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Johnson JL, Georgakilas G, Petrovic J, Kurachi M, Cai S, Harly C, Pear WS, Bhandoola A, Wherry EJ, Vahedi G. Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells. Immunity 2018; 48:243-257.e10. [PMID: 29466756 DOI: 10.1016/j.immuni.2018.01.012] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/05/2017] [Accepted: 01/26/2018] [Indexed: 11/17/2022]
Abstract
T cell development is orchestrated by transcription factors that regulate the expression of genes initially buried within inaccessible chromatin, but the transcription factors that establish the regulatory landscape of the T cell lineage remain unknown. Profiling chromatin accessibility at eight stages of T cell development revealed the selective enrichment of TCF-1 at genomic regions that became accessible at the earliest stages of development. TCF-1 was further required for the accessibility of these regulatory elements and at the single-cell level, it dictated a coordinate opening of chromatin in T cells. TCF-1 expression in fibroblasts generated de novo chromatin accessibility even at chromatin regions with repressive marks, inducing the expression of T cell-restricted genes. These results indicate that a mechanism by which TCF-1 controls T cell fate is through its widespread ability to target silent chromatin and establish the epigenetic identity of T cells.
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Affiliation(s)
- John L Johnson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Georgios Georgakilas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jelena Petrovic
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Makoto Kurachi
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stanley Cai
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christelle Harly
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20184, USA
| | - Warren S Pear
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Avinash Bhandoola
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20184, USA
| | - E John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Golnaz Vahedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Majumder K, Bassing CH, Oltz EM. Regulation of Tcrb Gene Assembly by Genetic, Epigenetic, and Topological Mechanisms. Adv Immunol 2015; 128:273-306. [PMID: 26477369 DOI: 10.1016/bs.ai.2015.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The adaptive immune system endows mammals with an ability to recognize nearly any foreign invader through antigen receptors that are expressed on the surface of all lymphocytes. This defense network is generated by V(D)J recombination, a set of sequentially controlled DNA cleavage and repair events that assemble antigen receptor genes from physically separated variable (V), joining (J), and sometimes diversity (D) gene segments. The recombination process itself must be stringently regulated to minimize oncogenic translocations involving chromosomes that harbor immunoglobulin and T cell receptor loci. Indeed, V(D)J recombination is controlled at several levels, including tissue-, developmental stage-, allele-, and gene segment-specificity. These levels of control are imposed by a collection of architectural and regulatory elements that are distributed throughout each antigen receptor locus. Together, the genetic elements regulate developmental changes in chromatin, transcription, and locus topology that promote or disfavor long-range recombination. This chapter focuses on the cross talk between these mechanisms at the T cell receptor beta (Tcrb) locus, and how they sculpt a diverse TCRβ repertoire while maintaining monospecificity of this antigen receptor on each mature T lymphocyte. We also discuss how insights obtained from studies of Tcrb are more generally relevant to our understanding of gene regulation strategies employed by mammals.
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Affiliation(s)
- Kinjal Majumder
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Craig H Bassing
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Institute, Cell and Molecular Biology Graduate Program, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA.
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3
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Influence of a CTCF-Dependent Insulator on Multiple Aspects of Enhancer-Mediated Chromatin Organization. Mol Cell Biol 2015; 35:3504-16. [PMID: 26240285 DOI: 10.1128/mcb.00514-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/24/2015] [Indexed: 01/07/2023] Open
Abstract
Developmental stage-specific enhancer-promoter-insulator interactions regulate the chromatin configuration necessary for transcription at various loci and additionally for VDJ recombination at antigen receptor loci that encode immunoglobulins and T-cell receptors. To investigate these regulatory interactions, we analyzed the epigenetic landscape of the murine T-cell receptor β (TCRβ) locus in the presence and absence of an ectopic CTCF-dependent enhancer-blocking insulator, H19-ICR, in genetically manipulated mice. Our analysis demonstrated the ability of the H19-ICR insulator to restrict several aspects of enhancer-based chromatin alterations that are observed during activation of the TCRβ locus for transcription and recombination. The H19-ICR insulator abrogated enhancer-promoter contact-dependent chromatin alterations and additionally prevented Eβ-mediated histone modifications that have been suggested to be independent of enhancer-promoter interaction. Observed enhancer-promoter-insulator interactions, in conjunction with the chromatin structure of the Eβ-regulated domain at the nucleosomal level, provide useful insights regarding the activity of the regulatory elements in addition to supporting the accessibility hypothesis of VDJ recombination. Analysis of H19-ICR in the heterologous context of the developmentally regulated TCRβ locus suggests that different mechanisms proposed for CTCF-dependent insulator action might be manifested simultaneously or selectively depending on the genomic context and the nature of enhancer activity being curtailed.
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Hernández-Munain C. Recent insights into the transcriptional control of the Tcra/Tcrd locus by distant enhancers during the development of T-lymphocytes. Transcription 2015; 6:65-73. [PMID: 26230488 DOI: 10.1080/21541264.2015.1078429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Tcra/Tcrd includes 2 genes with distinct developmental programs controlled by 2 distant enhancers, Eα and Eδ. These enhancers work as a developmental switch during thymocyte development and they are essential for generation of αβ and γδ T-lymphocytes. Tcra and Tcrd transit from an unrearranged configuration to a rearranged configuration during T-cell development. Eα and Eδ are responsible for transcription of their respective unrearranged genes in thymocytes but are dispensable for such functions in the context of the rearranged genes in mature T-cells. Interestingly, Eα activates transcription of the rearranged Tcrd in γδ T-lymphocytes but it is inactive in αβ T-lymphocytes.
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Affiliation(s)
- Cristina Hernández-Munain
- a Department of Cellular Biology and Immunology ; Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC); Parque Tecnológico de Ciencias de la Salud (PTS) ; Armilla , Granada , Spain
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5
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Wagatsuma K, Tani-ichi S, Liang B, Shitara S, Ishihara K, Abe M, Miyachi H, Kitano S, Hara T, Nanno M, Ishikawa H, Sakimura K, Nakao M, Kimura H, Ikuta K. STAT5 Orchestrates Local Epigenetic Changes for Chromatin Accessibility and Rearrangements by Direct Binding to the TCRγ Locus. THE JOURNAL OF IMMUNOLOGY 2015. [PMID: 26195811 DOI: 10.4049/jimmunol.1302456] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The transcription factor STAT5, which is activated by IL-7R, controls chromatin accessibility and rearrangements of the TCRγ locus. Although STAT-binding motifs are conserved in Jγ promoters and Eγ enhancers, little is known about their precise roles in rearrangements of the TCRγ locus in vivo. To address this question, we established two lines of Jγ1 promoter mutant mice: one harboring a deletion in the Jγ1 promoter, including three STAT motifs (Jγ1P(Δ/Δ)), and the other carrying point mutations in the three STAT motifs in that promoter (Jγ1P(mS/mS)). Both Jγ1P(Δ/Δ) and Jγ1P(mS/mS) mice showed impaired recruitment of STAT5 and chromatin remodeling factor BRG1 at the Jγ1 gene segment. This resulted in severe and specific reduction in germline transcription, histone H3 acetylation, and histone H4 lysine 4 methylation of the Jγ1 gene segment in adult thymus. Rearrangement and DNA cleavage of the segment were severely diminished, and Jγ1 promoter mutant mice showed profoundly decreased numbers of γδ T cells of γ1 cluster origin. Finally, compared with controls, both mutant mice showed a severe reduction in rearrangements of the Jγ1 gene segment, perturbed development of γδ T cells of γ1 cluster origin in fetal thymus, and fewer Vγ3(+) dendritic epidermal T cells. Furthermore, interaction with the Jγ1 promoter and Eγ1, a TCRγ enhancer, was dependent on STAT motifs in the Jγ1 promoter. Overall, this study strongly suggests that direct binding of STAT5 to STAT motifs in the Jγ promoter is essential for local chromatin accessibility and Jγ/Eγ chromatin interaction, triggering rearrangements of the TCRγ locus.
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Affiliation(s)
- Keisuke Wagatsuma
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan; Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shizue Tani-ichi
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Bingfei Liang
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan; Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Soichiro Shitara
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Ko Ishihara
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto 860-0811, Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Hitoshi Miyachi
- Reproductive Engineering Team, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Satsuki Kitano
- Reproductive Engineering Team, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Takahiro Hara
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Masanobu Nanno
- Yakult Central Institute, Kunitachi, Tokyo 186-8650, Japan
| | | | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Hiroshi Kimura
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan; Graduate School of Frontier Bioscience, Osaka University, Suita 565-0871, Japan; and Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Koichi Ikuta
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan;
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6
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Majumder K, Rupp LJ, Yang-Iott KS, Koues OI, Kyle KE, Bassing CH, Oltz EM. Domain-Specific and Stage-Intrinsic Changes in Tcrb Conformation during Thymocyte Development. THE JOURNAL OF IMMUNOLOGY 2015; 195:1262-72. [PMID: 26101321 DOI: 10.4049/jimmunol.1500692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/31/2015] [Indexed: 11/19/2022]
Abstract
Considerable cross-talk exists between mechanisms controlling genome architecture and gene expression. AgR loci are excellent models for these processes because they are regulated at both conformational and transcriptional levels to facilitate their assembly by V(D)J recombination. Upon commitment to the double-negative stage of T cell development, Tcrb adopts a compact conformation that promotes long-range recombination between Vβ gene segments (Trbvs) and their DβJβ targets. Formation of a functional VβDβJβ join signals for robust proliferation of double-negative thymocytes and their differentiation into double-positive (DP) cells, where Trbv recombination is squelched (allelic exclusion). DP differentiation also is accompanied by decontraction of Tcrb, which has been thought to separate the entire Trbv cluster from DβJβ segments (spatial segregation-based model for allelic exclusion). However, DP cells also repress transcription of unrearranged Trbvs, which may contribute to allelic exclusion. We performed a more detailed study of developmental changes in Tcrb topology and found that only the most distal portion of the Trbv cluster separates from DβJβ segments in DP thymocytes, leaving most Trbvs spatially available for rearrangement. Preferential dissociation of distal Trbvs is independent of robust proliferation or changes in transcription, chromatin, or architectural factors, which are coordinately regulated across the entire Trbv cluster. Segregation of distal Trbvs also occurs on alleles harboring a functional VβDβJβ join, suggesting that this process is independent of rearrangement status and is DP intrinsic. Our finding that most Trbvs remain associated with DβJβ targets in DP cells revises allelic exclusion models from their current conformation-dominant to a transcription-dominant formulation.
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Affiliation(s)
- Kinjal Majumder
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Levi J Rupp
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; and Abramson Family Cancer Research Institute, Cell and Molecular Biology Graduate Program, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the 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; and Abramson Family Cancer Research Institute, Cell and Molecular Biology Graduate Program, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
| | - Olivia I Koues
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Katherine E Kyle
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - 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; and Abramson Family Cancer Research Institute, Cell and Molecular Biology Graduate Program, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
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7
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The histone methyltransferase SETDB1 represses endogenous and exogenous retroviruses in B lymphocytes. Proc Natl Acad Sci U S A 2015; 112:8367-72. [PMID: 26100872 DOI: 10.1073/pnas.1422187112] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome stability relies on epigenetic mechanisms that enforce repression of endogenous retroviruses (ERVs). Current evidence suggests that distinct chromatin-based mechanisms repress ERVs in cells of embryonic origin (histone methylation dominant) vs. more differentiated cells (DNA methylation dominant). However, the latter aspect of this model has not been tested. Remarkably, and in contrast to the prevailing model, we find that repressive histone methylation catalyzed by the enzyme SETDB1 is critical for suppression of specific ERV families and exogenous retroviruses in committed B-lineage cells from adult mice. The profile of ERV activation in SETDB1-deficient B cells is distinct from that observed in corresponding embryonic tissues, despite the loss of repressive chromatin modifications at all ERVs. We provide evidence that, on loss of SETDB1, ERVs are activated in a lineage-specific manner depending on the set of transcription factors available to target proviral regulatory elements. These findings have important implications for genome stability in somatic cells, as well as the interface between epigenetic repression and viral latency.
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8
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Zacarías-Cabeza J, Belhocine M, Vanhille L, Cauchy P, Koch F, Pekowska A, Fenouil R, Bergon A, Gut M, Gut I, Eick D, Imbert J, Ferrier P, Andrau JC, Spicuglia S. Transcription-dependent generation of a specialized chromatin structure at the TCRβ locus. THE JOURNAL OF IMMUNOLOGY 2015; 194:3432-43. [PMID: 25732733 DOI: 10.4049/jimmunol.1400789] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
V(D)J recombination assembles Ag receptor genes during lymphocyte development. Enhancers at AR loci are known to control V(D)J recombination at associated alleles, in part by increasing chromatin accessibility of the locus, to allow the recombination machinery to gain access to its chromosomal substrates. However, whether there is a specific mechanism to induce chromatin accessibility at AR loci is still unclear. In this article, we highlight a specialized epigenetic marking characterized by high and extended H3K4me3 levels throughout the Dβ-Jβ-Cβ gene segments. We show that extended H3K4 trimethylation at the Tcrb locus depends on RNA polymerase II (Pol II)-mediated transcription. Furthermore, we found that the genomic regions encompassing the two DJCβ clusters are highly enriched for Ser(5)-phosphorylated Pol II and short-RNA transcripts, two hallmarks of transcription initiation and early transcription. Of interest, these features are shared with few other tissue-specific genes. We propose that the entire DJCβ regions behave as transcription "initiation" platforms, therefore linking a specialized mechanism of Pol II transcription with extended H3K4 trimethylation and highly accessible Dβ and Jβ gene segments.
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Affiliation(s)
- Joaquin Zacarías-Cabeza
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, UM2, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; Centre National de la Recherche Scientifique, UMR7280, F-13009 Marseille, France
| | - Mohamed Belhocine
- INSERM U1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France; Aix-Marseille University, UMR-S 1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France
| | - Laurent Vanhille
- INSERM U1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France; Aix-Marseille University, UMR-S 1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France
| | - Pierre Cauchy
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, UM2, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; Centre National de la Recherche Scientifique, UMR7280, F-13009 Marseille, France; INSERM U1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France; Aix-Marseille University, UMR-S 1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France
| | - Frederic Koch
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, UM2, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; Centre National de la Recherche Scientifique, UMR7280, F-13009 Marseille, France
| | - Aleksandra Pekowska
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, UM2, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; Centre National de la Recherche Scientifique, UMR7280, F-13009 Marseille, France
| | - Romain Fenouil
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, UM2, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; Centre National de la Recherche Scientifique, UMR7280, F-13009 Marseille, France
| | - Aurélie Bergon
- INSERM U1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France; Aix-Marseille University, UMR-S 1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France; Transcriptomic and Genomic Marseille-Luminy, Infrastructures en Biologie, Santé et Agronomie, 13288 Marseille, France
| | - Marta Gut
- Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac, 08028 Barcelona, Spain
| | - Ivo Gut
- Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac, 08028 Barcelona, Spain
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science, 80336 Munich, Germany; and
| | - Jean Imbert
- INSERM U1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France; Aix-Marseille University, UMR-S 1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France; Transcriptomic and Genomic Marseille-Luminy, Infrastructures en Biologie, Santé et Agronomie, 13288 Marseille, France
| | - Pierre Ferrier
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, UM2, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; Centre National de la Recherche Scientifique, UMR7280, F-13009 Marseille, France;
| | - Jean-Christophe Andrau
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, UM2, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; Centre National de la Recherche Scientifique, UMR7280, F-13009 Marseille, France; Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, UMR5535, 34293 Montpellier, France
| | - Salvatore Spicuglia
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, UM2, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; Centre National de la Recherche Scientifique, UMR7280, F-13009 Marseille, France; INSERM U1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France; Aix-Marseille University, UMR-S 1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France;
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9
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Majumder K, Koues OI, Chan EAW, Kyle KE, Horowitz JE, Yang-Iott K, Bassing CH, Taniuchi I, Krangel MS, Oltz EM. Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element. ACTA ACUST UNITED AC 2014; 212:107-20. [PMID: 25512470 PMCID: PMC4291525 DOI: 10.1084/jem.20141479] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Majumder et al. explore the large-scale looping architecture of the Tcrb locus early in murine thymocyte development during the generation of TCRβ diversity. They dissect novel DNA regulatory elements controlling V to D-J recombination and identify within an insulator region a distally located CTCF-containing element functioning as a tether, which facilitates looping of distal Vβ to Dβ-Jβ regions and promotes locus contraction. A second CTCF-containing element, proximal to the Dβ-Jβ region, acts as a boundary, preventing the spread of active chromatin associated with Dβ-Jβ regions. Removal of the proximal boundary element impairs the locus contraction capabilities of the tethering element. Gene regulation relies on dynamic changes in three-dimensional chromatin conformation, which are shaped by composite regulatory and architectural elements. However, mechanisms that govern such conformational switches within chromosomal domains remain unknown. We identify a novel mechanism by which cis-elements promote long-range interactions, inducing conformational changes critical for diversification of the TCRβ antigen receptor locus (Tcrb). Association between distal Vβ gene segments and the highly expressed DβJβ clusters, termed the recombination center (RC), is independent of enhancer function and recruitment of V(D)J recombinase. Instead, we find that tissue-specific folding of Tcrb relies on two distinct architectural elements located upstream of the RC. The first, a CTCF-containing element, directly tethers distal portions of the Vβ array to the RC. The second element is a chromatin barrier that protects the tether from hyperactive RC chromatin. When the second element is removed, active RC chromatin spreads upstream, forcing the tether to serve as a new barrier. Acquisition of barrier function by the CTCF element disrupts contacts between distal Vβ gene segments and significantly alters Tcrb repertoires. Our findings reveal a separation of function for RC-flanking regions, in which anchors for long-range recombination must be cordoned off from hyperactive RC landscapes by chromatin barriers.
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Affiliation(s)
- Kinjal Majumder
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Olivia I Koues
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Elizabeth A W Chan
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Katherine E Kyle
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Julie E Horowitz
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Katherine Yang-Iott
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Craig H Bassing
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
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10
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Fontes FL, Pinheiro DML, Oliveira AHSD, Oliveira RKDM, Lajus TBP, Agnez-Lima LF. Role of DNA repair in host immune response and inflammation. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:246-57. [PMID: 25795123 DOI: 10.1016/j.mrrev.2014.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 11/06/2014] [Accepted: 11/07/2014] [Indexed: 12/28/2022]
Abstract
In recent years, the understanding of how DNA repair contributes to the development of innate and acquired immunity has emerged. The DNA damage incurred during the inflammatory response triggers the activation of DNA repair pathways, which are required for host-cell survival. Here, we reviewed current understanding of the mechanism by which DNA repair contributes to protection against the oxidized DNA damage generated during infectious and inflammatory diseases and its involvement in innate and adaptive immunity. We discussed the functional role of DNA repair enzymes in the immune activation and the relevance of these processes to: transcriptional regulation of cytokines and other genes involved in the inflammatory response; V(D)J recombination; class-switch recombination (CSR); and somatic hypermutation (SHM). These three last processes of DNA damage repair are required for effective humoral adaptive immunity, creating genetic diversity in developing T and B cells. Furthermore, viral replication is also dependent on host DNA repair mechanisms. Therefore, the elucidation of the pathways of DNA damage and its repair that activate innate and adaptive immunity will be important for a better understanding of the immune and inflammatory disorders and developing new therapeutic interventions for treatment of these diseases and for improving their outcome.
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Affiliation(s)
- Fabrícia Lima Fontes
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, RN, Brazil.
| | - Daniele Maria Lopes Pinheiro
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, RN, Brazil.
| | - Ana Helena Sales de Oliveira
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, RN, Brazil.
| | | | - Tirzah Braz Petta Lajus
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, RN, Brazil; Liga Contra o Cancer, Natal, RN, Brazil.
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11
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Connelley TK, Degnan K, Longhi CW, Morrison WI. Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus. BMC Genomics 2014; 15:994. [PMID: 25408163 PMCID: PMC4289303 DOI: 10.1186/1471-2164-15-994] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 11/04/2014] [Indexed: 01/30/2023] Open
Abstract
Background The TRA/TRD locus contains the genes for V(D)J somatic rearrangement of TRA and TRD chains expressed by αβ and γδ T cells respectively. Previous studies have demonstrated that the bovine TRA/TRD locus contains an exceptionally large number of TRAV/TRDV genes. In this study we combine genomic and transcript analysis to provide insights into the evolutionary development of the bovine TRA/TRD locus and the remarkable TRAV/TRDV gene repertoire. Results Annotation of the UMD3.1 assembly identified 371 TRAV/TRDV genes (distributed in 42 subgroups), 3 TRDJ, 6 TRDD, 62 TRAJ and single TRAC and TRDC genes, most of which were located within a 3.5 Mb region of chromosome 10. Most of the TRAV/TRDV subgroups have multiple members and several have undergone dramatic expansion, most notably TRDV1 (60 genes). Wide variation in the proportion of pseudogenes within individual subgroups, suggest that differential ‘birth’ and ‘death’ rates have been used to form a functional bovine TRAV/TRDV repertoire which is phylogenetically distinct from that of humans and mice. The expansion of the bovine TRAV/TRDV gene repertoire has predominantly been achieved through a complex series of homology unit (regions of DNA containing multiple gene) replications. Frequent co-localisation within homology units of genes from subgroups with low and high pseudogene proportions suggest that replication of homology units driven by evolutionary selection for the former may have led to a ‘collateral’ expansion of the latter. Transcript analysis was used to define the TRAV/TRDV subgroups available for recombination of TRA and TRD chains and demonstrated preferential usage of different subgroups by the expressed TRA and TRD repertoires, indicating that TRA and TRD selection have had distinct impacts on the evolution of the TRAV/TRDV repertoire. Conclusion Both TRA and TRD selection have contributed to the evolution of the bovine TRAV/TRDV repertoire. However, our data suggest that due to homology unit duplication TRD selection for TRDV1 subgroup expansion may have substantially contributed to the genomic expansion of several TRAV subgroups. Such data demonstrate how integration of genomic and transcript data can provide a more nuanced appreciation of the evolutionary dynamics that have led to the dramatically expanded bovine TRAV/TRDV repertoire. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-994) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Timothy K Connelley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK.
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12
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Fugmann SD. Form follows function - the three-dimensional structure of antigen receptor gene loci. Curr Opin Immunol 2014; 27:33-7. [PMID: 24549092 DOI: 10.1016/j.coi.2014.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 01/22/2014] [Indexed: 01/17/2023]
Abstract
Antigen receptor genes are assembled during lymphocyte development from individual gene segments by a somatic gene rearrangement process named V(D)J recombination. This process is tightly regulated to ensure the generation of an unbiased broad primary repertoire of immunoglobulins and T cell receptors, and to prevent aberrant recombination products that could initiate lymphomagenesis. One important mode of regulation that has recently been discovered for the immunoglobulin heavy chain (IGH) gene locus is the adoption of distinct three-dimensional structures of the locus. Changes in the spatial conformation are thought to ensure the appropriate access of the V(D)J recombinase machinery at each developmental stage, and the formation of extensive chromosome loops has been implicated in allowing equal access to widely dispersed gene elements.
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Affiliation(s)
- Sebastian D Fugmann
- Department of Biomedical Sciences, Chang Gung University, 259 Wenhua 1st Rd, Kwei-Shan, Tao-Yuan 333, Taiwan.
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13
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Hauser J, Grundström C, Grundström T. Allelic exclusion of IgH through inhibition of E2A in a VDJ recombination complex. THE JOURNAL OF IMMUNOLOGY 2014; 192:2460-70. [PMID: 24470503 DOI: 10.4049/jimmunol.1302216] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A key feature of the immune system is the paradigm that one lymphocyte has only one Ag specificity that can be selected for or against. This requires that only one of the alleles of genes for AgR chains is made functional. However, the molecular mechanism of this allelic exclusion has been an enigma. In this study, we show that B lymphocytes with E2A that cannot be inhibited by calmodulin are dramatically defective in allelic exclusion of the IgH locus. Furthermore, we provide data supporting that E2A, PAX5, and the RAGs are in a VDJ recombination complex bound to key sequences on the Igh gene. We show that pre-BCR activation releases the VDJ recombination complex through calmodulin binding to E2A. We also show that pre-BCR signaling downregulates several components of the recombination machinery, including RAG1, RAG2, and PAX5, through calmodulin inhibition of E2A.
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Affiliation(s)
- Jannek Hauser
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
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14
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Predeus AV, Gopalakrishnan S, Huang Y, Tang J, Feeney AJ, Oltz EM, Artyomov MN. Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci. THE JOURNAL OF IMMUNOLOGY 2013; 192:1064-70. [PMID: 24353267 DOI: 10.4049/jimmunol.1302800] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The assembly and expression of mouse Ag receptor genes are controlled by a collection of cis-acting regulatory elements, including transcriptional promoters and enhancers. Although many powerful enhancers have been identified for Ig (Ig) and TCR (Tcr) loci, it remained unclear whether additional regulatory elements remain undiscovered. In this study, we use chromatin profiling of pro-B cells to define 38 epigenetic states in mouse Ag receptor loci, each of which reflects a distinct regulatory potential. One of these chromatin states corresponds to known transcriptional enhancers and identifies a new set of candidate elements in all three Ig loci. Four of the candidates were subjected to functional assays, and all four exhibit enhancer activity in B but not in T lineage cells. The new regulatory elements identified by focused chromatin profiling most likely have important functions in the creation, refinement, and expression of Ig repertoires.
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Affiliation(s)
- Alexander V Predeus
- Department of Pathology, Washington University School of Medicine, St. Louis, MO 63110
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15
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Perrin C, Lepesant JMJ, Roger E, Duval D, Fneich S, Thuillier V, Alliene JF, Mitta G, Grunau C, Cosseau C. Schistosoma mansoni mucin gene (SmPoMuc) expression: epigenetic control to shape adaptation to a new host. PLoS Pathog 2013; 9:e1003571. [PMID: 24009504 PMCID: PMC3757033 DOI: 10.1371/journal.ppat.1003571] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 06/27/2013] [Indexed: 11/28/2022] Open
Abstract
The digenetic trematode Schistosoma mansoni is a human parasite that uses the mollusc Biomphalaria glabrata as intermediate host. Specific S. mansoni strains can infect efficiently only certain B. glabrata strains (compatible strain) while others are incompatible. Strain-specific differences in transcription of a conserved family of polymorphic mucins (SmPoMucs) in S. mansoni are the principle determinants for this compatibility. In the present study, we investigated the bases of the control of SmPoMuc expression that evolved to evade B. glabrata diversified antigen recognition molecules. We compared the DNA sequences and chromatin structure of SmPoMuc promoters of two S. mansoni strains that are either compatible (C) or incompatible (IC) with a reference snail host. We reveal that although sequence differences are observed between active promoter regions of SmPoMuc genes, the sequences of the promoters are not diverse and are conserved between IC and C strains, suggesting that genetics alone cannot explain the evolution of compatibility polymorphism. In contrast, promoters carry epigenetic marks that are significantly different between the C and IC strains. Moreover, we show that modifications of the structure of the chromatin of the parasite modify transcription of SmPoMuc in the IC strain compared to the C strain and correlate with the presence of additional combinations of SmPoMuc transcripts only observed in the IC phenotype. Our results indicate that transcription polymorphism of a gene family that is responsible for an important adaptive trait of the parasite is epigenetically encoded. These strain-specific epigenetic marks are heritable, but can change while the underlying genetic information remains stable. This suggests that epigenetic changes may be important for the early steps in the adaptation of pathogens to new hosts, and might be an initial step in adaptive evolution in general. Schistosoma mansoni is a parasitic worm and agent of a disease that causes a considerable economic burden in African and South American countries. The propagation of the parasite requires passage through a freshwater snail of Biomphalaria genus. In the field, actually very few snails are infected. This is due to the fact that specific strains of the parasite can infect only specific strains of the snail. Comparative studies have shown that this so-called compatibility is based on the expression of a family of genes that are called SmPoMucs. We have shown previously that all parasites strains possess the repertoire of all SmPoMuc genes but every strain and even every individual parasite expresses only a subset. These differences could be due to DNA sequence differences in the regions that control gene expression, but here we show that these regions are nearly identical. Instead, the chromatin structure shows strain-specific characteristics. This means that the parasite can adapt to different snail strains simply by changing its chromatin structure and not necessarily the DNA sequence. If this holds true for other parasites, then we have to rethink the way parasite evolution is currently imagined but this also provides a new potential entry point to control the spread of diseases.
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Affiliation(s)
- Cecile Perrin
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Julie M. J. Lepesant
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Emmanuel Roger
- Center for Infection and Immunity of Lille, Inserm U1019, CNRS UMR 8204, Institut Pasteur de Lille, University Lille Nord de France, Lille, France
| | - David Duval
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Sara Fneich
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Virginie Thuillier
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Jean-Francois Alliene
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Guillaume Mitta
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Christoph Grunau
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Celine Cosseau
- Université de Perpignan Via Domitia, Perpignan, France
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan, France
- * E-mail:
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16
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Shih HY, Krangel MS. Chromatin architecture, CCCTC-binding factor, and V(D)J recombination: managing long-distance relationships at antigen receptor loci. THE JOURNAL OF IMMUNOLOGY 2013; 190:4915-21. [PMID: 23645930 DOI: 10.4049/jimmunol.1300218] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The rearrangement of T and B lymphocyte Ag receptor loci occurs within a highly complex chromosomal environment and is orchestrated through complex mechanisms. During the past decade, a large body of literature has highlighted the significance of chromatin architecture at Ag receptor loci in supporting the genomic assembly process: in preparation for recombination, these loci tend to contract and form multiple loops that shorten the distances between gene segments and facilitate recombination events. CCCTC-binding factor, CTCF, has received much attention in this regard since it has emerged as an important regulator of chromatin organization and transcription. In this review, we summarize recent work outlining conformational dynamics at Ag receptor loci during lymphocyte development and we discuss the role of CTCF in Ag receptor locus conformation and repertoire development.
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Affiliation(s)
- Han-Yu Shih
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA
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17
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Callen E, Faryabi RB, Luckey M, Hao B, Daniel JA, Yang W, Sun HW, Dressler G, Peng W, Chi H, Ge K, Krangel MS, Park JH, Nussenzweig A. The DNA damage- and transcription-associated protein paxip1 controls thymocyte development and emigration. Immunity 2012; 37:971-85. [PMID: 23159437 PMCID: PMC3525809 DOI: 10.1016/j.immuni.2012.10.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 10/04/2012] [Indexed: 01/21/2023]
Abstract
Histone 3 lysine 4 trimethylation (H3K4me3) is associated with promoters of active genes and found at hot spots for DNA recombination. Here we have shown that PAXIP1 (also known as PTIP), a protein associated with MLL3 and MLL4 methyltransferase and the DNA damage response, regulates RAG-mediated cleavage and repair during V(D)J recombination in CD4(+) CD8(+) DP thymocytes. Loss of PAXIP1 in developing thymocytes diminished Jα H3K4me3 and germline transcription, suppressed double strand break formation at 3' Jα segments, but resulted in accumulation of unresolved T cell receptor α-chain gene (Tcra) breaks. Moreover, PAXIP1 was essential for release of mature single positive (SP) αβ T cells from the thymus through transcriptional activation of sphingosine-1-phosphate receptor S1pr1 as well as for natural killer T cell development. Thus, in addition to maintaining genome integrity during Tcra rearrangements, PAXIP1 controls distinct transcriptional programs during DP differentiation necessary for Tcra locus accessibility, licensing mature thymocytes for trafficking and natural killer T cell development.
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Affiliation(s)
- Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
| | - Robert B. Faryabi
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
| | - Megan Luckey
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda MD 20892
| | - Bingtao Hao
- Department of Immunology, Campus Box 3010, Duke University Medical Center, Durham, NC 27710
| | - Jeremy A. Daniel
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wenjing Yang
- Department of Physics, The George Washington University, Washington, DC 20052
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, Office of Science and Technology, NIH, Bethesda MD 20892
| | - Greg Dressler
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA. 262 Danny Thomas Place, Room E-7013, Memphis, TN 38105-2794
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC 20052
| | - Hongbo Chi
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis TN 38105
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda MD 20892
| | - Michael S. Krangel
- Department of Immunology, Campus Box 3010, Duke University Medical Center, Durham, NC 27710
| | - Jung-Hyun Park
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda MD 20892
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
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18
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Subrahmanyam R, Du H, Ivanova I, Chakraborty T, Ji Y, Zhang Y, Alt FW, Schatz DG, Sen R. Localized epigenetic changes induced by DH recombination restricts recombinase to DJH junctions. Nat Immunol 2012; 13:1205-12. [PMID: 23104096 PMCID: PMC3685187 DOI: 10.1038/ni.2447] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/07/2012] [Indexed: 12/11/2022]
Abstract
Genes encoding immunoglobulin heavy chains (Igh) are assembled by rearrangement of variable (V(H)), diversity (D(H)) and joining (J(H)) gene segments. Three critical constraints govern V(H) recombination. These include timing (V(H) recombination follows D(H) recombination), precision (V(H) gene segments recombine only to DJ(H) junctions) and allele specificity (V(H) recombination is restricted to DJ(H)-recombined alleles). Here we provide a model for these universal features of V(H) recombination. Analyses of DJ(H)-recombined alleles showed that DJ(H) junctions were selectively epigenetically marked, became nuclease sensitive and bound RAG recombinase proteins, which thereby permitted D(H)-associated recombination signal sequences to initiate the second step of Igh gene assembly. We propose that V(H) recombination is precise, because these changes did not extend to germline D(H) segments located 5' of the DJ(H) junction.
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Affiliation(s)
- Ramesh Subrahmanyam
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, US National Institutes of Health, Baltimore, Maryland, USA
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19
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Stone JL, McMillan RE, Skaar DA, Bradshaw JM, Jirtle RL, Sikes ML. DNA double-strand breaks relieve USF-mediated repression of Dβ2 germline transcription in developing thymocytes. THE JOURNAL OF IMMUNOLOGY 2012; 188:2266-75. [PMID: 22287717 DOI: 10.4049/jimmunol.1002931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Activation of germline promoters is central to V(D)J recombinational accessibility, driving chromatin remodeling, nucleosome repositioning, and transcriptional read-through of associated DNA. We have previously shown that of the two TCRβ locus (Tcrb) D segments, Dβ1 is flanked by an upstream promoter that directs its transcription and recombinational accessibility. In contrast, transcription within the DJβ2 segment cluster is initially restricted to the J segments and only redirected upstream of Dβ2 after D-to-J joining. The repression of upstream promoter activity prior to Tcrb assembly correlates with evidence that suggests DJβ2 recombination is less efficient than that of DJβ1. Because inefficient DJβ2 assembly offers the potential for V-to-DJβ2 recombination to rescue frameshifted V-to-DJβ1 joints, we wished to determine how Dβ2 promoter activity is modulated upon Tcrb recombination. In this study, we show that repression of the otherwise transcriptionally primed 5'Dβ2 promoter requires binding of upstream stimulatory factor (USF)-1 to a noncanonical E-box within the Dβ2 12-recombination signal sequence spacer prior to Tcrb recombination. USF binding is lost from both rearranged and germline Dβ2 sites in DNA-dependent protein kinase, catalytic subunit-competent thymocytes. Finally, genotoxic dsDNA breaks lead to rapid loss of USF binding and gain of transcriptionally primed 5'Dβ2 promoter activity in a DNA-dependent protein kinase, catalytic subunit-dependent manner. Together, these data suggest a mechanism by which V(D)J recombination may feed back to regulate local Dβ2 recombinational accessibility during thymocyte development.
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Affiliation(s)
- Jennifer L Stone
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA
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Abstract
Vertebrate development requires the formation of multiple cell types from a single genetic blueprint, an extraordinary feat that is guided by the dynamic and finely tuned reprogramming of gene expression. The sophisticated orchestration of gene expression programs is driven primarily by changes in the patterns of covalent chromatin modifications. These epigenetic changes are directed by cis elements, positioned across the genome, which provide docking sites for transcription factors and associated chromatin modifiers. Epigenetic changes impact all aspects of gene regulation, governing association with the machinery that drives transcription, replication, repair and recombination, a regulatory relationship that is dramatically illustrated in developing lymphocytes. The program of somatic rearrangements that assemble antigen receptor genes in precursor B and T cells has proven to be a fertile system for elucidating relationships between the genetic and epigenetic components of gene regulation. This chapter describes our current understanding of the cross-talk between key genetic elements and epigenetic programs during recombination of the Tcrb locus in developing T cells, how each contributes to the regulation of chromatin accessibility at individual DNA targets for recombination, and potential mechanisms that coordinate their actions.
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Pinaud E, Marquet M, Fiancette R, Péron S, Vincent-Fabert C, Denizot Y, Cogné M. The IgH locus 3' regulatory region: pulling the strings from behind. Adv Immunol 2011; 110:27-70. [PMID: 21762815 DOI: 10.1016/b978-0-12-387663-8.00002-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antigen receptor gene loci are among the most complex in mammals. The IgH locus, encoding the immunoglobulin heavy chain (IgH) in B-lineage cells, undergoes major transcription-dependent DNA remodeling events, namely V(D)J recombination, Ig class-switch recombination (CSR), and somatic hypermutation (SHM). Various cis-regulatory elements (encompassing promoters, enhancers, and chromatin insulators) recruit multiple nuclear factors in order to ensure IgH locus regulation by tightly orchestrated physical and/or functional interactions. Among major IgH cis-acting regions, the large 3' regulatory region (3'RR) located at the 3' boundary of the locus includes several enhancers and harbors an intriguing quasi-palindromic structure. In this review, we report progress insights made over the past decade in order to describe in more details the structure and functions of IgH 3'RRs in mouse and human. Generation of multiple cellular, transgenic and knock-out models helped out to decipher the function of the IgH 3' regulatory elements in the context of normal and pathologic B cells. Beside its interest in physiology, the challenge of elucidating the locus-wide cross talk between distant cis-regulatory elements might provide useful insights into the mechanisms that mediate oncogene deregulation after chromosomal translocations onto the IgH locus.
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Affiliation(s)
- Eric Pinaud
- UMR CNRS 6101, Centre National de la Recherche Scientifique, Université de Limoges, Limoges, France
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