1
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Salataj E, Spilianakis CG, Chaumeil J. Single-cell detection of primary transcripts, their genomic loci and nuclear factors by 3D immuno-RNA/DNA FISH in T cells. Front Immunol 2023; 14:1156077. [PMID: 37215121 PMCID: PMC10193148 DOI: 10.3389/fimmu.2023.1156077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Over the past decades, it has become increasingly clear that higher order chromatin folding and organization within the nucleus is involved in the regulation of genome activity and serves as an additional epigenetic mechanism that modulates cellular functions and gene expression programs in diverse biological processes. In particular, dynamic allelic interactions and nuclear locations can be of functional importance during the process of lymphoid differentiation and the regulation of immune responses. Analyses of the proximity between chromatin and/or nuclear regions can be performed on populations of cells with high-throughput sequencing approaches such as chromatin conformation capture ("3C"-based) or DNA adenine methyltransferase identification (DamID) methods, or, in individual cells, by the simultaneous visualization of genomic loci, their primary transcripts and nuclear compartments within the 3-dimensional nuclear space using Fluorescence In Situ Hybridization (FISH) and immunostaining. Here, we present a detailed protocol to simultaneously detect nascent RNA transcripts (3D RNA FISH), their genomic loci (3D DNA FISH) and/or their chromosome territories (CT paint DNA FISH) combined with the antibody-based detection of various nuclear factors (immunofluorescence). We delineate the application and effectiveness of this robust and reproducible protocol in several murine T lymphocyte subtypes (from differentiating thymic T cells, to activated splenic and peripheral T cells) as well as other murine cells, including embryonic stem cells, B cells, megakaryocytes and macrophages.
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Affiliation(s)
- Eralda Salataj
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Charalampos G. Spilianakis
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Julie Chaumeil
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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2
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Glynn RA, Bassing CH. Nemo-Dependent, ATM-Mediated Signals from RAG DNA Breaks at Igk Feedback Inhibit V κ Recombination to Enforce Igκ Allelic Exclusion. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:371-383. [PMID: 34965965 PMCID: PMC8756740 DOI: 10.4049/jimmunol.2100696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/01/2021] [Indexed: 01/17/2023]
Abstract
Monoallelic AgR gene expression underlies specific adaptive immune responses. AgR allelic exclusion is achieved by sequential initiation of V(D)J recombination between alleles and resultant protein from one allele signaling to prevent recombination of the other. The ATM kinase, a regulator of the DNA double-strand break (DSB) response, helps enforce allelic exclusion through undetermined mechanisms. ATM promotes repair of RAG1/RAG2 (RAG) endonuclease-induced DSBs and transduces signals from RAG DSBs during Igk gene rearrangement on one allele to transiently inhibit RAG1 protein expression, Igk accessibility, and RAG cleavage of the other allele. Yet, the relative contributions of ATM functions in DSB repair versus signaling to enforce AgR allelic exclusion remain undetermined. In this study, we demonstrate that inactivation in mouse pre-B cells of the NF-κB essential modulator (Nemo) protein, an effector of ATM signaling, diminishes RAG DSB-triggered repression of Rag1/Rag2 transcription and Igk accessibility but does not result in aberrant repair of RAG DSBs like ATM inactivation. We show that Nemo deficiency increases simultaneous biallelic Igk cleavage in pre-B cells and raises the frequency of B cells expressing Igκ proteins from both alleles. In contrast, the incidence of biallelic Igκ expression is not elevated by inactivation of the SpiC transcriptional repressor, which is induced by RAG DSBs in an ATM-dependent manner and suppresses Igk accessibility. Thus, we conclude that Nemo-dependent, ATM-mediated DNA damage signals enforce Igκ allelic exclusion by orchestrating transient repression of RAG expression and feedback inhibition of additional Igk rearrangements in response to RAG cleavage on one Igk allele.
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Affiliation(s)
- Rebecca A. Glynn
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104,Department of Pathology and Laboratory Medicine, Children’s Hospital of Pennsylvania, Philadelphia, PA 19104
| | - Craig H. Bassing
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104,Department of Pathology and Laboratory Medicine, Children’s Hospital of Pennsylvania, Philadelphia, PA 19104,Corresponding Author: Craig H. Bassing, Ph.D., Children’s Hospital of Philadelphia, 4054 Colket Translational Research Building, 3501 Civic Center Blvd., Philadelphia, PA 19104, 267-426-0311,
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3
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Peters JM. How DNA loop extrusion mediated by cohesin enables V(D)J recombination. Curr Opin Cell Biol 2021; 70:75-83. [PMID: 33422934 DOI: 10.1016/j.ceb.2020.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 12/16/2022]
Abstract
'Structural maintenance of chromosomes' (SMC) complexes are required for the folding of genomic DNA into loops. Theoretical considerations and single-molecule experiments performed with the SMC complexes cohesin and condensin indicate that DNA folding occurs via loop extrusion. Recent work indicates that this process is essential for the assembly of antigen receptor genes by V(D)J recombination in developing B and T cells of the vertebrate immune system. Here, I review how recent studies of the mouse immunoglobulin heavy chain locus Igh have provided evidence for this hypothesis and how the formation of chromatin loops by cohesin and regulation of this process by CTCF and Wapl might ensure that all variable gene segments in this locus (VH segments) participate in recombination with a re-arranged DJH segment, to ensure generation of a maximally diverse repertoire of B-cell receptors and antibodies.
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Affiliation(s)
- Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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4
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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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5
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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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6
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Martinez MP, Cheng X, Joseph A, Al-Saleem J, Panfil AR, Palettas M, Dirksen WP, Ratner L, Green PL. HTLV-1 CTCF-binding site is dispensable for in vitro immortalization and persistent infection in vivo. Retrovirology 2019; 16:44. [PMID: 31864373 PMCID: PMC6925871 DOI: 10.1186/s12977-019-0507-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/13/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of adult T-cell leukemia/lymphoma (ATL) and the neurological disorder HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The exact mechanism(s) through which latency and disease progression are regulated are not fully understood. CCCTC-binding factor (CTCF) is an 11-zinc finger, sequence-specific, DNA-binding protein with thousands of binding sites throughout mammalian genomes. CTCF has been shown to play a role in organization of higher-order chromatin structure, gene expression, genomic imprinting, and serve as a barrier to epigenetic modification. A viral CTCF-binding site (vCTCF-BS) was previously identified within the overlapping p12 (sense) and Hbz (antisense) genes of the HTLV-1 genome. Thus, upon integration, HTLV-1 randomly inserts a vCTCF-BS into the host genome. vCTCF-BS studies to date have focused primarily on HTLV-1 chronically infected or tumor-derived cell lines. In these studies, HTLV-1 was shown to alter the structure and transcription of the surrounding host chromatin through the newly inserted vCTCF-BS. However, the effects of CTCF binding in the early stages of HTLV-1 infection remains unexplored. This study examines the effects of the vCTCF-BS on HTLV-1-induced in vitro immortalization and in vivo viral persistence in infected rabbits. RESULTS HTLV-1 and HTLV-1∆CTCF LTR-transactivation, viral particle production, and immortalization capacity were comparable in vitro. The total lymphocyte count, proviral load, and Hbz gene expression were not significantly different between HTLV-1 and HTLV-1∆CTCF-infected rabbits throughout a 12 week study. However, HTLV-1∆CTCF-infected rabbits displayed a significantly decreased HTLV-1-specific antibody response compared to HTLV-1-infected rabbits. CONCLUSIONS Mutation of the HTLV-1 vCTCF-BS does not significantly alter T-lymphocyte transformation capacity or early in vivo virus persistence, but results in a decreased HTLV-1-specific antibody response during early infection in rabbits. Ultimately, understanding epigenetic regulation of HTLV-1 gene expression and pathogenesis could provide meaningful insights into mechanisms of immune evasion and novel therapeutic targets.
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Affiliation(s)
- Michael P Martinez
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, USA.,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Xiaogang Cheng
- Division of Oncology, Washington University, St. Louis, MO, USA
| | - Ancy Joseph
- Division of Oncology, Washington University, St. Louis, MO, USA
| | - Jacob Al-Saleem
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, USA.,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Amanda R Panfil
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, USA.,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Marilly Palettas
- Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | - Wessel P Dirksen
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, USA.,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Lee Ratner
- Division of Oncology, Washington University, St. Louis, MO, USA
| | - Patrick L Green
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, USA. .,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA. .,Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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7
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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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8
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Lin SG, Ba Z, Alt FW, Zhang Y. RAG Chromatin Scanning During V(D)J Recombination and Chromatin Loop Extrusion are Related Processes. Adv Immunol 2018; 139:93-135. [PMID: 30249335 DOI: 10.1016/bs.ai.2018.07.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An effective adaptive immune system depends on the ability of developing B and T cells to generate diverse immunoglobulin (Ig) and T cell receptor repertoires, respectively. Such diversity is achieved through a programmed somatic recombination process whereby germline V, D, and J segments of antigen receptor loci are assembled to form the variable region V(D)J exons of Ig and TCRs. Studies of this process, termed V(D)J recombination, have provided key insights into our understanding of a variety of general gene regulatory and DNA repair processes over the last several decades. V(D)J recombination is initiated by the RAG endonuclease which generates DNA double-stranded breaks at the borders of V, D, and J segments. In this review, we cover recent work that has elucidated RAG structure and work that revealed that RAG has a novel chromatin scanning activity, likely mediated by chromatin loop extrusion, that contributes to its ability to locate V, D, J gene segment substrates within large chromosomal loop domains bounded by CTCF-binding elements (CBEs). This latter function, coupled with the role CBE-based chromatin loop domains and subdomains within them play in focusing V(D)J recombination activity within antigen receptor loci, provide mechanistic explanations for long-standing questions regarding V(D)J segment usage diversification and in limiting potentially deleterious off-target RAG-initiated recombination events genome-wide. This review will focus mainly on studies of the mouse Ig heavy chain locus, but the principles described also apply to other Ig loci and to TCR loci in mice and humans.
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Affiliation(s)
- Sherry G Lin
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States
| | - Zhaoqing Ba
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States
| | - Frederick W Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States.
| | - Yu Zhang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States
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9
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Abstract
CTCF, Zinc-finger protein, has been identified as a multifunctional transcription factor that regulates gene expression through various mechanisms, including recruitment of other co-activators and binding to promoter regions of target genes. Furthermore, it has been proposed to be an insulator protein that contributes to the establishment of functional three-dimensional chromatin structures. It can disrupt transcription through blocking the connection between an enhancer and a promoter. Previous studies revealed that the onset of various diseases, including breast cancer, could be attributed to the aberrant expression of CTCF itself or one or more of its target genes. In this review, we will describe molecular dysfunction involving CTCF that induces tumorigenesis and summarize the functional roles of CTCF in breast cancer.
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Affiliation(s)
- Sumin Oh
- Laboratory of Biomedical Genomics, Department of Biological Science, and Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Korea
| | - Chaeun Oh
- Laboratory of Biomedical Genomics, Department of Biological Science, Sookmyung Women's University, Seoul 04310, Korea
| | - Kyung Hyun Yoo
- Laboratory of Biomedical Genomics, Department of Biological Science, Sookmyung Women's University, Seoul 04310, Korea
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10
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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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11
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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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12
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Lee HK, Willi M, Wang C, Yang CM, Smith HE, Liu C, Hennighausen L. Functional assessment of CTCF sites at cytokine-sensing mammary enhancers using CRISPR/Cas9 gene editing in mice. Nucleic Acids Res 2017; 45:4606-4618. [PMID: 28334928 PMCID: PMC5416830 DOI: 10.1093/nar/gkx185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/15/2017] [Indexed: 01/05/2023] Open
Abstract
The zinc finger protein CTCF has been invoked in establishing boundaries between genes, thereby controlling spatial and temporal enhancer activities. However, there is limited genetic evidence to support the concept that these boundaries restrict the search space of enhancers. We have addressed this question in the casein locus containing five mammary and two non-mammary genes under the control of at least seven putative enhancers. We have identified two CTCF binding sites flanking the locus and two associated with a super-enhancer. Individual deletion of these sites from the mouse genome did not alter expression of any of the genes. However, deletion of the border CTCF site separating the Csn1s1 mammary enhancer from neighboring genes resulted in the activation of Sult1d1 at a distance of more than 95 kb but not the more proximal and silent Sult1e1 gene. Loss of this CTCF site led to de novo interactions between the Sult1d1 promoter and several enhancers in the casein locus. Our study demonstrates that only one out of the four CTCF sites in the casein locus had a measurable in vivo activity. Studies on additional loci are needed to determine the biological role of CTCF sites associated with enhancers.
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Affiliation(s)
- Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.,Department of Cell and Developmental Biology & Dental Research Institute, Seoul National University, Seoul 110-749, Korea
| | - Michaela Willi
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.,Division of Bioinformatics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Chaochen Wang
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Chul Min Yang
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Harold E Smith
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Chengyu Liu
- Transgenic Core,National Heart Lung and Blood Institute, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
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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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