1
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Dauba A, Näser E, Andrieux D, Cogné M, Denizot Y, Khamlichi AA. The immunoglobulin heavy chain super enhancer controls class switch recombination in developing B cells. Sci Rep 2024; 14:7370. [PMID: 38548819 PMCID: PMC10979011 DOI: 10.1038/s41598-024-57576-z] [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: 12/08/2023] [Accepted: 03/19/2024] [Indexed: 04/01/2024] Open
Abstract
Class switch recombination (CSR) plays an important role in adaptive immune response by enabling mature B cells to replace the initial IgM by another antibody class (IgG, IgE or IgA). CSR is preceded by transcription of the IgH constant genes and is controlled by the super-enhancer 3' regulatory region (3'RR) in an activation-specific manner. The 3'RR is composed of four enhancers (hs3a, hs1-2, hs3b and hs4). In mature B cells, 3'RR activity correlates with transcription of its enhancers. CSR can also occur in primary developing B cells though at low frequency, but in contrast to mature B cells, the transcriptional elements that regulate the process in developing B cells are ill-known. In particular, the role of the 3'RR in the control of constant genes' transcription and CSR has not been addressed. Here, by using a mouse line devoid of the 3'RR and a culture system that highly enriches in pro-B cells, we show that the 3'RR activity is indeed required for switch transcription and CSR, though its effect varies in an isotype-specific manner and correlates with transcription of hs4 enhancer only.
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Affiliation(s)
- Audrey Dauba
- Institut de Pharmacologie Et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), CNRS UMR5089, 205 Route de Narbonne, BP 64182, 31077, Toulouse, France
| | - Emmanuelle Näser
- Institut de Pharmacologie Et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), CNRS UMR5089, 205 Route de Narbonne, BP 64182, 31077, Toulouse, France
| | - Dylan Andrieux
- Institut de Pharmacologie Et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), CNRS UMR5089, 205 Route de Narbonne, BP 64182, 31077, Toulouse, France
| | - Michel Cogné
- MOBIDIC, INSERM U1236, Université de Rennes 1, Rennes, France
| | - Yves Denizot
- UMR CNRS 7276, INSERM U1262, Université de Limoges, CBRS, Limoges, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie Et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), CNRS UMR5089, 205 Route de Narbonne, BP 64182, 31077, Toulouse, France.
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2
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Ollikainen N, Sen R. Unraveling the Tcrb interactome. J Exp Med 2024; 221:e20232265. [PMID: 38284995 PMCID: PMC10824074 DOI: 10.1084/jem.20232265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024] Open
Abstract
In this issue of JEM, Allyn et al. (https://doi.org/10.1084/jem.20230985) provide mechanistic insights into the nuclear organization of the Tcrb locus that permits long-range genomic rearrangements.
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Affiliation(s)
- Noah Ollikainen
- Laboratory of Molecular Biology and Immunology, Intramural Research Program, National Institute on Aging, Baltimore, MD, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, Intramural Research Program, National Institute on Aging, Baltimore, MD, USA
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3
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Kabrani E, Saha T, Di Virgilio M. DNA repair and antibody diversification: the 53BP1 paradigm. Trends Immunol 2023; 44:782-791. [PMID: 37640588 DOI: 10.1016/j.it.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/31/2023]
Abstract
The DNA double-strand break (DSB) repair factor 53BP1 has long been implicated in V(D)J and class switch recombination (CSR) of mammalian lymphocyte receptors. However, the dissection of the underlying molecular activities is hampered by a paucity of studies [V(D)J] and plurality of phenotypes (CSR) associated with 53BP1 deficiency. Here, we revisit the currently accepted roles of 53BP1 in antibody diversification in view of the recent identification of its downstream effectors in DSB protection and latest advances in genome architecture. We propose that, in addition to end protection, 53BP1-mediated end-tethering stabilization is essential for CSR. Furthermore, we support a pre-DSB role during V(D)J recombination. Our perspective underscores the importance of evaluating repair of DSBs in relation to their dynamic architectural contexts.
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Affiliation(s)
- Eleni Kabrani
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
| | - Tannishtha Saha
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany; Freie Universität Berlin, Berlin 14195, Germany
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany; Charité-Universitätsmedizin Berlin, Berlin 10117, Germany.
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4
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Mielczarek O, Rogers CH, Zhan Y, Matheson LS, Stubbington MJT, Schoenfelder S, Bolland DJ, Javierre BM, Wingett SW, Várnai C, Segonds-Pichon A, Conn SJ, Krueger F, Andrews S, Fraser P, Giorgetti L, Corcoran AE. Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes. Cell Rep 2023; 42:113074. [PMID: 37676766 PMCID: PMC10548092 DOI: 10.1016/j.celrep.2023.113074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/28/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
To produce a diverse antibody repertoire, immunoglobulin heavy-chain (Igh) loci undergo large-scale alterations in structure to facilitate juxtaposition and recombination of spatially separated variable (VH), diversity (DH), and joining (JH) genes. These chromosomal alterations are poorly understood. Uncovering their patterns shows how chromosome dynamics underpins antibody diversity. Using tiled Capture Hi-C, we produce a comprehensive map of chromatin interactions throughout the 2.8-Mb Igh locus in progenitor B cells. We find that the Igh locus folds into semi-rigid subdomains and undergoes flexible looping of the VH genes to its 3' end, reconciling two views of locus organization. Deconvolution of single Igh locus conformations using polymer simulations identifies thousands of different structures. This heterogeneity may underpin the diversity of V(D)J recombination events. All three immunoglobulin loci also participate in a highly specific, developmentally regulated network of interchromosomal interactions with genes encoding B cell-lineage factors. This suggests a model of interchromosomal coordination of B cell development.
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Affiliation(s)
- Olga Mielczarek
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Carolyn H Rogers
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Louise S Matheson
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael J T Stubbington
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Daniel J Bolland
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Biola M Javierre
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Steven W Wingett
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Anne Segonds-Pichon
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Simon J Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Anne E Corcoran
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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5
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Qiu X, Liang G, Zhou W, Sen R, Atchison ML. Multiple lineage-specific epigenetic landscapes at the antigen receptor loci. AGING RESEARCH (HONG KONG, CHINA) 2023; 1:9340010. [PMID: 38770228 PMCID: PMC11103674 DOI: 10.26599/agr.2023.9340010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Antigen receptors (AgRs) expressed on B and T cells provide the adaptive immune system with ability to detect numerous foreign antigens. Epigenetic features of B cell receptor (BCR) and T cell receptor (TCR) genes were previously studied in lymphocytes, but little is known about their epigenetic features in other cells. Here, we explored histone modifications and transcription markers at the BCR and TCR loci in lymphocytes (pro-B, DP T cells, and mature CD4+ T cells), compared to embryonic stem (ES) cells and neurons. In B cells, the BCR loci exhibited active histone modifications and transcriptional markers indicative of active loci. Similar results were observed at the TCR loci in T cells. All loci were largely inactive in neurons. Surprisingly, in ES cells all AgR loci displayed a high degree of active histone modifications and markers of active transcription. Locations of these active histone modifications in ES cells were largely distinct from those in pro-B cells, and co-localized at numerous binding locations for transcription factors Oct4, Sox2, and Nanog. ES and pro-B cells also showed distinct binding patterns for the ubiquitous transcription factor YY1 and chromatin remodeler Brg1. On the contrary, there were many overlapping CCCTC-binding factor (CTCF) binding patterns when comparing ES cells, pro-B cells, and neurons. Our study identifies epigenetic features in ES cells and lymphocytes that may be related to ES cell pluripotency and lymphocyte tissue-specific activation at the AgR loci.
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Affiliation(s)
- Xiang Qiu
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland 21224, USA
| | - Guanxiang Liang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland 21224, USA
| | - Michael L. Atchison
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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6
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An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation. Nat Commun 2023; 14:1225. [PMID: 36869028 PMCID: PMC9984487 DOI: 10.1038/s41467-023-36414-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/31/2023] [Indexed: 03/05/2023] Open
Abstract
The mouse Igh locus is organized into a developmentally regulated topologically associated domain (TAD) that is divided into subTADs. Here we identify a series of distal VH enhancers (EVHs) that collaborate to configure the locus. EVHs engage in a network of long-range interactions that interconnect the subTADs and the recombination center at the DHJH gene cluster. Deletion of EVH1 reduces V gene rearrangement in its vicinity and alters discrete chromatin loops and higher order locus conformation. Reduction in the rearrangement of the VH11 gene used in anti-PtC responses is a likely cause of the observed reduced splenic B1 B cell compartment. EVH1 appears to block long-range loop extrusion that in turn contributes to locus contraction and determines the proximity of distant VH genes to the recombination center. EVH1 is a critical architectural and regulatory element that coordinates chromatin conformational states that favor V(D)J rearrangement.
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7
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Papadogkonas G, Papamatheakis DA, Spilianakis C. 3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells. Front Immunol 2022; 13:921375. [PMID: 35812421 PMCID: PMC9257000 DOI: 10.3389/fimmu.2022.921375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
In the heart of innate and adaptive immunity lies the proper spatiotemporal development of several immune cell lineages. Multiple studies have highlighted the necessity of epigenetic and transcriptional regulation in cell lineage specification. This mode of regulation is mediated by transcription factors and chromatin remodelers, controlling developmentally essential gene sets. The core of transcription and epigenetic regulation is formulated by different epigenetic modifications determining gene expression. Apart from “classic” epigenetic modifications, 3D chromatin architecture is also purported to exert fundamental roles in gene regulation. Chromatin conformation both facilitates cell-specific factor binding at specified regions and is in turn modified as such, acting synergistically. The interplay between global and tissue-specific protein factors dictates the epigenetic landscape of T and innate lymphoid cell (ILC) lineages. The expression of global genome organizers such as CTCF, YY1, and the cohesin complexes, closely cooperate with tissue-specific factors to exert cell type-specific gene regulation. Special AT-rich binding protein 1 (SATB1) is an important tissue-specific genome organizer and regulator controlling both long- and short-range chromatin interactions. Recent indications point to SATB1’s cooperation with the aforementioned factors, linking global to tissue-specific gene regulation. Changes in 3D genome organization are of vital importance for proper cell development and function, while disruption of this mechanism can lead to severe immuno-developmental defects. Newly emerging data have inextricably linked chromatin architecture deregulation to tissue-specific pathophysiological phenotypes. The combination of these findings may shed light on the mechanisms behind pathological conditions.
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Affiliation(s)
- George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
- *Correspondence: Charalampos Spilianakis,
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8
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Baizan-Edge A, Stubbs BA, Stubbington MJT, Bolland DJ, Tabbada K, Andrews S, Corcoran AE. IL-7R signaling activates widespread V H and D H gene usage to drive antibody diversity in bone marrow B cells. Cell Rep 2021; 36:109349. [PMID: 34260907 PMCID: PMC8293627 DOI: 10.1016/j.celrep.2021.109349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/05/2021] [Accepted: 06/15/2021] [Indexed: 01/09/2023] Open
Abstract
Generation of the primary antibody repertoire requires V(D)J recombination of hundreds of gene segments in the immunoglobulin heavy chain (Igh) locus. The role of interleukin-7 receptor (IL-7R) signaling in Igh recombination has been difficult to partition from its role in B cell survival and proliferation. With a detailed description of the Igh repertoire in murine IL-7Rα-/- bone marrow B cells, we demonstrate that IL-7R signaling profoundly influences VH gene selection during VH-to-DJH recombination. We find skewing toward 3' VH genes during de novo VH-to-DJH recombination more severe than the fetal liver (FL) repertoire and uncover a role for IL-7R signaling in DH-to-JH recombination. Transcriptome and accessibility analyses suggest reduced expression of B lineage transcription factors (TFs) and targets and loss of DH and VH antisense transcription in IL-7Rα-/- B cells. Thus, in addition to its roles in survival and proliferation, IL-7R signaling shapes the Igh repertoire by activating underpinning mechanisms.
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Affiliation(s)
- Amanda Baizan-Edge
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Bryony A Stubbs
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael J T Stubbington
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Daniel J Bolland
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Lymphocyte Signaling and Development Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Kristina Tabbada
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Lymphocyte Signaling and Development Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Anne E Corcoran
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Lymphocyte Signaling and Development Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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9
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Kasprzyk ME, Sura W, Dzikiewicz-Krawczyk A. Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer. Cancers (Basel) 2021; 13:3270. [PMID: 34210001 PMCID: PMC8269369 DOI: 10.3390/cancers13133270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 01/19/2023] Open
Abstract
B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.
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10
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Rogers CH, Mielczarek O, Corcoran AE. Dynamic 3D Locus Organization and Its Drivers Underpin Immunoglobulin Recombination. Front Immunol 2021; 11:633705. [PMID: 33679727 PMCID: PMC7930373 DOI: 10.3389/fimmu.2020.633705] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/30/2020] [Indexed: 01/10/2023] Open
Abstract
A functional adaptive immune system must generate enormously diverse antigen receptor (AgR) repertoires from a limited number of AgR genes, using a common mechanism, V(D)J recombination. The AgR loci are among the largest in the genome, and individual genes must overcome huge spatial and temporal challenges to co-localize with optimum variability. Our understanding of the complex mechanisms involved has increased enormously, due in part to new technologies for high resolution mapping of AgR structure and dynamic movement, underpinning mechanisms, and resulting repertoires. This review will examine these advances using the paradigm of the mouse immunoglobulin heavy chain (Igh) locus. We will discuss the key regulatory elements implicated in Igh locus structure. Recent next generation repertoire sequencing methods have shown that local chromatin state at V genes contribute to recombination efficiency. Next on the multidimensional scale, we will describe imaging studies that provided the first picture of the large-scale dynamic looping and contraction the Igh locus undergoes during recombination. We will discuss chromosome conformation capture (3C)-based technologies that have provided higher resolution pictures of Igh locus structure, including the different models that have evolved. We will consider the key transcription factors (PAX5, YY1, E2A, Ikaros), and architectural factors, CTCF and cohesin, that regulate these processes. Lastly, we will discuss a plethora of recent exciting mechanistic findings. These include Rag recombinase scanning for convergent RSS sequences within DNA loops; identification of Igh loop extrusion, and its putative role in Rag scanning; the roles of CTCF, cohesin and cohesin loading factor, WAPL therein; a new phase separation model for Igh locus compartmentalization. We will draw these together and conclude with some horizon-scanning and unresolved questions.
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Affiliation(s)
- Carolyn H Rogers
- Lymphocyte Signalling and Development Programme, Babraham Institute, Cambridge, United Kingdom
| | - Olga Mielczarek
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Anne E Corcoran
- Lymphocyte Signalling and Development Programme, Babraham Institute, Cambridge, United Kingdom
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11
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Qiu X, Ma F, Zhao M, Cao Y, Shipp L, Liu A, Dutta A, Singh A, Braikia FZ, De S, Wood WH, Becker KG, Zhou W, Ji H, Zhao K, Atchison ML, Sen R. Altered 3D chromatin structure permits inversional recombination at the IgH locus. SCIENCE ADVANCES 2020; 6:eaaz8850. [PMID: 32851160 PMCID: PMC7428332 DOI: 10.1126/sciadv.aaz8850] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/01/2020] [Indexed: 05/05/2023]
Abstract
Immunoglobulin heavy chain (IgH) genes are assembled by two sequential DNA rearrangement events that are initiated by recombination activating gene products (RAG) 1 and 2. Diversity (DH) gene segments rearrange first, followed by variable (VH) gene rearrangements. Here, we provide evidence that each rearrangement step is guided by different rules of engagement between rearranging gene segments. DH gene segments, which recombine by deletion of intervening DNA, must be located within a RAG1/2 scanning domain for efficient recombination. In the absence of intergenic control region 1, a regulatory sequence that delineates the RAG scanning domain on wild-type IgH alleles, VH and DH gene segments can recombine with each other by both deletion and inversion of intervening DNA. We propose that VH gene segments find their targets by distinct mechanisms from those that apply to DH gene segments. These distinctions may underlie differential allelic choice associated with each step of IgH gene assembly.
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Affiliation(s)
- Xiang Qiu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Fei Ma
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Mingming Zhao
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Lillian Shipp
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Angela Liu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Arun Dutta
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Fatima Zohra Braikia
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - William H. Wood
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Kevin G. Becker
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Michael L. Atchison
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
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12
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Allyn BM, Lee KD, Bassing CH. Genome Topology Control of Antigen Receptor Gene Assembly. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:2617-2626. [PMID: 32366683 PMCID: PMC7440635 DOI: 10.4049/jimmunol.1901356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/22/2020] [Indexed: 02/02/2023]
Abstract
The past decade has increased our understanding of how genome topology controls RAG endonuclease-mediated assembly of lymphocyte AgR genes. New technologies have illuminated how the large IgH, Igκ, TCRα/δ, and TCRβ loci fold into compact structures that place their numerous V gene segments in similar three-dimensional proximity to their distal recombination center composed of RAG-bound (D)J gene segments. Many studies have shown that CTCF and cohesin protein-mediated chromosome looping have fundamental roles in lymphocyte lineage- and developmental stage-specific locus compaction as well as broad usage of V segments. CTCF/cohesin-dependent loops have also been shown to direct and restrict RAG activity within chromosome domains. We summarize recent work in elucidating molecular mechanisms that govern three-dimensional chromosome organization and in investigating how these dynamic mechanisms control V(D)J recombination. We also introduce remaining questions for how CTCF/cohesin-dependent and -independent genome architectural mechanisms might regulate compaction and recombination of AgR loci.
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Affiliation(s)
- Brittney M Allyn
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Kyutae D Lee
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Craig H Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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13
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Barajas-Mora EM, Feeney AJ. Enhancers as regulators of antigen receptor loci three-dimensional chromatin structure. Transcription 2019; 11:37-51. [PMID: 31829768 DOI: 10.1080/21541264.2019.1699383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enhancers are defined as regulatory elements that control transcription in a cell-type and developmental stage-specific manner. They achieve this by physically interacting with their cognate gene promoters. Significantly, these interactions can occur through long genomic distances since enhancers may not be near their cognate promoters. The optimal coordination of enhancer-regulated transcription is essential for the function and identity of the cell. Although great efforts to fully understand the principles of this type of regulation are ongoing, other potential functions of the long-range chromatin interactions (LRCIs) involving enhancers are largely unexplored. We recently uncovered a new role for enhancer elements in determining the three-dimensional (3D) structure of the immunoglobulin kappa (Igκ) light chain receptor locus suggesting a structural function for these DNA elements. This enhancer-mediated locus configuration shapes the resulting Igκ repertoire. We also propose a role for enhancers as critical components of sub-topologically associating domain (subTAD) formation and nuclear spatial localization.
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Affiliation(s)
- E Mauricio Barajas-Mora
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ann J Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
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14
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Ciccone DN, Namiki Y, Chen C, Morshead KB, Wood AL, Johnston CM, Morris JW, Wang Y, Sadreyev R, Corcoran AE, Matthews AGW, Oettinger MA. The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF. J Biol Chem 2019; 294:13580-13592. [PMID: 31285261 PMCID: PMC6746451 DOI: 10.1074/jbc.ra118.007348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 06/13/2019] [Indexed: 01/03/2023] Open
Abstract
Antigen receptor assembly in lymphocytes involves stringently-regulated coordination of specific DNA rearrangement events across several large chromosomal domains. Previous studies indicate that transcription factors such as paired box 5 (PAX5), Yin Yang 1 (YY1), and CCCTC-binding factor (CTCF) play a role in regulating the accessibility of the antigen receptor loci to the V(D)J recombinase, which is required for these rearrangements. To gain clues about the role of CTCF binding at the murine immunoglobulin heavy chain (IgH) locus, we utilized a computational approach that identified 144 putative CTCF-binding sites within this locus. We found that these CTCF sites share a consensus motif distinct from other CTCF sites in the mouse genome. Additionally, we could divide these CTCF sites into three categories: intergenic sites remote from any coding element, upstream sites present within 8 kb of the VH-leader exon, and recombination signal sequence (RSS)-associated sites characteristically located at a fixed distance (∼18 bp) downstream of the RSS. We noted that the intergenic and upstream sites are located in the distal portion of the VH locus, whereas the RSS-associated sites are located in the DH-proximal region. Computational analysis indicated that the prevalence of CTCF-binding sites at the IgH locus is evolutionarily conserved. In all species analyzed, these sites exhibit a striking strand-orientation bias, with >98% of the murine sites being present in one orientation with respect to VH gene transcription. Electrophoretic mobility shift and enhancer-blocking assays and ChIP–chip analysis confirmed CTCF binding to these sites both in vitro and in vivo.
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Affiliation(s)
- David N Ciccone
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Yuka Namiki
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Changfeng Chen
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Katrina B Morshead
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Andrew L Wood
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Colette M Johnston
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - John W Morris
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Yanqun Wang
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Anne E Corcoran
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Adam G W Matthews
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114.,Department of Biological Sciences and Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481
| | - Marjorie A Oettinger
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
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15
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Kumari G, Gerasimova T, Du H, De S, Wood WH, Becker KG, Sen R. Misregulation of the IgH Locus in Thymocytes. Front Immunol 2018; 9:2426. [PMID: 30483245 PMCID: PMC6244664 DOI: 10.3389/fimmu.2018.02426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/02/2018] [Indexed: 12/27/2022] Open
Abstract
Functional antigen receptor genes are assembled by somatic rearrangements that are largely lymphocyte lineage specific. The immunoglobulin heavy chain (IgH) gene locus is unique amongst the seven antigen receptor loci in undergoing partial gene rearrangements in the wrong lineage. Here we demonstrate that breakdown of lineage-specificity is associated with inappropriate activation of the Eμ enhancer during T cell development by a different constellation of transcription factors than those used in developing B cells. This is reflected in reduced enhancer-induced epigenetic changes, eRNAs, formation of the RAG1/2-rich recombination center, attenuated chromatin looping and markedly different utilization of DH gene segments in CD4+CD8+ (DP) thymocytes. Additionally, CTCF-dependent VH locus compaction is disrupted in DP cells despite comparable transcription factor binding in both lineages. These observations identify multiple mechanisms that contribute to lineage-specific antigen receptor gene assembly.
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Affiliation(s)
- Gita Kumari
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, United States
| | - Tatiana Gerasimova
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, United States
| | - Hansen Du
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, United States
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, United States
| | - William H Wood
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, United States
| | - Kevin G Becker
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, United States
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, United States
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16
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Arzate-Mejía RG, Recillas-Targa F, Corces VG. Developing in 3D: the role of CTCF in cell differentiation. Development 2018; 145:dev137729. [PMID: 29567640 PMCID: PMC5897592 DOI: 10.1242/dev.137729] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
CTCF is a highly conserved zinc-finger DNA-binding protein that mediates interactions between distant sequences in the genome. As a consequence, CTCF regulates enhancer-promoter interactions and contributes to the three-dimensional organization of the genome. Recent studies indicate that CTCF is developmentally regulated, suggesting that it plays a role in cell type-specific genome organization. Here, we review these studies and discuss how CTCF functions during the development of various cell and tissue types, ranging from embryonic stem cells and gametes, to neural, muscle and cardiac cells. We propose that the lineage-specific control of CTCF levels, and its partnership with lineage-specific transcription factors, allows for the control of cell type-specific gene expression via chromatin looping.
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Affiliation(s)
- Rodrigo G Arzate-Mejía
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Victor G Corces
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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17
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Qiu X, Kumari G, Gerasimova T, Du H, Labaran L, Singh A, De S, Wood WH, Becker KG, Zhou W, Ji H, Sen R. Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus. Mol Cell 2018; 70:21-33.e6. [PMID: 29576529 DOI: 10.1016/j.molcel.2018.02.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 12/19/2017] [Accepted: 02/13/2018] [Indexed: 12/22/2022]
Abstract
Immunoglobulin heavy-chain (IgH) genes are assembled by DNA rearrangements that juxtapose a variable (VH), a diversity (DH), and a joining (JH) gene segment. Here, we report that in the absence of intergenic control region 1 (IGCR1), the intronic enhancer (Eμ) associates with the next available CTCF binding site located close to VH81X via putative heterotypic interactions involving YY1 and CTCF. The alternate Eμ/VH81X loop leads to formation of a distorted recombination center and altered DH rearrangements and disrupts chromosome conformation that favors distal VH recombination. Cumulatively, these features drive highly skewed, Eμ-dependent recombination of VH81X. Sequential deletion of CTCF binding regions on IGCR1-deleted alleles suggests that they influence recombination of single proximal VH gene segments. Our observations demonstrate that Eμ interacts differently with IGCR1- or VH-associated CTCF binding sites and thereby identify distinct roles for insulator-like elements in directing enhancer activity.
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Affiliation(s)
- Xiang Qiu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Gita Kumari
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Tatiana Gerasimova
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Hansen Du
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Lawal Labaran
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - William H Wood
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Kevin G Becker
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA.
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18
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Loguercio S, Barajas-Mora EM, Shih HY, Krangel MS, Feeney AJ. Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci. Front Immunol 2018; 9:425. [PMID: 29593713 PMCID: PMC5859386 DOI: 10.3389/fimmu.2018.00425] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/16/2018] [Indexed: 12/19/2022] Open
Abstract
CCCTC-binding factor (CTCF) is largely responsible for the 3D architecture of the genome, in concert with the action of cohesin, through the creation of long-range chromatin loops. Cohesin is hypothesized to be the main driver of these long-range chromatin interactions by the process of loop extrusion. Here, we performed ChIP-seq for CTCF and cohesin in two stages each of T and B cell differentiation and examined the binding pattern in all six antigen receptor (AgR) loci in these lymphocyte progenitors and in mature T and B cells, ES cells, and fibroblasts. The four large AgR loci have many bound CTCF sites, most of which are only occupied in lymphocytes, while only the CTCF sites at the end of each locus near the enhancers or J genes tend to be bound in non-lymphoid cells also. However, despite the generalized lymphocyte restriction of CTCF binding in AgR loci, the Igκ locus is the only locus that also shows significant lineage-specificity (T vs. B cells) and developmental stage-specificity (pre-B vs. pro-B) in CTCF binding. We show that cohesin binding shows greater lineage- and stage-specificity than CTCF at most AgR loci, providing more specificity to the loops. We also show that the culture of pro-B cells in IL7, a common practice to expand the number of cells before ChIP-seq, results in a CTCF-binding pattern resembling pre-B cells, as well as other epigenetic and transcriptional characteristics of pre-B cells. Analysis of the orientation of the CTCF sites show that all sites within the large V portions of the Igh and TCRβ loci have the same orientation. This suggests either a lack of requirement for convergent CTCF sites creating loops, or indicates an absence of any loops between CTCF sites within the V region portion of those loci but only loops to the convergent sites at the D-J-enhancer end of each locus. The V region portions of the Igκ and TCRα/δ loci, by contrast, have CTCF sites in both orientations, providing many options for creating CTCF-mediated convergent loops throughout the loci. CTCF/cohesin loops, along with transcription factors, drives contraction of AgR loci to facilitate the creation of a diverse repertoire of antibodies and T cell receptors.
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Affiliation(s)
- Salvatore Loguercio
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - E. Mauricio Barajas-Mora
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Han-Yu Shih
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Michael S. Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Ann J. Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
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19
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Gabriele M, Vulto-van Silfhout AT, Germain PL, Vitriolo A, Kumar R, Douglas E, Haan E, Kosaki K, Takenouchi T, Rauch A, Steindl K, Frengen E, Misceo D, Pedurupillay CRJ, Stromme P, Rosenfeld JA, Shao Y, Craigen WJ, Schaaf CP, Rodriguez-Buritica D, Farach L, Friedman J, Thulin P, McLean SD, Nugent KM, Morton J, Nicholl J, Andrieux J, Stray-Pedersen A, Chambon P, Patrier S, Lynch SA, Kjaergaard S, Tørring PM, Brasch-Andersen C, Ronan A, van Haeringen A, Anderson PJ, Powis Z, Brunner HG, Pfundt R, Schuurs-Hoeijmakers JHM, van Bon BWM, Lelieveld S, Gilissen C, Nillesen WM, Vissers LELM, Gecz J, Koolen DA, Testa G, de Vries BBA. YY1 Haploinsufficiency Causes an Intellectual Disability Syndrome Featuring Transcriptional and Chromatin Dysfunction. Am J Hum Genet 2017; 100:907-925. [PMID: 28575647 DOI: 10.1016/j.ajhg.2017.05.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/04/2017] [Indexed: 01/06/2023] Open
Abstract
Yin and yang 1 (YY1) is a well-known zinc-finger transcription factor with crucial roles in normal development and malignancy. YY1 acts both as a repressor and as an activator of gene expression. We have identified 23 individuals with de novo mutations or deletions of YY1 and phenotypic features that define a syndrome of cognitive impairment, behavioral alterations, intrauterine growth restriction, feeding problems, and various congenital malformations. Our combined clinical and molecular data define "YY1 syndrome" as a haploinsufficiency syndrome. Through immunoprecipitation of YY1-bound chromatin from affected individuals' cells with antibodies recognizing both ends of the protein, we show that YY1 deletions and missense mutations lead to a global loss of YY1 binding with a preferential retention at high-occupancy sites. Finally, we uncover a widespread loss of H3K27 acetylation in particular on the YY1-bound enhancers, underscoring a crucial role for YY1 in enhancer regulation. Collectively, these results define a clinical syndrome caused by haploinsufficiency of YY1 through dysregulation of key transcriptional regulators.
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Affiliation(s)
- Michele Gabriele
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | | | - Pierre-Luc Germain
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Alessandro Vitriolo
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Raman Kumar
- School of Medicine and Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Evelyn Douglas
- SA Clinical Genetics Service, SA Pathology, Adelaide, SA 5000, Australia; School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Eric Haan
- SA Clinical Genetics Service, SA Pathology, Adelaide, SA 5000, Australia; School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, 160-8582 Tokyo, Japan
| | - Toshiki Takenouchi
- Center for Medical Genetics, Keio University School of Medicine, 160-8582 Tokyo, Japan
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Eirik Frengen
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0315 Oslo, Norway
| | - Doriana Misceo
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0315 Oslo, Norway
| | | | - Petter Stromme
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital and University of Oslo, 0313 Oslo, Norway
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yunru Shao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Rodriguez-Buritica
- Division of Genetics, Department of Pediatrics, University of Texas Health, Houston, TX 77030, USA
| | - Laura Farach
- Division of Genetics, Department of Pediatrics, University of Texas Health, Houston, TX 77030, USA
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California, San Diego, and Rady Children's Hospital, San Diego, CA 92123, USA
| | - Perla Thulin
- Department of Neurology, University of Utah, San Diego, CA 92123, USA
| | - Scott D McLean
- Clinical Genetics Section, Children's Hospital of San Antonio, San Antonio, TX 78207, USA
| | - Kimberly M Nugent
- Clinical Genetics Section, Children's Hospital of San Antonio, San Antonio, TX 78207, USA
| | - Jenny Morton
- Birmingham Women's Hospital, B15 2TG Birmingham, UK
| | - Jillian Nicholl
- SA Clinical Genetics Service, SA Pathology, Adelaide, SA 5000, Australia; School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Joris Andrieux
- Institut de Génétique Médicale, Hopital Jeanne de Flandre, 59000 Lille, France
| | | | - Pascal Chambon
- Laboratory of Cytogenetics, Rouen University Hospital, 76031 Rouen, France
| | - Sophie Patrier
- Service d'Anatomie Pathologique, Rouen University Hospital, 76031 Rouen, France
| | - Sally A Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, D12 V004 Dublin, Ireland
| | - Susanne Kjaergaard
- Department of Clinical Genetics, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Pernille M Tørring
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | | | - Anne Ronan
- Hunter Genetics, Waratah, NSW 2298, Australia
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Peter J Anderson
- Australian Craniofacial Unit, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | | | - Bregje W M van Bon
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Stefan Lelieveld
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Willy M Nillesen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Jozef Gecz
- School of Medicine and Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - David A Koolen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Giuseppe Testa
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy; Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy.
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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20
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Chromatin Domain Organization of the TCRb Locus and Its Perturbation by Ectopic CTCF Binding. Mol Cell Biol 2017; 37:MCB.00557-16. [PMID: 28137913 DOI: 10.1128/mcb.00557-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/25/2017] [Indexed: 01/23/2023] Open
Abstract
CTCF-mediated chromatin interactions influence organization and function of mammalian genome in diverse ways. We analyzed the interactions among CTCF binding sites (CBS) at the murine TCRb locus to discern the role of CTCF-mediated interactions in the regulation of transcription and VDJ recombination. Chromosome conformation capture analysis revealed thymocyte-specific long-range intrachromosomal interactions among various CBS across the locus that were relevant for defining the limit of the enhancer Eb-regulated recombination center (RC) and for facilitating the spatial proximity of TCRb variable (V) gene segments to the RC. Ectopic CTCF binding in the RC region, effected via genetic manipulation, altered CBS-directed chromatin loops, interfered with RC establishment, and reduced the spatial proximity of the RC with Trbv segments. Changes in chromatin loop organization by ectopic CTCF binding were relatively modest but influenced transcription and VDJ recombination dramatically. Besides revealing the importance of CTCF-mediated chromatin organization for TCRb regulation, the observed chromatin loops were consistent with the emerging idea that CBS orientations influence chromatin loop organization and underscored the importance of CBS orientations for defining chromatin architecture that supports VDJ recombination. Further, our study suggests that in addition to mediating long-range chromatin interactions, CTCF influences intricate configuration of chromatin loops that govern functional interactions between elements.
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21
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Laffleur B, Basu U, Lim J. RNA Exosome and Non-coding RNA-Coupled Mechanisms in AID-Mediated Genomic Alterations. J Mol Biol 2017; 429:3230-3241. [PMID: 28069372 DOI: 10.1016/j.jmb.2016.12.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/21/2016] [Accepted: 12/27/2016] [Indexed: 12/31/2022]
Abstract
The eukaryotic RNA exosome is a well-conserved protein complex with ribonuclease activity implicated in RNA metabolism. Various families of non-coding RNAs have been identified as substrates of the complex, underscoring its role as a non-coding RNA processing/degradation unit. However, the role of RNA exosome and its RNA processing activity on DNA mutagenesis/alteration events have not been investigated until recently. B lymphocytes use two DNA alteration mechanisms, class switch recombination (CSR) and somatic hypermutation (SHM), to re-engineer their antibody gene expressing loci until a tailored antibody gene for a specific antigen is satisfactorily generated. CSR and SHM require the essential activity of the DNA activation-induced cytidine deaminase (AID). Causing collateral damage to the B-cell genome during CSR and SHM, AID induces unwanted (and sometimes oncogenic) mutations at numerous non-immunoglobulin gene sequences. Recent studies have revealed that AID's DNA mutator activity is regulated by the RNA exosome complex, thus providing an example of a mechanism that relates DNA mutagenesis to RNA processing. Here, we review the emergent functions of RNA exosome during CSR, SHM, and other chromosomal alterations in B cells, and discuss implications relevant to mechanisms that maintain B-cell genomic integrity.
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Affiliation(s)
- Brice Laffleur
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Uttiya Basu
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Junghyun Lim
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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22
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YY1 controls Eμ-3'RR DNA loop formation and immunoglobulin heavy chain class switch recombination. Blood Adv 2016; 1:15-20. [PMID: 29167838 DOI: 10.1182/bloodadvances.2016000372] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Key Points
Transcription factor YY1 regulates the IgH Eμ-3′RR long-distance DNA loop without the YY1 transcriptional activation domain. YY1 constructs that rescue the Eμ-3′RR DNA loop also restore CSR strongly arguing for the necessity of this long-distance DNA loop for CSR.
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23
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Abstract
Ghirlando and Felsenfeld review recent major advances in understanding the multiple roles of CTCF in gene regulation and genome organization and especially in how such domains are generated and organized. The role of the zinc finger protein CTCF in organizing the genome within the nucleus is now well established. Widely separated sites on DNA, occupied by both CTCF and the cohesin complex, make physical contacts that create large loop domains. Additional contacts between loci within those domains, often also mediated by CTCF, tend to be favored over contacts between loci in different domains. A large number of studies during the past 2 years have addressed the questions: How are these loops generated? What are the effects of disrupting them? Are there rules governing large-scale genome organization? It now appears that the strongest and evolutionarily most conserved of these CTCF interactions have specific rules for the orientation of the paired CTCF sites, implying the existence of a nonequilibrium mechanism of generation. Recent experiments that invert, delete, or inactivate one of a mating CTCF pair result in major changes in patterns of organization and gene expression in the surrounding regions. What remain to be determined are the detailed molecular mechanisms for re-establishing loop domains and maintaining them after replication and mitosis. As recently published data show, some mechanisms may involve interactions with noncoding RNAs as well as protein cofactors. Many CTCF sites are also involved in other functions such as modulation of RNA splicing and specific regulation of gene expression, and the relationship between these activities and loop formation is another unanswered question that should keep investigators occupied for some time.
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Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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24
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Abstract
Ying Yang 1 (YY1) is a ubiquitously expressed transcription factor shown to be essential for pro-B-cell development. However, the role of YY1 in other B-cell populations has never been investigated. Recent bioinformatics analysis data have implicated YY1 in the germinal center (GC) B-cell transcriptional program. In accord with this prediction, we demonstrated that deletion of YY1 by Cγ1-Cre completely prevented differentiation of GC B cells and plasma cells. To determine if YY1 was also required for the differentiation of other B-cell populations, we deleted YY1 with CD19-Cre and found that all peripheral B-cell subsets, including B1 B cells, require YY1 for their differentiation. Transitional 1 (T1) B cells were the most dependent upon YY1, being sensitive to even a half-dosage of YY1 and also to short-term YY1 deletion by tamoxifen-induced Cre. We show that YY1 exerts its effects, in part, by promoting B-cell survival and proliferation. ChIP-sequencing shows that YY1 predominantly binds to promoters, and pathway analysis of the genes that bind YY1 show enrichment in ribosomal functions, mitochondrial functions such as bioenergetics, and functions related to transcription such as mRNA splicing. By RNA-sequencing analysis of differentially expressed genes, we demonstrated that YY1 normally activates genes involved in mitochondrial bioenergetics, whereas it normally down-regulates genes involved in transcription, mRNA splicing, NF-κB signaling pathways, the AP-1 transcription factor network, chromatin remodeling, cytokine signaling pathways, cell adhesion, and cell proliferation. Our results show the crucial role that YY1 plays in regulating broad general processes throughout all stages of B-cell differentiation.
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25
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Rocha PP, Raviram R, Fu Y, Kim J, Luo VM, Aljoufi A, Swanzey E, Pasquarella A, Balestrini A, Miraldi ER, Bonneau R, Petrini J, Schotta G, Skok JA. A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination. Cell Rep 2016; 16:48-55. [PMID: 27320916 PMCID: PMC4927351 DOI: 10.1016/j.celrep.2016.05.073] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/27/2016] [Accepted: 05/17/2016] [Indexed: 01/03/2023] Open
Abstract
During class switch recombination (CSR), B cells replace the Igh Cμ or δ exons with another down-stream constant region exon (CH), altering the anti-body isotype. CSR occurs through the introduction of AID-mediated double-strand breaks (DSBs) in switch regions and subsequent ligation of broken ends. Here, we developed an assay to investigate the dynamics of DSB formation in individual cells. We demonstrate that the upstream switch region Sμ is first targeted during recombination and that the mechanism underlying this control relies on 53BP1. Surprisingly, regulation of break order occurs through residual binding of 53BP1 to chromatin before the introduction of damage and independent of its established role in DNA repair. Using chromosome conformation capture, we show that 53BP1 mediates changes in chromatin architecture that affect break order. Finally, our results explain how changes in Igh architecture in the absence of 53BP1 could promote inversional rearrangements that compromise CSR.
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Affiliation(s)
- Pedro P Rocha
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| | - Ramya Raviram
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Department of Biology, New York University, New York, NY 10003, USA
| | - Yi Fu
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - JungHyun Kim
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Vincent M Luo
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Arafat Aljoufi
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Emily Swanzey
- Department of Developmental Genetics, New York University School of Medicine, New York, NY 10016, USA
| | - Alessandra Pasquarella
- Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPSM), Biomedical Center, Planegg-Martinsried 80336, Germany
| | - Alessia Balestrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10003, USA; Department of Computer Science, Courant Institute of Mathematical Sciences, New York, NY 10012, USA; Simons Center for Data Analysis, New York, NY 10010, USA
| | - John Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gunnar Schotta
- Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPSM), Biomedical Center, Planegg-Martinsried 80336, Germany
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
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26
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Bolland DJ, Koohy H, Wood AL, Matheson LS, Krueger F, Stubbington MJT, Baizan-Edge A, Chovanec P, Stubbs BA, Tabbada K, Andrews SR, Spivakov M, Corcoran AE. Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination. Cell Rep 2016; 15:2475-87. [PMID: 27264181 PMCID: PMC4914699 DOI: 10.1016/j.celrep.2016.05.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/01/2016] [Accepted: 05/02/2016] [Indexed: 12/02/2022] Open
Abstract
Variable (V), diversity (D), and joining (J) (V(D)J) recombination is the first determinant of antigen receptor diversity. Understanding how recombination is regulated requires a comprehensive, unbiased readout of V gene usage. We have developed VDJ sequencing (VDJ-seq), a DNA-based next-generation-sequencing technique that quantitatively profiles recombination products. We reveal a 200-fold range of recombination efficiency among recombining V genes in the primary mouse Igh repertoire. We used machine learning to integrate these data with local chromatin profiles to identify combinatorial patterns of epigenetic features that associate with active VH gene recombination. These features localize downstream of VH genes and are excised by recombination, revealing a class of cis-regulatory element that governs recombination, distinct from expression. We detect two mutually exclusive chromatin signatures at these elements, characterized by CTCF/RAD21 and PAX5/IRF4, which segregate with the evolutionary history of associated VH genes. Thus, local chromatin signatures downstream of VH genes provide an essential layer of regulation that determines recombination efficiency. VDJ-seq enables precise quantification of antibody V(D)J recombination products Two distinct cis-regulatory designs characterize actively recombining V genes Putative recombination regulatory elements map downstream of mouse Igh V genes Recombination regulatory architecture reflects the V genes’ evolutionary history
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Affiliation(s)
- Daniel J Bolland
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Hashem Koohy
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Andrew L Wood
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Louise S Matheson
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael J T Stubbington
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Amanda Baizan-Edge
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Peter Chovanec
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Bryony A Stubbs
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Kristina Tabbada
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Simon R Andrews
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
| | - Anne E Corcoran
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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27
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Krangel MS. The Ties that Bind (the Igh Locus). Trends Genet 2016; 32:253-255. [PMID: 27012539 DOI: 10.1016/j.tig.2016.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Immunoglobulin heavy-chain locus V(D)J recombination requires a 3D chromatin organization which permits widely distributed variable (V) gene segments to contact distant diversity (D) and joining (J) gene segments. A recent study has identified key nodes in the locus interactome, paving the way for new molecular insights into how the locus is configured for recombination.
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Affiliation(s)
- Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA.
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28
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Chen L, Foreman DP, Sant'Angelo DB, Krangel MS. Yin Yang 1 Promotes Thymocyte Survival by Downregulating p53. THE JOURNAL OF IMMUNOLOGY 2016; 196:2572-82. [PMID: 26843327 DOI: 10.4049/jimmunol.1501916] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/07/2016] [Indexed: 12/13/2022]
Abstract
Yin Yang 1 (YY1) is a zinc finger protein that functions as a transcriptional activator or repressor and participates in multiple biological processes, including development and tumorigenesis. To investigate the role of YY1 in developing T cells, we used mouse models that depleted YY1 at two distinct stages of thymocyte development. When YY1 was depleted in CD4(-)CD8(-) double-negative thymocytes, development to the CD4(+)CD8(+) double-positive stage was impaired, due to increased apoptosis that prevented expansion of post-β-selection thymocytes. When YY1 was depleted in double-positive thymocytes, they underwent increased cell-autonomous apoptosis in vitro and displayed a shorter lifespan in vivo, as judged by their ability to undergo secondary Vα-to-Jα recombination. Mechanistically, we found that the increased apoptosis in YY1-deficient thymocytes was attributed to overexpression of p53, because concurrent loss of p53 completely rescued the developmental defects of YY1-deficient thymocytes. These results indicated that YY1 functions as a critical regulator of thymocyte survival and that it does so by suppressing the expression of p53.
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Affiliation(s)
- Liang Chen
- Department of Immunology, Duke University Medical Center, Durham, NC 27710; and
| | - Daniel P Foreman
- Department of Immunology, Duke University Medical Center, Durham, NC 27710; and
| | - Derek B Sant'Angelo
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC 27710; and
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29
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Xu C, Corces VG. Towards a predictive model of chromatin 3D organization. Semin Cell Dev Biol 2015; 57:24-30. [PMID: 26658098 DOI: 10.1016/j.semcdb.2015.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 01/19/2023]
Abstract
Architectural proteins mediate interactions between distant regions in the genome to bring together different regulatory elements while establishing a specific three-dimensional organization of the genetic material. Depletion of specific architectural proteins leads to miss regulation of gene expression and alterations in nuclear organization. The specificity of interactions mediated by architectural proteins depends on the nature, number, and orientation of their binding site at individual genomic locations. Knowledge of the mechanisms and rules governing interactions among architectural proteins may provide a code to predict the 3D organization of the genome.
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Affiliation(s)
- Chenhuan Xu
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA.
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30
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Outters P, Jaeger S, Zaarour N, Ferrier P. Long-Range Control of V(D)J Recombination & Allelic Exclusion: Modeling Views. Adv Immunol 2015; 128:363-413. [PMID: 26477371 DOI: 10.1016/bs.ai.2015.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Allelic exclusion of immunoglobulin (Ig) and T-cell receptor (TCR) genes ensures the development of B and T lymphocytes operating under the mode of clonal selection. This phenomenon associates asynchronous V(D)J recombination events at Ig or TCR alleles and inhibitory feedback control. Despite years of intense research, however, the mechanisms that sustain asymmetric choice in random Ig/TCR dual allele usage and the production of Ig/TCR monoallelic expressing B and T lymphocytes remain unclear and open for debate. In this chapter, we first recapitulate the biological evidence that almost from the start appeared to link V(D)J recombination and allelic exclusion. We review the theoretical models previously proposed to explain this connection. Finally, we introduce our own mathematical modeling views based on how the developmental dynamics of individual lymphoid cells combine to sustain allelic exclusion.
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Affiliation(s)
- Pernelle Outters
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Sébastien Jaeger
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Nancy Zaarour
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Pierre Ferrier
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France.
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