1
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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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2
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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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3
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Aubrey M, Warburg ZJ, Murre C. Helix-Loop-Helix Proteins in Adaptive Immune Development. Front Immunol 2022; 13:881656. [PMID: 35634342 PMCID: PMC9134016 DOI: 10.3389/fimmu.2022.881656] [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: 02/22/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The E/ID protein axis is instrumental for defining the developmental progression and functions of hematopoietic cells. The E proteins are dimeric transcription factors that activate gene expression programs and coordinate changes in chromatin organization. Id proteins are antagonists of E protein activity. Relative levels of E/Id proteins are modulated throughout hematopoietic development to enable the progression of hematopoietic stem cells into multiple adaptive and innate immune lineages including natural killer cells, B cells and T cells. In early progenitors, the E proteins promote commitment to the T and B cell lineages by orchestrating lineage specific programs of gene expression and regulating VDJ recombination of antigen receptor loci. In mature B cells, the E/Id protein axis functions to promote class switch recombination and somatic hypermutation. E protein activity further regulates differentiation into distinct CD4+ and CD8+ T cells subsets and instructs mature T cell immune responses. In this review, we discuss how the E/Id proteins define the adaptive immune system lineages, focusing on their role in directing developmental gene programs.
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Affiliation(s)
| | | | - Cornelis Murre
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, CA, United States
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4
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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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5
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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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6
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Prieto-Sánchez S, Moreno-Castro C, Hernández-Munain C, Suñé C. Drosophila Prp40 localizes to the histone locus body and regulates gene transcription and development. J Cell Sci 2020; 133:jcs.239509. [PMID: 32094262 DOI: 10.1242/jcs.239509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/09/2020] [Indexed: 12/12/2022] Open
Abstract
In eukaryotes, a large amount of histones need to be synthesized during the S phase of the cell cycle to package newly synthesized DNA into chromatin. The transcription and 3' end processing of histone pre-mRNAs are controlled by the histone locus body (HLB), which is assembled on the shared promoter for H3 and H4 Here, we identified the Drosophila Prp40 pre-mRNA processing factor (dPrp40, annotated as CG3542) as a novel HLB component. We showed that dPrp40 is essential for Drosophila development, with functionally conserved activity in vertebrates and invertebrates. We observed that dPrp40 is fundamental in endocycling cells, highlighting a role for this factor in mediating replication efficiency in vivo The depletion of dPrp40 from fly cells inhibited the transcription, but not the 3' end processing, of histone mRNA in a H3- and H4-promoter-dependent manner. Our results establish that dPrp40 is an essential protein for Drosophila development that can localize to the HLB and might participate in histone mRNA biosynthesis.
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Affiliation(s)
- Silvia Prieto-Sánchez
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Cristina Moreno-Castro
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Carlos Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
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7
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Saadi W, Kermezli Y, Dao LTM, Mathieu E, Santiago-Algarra D, Manosalva I, Torres M, Belhocine M, Pradel L, Loriod B, Aribi M, Puthier D, Spicuglia S. A critical regulator of Bcl2 revealed by systematic transcript discovery of lncRNAs associated with T-cell differentiation. Sci Rep 2019; 9:4707. [PMID: 30886319 PMCID: PMC6423290 DOI: 10.1038/s41598-019-41247-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/01/2019] [Indexed: 12/30/2022] Open
Abstract
Normal T-cell differentiation requires a complex regulatory network which supports a series of maturation steps, including lineage commitment, T-cell receptor (TCR) gene rearrangement, and thymic positive and negative selection. However, the underlying molecular mechanisms are difficult to assess due to limited T-cell models. Here we explore the use of the pro-T-cell line P5424 to study early T-cell differentiation. Stimulation of P5424 cells by the calcium ionophore ionomycin together with PMA resulted in gene regulation of T-cell differentiation and activation markers, partially mimicking the CD4-CD8- double negative (DN) to double positive (DP) transition and some aspects of subsequent T-cell maturation and activation. Global analysis of gene expression, along with kinetic experiments, revealed a significant association between the dynamic expression of coding genes and neighbor lncRNAs including many newly-discovered transcripts, thus suggesting potential co-regulation. CRISPR/Cas9-mediated genetic deletion of Robnr, an inducible lncRNA located downstream of the anti-apoptotic gene Bcl2, demonstrated a critical role of the Robnr locus in the induction of Bcl2. Thus, the pro-T-cell line P5424 is a powerful model system to characterize regulatory networks involved in early T-cell differentiation and maturation.
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Affiliation(s)
- Wiam Saadi
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France.,Equipe Labélisée Ligue Contre le Cancer, Marseille, France.,Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Tlemcen, Algeria
| | - Yasmina Kermezli
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France.,Equipe Labélisée Ligue Contre le Cancer, Marseille, France.,Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Tlemcen, Algeria
| | - Lan T M Dao
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France.,Equipe Labélisée Ligue Contre le Cancer, Marseille, France.,Vinmec Research Institute of Stem cell and Gene technology (VRISG), Hanoi, Vietnam
| | - Evelyne Mathieu
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France.,Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - David Santiago-Algarra
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France.,Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Iris Manosalva
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France.,Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Magali Torres
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France.,Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Mohamed Belhocine
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France.,Equipe Labélisée Ligue Contre le Cancer, Marseille, France.,Molecular Biology and Genetics Laboratory, Dubai, United Arab Emirates
| | - Lydie Pradel
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France.,Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Beatrice Loriod
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
| | - Mourad Aribi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Tlemcen, Algeria
| | - Denis Puthier
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France. .,Equipe Labélisée Ligue Contre le Cancer, Marseille, France.
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France. .,Equipe Labélisée Ligue Contre le Cancer, Marseille, France.
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8
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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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9
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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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10
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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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11
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Boudil A, Matei IR, Shih HY, Bogdanoski G, Yuan JS, Chang SG, Montpellier B, Kowalski PE, Voisin V, Bashir S, Bader GD, Krangel MS, Guidos CJ. IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte β-selection. Nat Immunol 2015; 16:397-405. [PMID: 25729925 PMCID: PMC4368453 DOI: 10.1038/ni.3122] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/10/2015] [Indexed: 12/15/2022]
Abstract
Signaling via the pre-T cell antigen receptor (pre-TCR) and the receptor Notch1 induces transient self-renewal (β-selection) of TCRβ(+) CD4(-)CD8(-) double-negative stage 3 (DN3) and DN4 progenitor cells that differentiate into CD4(+)CD8(+) double-positive (DP) thymocytes, which then rearrange the locus encoding the TCR α-chain (Tcra). Interleukin 7 (IL-7) promotes the survival of TCRβ(-) DN thymocytes by inducing expression of the pro-survival molecule Bcl-2, but the functions of IL-7 during β-selection have remained unclear. Here we found that IL-7 signaled TCRβ(+) DN3 and DN4 thymocytes to upregulate genes encoding molecules involved in cell growth and repressed the gene encoding the transcriptional repressor Bcl-6. Accordingly, IL-7-deficient DN4 cells lacked trophic receptors and did not proliferate but rearranged Tcra prematurely and differentiated rapidly. Deletion of Bcl6 partially restored the self-renewal of DN4 cells in the absence of IL-7, but overexpression of BCL2 did not. Thus, IL-7 critically acts cooperatively with signaling via the pre-TCR and Notch1 to coordinate proliferation, differentiation and Tcra recombination during β-selection.
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Affiliation(s)
- Amine Boudil
- 1] Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Canada. [2] Department of Immunology, University of Toronto, Toronto, Canada
| | - Irina R Matei
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Canada
| | - Han-Yu Shih
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Goce Bogdanoski
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Canada
| | - Julie S Yuan
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Canada
| | - Stephen G Chang
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Canada
| | - Bertrand Montpellier
- 1] Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Canada. [2] Department of Immunology, University of Toronto, Toronto, Canada
| | - Paul E Kowalski
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Canada
| | | | | | - Gary D Bader
- 1] The Donnelly Centre, University of Toronto, Toronto, Canada. [2] Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Cynthia J Guidos
- 1] Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Canada. [2] Department of Immunology, University of Toronto, Toronto, Canada
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12
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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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13
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Siggers T, Gordân R. Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res 2013; 42:2099-111. [PMID: 24243859 PMCID: PMC3936734 DOI: 10.1093/nar/gkt1112] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Binding of proteins to particular DNA sites across the genome is a primary determinant of specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded at multiple levels, from the detailed biophysical interactions between proteins and DNA, to the assembly of multi-protein complexes. At each level, variation in the mechanisms used to achieve specificity has led to difficulties in constructing and applying simple models of DNA binding. We review the complexities in protein–DNA binding found at multiple levels and discuss how they confound the idea of simple recognition codes. We discuss the impact of new high-throughput technologies for the characterization of protein–DNA binding, and how these technologies are uncovering new complexities in protein–DNA recognition. Finally, we review the concept of multi-protein recognition codes in which new DNA-binding specificities are achieved by the assembly of multi-protein complexes.
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Affiliation(s)
- Trevor Siggers
- Department of Biology, Boston University, Boston, MA 02215, USA, Departments of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
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14
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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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