1
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Naik AK, Dauphars DJ, Corbett E, Simpson L, Schatz DG, Krangel MS. RORγt up-regulates RAG gene expression in DP thymocytes to expand the Tcra repertoire. Sci Immunol 2024; 9:eadh5318. [PMID: 38489350 PMCID: PMC11005092 DOI: 10.1126/sciimmunol.adh5318] [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] [Received: 03/09/2023] [Accepted: 02/21/2024] [Indexed: 03/17/2024]
Abstract
Recombination activating gene (RAG) expression increases as thymocytes transition from the CD4-CD8- double-negative (DN) to the CD4+CD8+ double-positive (DP) stage, but the physiological importance and mechanism of transcriptional up-regulation are unknown. Here, we show that a DP-specific component of the recombination activating genes antisilencer (DPASE) provokes elevated RAG expression in DP thymocytes. Mouse DP thymocytes lacking the DPASE display RAG expression equivalent to that in DN thymocytes, but this supports only a partial Tcra repertoire due to inefficient secondary Vα-Jα rearrangement. These data indicate that RAG up-regulation is required for a replete Tcra repertoire and that RAG expression is fine-tuned during lymphocyte development to meet the requirements of distinct antigen receptor loci. We further show that transcription factor RORγt directs RAG up-regulation in DP thymocytes by binding to the DPASE and that RORγt influences the Tcra repertoire by binding to the Tcra enhancer. These data, together with prior work showing RORγt to control Tcra rearrangement by regulating DP thymocyte proliferation and survival, reveal RORγt to orchestrate multiple pathways that support formation of the Tcra repertoire.
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Affiliation(s)
- Abani Kanta Naik
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - Danielle J Dauphars
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - Elizabeth Corbett
- Department of Immunobiology and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Lunden Simpson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - David G Schatz
- Department of Immunobiology and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Michael S Krangel
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
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2
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Dai R, Zhu Y, Li Z, Qin L, Liu N, Liao S, Hao B. Three-way contact analysis characterizes the higher order organization of the Tcra locus. Nucleic Acids Res 2023; 51:8987-9000. [PMID: 37534534 PMCID: PMC10516640 DOI: 10.1093/nar/gkad641] [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] [Received: 12/02/2022] [Revised: 07/07/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023] Open
Abstract
The generation of highly diverse antigen receptors in T and B lymphocytes relies on V(D)J recombination. The enhancer Eα has been implicated in regulating the accessibility of Vα and Jα genes through long-range interactions during rearrangements of the T-cell antigen receptor gene Tcra. However, direct evidence for Eα physically mediating the interaction of Vα and Jα genes is still lacking. In this study, we utilized the 3C-HTGTS assay, a chromatin interaction technique based on 3C, to analyze the higher order chromatin structure of the Tcra locus. Our analysis revealed the presence of sufficient information in the 3C-HTGTS data to detect multiway contacts. Three-way contact analysis of the Tcra locus demonstrated the co-occurrence of the proximal Jα genes, Vα genes and Eα in CD4+CD8+ double-positive thymocytes. Notably, the INT2-TEAp loop emerged as a prominent structure likely to be responsible for bringing the proximal Jα genes and the Vα genes into proximity. Moreover, the enhancer Eα utilizes this loop to establish physical proximity with the proximal Vα gene region. This study provides insights into the higher order chromatin structure of the Tcra locus, shedding light on the spatial organization of chromatin and its impact on V(D)J recombination.
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Affiliation(s)
- Ranran Dai
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, China
| | - Yongchang Zhu
- Department of Immunology, School of Basic Medical, Zhengzhou University, Zhengzhou 450001, China
- Medical Genetic Institute of Henan Province, Henan Key Laboratory of Genetic Diseases and Functional Genomics, National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province 450003, China
| | - Zhaoqiang Li
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, China
| | - Litao Qin
- Medical Genetic Institute of Henan Province, Henan Key Laboratory of Genetic Diseases and Functional Genomics, National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province 450003, China
| | - Nan Liu
- Division of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province 510515, China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Key Laboratory of Genetic Diseases and Functional Genomics, National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province 450003, China
| | - Bingtao Hao
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, China
- Department of Immunology, School of Basic Medical, Zhengzhou University, Zhengzhou 450001, China
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3
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Mihai A, Roy S, Krangel MS, Zhuang Y. E protein binding at the Tcra enhancer promotes Tcra repertoire diversity. Front Immunol 2023; 14:1188738. [PMID: 37483636 PMCID: PMC10358851 DOI: 10.3389/fimmu.2023.1188738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023] Open
Abstract
V(D)J recombination of antigen receptor loci is a highly developmentally regulated process. During T lymphocyte development, recombination of the Tcra gene occurs in CD4+CD8+ double positive (DP) thymocytes and requires the Tcra enhancer (Eα). E proteins are known regulators of DP thymocyte development and have three identified binding sites in Eα. To understand the contribution of E proteins to Eα function, mutants lacking one or two of the respective binding sites were generated. The double-binding site mutant displayed a partial block at the positive selection stage of αβ T cell development. Further investigation revealed loss of germline transcription within the Tcra locus at the Jα array, along with dysregulated primary and impaired secondary Vα-Jα rearrangement. Eα E protein binding increases Tcra locus accessibility and regulates TCRα recombination, thus directly promoting Tcra repertoire diversity.
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Affiliation(s)
| | | | - Michael S. Krangel
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
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4
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Kumar D, Sahoo SS, Chauss D, Kazemian M, Afzali B. Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations. J Autoimmun 2023; 134:102982. [PMID: 36592512 PMCID: PMC9908861 DOI: 10.1016/j.jaut.2022.102982] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/02/2023]
Abstract
Immune cell function is critically dependent on precise control over transcriptional output from the genome. In this respect, integration of environmental signals that regulate gene expression, specifically by transcription factors, enhancer DNA elements, genome topography and non-coding RNAs (ncRNAs), are key components. The first three have been extensively investigated. Even though non-coding RNAs represent the vast majority of cellular RNA species, this class of RNA remains historically understudied. This is partly because of a lag in technological and bioinformatic innovations specifically capable of identifying and accurately measuring their expression. Nevertheless, recent progress in this domain has enabled a profusion of publications identifying novel sub-types of ncRNAs and studies directly addressing the function of ncRNAs in human health and disease. Many ncRNAs, including circular and enhancer RNAs, have now been demonstrated to play key functions in the regulation of immune cells and to show associations with immune-mediated diseases. Some ncRNAs may function as biomarkers of disease, aiding in diagnostics and in estimating response to treatment, while others may play a direct role in the pathogenesis of disease. Importantly, some are relatively stable and are amenable to therapeutic targeting, for example through gene therapy. Here, we provide an overview of ncRNAs and review technological advances that enable their study and hold substantial promise for the future. We provide context-specific examples by examining the associations of ncRNAs with four prototypical human autoimmune diseases, specifically rheumatoid arthritis, psoriasis, inflammatory bowel disease and multiple sclerosis. We anticipate that the utility and mechanistic roles of these ncRNAs in autoimmunity will be further elucidated in the near future.
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Affiliation(s)
- Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Subhransu Sekhar Sahoo
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
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5
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Rodríguez-Caparrós A, Tani-ichi S, Casal Á, López-Ros J, Suñé C, Ikuta K, Hernández-Munain C. Interleukin-7 receptor signaling is crucial for enhancer-dependent TCRδ germline transcription mediated through STAT5 recruitment. Front Immunol 2022; 13:943510. [PMID: 36059467 PMCID: PMC9437428 DOI: 10.3389/fimmu.2022.943510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
γδ T cells play important roles in immune responses by rapidly producing large quantities of cytokines. Recently, γδ T cells have been found to be involved in tissue homeostatic regulation, playing roles in thermogenesis, bone regeneration and synaptic plasticity. Nonetheless, the mechanisms involved in γδ T-cell development, especially the regulation of TCRδ gene transcription, have not yet been clarified. Previous studies have established that NOTCH1 signaling plays an important role in the Tcrg and Tcrd germline transcriptional regulation induced by enhancer activation, which is mediated through the recruitment of RUNX1 and MYB. In addition, interleukin-7 signaling has been shown to be required for Tcrg germline transcription, VγJγ rearrangement and γδ T-lymphocyte generation as well as for promoting T-cell survival. In this study, we discovered that interleukin-7 is required for the activation of enhancer-dependent Tcrd germline transcription during thymocyte development. These results indicate that the activation of both Tcrg and Tcrd enhancers during γδ T-cell development in the thymus depends on the same NOTCH1- and interleukin-7-mediated signaling pathways. Understanding the regulation of the Tcrd enhancer during thymocyte development might lead to a better understanding of the enhancer-dependent mechanisms involved in the genomic instability and chromosomal translocations that cause leukemia.
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Affiliation(s)
- Alonso Rodríguez-Caparrós
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Shizue Tani-ichi
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Áurea Casal
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Jennifer López-Ros
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Carlos Suñé
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Cristina Hernández-Munain
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
- *Correspondence: Cristina Hernández-Munain,
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6
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Kissiov DU, Ethell A, Chen S, Wolf NK, Zhang C, Dang SM, Jo Y, Madsen KN, Paranjpe I, Lee AY, Chim B, Muljo SA, Raulet DH. Binary outcomes of enhancer activity underlie stable random monoallelic expression. eLife 2022; 11:e74204. [PMID: 35617021 PMCID: PMC9135403 DOI: 10.7554/elife.74204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Mitotically stable random monoallelic gene expression (RME) is documented for a small percentage of autosomal genes. We developed an in vivo genetic model to study the role of enhancers in RME using high-resolution single-cell analysis of natural killer (NK) cell receptor gene expression and enhancer deletions in the mouse germline. Enhancers of the RME NK receptor genes were accessible and enriched in H3K27ac on silent and active alleles alike in cells sorted according to allelic expression status, suggesting enhancer activation and gene expression status can be decoupled. In genes with multiple enhancers, enhancer deletion reduced gene expression frequency, in one instance converting the universally expressed gene encoding NKG2D into an RME gene, recapitulating all aspects of natural RME including mitotic stability of both the active and silent states. The results support the binary model of enhancer action, and suggest that RME is a consequence of general properties of gene regulation by enhancers rather than an RME-specific epigenetic program. Therefore, many and perhaps all genes may be subject to some degree of RME. Surprisingly, this was borne out by analysis of several genes that define different major hematopoietic lineages, that were previously thought to be universally expressed within those lineages: the genes encoding NKG2D, CD45, CD8α, and Thy-1. We propose that intrinsically probabilistic gene allele regulation is a general property of enhancer-controlled gene expression, with previously documented RME representing an extreme on a broad continuum.
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Affiliation(s)
- Djem U Kissiov
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Alexander Ethell
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sean Chen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Natalie K Wolf
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Chenyu Zhang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Susanna M Dang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Yeara Jo
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Katrine N Madsen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Ishan Paranjpe
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Angus Y Lee
- Cancer Research Laboratory, University of California, BerkeleyBerkeleyUnited States
| | - Bryan Chim
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Stefan A Muljo
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - David H Raulet
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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7
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Rodríguez-Caparrós A, Álvarez-Santiago J, López-Castellanos L, Ruiz-Rodríguez C, Valle-Pastor MJ, López-Ros J, Angulo Ú, Andrés-León E, Suñé C, Hernández-Munain C. Differently Regulated Gene-Specific Activity of Enhancers Located at the Boundary of Subtopologically Associated Domains: TCRα Enhancer. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:910-928. [PMID: 35082160 DOI: 10.4049/jimmunol.2000864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/05/2021] [Indexed: 11/19/2022]
Abstract
Enhancers activate transcription through long-distance interactions with their cognate promoters within a particular subtopologically associated domain (sub-TAD). The TCRα enhancer (Eα) is located at the sub-TAD boundary between the TCRα and DAD1 genes and regulates transcription toward both sides in an ∼1-Mb region. Analysis of Eα activity in transcribing the unrearranged TCRα gene at the 5'-sub-TAD has defined Eα as inactive in CD4-CD8- thymocytes, active in CD4+CD8+ thymocytes, and strongly downregulated in CD4+ and CD8+ thymocytes and αβ T lymphocytes. Despite its strongly reduced activity, Eα is still required for high TCRα transcription and expression of TCRαβ in mouse and human T lymphocytes, requiring collaboration with distant sequences for such functions. Because VαJα rearrangements in T lymphocytes do not induce novel long-range interactions between Eα and other genomic regions that remain in cis after recombination, strong Eα connectivity with the 3'-sub-TAD might prevent reduced transcription of the rearranged TCRα gene. Our analyses of transcriptional enhancer dependence during T cell development and non-T lineage tissues at the 3'-sub-TAD revealed that Eα can activate the transcription of specific genes, even when it is inactive to transcribe the TCRα gene at the 5'-sub-TAD. Hence distinct requirements for Eα function are necessary at specific genes at both sub-TADs, implying that enhancers do not merely function as chromatin loop anchors that nucleate the formation of factor condensates to increase gene transcription initiated at their cognate promoters. The observed different regulated Eα activity for activating specific genes at its flanking sub-TADs may be a general feature for enhancers located at sub-TAD boundaries.
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Affiliation(s)
- Alonso Rodríguez-Caparrós
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Jesús Álvarez-Santiago
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Laura López-Castellanos
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Candela Ruiz-Rodríguez
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - María Jesús Valle-Pastor
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Jennifer López-Ros
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Úrsula Angulo
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Eduardo Andrés-León
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Carlos Suñé
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Cristina Hernández-Munain
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
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8
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Pongubala JMR, Murre C. Spatial Organization of Chromatin: Transcriptional Control of Adaptive Immune Cell Development. Front Immunol 2021; 12:633825. [PMID: 33854505 PMCID: PMC8039525 DOI: 10.3389/fimmu.2021.633825] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Higher-order spatial organization of the genome into chromatin compartments (permissive and repressive), self-associating domains (TADs), and regulatory loops provides structural integrity and offers diverse gene regulatory controls. In particular, chromatin regulatory loops, which bring enhancer and associated transcription factors in close spatial proximity to target gene promoters, play essential roles in regulating gene expression. The establishment and maintenance of such chromatin loops are predominantly mediated involving CTCF and the cohesin machinery. In recent years, significant progress has been made in revealing how loops are assembled and how they modulate patterns of gene expression. Here we will discuss the mechanistic principles that underpin the establishment of three-dimensional (3D) chromatin structure and how changes in chromatin structure relate to alterations in gene programs that establish immune cell fate.
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Affiliation(s)
| | - Cornelis Murre
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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9
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Wu GS, Yang-Iott KS, Klink MA, Hayer KE, Lee KD, Bassing CH. Poor quality Vβ recombination signal sequences stochastically enforce TCRβ allelic exclusion. J Exp Med 2021; 217:151853. [PMID: 32526772 PMCID: PMC7478721 DOI: 10.1084/jem.20200412] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 12/15/2022] Open
Abstract
The monoallelic expression of antigen receptor (AgR) genes, called allelic exclusion, is fundamental for highly specific immune responses to pathogens. This cardinal feature of adaptive immunity is achieved by the assembly of a functional AgR gene on one allele, with subsequent feedback inhibition of V(D)J recombination on the other allele. A range of epigenetic mechanisms have been implicated in sequential recombination of AgR alleles; however, we now demonstrate that a genetic mechanism controls this process for Tcrb. Replacement of V(D)J recombinase targets at two different mouse Vβ gene segments with a higher quality target elevates Vβ rearrangement frequency before feedback inhibition, dramatically increasing the frequency of T cells with TCRβ chains derived from both Tcrb alleles. Thus, TCRβ allelic exclusion is enforced genetically by the low quality of Vβ recombinase targets that stochastically restrict the production of two functional rearrangements before feedback inhibition silences one allele.
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Affiliation(s)
- Glendon S Wu
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Katherine S Yang-Iott
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Morgann A Klink
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Katharina E Hayer
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kyutae D Lee
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Craig H Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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10
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Cieslak A, Charbonnier G, Tesio M, Mathieu EL, Belhocine M, Touzart A, Smith C, Hypolite G, Andrieu GP, Martens JHA, Janssen-Megens E, Gut M, Gut I, Boissel N, Petit A, Puthier D, Macintyre E, Stunnenberg HG, Spicuglia S, Asnafi V. Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation. J Exp Med 2021; 217:151947. [PMID: 32667968 PMCID: PMC7478722 DOI: 10.1084/jem.20192360] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/03/2020] [Accepted: 05/15/2020] [Indexed: 01/30/2023] Open
Abstract
Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition and cell identity. Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an integrative analysis of other hematopoietic populations. Although T cell commitment is accompanied by large scale epigenetic changes, we observed that the majority of distal regulatory elements are constitutively unmethylated throughout T cell differentiation, irrespective of their activation status. Among these, the TCRA gene enhancer (Eα) is in an open and unmethylated chromatin structure well before activation. Integrative analyses revealed that the HOXA5-9 transcription factors repress the Eα enhancer at early stages of T cell differentiation, while their decommission is required for TCRA locus activation and enforced αβ T lineage differentiation. Remarkably, the HOXA-mediated repression of Eα is paralleled by the ectopic expression of homeodomain-related oncogenes in T cell acute lymphoblastic leukemia. These results highlight an analogous enhancer repression mechanism at play in normal and cancer conditions, but imposing distinct developmental constraints.
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Affiliation(s)
- Agata Cieslak
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Melania Tesio
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Eve-Lyne Mathieu
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Mohamed Belhocine
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Aurore Touzart
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France.,Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Charlotte Smith
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Guillaume Hypolite
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Guillaume P Andrieu
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Joost H A Martens
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Eva Janssen-Megens
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Marta Gut
- Centro Nacional de Análisis Genómico-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Ivo Gut
- Centro Nacional de Análisis Genómico-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicolas Boissel
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, Paris, France
| | - Arnaud Petit
- Department of Pediatric Hematology and Oncology, Assistance Publique-Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, France
| | - Denis Puthier
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Elizabeth Macintyre
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Salvatore Spicuglia
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
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11
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Mendes J, Areia AL, Rodrigues-Santos P, Santos-Rosa M, Mota-Pinto A. Innate Lymphoid Cells in Human Pregnancy. Front Immunol 2020; 11:551707. [PMID: 33329512 PMCID: PMC7734178 DOI: 10.3389/fimmu.2020.551707] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/28/2020] [Indexed: 12/26/2022] Open
Abstract
Innate lymphoid cells (ILCs) are a new set of cells considered to be a part of the innate immune system. ILCs are classified into five subsets (according to their transcription factors and cytokine profile) as natural killer cells (NK cells), group 1 ILCs, group 2 ILCs, group 3 ILCs, and lymphoid tissue inducers (LTi). Functionally, these cells resemble the T helper population but lack the expression of recombinant genes, which is essential for the formation of T cell receptors. In this work, the authors address the distinction between peripheral and decidual NK cells, highlighting their diversity in ILC biology and its relevance to human pregnancy. ILCs are effector cells that are important in promoting immunity, inflammation, and tissue repair. Recent studies have directed their attention to ILC actions in pregnancy. Dysregulation or expansion of pro-inflammatory ILC populations as well as abnormal tolerogenic responses may directly interfere with pregnancy, ultimately resulting in pregnancy loss or adverse outcomes. In this review, we characterize these cells, considering recent findings and addressing knowledge gaps in perinatal medicine in the context of ILC biology. Moreover, we discuss the relevance of these cells not only to the process of immune tolerance, but also in disease.
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Affiliation(s)
- João Mendes
- Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, Center of Investigation in Environment, Genetics and Oncobiology (CIMAGO), University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, General Pathology Institute, University of Coimbra, Coimbra, Portugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Ana Luísa Areia
- Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, Center of Investigation in Environment, Genetics and Oncobiology (CIMAGO), University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, General Pathology Institute, University of Coimbra, Coimbra, Portugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
- Obstetrics Department, Coimbra University Hospital Center, Coimbra, Portugal
| | - Paulo Rodrigues-Santos
- Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, Center of Investigation in Environment, Genetics and Oncobiology (CIMAGO), University of Coimbra, Coimbra, Portugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
- Faculty of Medicine (FMUC), Institute of Immunology, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology (CNC), Laboratory of Immunology and Oncology, University of Coimbra, Coimbra, Portugal
| | - Manuel Santos-Rosa
- Faculty of Medicine (FMUC), Institute of Immunology, University of Coimbra, Coimbra, Portugal
| | - Anabela Mota-Pinto
- Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, Center of Investigation in Environment, Genetics and Oncobiology (CIMAGO), University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, General Pathology Institute, University of Coimbra, Coimbra, Portugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
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12
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Rodríguez-Caparrós A, Álvarez-Santiago J, del Valle-Pastor MJ, Suñé C, López-Ros J, Hernández-Munain C. Regulation of T-cell Receptor Gene Expression by Three-Dimensional Locus Conformation and Enhancer Function. Int J Mol Sci 2020; 21:E8478. [PMID: 33187197 PMCID: PMC7696796 DOI: 10.3390/ijms21228478] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022] Open
Abstract
The adaptive immune response in vertebrates depends on the expression of antigen-specific receptors in lymphocytes. T-cell receptor (TCR) gene expression is exquisitely regulated during thymocyte development to drive the generation of αβ and γδ T lymphocytes. The TCRα, TCRβ, TCRγ, and TCRδ genes exist in two different configurations, unrearranged and rearranged. A correctly rearranged configuration is required for expression of a functional TCR chain. TCRs can take the form of one of three possible heterodimers, pre-TCR, TCRαβ, or TCRγδ which drive thymocyte maturation into αβ or γδ T lymphocytes. To pass from an unrearranged to a rearranged configuration, global and local three dimensional (3D) chromatin changes must occur during thymocyte development to regulate gene segment accessibility for V(D)J recombination. During this process, enhancers play a critical role by modifying the chromatin conformation and triggering noncoding germline transcription that promotes the recruitment of the recombination machinery. The different signaling that thymocytes receive during their development controls enhancer activity. Here, we summarize the dynamics of long-distance interactions established through chromatin regulatory elements that drive transcription and V(D)J recombination and how different signaling pathways are orchestrated to regulate the activity of enhancers to precisely control TCR gene expression during T-cell maturation.
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Affiliation(s)
| | | | | | | | | | - Cristina Hernández-Munain
- Institute of Parasitology and Biomedicine “López-Neyra”—Spanish Scientific Research Council (IPBLN-CSIC), Parque Tecnológico de Ciencias de la Salud (PTS), 18016 Granada, Spain; (A.R.-C.); (J.Á.-S.); (M.J.d.V.-P.); (C.S.); (J.L.-R.)
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13
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Zhao H, Li Z, Zhu Y, Bian S, Zhang Y, Qin L, Naik AK, He J, Zhang Z, Krangel MS, Hao B. A role of the CTCF binding site at enhancer Eα in the dynamic chromatin organization of the Tcra-Tcrd locus. Nucleic Acids Res 2020; 48:9621-9636. [PMID: 32853367 PMCID: PMC7515734 DOI: 10.1093/nar/gkaa711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/03/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022] Open
Abstract
The regulation of T cell receptor Tcra gene rearrangement has been extensively studied. The enhancer Eα plays an essential role in Tcra rearrangement by establishing a recombination centre in the Jα array and a chromatin hub for interactions between Vα and Jα genes. But the mechanism of the Eα and its downstream CTCF binding site (here named EACBE) in dynamic chromatin regulation is unknown. The Hi-C data showed that the EACBE is located at the sub-TAD boundary which separates the Tcra–Tcrd locus and the downstream region including the Dad1 gene. The EACBE is required for long-distance regulation of the Eα on the proximal Vα genes, and its deletion impaired the Tcra rearrangement. We also noticed that the EACBE and Eα regulate the genes in the downstream sub-TAD via asymmetric chromatin extrusion. This study provides a new insight into the role of CTCF binding sites at TAD boundaries in gene regulation.
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Affiliation(s)
- Hao Zhao
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Zhaoqiang Li
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yongchang Zhu
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Shasha Bian
- Henan Medical Genetics Institute, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan Province, China
| | - Yan Zhang
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Litao Qin
- Henan Medical Genetics Institute, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan Province, China
| | - Abani Kanta Naik
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Jiangtu He
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhenhai Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Bingtao Hao
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Henan Medical Genetics Institute, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan Province, China
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14
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Rodríguez-Caparrós A, García V, Casal Á, López-Ros J, García-Mariscal A, Tani-ichi S, Ikuta K, Hernández-Munain C. Notch Signaling Controls Transcription via the Recruitment of RUNX1 and MYB to Enhancers during T Cell Development. THE JOURNAL OF IMMUNOLOGY 2019; 202:2460-2472. [DOI: 10.4049/jimmunol.1801650] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/11/2019] [Indexed: 12/11/2022]
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15
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Affiliation(s)
- Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
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16
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Villarese P, Lours C, Trinquand A, Le Noir S, Belhocine M, Lhermitte L, Cieslak A, Tesio M, Petit A, LeLorch M, Spicuglia S, Ifrah N, Dombret H, Langerak AW, Boissel N, Macintyre E, Asnafi V. TCRα rearrangements identify a subgroup of NKL-deregulated adult T-ALLs associated with favorable outcome. Leukemia 2017; 32:61-71. [PMID: 28592888 DOI: 10.1038/leu.2017.176] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 05/16/2017] [Accepted: 05/25/2017] [Indexed: 12/18/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) results from leukemic transformation of T-cell precursors arrested at specific differentiation stages, including an 'early-cortical' thymic maturation arrest characterized by expression of cytoplasmic TCRβ but no surface T-cell receptor (TCR) and frequent ectopic expression of the TLX1/3 NK-like homeotic proteins (NKL). We designed a TCRα VJC PCR to identify clonal TCRα rearrangements in 32% of 127 T-ALLs, including 0/52 immature/TCRγδ lineage cases and 41/75 (55%) TCRαβ lineage cases. Amongst the latter, TCRα rearrangements were not identified in 30/54 (56%) of IMβ/pre-αβ early-cortical T-ALLs, of which the majority (21/30) expressed TLX1/3. We reasoned that the remaining T-ALLs might express other NKL proteins, so compared transcript levels of 46 NKL in T-ALL and normal thymic subpopulations. Ectopic overexpression of 10 NKL genes, of which six are unreported in T-ALL (NKX2-3, BARHL1, BARX2, EMX2, LBX2 and MSX2), was detectable in 17/104 (16%) T-ALLs. Virtually all NKL overexpressing T-ALLs were TCRα unrearranged and ectopic NKL transcript expression strongly repressed Eα activity, suggesting that ectopic NKL expression is the major determinant in early-cortical thymic T-ALL maturation arrest. This immunogenetic T-ALL subtype, defined by TCRβ VDJ but no TCRα VJ rearrangement, is associated with a favorable outcome in GRAALL-treated adult T-ALLs.
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Affiliation(s)
- P Villarese
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants-Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - C Lours
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants-Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - A Trinquand
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants-Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - S Le Noir
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants-Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France
| | - M Belhocine
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants-Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France.,Aix Marseille Univ, INSERM, TAGC UMR1090, Marseille, France
| | - L Lhermitte
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants-Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - A Cieslak
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants-Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France
| | - M Tesio
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants-Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France
| | - A Petit
- Department of Hematology and Oncologie Pédiatrique, Hôpital Trousseau Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - M LeLorch
- Laboratory of Cytogenetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - S Spicuglia
- Aix Marseille Univ, INSERM, TAGC UMR1090, Marseille, France
| | - N Ifrah
- Department of Hematology, Centre Hospitalier, Angers, France
| | - H Dombret
- University Paris 7, Hôpital Saint-Louis, AP-HP, Department of Hematology and Institut Universitaire d'Hématologie, Paris, France
| | - A W Langerak
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - N Boissel
- University Paris 7, Hôpital Saint-Louis, AP-HP, Department of Hematology and Institut Universitaire d'Hématologie, Paris, France
| | - E Macintyre
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants-Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France
| | - V Asnafi
- Université Paris Descartes Sorbonne Cité, Institut Necker Enfants-Malades (INEM), Institut National de Recherche Médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
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17
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Chen L, Zhao L, Alt FW, Krangel MS. An Ectopic CTCF Binding Element Inhibits Tcrd Rearrangement by Limiting Contact between Vδ and Dδ Gene Segments. THE JOURNAL OF IMMUNOLOGY 2016; 197:3188-3197. [PMID: 27613698 DOI: 10.4049/jimmunol.1601124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/16/2016] [Indexed: 11/19/2022]
Abstract
Chromatin looping mediated by the CCCTC binding factor (CTCF) regulates V(D)J recombination at Ag receptor loci. CTCF-mediated looping can influence recombination signal sequence (RSS) accessibility by regulating enhancer activation of germline promoters. CTCF-mediated looping has also been shown to limit directional tracking of the RAG recombinase along chromatin, and to regulate long-distance interactions between RSSs, independent of the RAG recombinase. However, in all prior instances in which CTCF-mediated looping was shown to influence V(D)J recombination, it was not possible to fully resolve the relative contributions to the V(D)J recombination phenotype of changes in accessibility, RAG tracking, and RAG-independent long-distance interactions. In this study, to assess mechanisms by which CTCF-mediated looping can impact V(D)J recombination, we introduced an ectopic CTCF binding element (CBE) immediately downstream of Eδ in the murine Tcra-Tcrd locus. The ectopic CBE impaired inversional rearrangement of Trdv5 in the absence of measurable effects on Trdv5 transcription and chromatin accessibility. The ectopic CBE also limited directional RAG tracking from the Tcrd recombination center, demonstrating that a single CBE can impact the distribution of RAG proteins along chromatin. However, such tracking cannot account for Trdv5-to-Trdd2 inversional rearrangement. Rather, the defect in Trdv5 rearrangement could only be attributed to a reconfigured chromatin loop organization that limited RAG-independent contacts between the Trdv5 and Trdd2 RSSs. We conclude that CTCF can regulate V(D)J recombination by segregating RSSs into distinct loop domains and inhibiting RSS synapsis, independent of any effects on transcription, RSS accessibility, and RAG tracking.
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Affiliation(s)
- Liang Chen
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Lijuan Zhao
- Howard Hughes Medical Institute, Boston, MA 02115.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; and.,Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Frederick W Alt
- Howard Hughes Medical Institute, Boston, MA 02115.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; and.,Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC 27710;
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18
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Zhao L, Frock RL, Du Z, Hu J, Chen L, Krangel MS, Alt FW. Orientation-specific RAG activity in chromosomal loop domains contributes to Tcrd V(D)J recombination during T cell development. J Exp Med 2016; 213:1921-36. [PMID: 27526713 PMCID: PMC4995090 DOI: 10.1084/jem.20160670] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 06/24/2016] [Indexed: 12/17/2022] Open
Abstract
T cell antigen receptor δ (Tcrd) variable region exons are assembled by RAG-initiated V(D)J recombination events in developing γδ thymocytes. Here, we use linear amplification-mediated high-throughput genome-wide translocation sequencing (LAM-HTGTS) to map hundreds of thousands of RAG-initiated Tcrd D segment (Trdd1 and Trdd2) rearrangements in CD4(-)CD8(-) double-negative thymocyte progenitors differentiated in vitro from bone marrow-derived hematopoietic stem cells. We find that Trdd2 joins directly to Trdv, Trdd1, and Trdj segments, whereas Trdd1 joining is ordered with joining to Trdd2, a prerequisite for further rearrangement. We also find frequent, previously unappreciated, Trdd1 and Trdd2 rearrangements that inactivate Tcrd, including sequential rearrangements from V(D)J recombination signal sequence fusions. Moreover, we find dozens of RAG off-target sequences that are generated via RAG tracking both upstream and downstream from the Trdd2 recombination center across the Tcrd loop domain that is bounded by the upstream INT1-2 and downstream TEA elements. Disruption of the upstream INT1-2 boundary of this loop domain allows spreading of RAG on- and off-target activity to the proximal Trdv domain and, correspondingly, shifts the Tcrd V(D)J recombination landscape by leading to predominant V(D)J joining to a proximal Trdv3 pseudogene that lies just upstream of the normal boundary.
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Affiliation(s)
- Lijuan Zhao
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Richard L Frock
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Zhou Du
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Jiazhi Hu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Liang Chen
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, MA 02115
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19
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Proudhon C, Hao B, Raviram R, Chaumeil J, Skok JA. Long-Range Regulation of V(D)J Recombination. Adv Immunol 2015; 128:123-82. [PMID: 26477367 DOI: 10.1016/bs.ai.2015.07.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Given their essential role in adaptive immunity, antigen receptor loci have been the focus of analysis for many years and are among a handful of the most well-studied genes in the genome. Their investigation led initially to a detailed knowledge of linear structure and characterization of regulatory elements that confer control of their rearrangement and expression. However, advances in DNA FISH and imaging combined with new molecular approaches that interrogate chromosome conformation have led to a growing appreciation that linear structure is only one aspect of gene regulation and in more recent years, the focus has switched to analyzing the impact of locus conformation and nuclear organization on control of recombination. Despite decades of work and intense effort from numerous labs, we are still left with an incomplete picture of how the assembly of antigen receptor loci is regulated. This chapter summarizes our advances to date and points to areas that need further investigation.
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Affiliation(s)
- Charlotte Proudhon
- Department of Pathology, New York University School of Medicine, New York, USA
| | - Bingtao Hao
- Department of Pathology, New York University School of Medicine, New York, USA
| | - Ramya Raviram
- Department of Pathology, New York University School of Medicine, New York, USA
| | - Julie Chaumeil
- Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, USA.
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20
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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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21
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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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22
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The 3'-Jα Region of the TCRα Locus Bears Gene Regulatory Activity in Thymic and Peripheral T Cells. PLoS One 2015; 10:e0132856. [PMID: 26177549 PMCID: PMC4503570 DOI: 10.1371/journal.pone.0132856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/18/2015] [Indexed: 11/19/2022] Open
Abstract
Much progress has been made in understanding the important cis-mediated controls on mouse TCRα gene function, including identification of the Eα enhancer and TCRα locus control region (LCR). Nevertheless, previous data have suggested that other cis-regulatory elements may reside in the locus outside of the Eα/LCR. Based on prior findings, we hypothesized the existence of gene regulatory elements in a 3.9-kb region 5’ of the Cα exons. Using DNase hypersensitivity assays and TCRα BAC reporter transgenes in mice, we detected gene regulatory activity within this 3.9-kb region. This region is active in both thymic and peripheral T cells, and selectively affects upstream, but not downstream, gene expression. Together, these data indicate the existence of a novel cis-acting regulatory complex that contributes to TCRα transgene expression in vivo. The active chromatin sites we discovered within this region would remain in the locus after TCRα gene rearrangement, and thus may contribute to endogenous TCRα gene activity, particularly in peripheral T cells, where the Eα element has been found to be inactive.
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23
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Abstract
The Tcra enhancer (Eα) is essential for Tcra locus germ-line transcription and primary Vα-to-Jα recombination during thymocyte development. We found that Eα is inhibited late during thymocyte differentiation and in αβ T lymphocytes, indicating that it is not required to drive transcription of rearranged Tcra genes. Eα inactivation resulted in the disruption of functional long-range enhancer-promoter interactions and was associated with loss of Eα-dependent histone modifications at promoter and enhancer regions, and reduced expression and recruitment of E2A to the Eα enhanceosome in T cells. Enhancer activity could not be recovered by T-cell activation, by forced expression of E2A or by the up-regulation of this and other transcription factors in the context of T helper differentiation. Our results argue that the major function of Eα is to coordinate the formation of a chromatin hub that drives Vα and Jα germ-line transcription and primary rearrangements in thymocytes and imply the existence of an Eα-independent mechanism to activate transcription of the rearranged Tcra locus in αβ T cells.
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24
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Aberrant TCRδ rearrangement underlies the T-cell lymphocytopenia and t(12;14) translocation associated with ATM deficiency. Blood 2015; 125:2665-8. [PMID: 25721125 DOI: 10.1182/blood-2015-01-622621] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/21/2015] [Indexed: 11/20/2022] Open
Abstract
Ataxia telangiectasia mutated (ATM) is a protein kinase and a master regulator of DNA-damage responses. Germline ATM inactivation causes ataxia-telangiectasia (A-T) syndrome with severe lymphocytopenia and greatly increased risk for T-cell lymphomas/leukemia. Both A-T and T-cell prolymphoblastic leukemia patients with somatic mutations of ATM frequently carry inv(14;14) between the T-cell receptor α/δ (TCRα/δ) and immunoglobulin H loci, but the molecular origin of this translocation remains elusive. ATM(-/-) mice recapitulate lymphocytopenia of A-T patients and routinely succumb to thymic lymphomas with t(12;14) translocation, syntenic to inv(14;14) in humans. Here we report that deletion of the TCRδ enhancer (Eδ), which initiates TCRδ rearrangement, significantly improves αβ T cell output and effectively prevents t(12;14) translocations in ATM(-/-) mice. These findings identify the genomic instability associated with V(D)J recombination at the TCRδ locus as the molecular origin of both lymphocytopenia and the signature t(12;14) translocations associated with ATM deficiency.
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25
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Carico Z, Krangel MS. Chromatin Dynamics and the Development of the TCRα and TCRδ Repertoires. Adv Immunol 2015; 128:307-61. [DOI: 10.1016/bs.ai.2015.07.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Ehrlich LA, Yang-Iott K, DeMicco A, Bassing CH. Somatic inactivation of ATM in hematopoietic cells predisposes mice to cyclin D3 dependent T cell acute lymphoblastic leukemia. Cell Cycle 2015; 14:388-98. [PMID: 25659036 PMCID: PMC4614830 DOI: 10.4161/15384101.2014.988020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 11/07/2014] [Indexed: 11/19/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a cancer of immature T cells that exhibits heterogeneity of oncogenic lesions, providing an obstacle for development of more effective and less toxic therapies. Inherited deficiency of ATM, a regulator of the cellular DNA damage response, predisposes young humans and mice to T-ALLs with clonal chromosome translocations. While acquired ATM mutation or deletion occurs in pediatric T-ALLs, the role of somatic ATM alterations in T-ALL pathogenesis remains unknown. We demonstrate here that somatic Atm inactivation in haematopoietic cells starting as these cells differentiate in utero predisposes mice to T-ALL at similar young ages and harboring analogous translocations as germline Atm-deficient mice. However, some T-ALLs from haematopoietic cell specific deletion of Atm were of more mature thymocytes, revealing that the developmental timing and celluar origin of Atm inactivation influences the phenotype of ATM-deficient T-ALLs. Although it has been hypothesized that ATM suppresses cancer by preventing deletion and inactivation of TP53, we find that Atm inhibits T-ALL independent of Tp53 deletion. Finally, we demonstrate that the Cyclin D3 protein that drives immature T cell proliferation is essential for transformation of Atm-deficient thymocytes. Our study establishes a pre-clinical model for pediatric T-ALLs with acquired ATM inactivation and identifies the cell cycle machinery as a therapeutic target for this aggressive childhood T-ALL subtype.
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Affiliation(s)
- Lori A Ehrlich
- Division of Oncology, Department of Pediatrics; Children's Hospital of Philadelphia; Philadelphia, PA USA
- Division of Cancer Pathobiology; Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia; Philadelphia, PA USA
- Abramson Family Cancer Research Institute; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA USA
| | - Katherine Yang-Iott
- Division of Cancer Pathobiology; Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia; Philadelphia, PA USA
- Abramson Family Cancer Research Institute; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA USA
| | - Amy DeMicco
- Division of Cancer Pathobiology; Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia; Philadelphia, PA USA
- Abramson Family Cancer Research Institute; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA USA
- Cell and Molecular Biology Graduate Group; Perelman School of Medicine of the University of Pennsylvania; Philadelphia, PA 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, PA USA
- Abramson Family Cancer Research Institute; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA USA
- Cell and Molecular Biology Graduate Group; Perelman School of Medicine of the University of Pennsylvania; Philadelphia, PA USA
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27
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Ziegler H, Welker C, Sterk M, Haarer J, Rammensee HG, Handgretinger R, Schilbach K. Human Peripheral CD4(+) Vδ1(+) γδT Cells Can Develop into αβT Cells. Front Immunol 2014; 5:645. [PMID: 25709606 PMCID: PMC4329445 DOI: 10.3389/fimmu.2014.00645] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/03/2014] [Indexed: 11/16/2022] Open
Abstract
The lifelong generation of αβT cells enables us to continuously build immunity against pathogens and malignancies despite the loss of thymic function with age. Homeostatic proliferation of post-thymic naïve and memory T cells and their transition into effector and long-lived memory cells balance the decreasing output of naïve T cells, and recent research suggests that also αβT-cell development independent from the thymus may occur. However, the sites and mechanisms of extrathymic T-cell development are not yet understood in detail. γδT cells represent a small fraction of the overall T-cell pool, and are endowed with tremendous phenotypic and functional plasticity. γδT cells that express the Vδ1 gene segment are a minor population in human peripheral blood but predominate in epithelial (and inflamed) tissues. Here, we characterize a CD4+ peripheral Vδ1+ γδT-cell subpopulation that expresses stem-cell and progenitor markers and is able to develop into functional αβT cells ex vivo in a simple culture system and in vivo. The route taken by this process resembles thymic T-cell development. However, it involves the re-organization of the Vδ1+ γδTCR into the αβTCR as a consequence of TCR-γ chain downregulation and the expression of surface Vδ1+Vβ+ TCR components, which we believe function as surrogate pre-TCR. This transdifferentiation process is readily detectable in vivo in inflamed tissue. Our study provides a conceptual framework for extrathymic T-cell development and opens up a new vista in immunology that requires adaptive immune responses in infection, autoimmunity, and cancer to be reconsidered.
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Affiliation(s)
- Hendrik Ziegler
- Department of Hematology and Oncology, University Children's Hospital, University of Tübingen , Tübingen , Germany
| | - Christian Welker
- Department of Hematology and Oncology, University Children's Hospital, University of Tübingen , Tübingen , Germany
| | - Marco Sterk
- Department of Hematology and Oncology, University Children's Hospital, University of Tübingen , Tübingen , Germany
| | - Jan Haarer
- Department of Hematology and Oncology, University Children's Hospital, University of Tübingen , Tübingen , Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen , Tübingen , Germany
| | - Rupert Handgretinger
- Department of Hematology and Oncology, University Children's Hospital, University of Tübingen , Tübingen , Germany
| | - Karin Schilbach
- Department of Hematology and Oncology, University Children's Hospital, University of Tübingen , Tübingen , Germany
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28
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Naik AK, Hawwari A, Krangel MS. Specification of Vδ and Vα usage by Tcra/Tcrd locus V gene segment promoters. THE JOURNAL OF IMMUNOLOGY 2014; 194:790-4. [PMID: 25472997 DOI: 10.4049/jimmunol.1402423] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Tcra/Tcrd locus undergoes V-Dδ-Jδ rearrangement in CD4(-)CD8(-) thymocytes to form the TCRδ chain of the γδ TCR and V-Jα rearrangement in CD4(+)CD8(+) thymocytes to form the TCRα-chain of the αβ TCR. Most V segments in the locus participate in V-Jα rearrangement, but only a small and partially overlapping subset participates in V-Dδ-Jδ rearrangement. What specifies any particular Tcra/Tcrd locus V gene segment as a Vδ, a Vα, or both is currently unknown. We tested the hypothesis that V segment usage is specified by V segment promoter-dependent chromatin accessibility in developing thymocytes. TRAV15/DV6 family V gene segments contribute to both the Tcrd and the Tcra repertoires, whereas TRAV12 family V gene segments contribute almost exclusively to the Tcra repertoire. To understand whether the TRAV15/DV6 promoter region specifies TRAV15/DV6 as a Vδ, we used gene targeting to replace the promoter region of a TRAV12 family member with one from a TRAV15/DV6 family member. The TRAV15/DV6 promoter region conferred increased germline transcription and histone modifications to TRAV12 in double-negative thymocytes and caused a substantial increase in usage of TRAV12 in Tcrd recombination events. Our results demonstrate that usage of TRAV15/DV6 family V gene segments for Tcrd recombination in double-negative thymocytes is regulated, at least in part, by intrinsic features of TRAV15/DV6 promoters, and argue that Tcra/Tcrd locus Vδ gene segments are defined by their local chromatin accessibility in CD4(-)CD8(-) thymocytes.
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Affiliation(s)
- Abani Kanta Naik
- Department of Immunology, Duke University Medical Center, Durham, NC 27710; and
| | - Abbas Hawwari
- Department of Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC 27710; and
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29
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Cieslak A, Le Noir S, Trinquand A, Lhermitte L, Franchini DM, Villarese P, Gon S, Bond J, Simonin M, Vanhille L, Vanhile L, Reimann C, Verhoeyen E, Larghero J, Six E, Spicuglia S, André-Schmutz I, Langerak A, Nadel B, Macintyre E, Payet-Bornet D, Asnafi V. RUNX1-dependent RAG1 deposition instigates human TCR-δ locus rearrangement. ACTA ACUST UNITED AC 2014; 211:1821-32. [PMID: 25135298 PMCID: PMC4144731 DOI: 10.1084/jem.20132585] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Within the human TCR-α/δ locus, ordered rearrangements requires RUNX1, which binds to the Dδ2-23RSS and interacts with RAG1 to enhance RAG1 deposition at this site. Absence of this RUNX1 binding site in the homologous murine Dδ1-23RSS offers an explanation for the lack of ordered TCR-δ gene assembly in mice. V(D)J recombination of TCR loci is regulated by chromatin accessibility to RAG1/2 proteins, rendering RAG1/2 targeting a potentially important regulator of lymphoid differentiation. We show that within the human TCR-α/δ locus, Dδ2-Dδ3 rearrangements occur at a very immature thymic, CD34+/CD1a−/CD7+dim stage, before Dδ2(Dδ3)-Jδ1 rearrangements. These strictly ordered rearrangements are regulated by mechanisms acting beyond chromatin accessibility. Importantly, direct Dδ2-Jδ1 rearrangements are prohibited by a B12/23 restriction and ordered human TCR-δ gene assembly requires RUNX1 protein, which binds to the Dδ2-23RSS, interacts with RAG1, and enhances RAG1 deposition at this site. This RUNX1-mediated V(D)J recombinase targeting imposes the use of two Dδ gene segments in human TCR-δ chains. Absence of this RUNX1 binding site in the homologous mouse Dδ1-23RSS provides a molecular explanation for the lack of ordered TCR-δ gene assembly in mice and may underlie differences in early lymphoid differentiation between these species.
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Affiliation(s)
- Agata Cieslak
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Sandrine Le Noir
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Amélie Trinquand
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Ludovic Lhermitte
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Don-Marc Franchini
- CNRS-Pierre Fabre USR3388, Epigenetic Targeting of Cancer (ETaC), and INSERM UMR1037, Cancer Research Center of Toulouse (CRCT), 31035 Toulouse, France
| | - Patrick Villarese
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Stéphanie Gon
- Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille Université UM 2, INSERM UMR 1104, CNRS UMR 7280, 13288 Marseille, France
| | - Jonathan Bond
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Mathieu Simonin
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Laurent Vanhille
- Technological Advances for Genomics and Clinics (TAGC), INSERM U1090, Université de la Méditerranée, 13288 Marseille, France
| | - Laurent Vanhile
- Technological Advances for Genomics and Clinics (TAGC), INSERM U1090, Université de la Méditerranée, 13288 Marseille, France
| | - Christian Reimann
- Université Paris-Descartes, Faculté de Médecine René Descartes, IFR94 and INSERM, U768, F-75015 Paris, France
| | - Els Verhoeyen
- CIRI, International center for Infectiology Research, EVIR team, Université de Lyon, INSERM U1111, Lyon, France and Centre Méditerranéen de Médecine Moléculaire (C3M), team "contrôle métabolique des morts cellulaires" Inserm, U1065, 06204 Nice, France
| | - Jerome Larghero
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Saint-Louis, Unité de Thérapie Cellulaire, Université Paris Diderot, Sorbonne Paris Cité, Inserm CICBT501 et UMR1160, Institut Universitaire d'Hématologie, 75010 Paris, France
| | - Emmanuelle Six
- Université Paris-Descartes, Faculté de Médecine René Descartes, IFR94 and INSERM, U768, F-75015 Paris, France
| | - Salvatore Spicuglia
- Technological Advances for Genomics and Clinics (TAGC), INSERM U1090, Université de la Méditerranée, 13288 Marseille, France
| | - Isabelle André-Schmutz
- Université Paris-Descartes, Faculté de Médecine René Descartes, IFR94 and INSERM, U768, F-75015 Paris, France
| | - Anton Langerak
- Department of Immunology, Erasmus MC, University Medical Center, 3016 Rotterdam, Netherlands
| | - Bertrand Nadel
- Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille Université UM 2, INSERM UMR 1104, CNRS UMR 7280, 13288 Marseille, France
| | - Elizabeth Macintyre
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Dominique Payet-Bornet
- Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille Université UM 2, INSERM UMR 1104, CNRS UMR 7280, 13288 Marseille, France
| | - Vahid Asnafi
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, 75015 Paris, France
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30
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Kondilis-Mangum HD, Wade PA. Epigenetics and the adaptive immune response. Mol Aspects Med 2013; 34:813-25. [PMID: 22789989 PMCID: PMC3508324 DOI: 10.1016/j.mam.2012.06.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 06/27/2012] [Indexed: 01/31/2023]
Abstract
Cells of the adaptive immune response undergo dynamic epigenetic changes as they develop and respond to immune challenge. Plasticity is a necessary prerequisite for the chromosomal dynamics of lineage specification, development, and the immune effector function of the mature cell types. The alterations in DNA methylation and histone modification that characterize activation may be integral to the generation of immunologic memory, thereby providing an advantage on secondary exposure to pathogens. While the immune system benefits from the dynamic nature of the epigenome, such benefit comes at a cost - increased likelihood of disease-causing mutation.
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Affiliation(s)
- Hrisavgi D Kondilis-Mangum
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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31
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Winandy S. Ikaros to the rescue of TCR-α chain gene rearrangement. Eur J Immunol 2013; 43:314-7. [PMID: 23299235 DOI: 10.1002/eji.201243272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 12/18/2012] [Accepted: 01/03/2013] [Indexed: 12/15/2022]
Abstract
Ikaros is a transcriptional regulator critical for B- and T-cell development. Recently, it has been shown to play a central role in facilitating rearrangement of antigen-receptor genes in B cells. Whether or not it had a similar function in this process in T cells, however, was a mystery. In this issue of the European Journal of Immunology, a role for Ikaros in T-cell receptor (TCR) rearrangement and expression of TCR-α chain genes is revealed in the study by Collins et al. [Eur. J. Immunol. 2013. 43: 521-532]. Ikaros functions in this capacity as an "accessibility factor," facilitating increased TCR-α chain gene transcription and accessibility of the locus to promote rearrangement. Interestingly, this study has also revealed differences in the mechanisms by which Ikaros promotes antigen-receptor rearrangement in B versus T cells, thereby suggesting that Ikaros may have lineage-specific functions in coordinating antigen-receptor rearrangement.
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Affiliation(s)
- Susan Winandy
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA.
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32
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Jaeger S, Fernandez B, Ferrier P. Epigenetic aspects of lymphocyte antigen receptor gene rearrangement or 'when stochasticity completes randomness'. Immunology 2013; 139:141-50. [PMID: 23278765 DOI: 10.1111/imm.12057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 01/05/2023] Open
Abstract
To perform their specific functional role, B and T lymphocytes, cells of the adaptive immune system of jawed vertebrates, need to express one (and, preferably, only one) form of antigen receptor, i.e. the immunoglobulin or T-cell receptor (TCR), respectively. This end goal depends initially on a series of DNA cis-rearrangement events between randomly chosen units from separate clusters of V, D (at some immunoglobulin and TCR loci) and J gene segments, a biomolecular process collectively referred to as V(D)J recombination. V(D)J recombination takes place in immature T and B cells and relies on the so-called RAG nuclease, a site-specific DNA cleavage apparatus that corresponds to the lymphoid-specific moiety of the VDJ recombinase. At the genome level, this recombinase's mission presents substantial biochemical challenges. These relate to the huge distance between (some of) the gene segments that it eventually rearranges and the need to achieve cell-lineage-restricted and developmentally ordered routines with at times, mono-allelic versus bi-allelic discrimination. The entire process must be completed without any recombination errors, instigators of chromosome instability, translocation and, potentially, tumorigenesis. As expected, such a precisely choreographed and yet potentially risky process demands sophisticated controls; epigenetics demonstrates what is possible when calling upon its many facets. In this vignette, we will recall the evidence that almost from the start appeared to link the two topics, V(D)J recombination and epigenetics, before reviewing the latest advances in our knowledge of this joint venture.
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Affiliation(s)
- Sébastien Jaeger
- Centre d'Immunologie de Marseille-Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (Inserm) U1104, Centre National de la Recherche Scientifique (CNRS)UMR7280, Aix-Marseille University UM2, Marseille, France
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Collins B, Clambey ET, Scott-Browne J, White J, Marrack P, Hagman J, Kappler JW. Ikaros promotes rearrangement of TCR α genes in an Ikaros null thymoma cell line. Eur J Immunol 2012; 43:521-32. [PMID: 23172374 DOI: 10.1002/eji.201242757] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 10/09/2012] [Accepted: 11/16/2012] [Indexed: 12/27/2022]
Abstract
Ikaros is important in the development and maintenance of the lymphoid system, functioning in part by associating with chromatin-remodeling complexes. We have studied the functions of Ikaros in the transition from pre-T cell to the CD4(+) CD8(+) thymocyte using an Ikaros null CD4(-) CD8(-) mouse thymoma cell line (JE131). We demonstrate that this cell line carries a single functional TCR β gene rearrangement and expresses a surface pre-TCR. JE131 cells also carry nonfunctional rearrangements on both alleles of their TCR α loci. Retroviral reintroduction of Ikaros dramatically increased the rate of transcription in the α locus and TCR Vα/Jα recombination resulting in the appearance of many new αβTCR(+) cells. The process is RAG dependent, requires switch/sucrose nonfermentable chromatin-remodeling complexes and is coincident with the binding of Ikaros to the TCR α enhancer. Furthermore, knockdown of Mi2/nucleosome remodeling and deacetylase complexes increased the frequency of TCR α rearrangement. Our data suggest that Ikaros controls Vα/Jα recombination in T cells by controlling access of the transcription and recombination machinery to the TCR α loci. The JE131 cell line should prove to be a very useful tool for studying the molecular details of this and other processes involved in the pre-T cell to αβTCR(+) CD4(+) CD8(+) thymocyte transition.
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Affiliation(s)
- Bernard Collins
- Howard Hughes Medical Institute, National Jewish Health, Denver, CO 80206, USA
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Tcra gene recombination is supported by a Tcra enhancer- and CTCF-dependent chromatin hub. Proc Natl Acad Sci U S A 2012; 109:E3493-502. [PMID: 23169622 DOI: 10.1073/pnas.1214131109] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Antigen receptor locus V(D)J recombination requires interactions between widely separated variable (V), diversity (D), and joining (J) gene segments, but the mechanisms that generate these interactions are not well understood. Here we assessed mechanisms that direct developmental stage-specific long-distance interactions at the Tcra/Tcrd locus. The Tcra/Tcrd locus recombines Tcrd gene segments in CD4(-)CD8(-) double-negative thymocytes and Tcra gene segments in CD4(+)CD8(+) double-positive thymocytes. Initial V(α)-to-J(α) recombination occurs within a chromosomal domain that displays a contracted conformation in both thymocyte subsets. We used chromosome conformation capture to demonstrate that the Tcra enhancer (E(α)) interacts directly with V(α) and J(α) gene segments distributed across this domain, specifically in double-positive thymocytes. Moreover, E(α) promotes interactions between these V(α) and J(α) segments that should facilitate their synapsis. We found that the CCCTC-binding factor (CTCF) binds to E(α) and to many locus promoters, biases E(α) to interact with these promoters, and is required for efficient V(α)-J(α) recombination. Our data indicate that E(α) and CTCF cooperate to create a developmentally regulated chromatin hub that supports V(α)-J(α) synapsis and recombination.
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TRIM28 mediates chromatin modifications at the TCRα enhancer and regulates the development of T and natural killer T cells. Proc Natl Acad Sci U S A 2012; 109:20083-8. [PMID: 23169648 DOI: 10.1073/pnas.1214704109] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
T-cell receptor-α (TCRα) rearrangement in CD4(+)CD8(+) double-positive immature thymocytes is a prerequisite for production of αβ T cells and invariant natural killer T cells. This developmental event is regulated by the TCRα enhancer (Eα), which induces chromatin modification and recruitment of the recombination-activating proteins Rag1 and Rag2. However, the molecular mechanism underlying the activation and long-range action of Eα remains incompletely understood. We show here that the chromatin-modifying factor TRIM28 is highly expressed in double-positive thymocytes and persistently phosphorylated at serine 473. TRIM28 binds to Eα and induces histone 3 lysine 4 trimethylation in the Eα and distant regions of the TCRα locus, coupled with recruitment of Rag proteins. T-cell-conditional ablation of TRIM28 impaired TCRα gene rearrangement and compromised the development of αβ T cells and invariant natural killer T cells. These findings establish TRIM28 as a unique regulator of thymocyte development and highlight an epigenetic mechanism involving TRIM28-mediated active chromatin modification in the TCRα locus.
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Dadi S, Le Noir S, Payet-Bornet D, Lhermitte L, Zacarias-Cabeza J, Bergeron J, Villarèse P, Vachez E, Dik WA, Millien C, Radford I, Verhoeyen E, Cosset FL, Petit A, Ifrah N, Dombret H, Hermine O, Spicuglia S, Langerak AW, Macintyre EA, Nadel B, Ferrier P, Asnafi V. TLX homeodomain oncogenes mediate T cell maturation arrest in T-ALL via interaction with ETS1 and suppression of TCRα gene expression. Cancer Cell 2012; 21:563-76. [PMID: 22516263 DOI: 10.1016/j.ccr.2012.02.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 01/03/2012] [Accepted: 02/13/2012] [Indexed: 10/28/2022]
Abstract
Acute lymphoblastic leukemias (ALLs) are characterized by multistep oncogenic processes leading to cell-differentiation arrest and proliferation. Specific abrogation of maturation blockage constitutes a promising therapeutic option in cancer, which requires precise understanding of the underlying molecular mechanisms. We show that the cortical thymic maturation arrest in T-lineage ALLs that overexpress TLX1 or TLX3 is due to binding of TLX1/TLX3 to ETS1, leading to repression of T cell receptor (TCR) α enhanceosome activity and blocked TCR-Jα rearrangement. TLX1/TLX3 abrogation or enforced TCRαβ expression leads to TCRα rearrangement and apoptosis. Importantly, the autoextinction of clones carrying TCRα-driven TLX1 expression supports TLX "addiction" in TLX-positive leukemias and provides further rationale for targeted therapy based on disruption of TLX1/TLX3.
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Affiliation(s)
- Saïda Dadi
- Department of Hematologye, Université de Médecine Paris Descartes Sorbonne Cité, Centre National de la Recherche Scientifique (CNRS), France
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del Blanco B, García-Mariscal A, Wiest DL, Hernández-Munain C. Tcra enhancer activation by inducible transcription factors downstream of pre-TCR signaling. THE JOURNAL OF IMMUNOLOGY 2012; 188:3278-93. [PMID: 22357628 DOI: 10.4049/jimmunol.1100271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Tcra enhancer (Eα) is essential for pre-TCR-mediated activation of germline transcription and V(D)J recombination. Eα is considered an archetypical enhanceosome that acts through the functional synergy and cooperative binding of multiple transcription factors. Based on dimethylsulfate genomic footprinting experiments, there has been a long-standing paradox regarding Eα activation in the absence of differences in enhancer occupancy. Our data provide the molecular mechanism of Eα activation and an explanation of this paradox. We found that germline transcriptional activation of Tcra is dependent on constant phospholipase Cγ, as well as calcineurin- and MAPK/ERK-mediated signaling, indicating that inducible transcription factors are crucially involved. NFAT, AP-1, and early growth response factor 1, together with CREB-binding protein/p300 coactivators, bind to Eα as part of an active enhanceosome assembled during pre-TCR signaling. We favor a scenario in which the binding of lymphoid-restricted and constitutive transcription factors to Eα prior to its activation forms a regulatory scaffold to recruit factors induced by pre-TCR signaling. Thus, the combinatorial assembly of tissue- and signal-specific transcription factors dictates the Eα function. This mechanism for enhancer activation may represent a general paradigm in tissue-restricted and stimulus-responsive gene regulation.
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Affiliation(s)
- Beatriz del Blanco
- Departamento de Biología Celular e Inmunología, Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), Consejo Superior de Investigaciones Científicas, 18100-Armilla, Granada, Spain
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Del Blanco B, García V, García-Mariscal A, Hernández-Munain C. Control of V(D)J Recombination through Transcriptional Elongation and Changes in Locus Chromatin Structure and Nuclear Organization. GENETICS RESEARCH INTERNATIONAL 2011; 2011:970968. [PMID: 22567371 PMCID: PMC3335570 DOI: 10.4061/2011/970968] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 07/29/2011] [Indexed: 01/29/2023]
Abstract
V(D)J recombination is the assembly of gene segments at the antigen receptor loci to
generate antigen receptor diversity in T and B lymphocytes. This process is regulated,
according to defined developmental programs, by the action of a single specific
recombinase complex formed by the recombination antigen gene (RAG-1/2) proteins
that are expressed in immature lymphocytes. V(D)J recombination is strictly controlled
by RAG-1/2 accessibility to specific recombination signal sequences in chromatin at
several levels: cellular lineage, temporal regulation, gene segment order, and allelic
exclusion. DNA cleavage by RAG-1/2 is regulated by the chromatin structure,
transcriptional elongation, and three-dimensional architecture and position of the
antigen receptor loci in the nucleus. Cis-elements specifically direct transcription and
V(D)J recombination at these loci through interactions with transacting factors that form
molecular machines that mediate a sequence of structural events. These events open
chromatin to activate transcriptional elongation and to permit the access of RAG-1/2 to
their recombination signal sequences to drive the juxtaposition of the V, D, and J
segments and the recombination reaction itself. This chapter summarizes the advances
in this area and the important role of the structure and position of antigen receptor loci
within the nucleus to control this process.
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Affiliation(s)
- Beatriz Del Blanco
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento s/n. 18100 Armilla, Spain
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Jones ME, Zhuang Y. Stage-specific functions of E-proteins at the β-selection and T-cell receptor checkpoints during thymocyte development. Immunol Res 2011; 49:202-15. [PMID: 21128008 DOI: 10.1007/s12026-010-8182-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The E-protein transcription factors E2A and HEB function in a lineage- and stage-specific manner to orchestrate many critical events throughout lymphocyte development. The function of E-proteins in both B- and T-lymphocyte development has been extensively studied through the use of single-gene knockout animals. Unlike B cells, which rely primarily on E2A alone, T cells are regulated by the combinatorial expression of both E2A and HEB. Therefore, many of the roles of E-proteins during T-cell development may be masked in single-gene knockout studies due to the compensatory function of E2A and HEB. More recently, our laboratory has established double-conditional knockout models to eliminate both E2A and HEB in a stage-specific manner throughout T-cell development. These models, in combination with other complimentary genetic approaches, have identified new E-protein functions at each of the two major T-cell developmental checkpoints. Here, we will discuss how E-proteins function to regulate the expression of T-cell receptor components and cell cycle at the β-selection checkpoint, and how they control positive selection, survival, and lineage-specific gene expression at the subsequent T-cell receptor checkpoint.
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Affiliation(s)
- Mary Elizabeth Jones
- Department of Immunology, Duke University Medical Center, Box 3010, Durham, NC 27710, USA.
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Shih HY, Hao B, Krangel MS. Orchestrating T-cell receptor α gene assembly through changes in chromatin structure and organization. Immunol Res 2011; 49:192-201. [PMID: 21128009 DOI: 10.1007/s12026-010-8181-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
V(D)J recombination is regulated through changes in chromatin structure that allow recombinase proteins access to recombination signal sequences and through changes in three-dimensional chromatin organization that bring pairs of distant recombination signal sequences into proximity. The Tcra/Tcrd locus is complex and undergoes distinct recombination programs in double negative and double positive thymocytes that lead to the assembly of Tcrd and Tcra genes, respectively. Our studies provide insights into how locus chromatin structure is regulated and how changes in locus chromatin structure can target and then retarget the recombinase to create developmental progressions of recombination events. Our studies also reveal distinct locus conformations in double negative and double positive thymocytes and suggest how these conformations may support the distinct recombination programs in the two compartments.
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Affiliation(s)
- Han-Yu Shih
- Department of Immunology, Duke University Medical Center, PO Box 3010, Durham, NC 27710, USA
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Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau JC, Ferrier P, Spicuglia S. H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J 2011; 30:4198-210. [PMID: 21847099 DOI: 10.1038/emboj.2011.295] [Citation(s) in RCA: 236] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 07/12/2011] [Indexed: 11/09/2022] Open
Abstract
Combinations of post-translational histone modifications shape the chromatin landscape during cell development in eukaryotes. However, little is known about the modifications exactly delineating functionally engaged regulatory elements. For example, although histone H3 lysine 4 mono-methylation (H3K4me1) indicates the presence of transcriptional gene enhancers, it does not provide clearcut information about their actual position and stage-specific activity. Histone marks were, therefore, studied here at genomic loci differentially expressed in early stages of T-lymphocyte development. The concomitant presence of the three H3K4 methylation states (H3K4me1/2/3) was found to clearly reflect the activity of bona fide T-cell gene enhancers. Globally, gain or loss of H3K4me2/3 at distal genomic regions correlated with, respectively, the induction or the repression of associated genes during T-cell development. In the Tcrb gene enhancer, the H3K4me3-to-H3K4me1 ratio decreases with the enhancer's strength. Lastly, enhancer association of RNA-polymerase II (Pol II) correlated with the presence of H3K4me3 and Pol II accumulation resulted in local increase of H3K4me3. Our results suggest the existence of functional links between Pol II occupancy, H3K4me3 enrichment and enhancer activity.
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Affiliation(s)
- Aleksandra Pekowska
- Centre d'Immunologie de Marseille-Luminy, Parc Scientifique de Luminy, Case 906, Marseille, France
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Hao B, Krangel MS. Long-distance regulation of fetal V(δ) gene segment TRDV4 by the Tcrd enhancer. THE JOURNAL OF IMMUNOLOGY 2011; 187:2484-91. [PMID: 21784972 DOI: 10.4049/jimmunol.1100468] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Murine Tcra and Tcrd gene segments are organized into a single genetic locus (Tcra/Tcrd locus) that undergoes V(D)J recombination in CD4(-)CD8(-) double-negative (DN) thymocytes to assemble Tcrd genes and in CD4(+)CD8(+) double-positive thymocytes to assemble Tcra genes. Recombination events are regulated by two developmental stage-specific enhancers, E(δ) and E(α). Effects of E(α) on Trca/Tcrd locus chromatin have been well documented, but effects of E(δ) have not. In this regard, E(α) acts over long distances to activate many V(α) and J(α) segments for recombination in double-positive thymocytes. However, in DN thymocytes, it is unclear whether E(δ) functions over long distances to regulate V(δ) gene segments or functions only locally to regulate D(δ) and J(δ) gene segments. In this study, we analyzed germline transcription, histone modifications, and recombination on wild-type and E(δ)-deficient alleles in adult and fetal thymocytes. We found that E(δ) functions as a local enhancer whose influence is limited to no more than ∼10 kb in either direction (including D(δ), J(δ), and TRDV5 gene segments) in adult DN thymocytes. However, we identified a unique long-distance role for E(δ) promoting accessibility and recombination of fetal V(δ) gene segment TRDV4, over a distance of 55 kb, in fetal thymocytes. TRDV4 recombination is specifically repressed in adult thymocytes. We found that this repression is enforced by a developmentally regulated loss of histone acetylation. Constitutively high levels of a suppressive modification, histone H3 lysine 9 dimethylation, may contribute to repression as well.
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Affiliation(s)
- Bingtao Hao
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA
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Giallourakis CC, Franklin A, Guo C, Cheng HL, Yoon HS, Gallagher M, Perlot T, Andzelm M, Murphy AJ, Macdonald LE, Yancopoulos GD, Alt FW. Elements between the IgH variable (V) and diversity (D) clusters influence antisense transcription and lineage-specific V(D)J recombination. Proc Natl Acad Sci U S A 2010; 107:22207-12. [PMID: 21123744 PMCID: PMC3009784 DOI: 10.1073/pnas.1015954107] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ig and T-cell receptor (TCR) variable-region gene exons are assembled from component variable (V), diversity (D) and joining (J) gene segments during early B and T cell development. The RAG1/2 endonuclease initiates V(D)J recombination by introducing DNA double-strand breaks at borders of the germ-line segments. In mice, the Ig heavy-chain (IgH) locus contains, from 5' to 3', several hundred V(H) gene segments, 13 D segments, and 4 J(H) segments within a several megabase region. In developing B cells, IgH variable-region exon assembly is ordered with D to J(H) rearrangement occurring on both alleles before appendage of a V(H) segment. Also, IgH V(H) to DJ(H) rearrangement does not occur in T cells, even though DJ(H) rearrangements occur at low levels. In these contexts, V(D)J recombination is controlled by modulating substrate gene segment accessibility to RAG1/2 activity. To elucidate control elements, we deleted the 100-kb intergenic region that separates the V(H) and D clusters (generating ΔV(H)-D alleles). In both B and T cells, ΔV(H)-D alleles initiated high-level antisense and, at lower levels, sense transcription from within the downstream D cluster, with antisense transcripts extending into proximal V(H) segments. In developing T lymphocytes, activated germ-line antisense transcription was accompanied by markedly increased IgH D-to-J(H) rearrangement and substantial V(H) to DJ(H) rearrangement of proximal IgH V(H) segments. Thus, the V(H)-D intergenic region, and likely elements within it, can influence silencing of sense and antisense germ-line transcription from the IgH D cluster and thereby influence targeting of V(D)J recombination.
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Affiliation(s)
- Cosmas C. Giallourakis
- The Howard Hughes Medical Institute, Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114; and
| | - Andrew Franklin
- The Howard Hughes Medical Institute, Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Chunguang Guo
- The Howard Hughes Medical Institute, Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Hwei-Ling Cheng
- The Howard Hughes Medical Institute, Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Hye Suk Yoon
- The Howard Hughes Medical Institute, Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Michael Gallagher
- The Howard Hughes Medical Institute, Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Thomas Perlot
- The Howard Hughes Medical Institute, Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Milena Andzelm
- The Howard Hughes Medical Institute, Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | | | | | - Frederick W. Alt
- The Howard Hughes Medical Institute, Children's Hospital, Immune Disease Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115
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Subrahmanyam R, Sen R. RAGs' eye view of the immunoglobulin heavy chain gene locus. Semin Immunol 2010; 22:337-45. [PMID: 20864355 DOI: 10.1016/j.smim.2010.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 08/12/2010] [Indexed: 10/19/2022]
Abstract
The immunoglobulin heavy chain (IgH) gene locus is activated at a precise stage of B lymphocyte development to undergo gene rearrangements that assemble the functional gene. In this review we summarize our current understanding of the chromatin state of the IgH as it appears just prior to the initiation of V(D)J recombination, and the implications of this structure for regulation of recombination. We also examine the role of the intron enhancer, Eμ, in establishing the pre-rearrangement chromatin structure. The emerging picture shows that the IgH locus consists of independently regulated domains, each of which requires multiple levels of epigenetic changes to reach the fully activated state.
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Affiliation(s)
- Ramesh Subrahmanyam
- Gene Regulation Section, Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, 251 Bayview Blvd., Room 06C214, Baltimore, MD 21224, United States
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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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Ji Y, Little AJ, Banerjee JK, Hao B, Oltz EM, Krangel MS, Schatz DG. Promoters, enhancers, and transcription target RAG1 binding during V(D)J recombination. ACTA ACUST UNITED AC 2010; 207:2809-16. [PMID: 21115692 PMCID: PMC3005232 DOI: 10.1084/jem.20101136] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
RAG1 binding to TCR gene elements is dictated by transcriptional control elements and by transcription itself; these findings provide direct confirmation of the long-held accessibility model. V(D)J recombination assembles antigen receptor genes in a well-defined order during lymphocyte development. This sequential process has long been understood in the context of the accessibility model, which states that V(D)J recombination is regulated by controlling the ability of the recombination machinery to gain access to its chromosomal substrates. Indeed, many features of “open” chromatin correlate with V(D)J recombination, and promoters and enhancers have been strongly implicated in creating a recombinase-accessible configuration in neighboring chromatin. An important prediction of the accessibility model is that cis-elements and transcription control binding of the recombination-activating gene 1 (RAG1) and RAG2 proteins to their DNA targets. However, this prediction has not been tested directly. In this study, we use mutant Tcra and Tcrb alleles to demonstrate that enhancers control RAG1 binding globally at Jα or Dβ/Jβ gene segments, that promoters and transcription direct RAG1 binding locally, and that RAG1 binding can be targeted in the absence of RAG2. These findings reveal important features of the genetic mechanisms that regulate RAG binding and provide a direct confirmation of the accessibility model.
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Affiliation(s)
- Yanhong Ji
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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Analysis of mice lacking DNaseI hypersensitive sites at the 5' end of the IgH locus. PLoS One 2010; 5:e13992. [PMID: 21085586 PMCID: PMC2981565 DOI: 10.1371/journal.pone.0013992] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 10/26/2010] [Indexed: 12/24/2022] Open
Abstract
The 5′ end of the IgH locus contains a cluster of DNaseI hypersensitive sites, one of which (HS1) was shown to be pro-B cell specific and to contain binding sites for the transcription factors PU.1, E2A, and Pax5. These data as well as the location of the hypersensitive sites at the 5′ border of the IgH locus suggested a possible regulatory function for these elements with respect to the IgH locus. To test this notion, we generated mice carrying targeted deletions of either the pro-B cell specific site HS1 or the whole cluster of DNaseI hypersensitive sites. Lymphocytes carrying these deletions appear to undergo normal development, and mutant B cells do not exhibit any obvious defects in V(D)J recombination, allelic exclusion, or class switch recombination. We conclude that deletion of these DNaseI hypersensitive sites does not have an obvious impact on the IgH locus or B cell development.
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48
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Cellular context-dependent effects of H2ax and p53 deletion on the development of thymic lymphoma. Blood 2010; 117:175-85. [PMID: 20947684 DOI: 10.1182/blood-2010-03-273045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
H2AX and Artemis each cooperate with p53 to suppress lymphoma. Germline H2ax(-/-)p53(-/-) mice die of T-cell receptor-β(-) (TCR-β(-)) thymic lymphomas with translocations and other lesions characteristic of human T-cell acute lymphoblastic leukemia. Here, we demonstrate that mice with inactivation of H2ax and p53 in thymocytes die at later ages to TCR-β(-) or TCR-β(+) thymic lymphomas containing a similar pattern of translocations as H2ax(-/-)p53(-/-) tumors. Germline Artemis(-/-) p53(-/-) mice die of lymphomas with antigen receptor locus translocations, whereas Artemis(-/-)H2ax(-/-)p53(-/-) mice die at earlier ages from multiple malignancies. We show here that Artemis(-/-) mice with p53 deletion in thymocytes die of TCR-β(-) tumors containing Tcrα/δ translocations, other clonal translocations, or aneuploidy, as well as Notch1 mutations. Strikingly, Artemis(-/-) mice with H2ax and p53 deletion in thymocytes exhibited a lower rate of mortality from TCR-β(-) tumors, which harbored significantly elevated levels of genomic instability. Our data reveal that the cellular origin of H2ax and p53 loss impacts the rate of mortality from and developmental stage of thymic lymphomas, and suggest that conditional deletion of tumor suppressor genes may provide more physiologic models for human lymphoid malignancies than germline inactivation.
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Sikes ML, McMillan RE, Bradshaw JM. The center of accessibility: Dβ control of V(D)J recombination. Arch Immunol Ther Exp (Warsz) 2010; 58:427-33. [PMID: 20890731 DOI: 10.1007/s00005-010-0101-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 07/23/2010] [Indexed: 12/26/2022]
Abstract
Developmental patterning of antigen receptor gene assembly in lymphocyte precursors correlates with decondensation of the chromatin surrounding individual gene segments. Ongoing V(D)J recombination is associated with hyperacetylation of histones H3 and H4 and the expression of sterile germline transcripts across the region of recombinational accessibility. Likewise, histone acetyltransferase and SWI/SNF chromatin remodeling complexes each appear to be required for recombination, and the PHD-finger of RAG-2 preferentially associates with recombination signal sequence (RSS) chromatin that contains H3 trimethylated on lysine 4. However, the regulatory mechanisms that direct chromatin alteration and rearrangement have proven elusive, due in large part to the interdependency of individual stages in gene activation, our limited understanding of functional significance of changes to the histone code, and the difficulty of modeling recombinational accessibility in existing experimental systems. Examining Tcrb assembly in developing thymocytes, we review the central roles of RSS elements and germline promoters as foci for epigenetic reorganization of recombinationally accessible gene segments in light of recent findings and persistent questions.
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Affiliation(s)
- Michael L Sikes
- Department of Microbiology, North Carolina State University, 100 Derieux Place, Campus Box 7615, Raleigh, NC 27695, USA.
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Shih HY, Krangel MS. Distinct contracted conformations of the Tcra/Tcrd locus during Tcra and Tcrd recombination. ACTA ACUST UNITED AC 2010; 207:1835-41. [PMID: 20696701 PMCID: PMC2931158 DOI: 10.1084/jem.20100772] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Studies have suggested that antigen receptor loci adopt contracted conformations to promote long-distance interactions between gene segments during V(D)J recombination. The Tcra/Tcrd locus is unique because it undergoes highly divergent Tcrd and Tcra recombination programs in CD4−CD8− double negative (DN) and CD4+CD8+ double positive (DP) thymocytes, respectively. Using three-dimensional fluorescence in situ hybridization, we asked whether these divergent recombination programs are supported by distinct conformational states of the Tcra/Tcrd locus. We found that the 3′ portion of the locus is contracted in DN and DP thymocytes but not in B cells. Remarkably, the 5′ portion of the locus is contracted in DN thymocytes but is decontracted in DP thymocytes. We propose that the fully contracted conformation in DN thymocytes allows Tcrd rearrangements involving Vδ gene segments distributed over 1 Mb, whereas the unique 3′-contracted, 5′-decontracted conformation in DP thymocytes biases initial Tcra rearrangements to the most 3′ of the available Vα gene segments. This would maintain a large pool of distal 5′ Vα gene segments for subsequent rounds of recombination. Thus, distinct contracted conformations of the Tcra/Tcrd locus may facilitate a transition from a Tcrd to a Tcra mode of recombination during thymocyte 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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