large-Scale Chromatin Remodeling at the Immunoglobulin Heavy Chain Locus: A Paradigm for Multigene Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 650:59-72. [DOI: 10.1007/978-1-4419-0296-2_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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34
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Temporal and spatial regulation of V(D)J recombination: interactions of extrinsic factors with the RAG complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 650:157-65. [PMID: 19731809 DOI: 10.1007/978-1-4419-0296-2_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In the course of lymphoid development, V(D)J recombination is subject to stringent locus-specific and temporal regulation. These constraints are ultimately responsible for several features peculiar to lymphoid development, including the lineage specificity of antigen receptor assembly, allelic exclusion and receptor editing. In addition, cell cycle phase-dependent regulation of V(D)J recombinase activity ensures that DNA rearrangement is completed by the appropriate mechanism of DNA repair. Regulation of V(D)J recombination involves interactions between the V(D)J recombinase--a heteromeric complex consisting of RAG-1 and RAG-2 subunits--and macromolecular assemblies extrinsic to the recombinase. This chapter will focus on those features of the recombinase itself--and in particular the RAG-2 subunit--that interact with extrinsic factors to establish patterns of temporal control and locus specificity in developing lymphocytes.
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35
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Biallelic, ubiquitous transcription from the distal germline Ig{kappa} locus promoter during B cell development. Proc Natl Acad Sci U S A 2008; 106:522-7. [PMID: 19116268 DOI: 10.1073/pnas.0808895106] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Allelic exclusion of Ig gene expression is necessary to limit the number of functional receptors to one per B cell. The mechanism underlying allelic exclusion is unknown. Because germline transcription of Ig and TCR loci is tightly correlated with rearrangement, we created two novel knock-in mice that report transcriptional activity of the Jkappa germline promoters in the Igkappa locus. Analysis of these mice revealed that germline transcription is biallelic and occurs in all pre-B cells. Moreover, we found that the two germline promoters in this region are not equivalent but that the distal promoter accounts for the vast majority of observed germline transcript in pre-B cells while the activity of the proximal promoter increases later in development. Allelic exclusion of the Igkappa locus thus occurs at the level of rearrangement, but not germline transcription.
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36
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A reappraisal of evidence for probabilistic models of allelic exclusion. Proc Natl Acad Sci U S A 2008; 106:516-21. [PMID: 19116266 DOI: 10.1073/pnas.0808764105] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
B cell development requires the coordinated rearrangement of Ig heavy (IgH) and light chain loci (IgL). Most mature B cells express a single B cell receptor of unique specificity, and a central question in immunology concerns the mechanisms that prevent the productive rearrangement of >1 IgH and IgL allele per cell. Probabilistic models of allelic exclusion maintain that simultaneous rearrangement of both alleles is rare, because the likelihood of undergoing rearrangement is low for a given Ig allele. Strong support for this idea came from studies in which a GFP marker was inserted into the Igk locus. In this system, the probability of high-level germ-line transcription and subsequent locus rearrangement appeared to be low in pre-B cells. Readdressing the validity of GFP expression as a reporter for the level of germ-line transcription, we found a striking discordance between GFP transcript and protein levels at the pre-B cell stage, which is explained at least in part by the developmentally regulated usage of 2 alternative Igk-J germ-line promoters. These results question the validity of the kappa-GFP system as evidence for probabilistic models of allelic exclusion.
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37
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Abstract
The adaptive immune system depends on specific antigen receptors, immunoglobulins (Ig) in B lymphocytes and T cell receptors (TCR) in T lymphocytes. Adaptive responses to immune challenge are based on the expression of a single species of antigen receptor per cell; and in B cells, this is mediated in part by allelic exclusion at the Ig heavy (H) chain locus. How allelic exclusion is regulated is unclear; we considered that sharks, the oldest vertebrates possessing the Ig/TCR-based immune system, would yield insights not previously approachable and reveal the primordial basis of the regulation of allelic exclusion. Sharks have an IgH locus organization consisting of 15–200 independently rearranging miniloci (VH-D1-D2-JH-Cμ), a gene organization that is considered ancestral to the tetrapod and bony fish IgH locus. We found that rearrangement takes place only within a minilocus, and the recombining gene segments are assembled simultaneously and randomly. Only one or few H chain genes were fully rearranged in each shark B cell, whereas the other loci retained their germline configuration. In contrast, most IgH were partially rearranged in every thymocyte (developing T cell) examined, but no IgH transcripts were detected. The distinction between B and T cells in their IgH configurations and transcription reveals a heretofore unsuspected chromatin state permissive for rearrangement in precursor lymphocytes, and suggests that controlled limitation of B cell lineage-specific factors mediate regulated rearrangement and allelic exclusion. This regulation may be shared by higher vertebrates in which additional mechanistic and regulatory elements have evolved with their structurally complex IgH locus. Lymphocytes provide a limitless repertoire of antigen receptors, but each lymphocyte expresses only one kind of receptor per cell in order to provide specific recognition and response to pathogen invasion. The restriction, called allelic exclusion, operates in tetrapod vertebrates from frogs to human beings. In mouse, immunoglobulin (Ig) heavy chain (H) exclusion depends on ordered activation of component parts of the highly complex, three-megabase IgH locus in a process that differentiates between the two alleles. However, the regulation and mechanisms ensuring allelic exclusion remain uncertain. Sharks represent the earliest vertebrates with an adaptive immune system; their IgH organization, consisting of multiple miniloci, is considered primitive and ancestral to the classical IgH locus in other vertebrates. We show that allelic exclusion nonetheless exists in shark B lymphocytes, although attained by alternative means. Thus, major aspects of the complex pathway described for allelic exclusion in mammals evolved with their IgH organization. Elucidating shared and divergent regulatory processes allows us to gain insight into the basis and evolution of allelic exclusion, which provides the foundation for the functioning of the adaptive immune system. In B lymphocytes of most animals, only one allele is expressed at the antibody heavy-chain locus, while the other is shut down. Sharks have 15-200 such loci. How is antibody expression regulated in this early vertebrate?
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38
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Kuzin II, Bagaeva L, Young FM, Bottaro A. Requirement for enhancer specificity in immunoglobulin heavy chain locus regulation. THE JOURNAL OF IMMUNOLOGY 2008; 180:7443-50. [PMID: 18490744 DOI: 10.4049/jimmunol.180.11.7443] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The intronic Emicro enhancer has been implicated in IgH locus transcription, VDJ recombination, class switch recombination, and somatic hypermutation. How Emicro controls these diverse mechanisms is still largely unclear, but transcriptional enhancer activity is thought to play a central role. In this study we compare the phenotype of mice lacking the Emicro element (DeltaEmicro) with that of mice in which Emu was replaced with the ubiquitous SV40 transcriptional enhancer (SV40eR mutation) and show that SV40e cannot functionally complement Emu loss in pro-B cells. Surprisingly, in fact, the SV40eR mutation yields a more profound defect than DeltaEmicro, with an almost complete block in micro0 germline transcription in pro-B cells. This active transcriptional suppression caused by enhancer replacement appears to be specific to the early stages of B cell development, as mature SV40eR B cells express micro0 transcripts at higher levels than DeltaEmicro mice and undergo complete DNA demethylation at the IgH locus. These results indicate an unexpectedly stringent, developmentally restricted requirement for enhancer specificity in regulating IgH function during the early phases of B cell differentiation, consistent with the view that coordination of multiple independent regulatory mechanisms and elements is essential for locus activation and VDJ recombination.
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Affiliation(s)
- Igor I Kuzin
- Department of Medicine, J.P Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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39
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Initiation of allelic exclusion by stochastic interaction of Tcrb alleles with repressive nuclear compartments. Nat Immunol 2008; 9:802-9. [PMID: 18536719 DOI: 10.1038/ni.1624] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 05/20/2008] [Indexed: 12/12/2022]
Abstract
Studies of antigen-receptor loci have linked directed monoallelic association with pericentromeric heterochromatin to the initiation or maintenance of allelic exclusion. Here we provide evidence for a fundamentally different basis for T cell antigen receptor-beta (Tcrb) allelic exclusion. Using three-dimensional immunofluorescence in situ hybridization, we found that germline Tcrb alleles associated stochastically and at high frequency with the nuclear lamina or with pericentromeric heterochromatin in developing thymocytes and that such interactions inhibited variable-to-diversity-joining (V(beta)-to-D(beta)J(beta)) recombination before beta-selection. The introduction of an ectopic enhancer into Tcrb resulted in fewer such interactions and impaired allelic exclusion. We propose that initial V(beta)-to-D(beta)J(beta) recombination events are generally monoallelic in developing thymocytes because of frequent stochastic, rather than directed, interactions of Tcrb alleles with repressive nuclear compartments. Such interactions may be essential for Tcrb allelic exclusion.
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40
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Xiang Y, Garrard WT. The Downstream Transcriptional Enhancer, Ed, positively regulates mouse Ig kappa gene expression and somatic hypermutation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2008; 180:6725-32. [PMID: 18453592 PMCID: PMC2424255 DOI: 10.4049/jimmunol.180.10.6725] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The mouse Igkappa locus has three known transcriptional enhancers: the matrix association region/intronic enhancer, the 3' enhancer (E3'), and the further downstream enhancer (Ed). Previous studies have shown that both matrix association region/intronic and E3' enhancers are required for maximal gene rearrangement of the locus, and that E3' is also required for maximal expression and somatic hypermutation (SHM). To functionally elucidate Ed in vivo, we generated knockout mice with a targeted germline deletion of Ed. Ed deleted homozygous mice (Ed-/-) have moderately reduced numbers of Igkappa expressing B cells and correspondingly increased numbers of Iglambda expressing B cells in spleen. Ed-/- mice also have decreased Igkappa mRNA expression in resting and T cell-dependent activated splenic B cells and reduced Igkappa chains in sera. However, our analysis indicates that Igkappa gene rearrangement is normal in Ed-/- mice. In addition, our results show that Ed-/- mice exhibit reduced SHM in the Igkappa gene J-C intronic region in germinal center B cells from Peyer's patches. We conclude that Ed positively regulates Igkappa gene expression and SHM, but not gene rearrangement.
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Affiliation(s)
- Yougui Xiang
- Department of Molecular Biology University of Texas, Southwestern Medical Center, Dallas, TX 75390, USA
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41
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Cedar H, Bergman Y. Choreography of Ig allelic exclusion. Curr Opin Immunol 2008; 20:308-17. [PMID: 18400481 DOI: 10.1016/j.coi.2008.02.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 02/22/2008] [Indexed: 12/24/2022]
Abstract
Allelic exclusion guarantees that each B or T cell only produces a single antigen receptor, and in this way contributes to immune diversity. This process is actually initiated in the early embryo when the immune receptor loci become asynchronously replicating in a stochastic manner with one early and one late allele in each cell. This distinct differential replication timing feature then serves an instructive mark that directs a series of allele-specific epigenetic events in the immune system, including programmed histone modification, nuclear localization and DNA demethylation that ultimately bring about preferred rearrangement on a single allele, and this decision is temporally stabilized by feedback mechanisms that inhibit recombination on the second allele. In principle, these same molecular components are also used for controlling monoallelic expression at other genomic loci, such as those carrying interleukins and olfactory receptor genes that require the choice of one gene out of a large array. Thus, allelic exclusion appears to represent a general epigenetic phenomenon that is modeled on the same basis as X chromosome inactivation.
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Affiliation(s)
- Howard Cedar
- Department of Cellular Biochemistry and Human Genetics, Hebrew University Medical School, Jerusalem 91120, Israel.
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42
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Agata Y, Tamaki N, Sakamoto S, Ikawa T, Masuda K, Kawamoto H, Murre C. Regulation of T cell receptor beta gene rearrangements and allelic exclusion by the helix-loop-helix protein, E47. Immunity 2008; 27:871-84. [PMID: 18093539 DOI: 10.1016/j.immuni.2007.11.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 10/06/2007] [Accepted: 11/09/2007] [Indexed: 11/16/2022]
Abstract
Allelic exclusion of antigen-receptor genes is ensured primarily by monoallelic locus activation upon rearrangement and subsequently by feedback inhibition of continued rearrangement. Here, we demonstrated that the basic helix-loop-helix protein, E47, promoted T cell receptor beta (TCRbeta) gene rearrangement by directly binding to target gene segments to increase chromatin accessibility in a dosage-sensitive manner. Feedback signaling abrogated E47 binding, leading to a decline in accessibility. Conversely, enforced expression of E47 induced TCRbeta gene rearrangement by antagonizing feedback inhibition. Thus, the abundance of E47 is rate limiting in locus activation, and feedback signaling downregulates E47 activity to ensure allelic exclusion.
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Affiliation(s)
- Yasutoshi Agata
- Horizontal Medical Research Organization, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.
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43
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Shen L, Catalano PJ, Benson AB, O'Dwyer P, Hamilton SR, Issa JPJ. Association between DNA methylation and shortened survival in patients with advanced colorectal cancer treated with 5-fluorouracil based chemotherapy. Clin Cancer Res 2007; 13:6093-8. [PMID: 17947473 DOI: 10.1158/1078-0432.ccr-07-1011] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
PURPOSE There are no good genomic markers of survival in patients with advanced colorectal cancer. The CpG island methylator phenotype (CIMP) marks a distinctive pathway in colorectal cancer. We sought to determine the prognostic significance of CIMP in advanced colorectal cancer patients treated with 5-fluorouracil (5-FU) in an Eastern Cooperative Oncology Group clinical trial. EXPERIMENTAL DESIGN We studied 188 patients enrolled on protocol E2290, a five-arm trial comparing 5-FU, 5-FU in combination with N-phosphonoacetyl-l-aspartic acid, oral leucovorin, i.v. leucovorin, or IFNalpha-2a in patients with advanced colorectal cancer. Methylation of MINT1, MINT31, hMLH1, p14ARF, and p16INK4a in DNA extracted from formalin-fixed paraffin-embedded specimens was evaluated by combined bisulfite restriction analysis, and methylation of MINT2 was studied by methylation-specific PCR. RESULTS Methylation frequencies were 21% for MINT1, 23% for MINT2, 24% for MINT31, 4% for hMLH1, 11% for p14ARF, and 17% for p16INK4a. Methylation of MINT1, MINT31, p14ARF, and p16INK4a were correlated, as expected. There was no association between methylation and clinicopathologic factors or response to therapy. Methylation of MINT1, MINT31, p14ARF, or p16INK4a was associated individually with shortened overall survival. Hazard ratios were 1.51 (P = 0.05) for MINT1, 1.70 (P = 0.006) for MINT31, 2.22 (P = 0.001) for p14ARF, and 1.51 (P = 0.05) for p16INK4a. Concurrent methylation of two or more genes of the CIMP-associated subset (MINT1, MINT31, p14ARF and p16INK4a) defined a group of cases with markedly reduced overall survival and hazard ratio was 3.22 (P < 0.0001 in multivariate analyses). CONCLUSIONS CIMP is associated with poor survival in advanced colorectal cancer patients.
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Affiliation(s)
- Lanlan Shen
- The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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44
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Gimelbrant A, Hutchinson JN, Thompson BR, Chess A. Widespread monoallelic expression on human autosomes. Science 2007; 318:1136-40. [PMID: 18006746 DOI: 10.1126/science.1148910] [Citation(s) in RCA: 432] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Monoallelic expression with random choice between the maternal and paternal alleles defines an unusual class of genes comprising X-inactivated genes and a few autosomal gene families. Using a genome-wide approach, we assessed allele-specific transcription of about 4000 human genes in clonal cell lines and found that more than 300 were subject to random monoallelic expression. For a majority of monoallelic genes, we also observed some clonal lines displaying biallelic expression. Clonal cell lines reflect an independent choice to express the maternal, the paternal, or both alleles for each of these genes. This can lead to differences in expressed protein sequence and to differences in levels of gene expression. Unexpectedly widespread monoallelic expression suggests a mechanism that generates diversity in individual cells and their clonal descendants.
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Affiliation(s)
- Alexander Gimelbrant
- Center for Human Genetic Research and Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA
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45
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Murre C. Epigenetics of antigen-receptor gene assembly. Curr Opin Genet Dev 2007; 17:415-21. [PMID: 17920858 PMCID: PMC2151926 DOI: 10.1016/j.gde.2007.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 07/17/2007] [Accepted: 08/17/2007] [Indexed: 02/05/2023]
Abstract
The antigen receptor genes are organized into distinct DNA elements that encode the variable (V), diversity (D) and joining (J) regions. It is now well established that the rearrangement of antigen receptor genes is regulated by developmental-specific modulation of chromatin structure. Further studies involving statistical mechanics should provide physical insight into the physical mechanisms that underlie the association of antigen receptor gene segments.
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Affiliation(s)
- Cornelis Murre
- Division of Biological Sciences, 03777, University of California, San Diego, La Jolla, CA 92093, United States.
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46
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Fraenkel S, Mostoslavsky R, Novobrantseva TI, Pelanda R, Chaudhuri J, Esposito G, Jung S, Alt FW, Rajewsky K, Cedar H, Bergman Y. Allelic 'choice' governs somatic hypermutation in vivo at the immunoglobulin kappa-chain locus. Nat Immunol 2007; 8:715-22. [PMID: 17546032 DOI: 10.1038/ni1476] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2007] [Accepted: 05/02/2007] [Indexed: 12/29/2022]
Abstract
Monoallelic demethylation and rearrangement control allelic exclusion of the immunoglobulin kappa-chain locus (Igk locus) in B cells. Here, through the introduction of pre-rearranged Igk genes into their physiological position, the critical rearrangement step was bypassed, thereby generating mice producing B cells simultaneously expressing two different immunoglobulin-kappa light chains. Such 'double-expressing' B cells still underwent monoallelic demethylation at the Igk locus, and the demethylated allele was the 'preferred' substrate for somatic hypermutation in each cell. However, methylation itself did not directly inhibit the activation-induced cytidine-deaminase reaction in vitro. Thus, it seems that the epigenetic mechanisms that initially bring about monoallelic variable-(diversity)-joining rearrangement continue to be involved in the control of antibody diversity at later stages of B cell development.
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Affiliation(s)
- Shira Fraenkel
- The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
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47
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Melchers F, Yamagami T, Rolink A, Andersson J. Rules for the rearrangement events at the L chain gene loci of the mouse. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 596:63-70. [PMID: 17338176 DOI: 10.1007/0-387-46530-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Fritz Melchers
- Department of Cell Biology, Biozentrum, University of Basel, Basel, Switzerland
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48
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Jia J, Kondo M, Zhuang Y. Germline transcription from T-cell receptor Vbeta gene is uncoupled from allelic exclusion. EMBO J 2007; 26:2387-99. [PMID: 17410206 PMCID: PMC1864970 DOI: 10.1038/sj.emboj.7601671] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 03/05/2007] [Indexed: 11/09/2022] Open
Abstract
Allelic exclusion operates in B and T lymphocytes to ensure clonal expression of antigen receptors after V(D)J recombination. Germline transcription, which proceeds V(D)J recombination, has been postulated to provide an instructive signal for allelic exclusion. Here, we use a genetic marker to track germline transcription from a Vbeta gene within the TCRbeta locus. We find that developing thymocytes exhibit uniformed, bi-allelic activation of the Vbeta gene before V-DJ recombination, a process subject to allelic exclusion. We further show that V-DJ rearrangement promotes activation rather than silencing of germline transcription from the remaining Vbeta genes on either the functionally or non-functionally rearranged chromosome. Results presented here suggest that germline transcription, although necessary for V(D)J recombination, is not sufficient to instruct allelic exclusion.
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Affiliation(s)
- Jingquan Jia
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Motonari Kondo
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Yuan Zhuang
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
- Department of Immunology, Duke University Medical Center, Box 3010, Jones 329, Durham, NC 27710, USA. Tel.: +1 919 613 7824; Fax: +1 919 613 7853; E-mail:
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49
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Espinoza CR, Feeney AJ. Chromatin accessibility and epigenetic modifications differ between frequently and infrequently rearranging VH genes. Mol Immunol 2007; 44:2675-85. [PMID: 17218014 PMCID: PMC2570232 DOI: 10.1016/j.molimm.2006.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 11/16/2006] [Accepted: 12/06/2006] [Indexed: 11/30/2022]
Abstract
The molecular mechanisms that control the temporal and lineage-specific accessibility, as well as the rearrangement frequency of V(H) genes for V(H)-to-DJ(H) recombination, are not fully understood. We previously found a positive correlation between the extent of histone acetylation and the differential rearrangement frequency of individual V(H) genes. Here, we demonstrated that poorly rearranging V(H) genes are more highly associated with histone H3 dimethylated at lysine 9, a marker of repressive chromatin, than frequently rearranging V(H) genes. We also observed a positive relationship between the differential binding of Pax5 to individual V(H)S107 genes and rearrangement frequency. Furthermore, we showed that accessibility of the regions flanking the Pax5 binding site and the recombination signal sequence (RSS) to restriction enzyme cleavage correspond with the differential rearrangement frequency of the V(H)S107 family members. In addition, we found that the CpG sites located in the coding regions of V(H) genes are methylated in general, while the extent of DNA methylation drops dramatically near the RSS. For the V(H)S107 family, one CpG site located 101bp upstream of the RSS showed variable methylation that correlates with rearrangement frequency, and the methylation status of a CpG site located 34bp downstream of the RSS could also favor the rearrangement of V1 over V11. These findings suggest that the extent of histone modifications, chromatin accessibility, DNA methylation, as well as the differential binding of Pax5 to V(H) coding regions, could all influence the rearrangement frequency of individual V(H) genes, although some of these mechanisms are not strictly B cell specific.
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Affiliation(s)
- Celia R Espinoza
- The Scripps Research Institute, Department of Immunology IMM-22, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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50
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Skok JA, Gisler R, Novatchkova M, Farmer D, de Laat W, Busslinger M. Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes. Nat Immunol 2007; 8:378-87. [PMID: 17334367 DOI: 10.1038/ni1448] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Accepted: 02/05/2007] [Indexed: 02/06/2023]
Abstract
Reversible contraction of immunoglobulin loci juxtaposes the variable (V) genes next to the (diversity)-joining-constant ((D)JC) gene domain, thus facilitating V-(D)J recombination. Here we show that the T cell receptor beta (Tcrb) and T cell receptor alphadelta (Tcra-Tcrd) loci also underwent long-range interactions by looping in double-negative and double-positive thymocytes, respectively. Contraction of the Tcrb and Tcra loci occurred in rearranging thymocytes and was reversed at the next developmental stage. Decontraction of the Tcrb locus probably prevented further V(beta)-DJ(beta) rearrangements in double-positive thymocytes by separating the V(beta) genes from the DJC(beta) domain. In most double-negative cells, one Tcrb allele was recruited to pericentromeric heterochromatin. Such allelic positioning may facilitate asynchronous V(beta)-DJ(beta) recombination. Hence, pericentromeric recruitment and locus 'decontraction' seem to contribute to the initiation and maintenance of allelic exclusion at the Tcrb locus.
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Affiliation(s)
- Jane A Skok
- Department of Immunology and Molecular Pathology, Division of Infection and Immunity, University College London, London W1T 4JF, UK
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