1
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Allyn BM, Hayer KE, Oyeniran C, Nganga V, Lee K, Mishra B, Sacan A, Oltz EM, Bassing CH. Locus folding mechanisms determine modes of antigen receptor gene assembly. J Exp Med 2024; 221:e20230985. [PMID: 38189780 PMCID: PMC10772921 DOI: 10.1084/jem.20230985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/12/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
The dynamic folding of genomes regulates numerous biological processes, including antigen receptor (AgR) gene assembly. We show that, unlike other AgR loci, homotypic chromatin interactions and bidirectional chromosome looping both contribute to structuring Tcrb for efficient long-range V(D)J recombination. Inactivation of the CTCF binding element (CBE) or promoter at the most 5'Vβ segment (Trbv1) impaired loop extrusion originating locally and extending to DβJβ CBEs at the opposite end of Tcrb. Promoter or CBE mutation nearly eliminated Trbv1 contacts and decreased RAG endonuclease-mediated Trbv1 recombination. Importantly, Trbv1 rearrangement can proceed independent of substrate orientation, ruling out scanning by DβJβ-bound RAG as the sole mechanism of Vβ recombination, distinguishing it from Igh. Our data indicate that CBE-dependent generation of loops cooperates with promoter-mediated activation of chromatin to juxtapose Vβ and DβJβ segments for recombination through diffusion-based synapsis. Thus, the mechanisms that fold a genomic region can influence molecular processes occurring in that space, which may include recombination, repair, and transcriptional programming.
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Affiliation(s)
- Brittney M. Allyn
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharina E. Hayer
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Perelman School of Medicine, Philadelphia, PA, USA
| | - Clement Oyeniran
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Vincent Nganga
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Kyutae Lee
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bikash Mishra
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Ahmet Sacan
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Craig H. Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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2
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Barajas-Mora EM, Feeney AJ. Enhancers within the Ig V Gene Region Orchestrate Chromatin Topology and Regulate V Gene Rearrangement Frequency to Shape the B Cell Receptor Repertoire Specificities. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1613-1622. [PMID: 37983521 PMCID: PMC10662671 DOI: 10.4049/jimmunol.2300261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 11/22/2023]
Abstract
Effective Ab-mediated responses depend on a highly diverse Ab repertoire with the ability to bind a wide range of epitopes in disease-causing agents. The generation of this repertoire depends on the somatic recombination of the variable (V), diversity (D), and joining (J) genes in the Ig loci of developing B cells. It has been known for some time that individual V, D, and J gene segments rearrange at different frequencies, but the mechanisms behind this unequal V gene usage have not been well understood. However, recent work has revealed that newly described enhancers scattered throughout the V gene-containing portion of the Ig loci regulate the V gene recombination frequency in a regional manner. Deletion of three of these enhancers revealed that these elements exert many layers of control during V(D)J recombination, including long-range chromatin interactions, epigenetic milieu, chromatin accessibility, and compartmentalization.
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Affiliation(s)
- E. Mauricio Barajas-Mora
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA, Current address: Poseida Therapeutics, Inc. San Diego, CA
| | - Ann J. Feeney
- Scripps Research, Department of Immunology and Microbiology, La Jolla, CA 92014
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3
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Hill L, Wutz G, Jaritz M, Tagoh H, Calderón L, Peters JM, Goloborodko A, Busslinger M. Igh and Igk loci use different folding principles for V gene recombination due to distinct chromosomal architectures of pro-B and pre-B cells. Nat Commun 2023; 14:2316. [PMID: 37085514 PMCID: PMC10121685 DOI: 10.1038/s41467-023-37994-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 04/04/2023] [Indexed: 04/23/2023] Open
Abstract
Extended loop extrusion across the immunoglobulin heavy-chain (Igh) locus facilitates VH-DJH recombination following downregulation of the cohesin-release factor Wapl by Pax5, resulting in global changes in the chromosomal architecture of pro-B cells. Here, we demonstrate that chromatin looping and VK-JK recombination at the Igk locus were insensitive to Wapl upregulation in pre-B cells. Notably, the Wapl protein was expressed at a 2.2-fold higher level in pre-B cells compared with pro-B cells, which resulted in a distinct chromosomal architecture with normal loop sizes in pre-B cells. High-resolution chromosomal contact analysis of the Igk locus identified multiple internal loops, which likely juxtapose VK and JK elements to facilitate VK-JK recombination. The higher Wapl expression in Igμ-transgenic pre-B cells prevented extended loop extrusion at the Igh locus, leading to recombination of only the 6 most 3' proximal VH genes and likely to allelic exclusion of all other VH genes in pre-B cells. These results suggest that pro-B and pre-B cells with their distinct chromosomal architectures use different chromatin folding principles for V gene recombination, thereby enabling allelic exclusion at the Igh locus, when the Igk locus is recombined.
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Affiliation(s)
- Louisa Hill
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Hiromi Tagoh
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Lesly Calderón
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Anton Goloborodko
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, A-1030, Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria.
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4
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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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5
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Kenter AL, Priyadarshi S, Drake EB. Locus architecture and RAG scanning determine antibody diversity. Trends Immunol 2023; 44:119-128. [PMID: 36706738 PMCID: PMC10128066 DOI: 10.1016/j.it.2022.12.005] [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: 12/01/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/27/2023]
Abstract
Diverse mammalian antibody repertoires are produced via distant genomic contacts involving immunoglobulin Igh variable (V), diversity (D), and joining (J) gene segments and result in V(D)J recombination. How such interactions determine V gene usage remains unclear. The recombination-activating gene (RAG) chromatin scanning model posits that RAG recombinase bound to the recombination center (RC) linearly tracks along chromatin by means of cohesin-mediated loop extrusion; a proposition supported by cohesin depletion studies. A mechanistic role for chromatin loop extrusion has also been implicated for Igh locus contraction. In this opinion, we provide perspective on how loop extrusion interfaces with the 3D conformation of the Igh locus and newly identified enhancers that regionally regulate VH gene usage during V(D)J recombination, shaping the preselected repertoire.
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Affiliation(s)
- Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA.
| | - Saurabh Priyadarshi
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Ellen B Drake
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
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6
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Barajas-Mora EM, Lee L, Lu H, Valderrama JA, Bjanes E, Nizet V, Feeney AJ, Hu M, Murre C. Enhancer-instructed epigenetic landscape and chromatin compartmentalization dictate a primary antibody repertoire protective against specific bacterial pathogens. Nat Immunol 2023; 24:320-336. [PMID: 36717722 PMCID: PMC10917333 DOI: 10.1038/s41590-022-01402-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/06/2022] [Indexed: 01/31/2023]
Abstract
Antigen receptor loci are organized into variable (V), diversity (D) and joining (J) gene segments that rearrange to generate antigen receptor repertoires. Here, we identified an enhancer (E34) in the murine immunoglobulin kappa (Igk) locus that instructed rearrangement of Vκ genes located in a sub-topologically associating domain, including a Vκ gene encoding for antibodies targeting bacterial phosphorylcholine. We show that E34 instructs the nuclear repositioning of the E34 sub-topologically associating domain from a recombination-repressive compartment to a recombination-permissive compartment that is marked by equivalent activating histone modifications. Finally, we found that E34-instructed Vκ-Jκ rearrangement was essential to combat Streptococcus pneumoniae but not methicillin-resistant Staphylococcus aureus or influenza infections. We propose that the merging of Vκ genes with Jκ elements is instructed by one-dimensional epigenetic information imposed by enhancers across Vκ and Jκ genomic regions. The data also reveal how enhancers generate distinct antibody repertoires that provide protection against lethal bacterial infection.
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Affiliation(s)
| | - Lindsay Lee
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Hanbin Lu
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - J Andrés Valderrama
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elisabet Bjanes
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Victor Nizet
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA
| | - Ann J Feeney
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
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7
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The role of chromatin loop extrusion in antibody diversification. Nat Rev Immunol 2022; 22:550-566. [PMID: 35169260 PMCID: PMC9376198 DOI: 10.1038/s41577-022-00679-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2022] [Indexed: 12/15/2022]
Abstract
Cohesin mediates chromatin loop formation across the genome by extruding chromatin between convergently oriented CTCF-binding elements. Recent studies indicate that cohesin-mediated loop extrusion in developing B cells presents immunoglobulin heavy chain (Igh) variable (V), diversity (D) and joining (J) gene segments to RAG endonuclease through a process referred to as RAG chromatin scanning. RAG initiates V(D)J recombinational joining of these gene segments to generate the large number of different Igh variable region exons that are required for immune responses to diverse pathogens. Antigen-activated mature B cells also use chromatin loop extrusion to mediate the synapsis, breakage and end joining of switch regions flanking Igh constant region exons during class-switch recombination, which allows for the expression of different antibody constant region isotypes that optimize the functions of antigen-specific antibodies to eliminate pathogens. Here, we review recent advances in our understanding of chromatin loop extrusion during V(D)J recombination and class-switch recombination at the Igh locus.
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8
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Xu WD, Huang Q, Huang AF. Emerging role of EZH2 in rheumatic diseases: A comprehensive review. Int J Rheum Dis 2022; 25:1230-1238. [PMID: 35933601 DOI: 10.1111/1756-185x.14416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/03/2022] [Accepted: 07/23/2022] [Indexed: 11/29/2022]
Abstract
Enhancer of zeste homolog 2 (EZH2) is a histone methylated enzyme. It trimethylates histone 3 lysine 27 (H3K27) to regulate epigenetic processes. Recently, studies showed excessive expression of EZH2 in rheumatic diseases, such as systemic lupus erythematosus, rheumatoid arthritis, osteoarthritis, and systemic sclerosis. Moreover, epigenetic modification of EZH2 regulates differentiation and proliferation of different immune cells. Therefore, in this review, we comprehensively discuss the role of EZH2 in rheumatic diseases. Collection of the evidence may provide a basis for further understanding the role of EZH2 and give potential for targeting these diseases.
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Affiliation(s)
- Wang-Dong Xu
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, China
| | - Qi Huang
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, China
| | - An-Fang Huang
- Department of Rheumatology and Immunology, Affiliated Hospital of Southwest Medical University, Luzhou, China
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9
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Luo S, Qiao R, Zhang X. DNA Damage Response and Repair in Adaptive Immunity. Front Cell Dev Biol 2022; 10:884873. [PMID: 35663402 PMCID: PMC9157429 DOI: 10.3389/fcell.2022.884873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/31/2022] [Indexed: 11/16/2022] Open
Abstract
The diversification of B-cell receptor (BCR), as well as its secreted product, antibody, is a hallmark of adaptive immunity, which has more specific roles in fighting against pathogens. The antibody diversification is from recombination-activating gene (RAG)-initiated V(D)J recombination, activation-induced cytidine deaminase (AID)-initiated class switch recombination (CSR), and V(D)J exon somatic hypermutation (SHM). The proper repair of RAG- and AID-initiated DNA lesions and double-strand breaks (DSBs) is required for promoting antibody diversification, suppressing genomic instability, and oncogenic translocations. DNA damage response (DDR) factors and DSB end-joining factors are recruited to the RAG- and AID-initiated DNA lesions and DSBs to coordinately resolve them for generating productive recombination products during antibody diversification. Recently, cohesin-mediated loop extrusion is proposed to be the underlying mechanism of V(D)J recombination and CSR, which plays essential roles in promoting the orientation-biased deletional end-joining . Here, we will discuss the mechanism of DNA damage repair in antibody diversification.
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Affiliation(s)
- Sha Luo
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing, China
- Academy for Advanced Interdisciplinery Studies, Peking University, Beijing, China
| | - Ruolin Qiao
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing, China
- Academy for Advanced Interdisciplinery Studies, Peking University, Beijing, China
| | - Xuefei Zhang
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing, China
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10
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Ruan GX, Li Y, Chen W, Huang H, Zhang R, Chen C, Lam KP, Xu S, Ou X. The spliceosome component Usp39 controls B cell development by regulating immunoglobulin gene rearrangement. Cell Rep 2022; 38:110338. [PMID: 35139388 DOI: 10.1016/j.celrep.2022.110338] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/18/2021] [Accepted: 01/13/2022] [Indexed: 12/17/2022] Open
Abstract
The spliceosome is a large ribonucleoprotein complex responsible for pre-mRNA splicing and genome stability maintenance. Disruption of the spliceosome activity may lead to developmental disorders and tumorigenesis. However, the physiological role that the spliceosome plays in B cell development and function is still poorly defined. Here, we demonstrate that ubiquitin-specific peptidase 39 (Usp39), a spliceosome component of the U4/U6.U5 tri-snRNP complex, is essential for B cell development. Ablation of Usp39 in B cell lineage blocks pre-pro-B to pro-B cell transition in the bone marrow, leading to a profound reduction of mature B cells in the periphery. We show that Usp39 specifically regulates immunoglobulin gene rearrangement in a spliceosome-dependent manner, which involves modulating chromatin interactions at the Igh locus. Moreover, our results indicate that Usp39 deletion reduces the pre-malignant B cells in Eμ-Myc transgenic mice and significantly improves their survival.
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Affiliation(s)
- Gui-Xin Ruan
- Harbin Institute of Technology, Harbin 150001, China; Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuxing Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenjing Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hengjun Huang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Rui Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Changxu Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Kong-Peng Lam
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore; Departments of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore; Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Shengli Xu
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Xijun Ou
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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11
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Libri A, Marton T, Deriano L. The (Lack of) DNA Double-Strand Break Repair Pathway Choice During V(D)J Recombination. Front Genet 2022; 12:823943. [PMID: 35082840 PMCID: PMC8785701 DOI: 10.3389/fgene.2021.823943] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023] Open
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that can be mended via several DNA repair pathways. Multiple factors can influence the choice and the restrictiveness of repair towards a given pathway in order to warrant the maintenance of genome integrity. During V(D)J recombination, RAG-induced DSBs are (almost) exclusively repaired by the non-homologous end-joining (NHEJ) pathway for the benefit of antigen receptor gene diversity. Here, we review the various parameters that constrain repair of RAG-generated DSBs to NHEJ, including the peculiarity of DNA DSB ends generated by the RAG nuclease, the establishment and maintenance of a post-cleavage synaptic complex, and the protection of DNA ends against resection and (micro)homology-directed repair. In this physiological context, we highlight that certain DSBs have limited DNA repair pathway choice options.
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Affiliation(s)
- Alice Libri
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| | - Timea Marton
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
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12
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Kumar S, Kaur S, Seem K, Kumar S, Mohapatra T. Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective. Front Cell Dev Biol 2021; 9:774719. [PMID: 34957106 PMCID: PMC8692796 DOI: 10.3389/fcell.2021.774719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/23/2021] [Indexed: 01/17/2023] Open
Abstract
The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
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13
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Hagman JR, Arends T, Laborda C, Knapp JR, Harmacek L, O'Connor BP. Chromodomain helicase DNA-binding 4 (CHD4) regulates early B cell identity and V(D)J recombination. Immunol Rev 2021; 305:29-42. [PMID: 34927255 DOI: 10.1111/imr.13054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022]
Abstract
B lymphocytes develop from uncommitted precursors into immunoglobulin (antibody)-producing B cells, a major arm of adaptive immunity. Progression of early progenitors to antibody-expressing cells in the bone marrow is orchestrated by the temporal regulation of different gene programs at discrete developmental stages. A major question concerns how B cells control the accessibility of these genes to transcription factors. Research has implicated nucleosome remodeling ATPases as mediators of chromatin accessibility. Here, we describe studies of chromodomain helicase DNA-binding 4 (CHD4; also known as Mi-2β) in early B cell development. CHD4 comprises multiple domains that function in nucleosome mobilization and histone binding. CHD4 is a key component of Nucleosome Remodeling and Deacetylase, or NuRD (Mi-2) complexes, which assemble with other proteins that mediate transcriptional repression. We review data demonstrating that CHD4 is necessary for B lineage identity: early B lineage progression, proliferation in response to interleukin-7, responses to DNA damage, and cell survival in vivo. CHD4-NuRD is also required for the Ig heavy-chain repertoire by promoting utilization of distal variable (VH ) gene segments in V(D)J recombination. In conclusion, the regulation of chromatin accessibility by CHD4 is essential for production of antibodies by B cells, which in turn mediate humoral immune responses to pathogens and disease.
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Affiliation(s)
- James R Hagman
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Tessa Arends
- Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Curtis Laborda
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Jennifer R Knapp
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Laura Harmacek
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Brian P O'Connor
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
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14
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Antonio-Andres G, Jiménez-Hernandez E, Estrada-Abreo LA, Garfias-Gómez Y, Patino-Lopez G, Juarez-Mendez S, Huerta-Yepez S. Expression of YY1 in pro-B and T phenotypes correlation with poor survival in pediatric acute lymphoblastic leukemia. Pediatr Hematol Oncol 2021; 38:456-470. [PMID: 33900899 DOI: 10.1080/08880018.2020.1871139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer, constituting 80% of all acute leukemias in minors. Despite the increase in the success of therapies, disease-free survival is over 80% in most cases. For the remaining 20% of patients, new strategies are needed to allow us to know and select those at greatest risk of relapse. We evaluated by immunohistochemistry the expression of the transcription factor YY1 and found that it is overexpressed in peripheral blood leukemia cells of pediatric patients with ALL with Pro-B and T phenotype compared to control samples. Over expression of YY1 was associated with a significantly lower chance of survival. We also evaluated by RT-PCR in bone marrow samples from ALL pediatric patients the association of YY1 expression with the percentage of blasts. High levels of YY1 were present in samples with higher percent of blasts in these patients. In addition, ALL pediatric patients with a poor response to therapy had higher levels at the nuclear level of YY1 than those who responded well to chemotherapy. In conclusion, our data suggest that YY1 could serve in pediatric ALL as markers of evolution and response for this disease, mainly in patients with pro-B and T immunophenotype. It is also suggested that YY1 is implicated in the expanse of blast in these patients.
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Affiliation(s)
- Gabriela Antonio-Andres
- Oncology Disease Research Unit, Children's Hospital of Mexico, Federico Gomez, Mexico City, Mexico
| | | | - Laura A Estrada-Abreo
- Immunology and Proteomics Laboratory, Hospital Infantil de México, Federico Gómez, Mexico City, Mexico
| | - Yanelly Garfias-Gómez
- Immunology and Proteomics Laboratory, Hospital Infantil de México, Federico Gómez, Mexico City, Mexico
| | - Genaro Patino-Lopez
- Immunology and Proteomics Laboratory, Hospital Infantil de México, Federico Gómez, Mexico City, Mexico
| | - Sergio Juarez-Mendez
- Laboratorio de Oncologia Experimental, Instituto Nacional de Pediatria, S.S.A, Mexico City, Mexico
| | - Sara Huerta-Yepez
- Oncology Disease Research Unit, Children's Hospital of Mexico, Federico Gomez, Mexico City, Mexico
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15
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Yuan M, Wang Y, Qin M, Zhao X, Chen X, Li D, Miao Y, Otieno Odhiambo W, Liu H, Ma Y, Ji Y. RAG enhances BCR-ABL1-positive leukemic cell growth through its endonuclease activity in vitro and in vivo. Cancer Sci 2021; 112:2679-2691. [PMID: 33949040 PMCID: PMC8253288 DOI: 10.1111/cas.14939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/15/2021] [Accepted: 04/30/2021] [Indexed: 12/14/2022] Open
Abstract
BCR-ABL1 gene fusion associated with additional DNA lesions involves the pathogenesis of chronic myelogenous leukemia (CML) from a chronic phase (CP) to a blast crisis of B lymphoid (CML-LBC) lineage and BCR-ABL1+ acute lymphoblastic leukemia (BCR-ABL1+ ALL). The recombination-activating gene RAG1 and RAG2 (collectively, RAG) proteins that assemble a diverse set of antigen receptor genes during lymphocyte development are abnormally expressed in CML-LBC and BCR-ABL1+ ALL. However, the direct involvement of dysregulated RAG in disease progression remains unclear. Here, we generate human wild-type (WT) RAG and catalytically inactive RAG-expressing BCR-ABL1+ and BCR-ABL1- cell lines, respectively, and demonstrate that BCR-ABL1 specifically collaborates with RAG recombinase to promote cell survival in vitro and in xenograft mice models. WT RAG-expressing BCR-ABL1+ cell lines and primary CD34+ bone marrow cells from CML-LBC samples maintain more double-strand breaks (DSB) compared to catalytically inactive RAG-expressing BCR-ABL1+ cell lines and RAG-deficient CML-CP samples, which are measured by γ-H2AX. WT RAG-expressing BCR-ABL1+ cells are biased to repair RAG-mediated DSB by the alternative non-homologous end joining pathway (a-NHEJ), which could contribute genomic instability through increasing the expression of a-NHEJ-related MRE11 and RAD50 proteins. As a result, RAG-expressing BCR-ABL1+ cells decrease sensitivity to tyrosine kinase inhibitors (TKI) by activating BCR-ABL1 signaling but independent of the levels of BCR-ABL1 expression and mutations in the BCR-ABL1 tyrosine kinase domain. These findings identify a surprising and novel role of RAG in the functional specialization of disease progression in BCR-ABL1+ leukemia through its endonuclease activity.
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MESH Headings
- Acid Anhydride Hydrolases/metabolism
- Animals
- Blast Crisis/genetics
- Blast Crisis/metabolism
- Cell Line, Tumor
- Cell Proliferation
- Cell Survival
- DNA Breaks, Double-Stranded
- DNA End-Joining Repair
- DNA-Binding Proteins/deficiency
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Disease Progression
- Endonucleases/metabolism
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Genomic Instability
- Heterografts
- Histones/analysis
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- In Vitro Techniques
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- MRE11 Homologue Protein/metabolism
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Nuclear Proteins/deficiency
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Protein Kinase Inhibitors/therapeutic use
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Affiliation(s)
- Meng Yuan
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Yang Wang
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Mengting Qin
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Xiaohui Zhao
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Xiaodong Chen
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Dandan Li
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Yinsha Miao
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
- Department of Clinical laboratoryXi’an No. 3 HospitalThe Affiliated Hospital of Northwest UniversityXi’anChina
| | - Wood Otieno Odhiambo
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Huasheng Liu
- Department of HematologyThe First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
| | - Yunfeng Ma
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
| | - Yanhong Ji
- Department of Pathogenic Biology and Immunology, School of Basic Medical SciencesXi’an Jiaotong University Health Science CenterXi’anChina
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16
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Rausch JW, Le Grice SFJ. Characterizing the Latent HIV-1 Reservoir in Patients with Viremia Suppressed on cART: Progress, Challenges, and Opportunities. Curr HIV Res 2021; 18:99-113. [PMID: 31889490 PMCID: PMC7475929 DOI: 10.2174/1570162x18666191231105438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Modern combination antiretroviral therapy (cART) can bring HIV-1 in blood plasma to level undetectable by standard tests, prevent the onset of acquired immune deficiency syndrome (AIDS), and allow a near-normal life expectancy for HIV-infected individuals. Unfortunately, cART is not curative, as within a few weeks of treatment cessation, HIV viremia in most patients rebounds to pre-cART levels. The primary source of this rebound, and the principal barrier to a cure, is the highly stable reservoir of latent yet replication-competent HIV-1 proviruses integrated into the genomic DNA of resting memory CD4+ T cells. In this review, prevailing models for how the latent reservoir is established and maintained, residual viremia and viremic rebound upon withdrawal of cART, and the types and characteristics of cells harboring latent HIV-1 will be discussed. Selected technologies currently being used to advance our understanding of HIV latency will also be presented, as will a perspective on which areas of advancement are most essential for producing the next generation of HIV-1 therapeutics.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
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17
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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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18
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Dai HQ, Hu H, Lou J, Ye AY, Ba Z, Zhang X, Zhang Y, Zhao L, Yoon HS, Chapdelaine-Williams AM, Kyritsis N, Chen H, Johnson K, Lin S, Conte A, Casellas R, Lee CS, Alt FW. Loop extrusion mediates physiological Igh locus contraction for RAG scanning. Nature 2021; 590:338-343. [PMID: 33442057 PMCID: PMC9037962 DOI: 10.1038/s41586-020-03121-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023]
Abstract
RAG endonuclease initiates Igh V(D)J recombination in progenitor B cells by binding a JH-recombination signal sequence (RSS) within a recombination centre (RC) and then linearly scanning upstream chromatin, presented by loop extrusion mediated by cohesin, for convergent D-RSSs1,2. The utilization of convergently oriented RSSs and cryptic RSSs is intrinsic to long-range RAG scanning3. Scanning of RAG from the DJH-RC-RSS to upstream convergent VH-RSSs is impeded by D-proximal CTCF-binding elements (CBEs)2-5. Primary progenitor B cells undergo a mechanistically undefined contraction of the VH locus that is proposed to provide distal VHs access to the DJH-RC6-9. Here we report that an inversion of the entire 2.4-Mb VH locus in mouse primary progenitor B cells abrogates rearrangement of both VH-RSSs and normally convergent cryptic RSSs, even though locus contraction still occurs. In addition, this inversion activated both the utilization of cryptic VH-RSSs that are normally in opposite orientation and RAG scanning beyond the VH locus through several convergent CBE domains to the telomere. Together, these findings imply that broad deregulation of CBE impediments in primary progenitor B cells promotes RAG scanning of the VH locus mediated by loop extrusion. We further found that the expression of wings apart-like protein homologue (WAPL)10, a cohesin-unloading factor, was low in primary progenitor B cells compared with v-Abl-transformed progenitor B cell lines that lacked contraction and RAG scanning of the VH locus. Correspondingly, depletion of WAPL in v-Abl-transformed lines activated both processes, further implicating loop extrusion in the locus contraction mechanism.
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Affiliation(s)
- Hai-Qiang Dai
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Correspondence: ; ; . Correspondence and requests for materials should be addressed to F.W.A
| | - Hongli Hu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jiangman Lou
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Adam Yongxin Ye
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Zhaoqing Ba
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Xuefei Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yiwen Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lijuan Zhao
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hye Suk Yoon
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aimee M. Chapdelaine-Williams
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nia Kyritsis
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Huan Chen
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kerstin Johnson
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sherry Lin
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea Conte
- Lymphocyte Nuclear Biology, NIAMS, NIH, and Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, and Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Cheng-Sheng Lee
- Institute of Molecular and Cellular Biology, Department of Life Sciences, Hsinchu, Taiwan, 30013, R.O.C.,Correspondence: ; ; . Correspondence and requests for materials should be addressed to F.W.A
| | - Frederick W. Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Correspondence: ; ; . Correspondence and requests for materials should be addressed to F.W.A
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19
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Meluzzi D, Arya G. Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data. Methods 2020; 181-182:24-34. [PMID: 31470090 PMCID: PMC7044057 DOI: 10.1016/j.ymeth.2019.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/24/2019] [Accepted: 08/23/2019] [Indexed: 02/08/2023] Open
Abstract
Chromosome conformation capture (3C) and its variants are powerful experimental techniques for probing intra- and inter-chromosomal interactions within cell nuclei at high resolution and in a high-throughput, quantitative manner. The contact maps derived from such experiments provide an avenue for inferring the 3D spatial organization of the genome. This review provides an overview of the various computational methods developed in the past decade for addressing the very important but challenging problem of deducing the detailed 3D structure or structure population of chromosomal domains, chromosomes, and even entire genomes from 3C contact maps.
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Affiliation(s)
- Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, United States.
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20
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Ba Z, Lou J, Ye AY, Dai HQ, Dring EW, Lin SG, Jain S, Kyritsis N, Kieffer-Kwon KR, Casellas R, Alt FW. CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning. Nature 2020; 586:305-310. [PMID: 32717742 PMCID: PMC7554077 DOI: 10.1038/s41586-020-2578-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 05/18/2020] [Indexed: 12/17/2022]
Abstract
The RAG endonuclease initiates Igh locus V(D)J recombination in progenitor (pro)-B cells1. Upon binding a recombination centre-based JH, RAG scans upstream chromatin via loop extrusion, potentially mediated by cohesin, to locate Ds and assemble a DJH-based recombination centre2. CTCF looping factor-bound elements (CBEs) within IGCR1 upstream of Ds impede RAG scanning3-5; however, their inactivation allows scanning to proximal VHs, where additional CBEs activate rearrangement and impede scanning any further upstream5. Distal VH utilization is thought to involve diffusional access to the recombination centre following large-scale Igh locus contraction6-8. Here we test the potential of linear RAG scanning to mediate distal VH usage in G1-arrested v-Abl pro-B cell lines9, which undergo robust D-to-JH but little VH-to-DJH rearrangements, presumably owing to lack of locus contraction2,5. Through an auxin-inducible approach10, we degraded the cohesin component RAD2110-12 or CTCF12,13 in these G1-arrested lines. Degradation of RAD21 eliminated all V(D)J recombination and interactions associated with RAG scanning, except for reecombination centre-located DQ52-to-JH joining, in which synapsis occurs by diffusion2. Remarkably, while degradation of CTCF suppressed most CBE-based chromatin interactions, it promoted robust recombination centre interactions with, and robust VH-to-DJH joining of, distal VHs, with patterns similar to those of 'locus-contracted' primary pro-B cells. Thus, downmodulation of CTCF-bound scanning-impediment activity promotes cohesin-driven RAG scanning across the 2.7-Mb Igh locus.
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Affiliation(s)
- Zhaoqing Ba
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Jiangman Lou
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Adam Yongxin Ye
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hai-Qiang Dai
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Edward W Dring
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sherry G Lin
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Suvi Jain
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nia Kyritsis
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Kyong-Rim Kieffer-Kwon
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA
- Center of Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA.
- Center of Cancer Research, NCI, NIH, Bethesda, MD, USA.
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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21
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Wu Q, Liu P, Wang L. Many facades of CTCF unified by its coding for three-dimensional genome architecture. J Genet Genomics 2020; 47:407-424. [PMID: 33187878 DOI: 10.1016/j.jgg.2020.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/15/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
Abstract
CCCTC-binding factor (CTCF) is a multifunctional zinc finger protein that is conserved in metazoan species. CTCF is consistently found to play an important role in many diverse biological processes. CTCF/cohesin-mediated active chromatin 'loop extrusion' architects three-dimensional (3D) genome folding. The 3D architectural role of CTCF underlies its multifarious functions, including developmental regulation of gene expression, protocadherin (Pcdh) promoter choice in the nervous system, immunoglobulin (Ig) and T-cell receptor (Tcr) V(D)J recombination in the immune system, homeobox (Hox) gene control during limb development, as well as many other aspects of biology. Here, we review the pleiotropic functions of CTCF from the perspective of its essential role in 3D genome architecture and topological promoter/enhancer selection. We envision the 3D genome as an enormous complex architecture, with tens of thousands of CTCF sites as connecting nodes and CTCF proteins as mysterious bonds that glue together genomic building parts with distinct articulation joints. In particular, we focus on the internal mechanisms by which CTCF controls higher order chromatin structures that manifest its many façades of physiological and pathological functions. We also discuss the dichotomic role of CTCF sites as intriguing 3D genome nodes for seemingly contradictory 'looping bridges' and 'topological insulators' to frame a beautiful magnificent house for a cell's nuclear home.
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Affiliation(s)
- Qiang Wu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China.
| | - Peifeng Liu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Leyang Wang
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
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22
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Nutt SL, Keenan C, Chopin M, Allan RS. EZH2 function in immune cell development. Biol Chem 2020; 401:933-943. [DOI: 10.1515/hsz-2019-0436] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/31/2020] [Indexed: 12/17/2022]
Abstract
AbstractThe polycomb repressive complex 2 (PRC2) consists of three core components EZH2, SUZ12 and EED. EZH2 catalyzes the methylation of lysine 27 of histone H3, a modification associated with gene silencing. Through gene duplication higher vertebrate genomes also encode a second partially redundant methyltransferase, EZH1. Within the mammalian immune system most research has concentrated on EZH2 which is expressed predominantly in proliferating cells. EZH2 and other PRC2 components are required for hematopoietic stem cell function and lymphocyte development, at least in part by repressing cell cycle inhibitors. At later stages of immune cell differentiation, EZH2 plays essential roles in humoral and cell-mediated adaptive immunity, as well as the maintenance of immune homeostasis. EZH2 is often overactive in cancers, through both gain-of-function mutations and over-expression, an observation that has led to the development and clinical testing of specific EZH2 inhibitors. Such inhibitors may also be of use in inflammatory and autoimmune settings, as EZH2 inhibition dampens the immune response. Here, we will review the current state of understanding of the roles for EZH2, and PRC2 more generally, in the development and function of the immune system.
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Affiliation(s)
- Stephen L. Nutt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Christine Keenan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michaël Chopin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rhys S. Allan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
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23
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Dangerous Liaisons: Gammaherpesvirus Subversion of the Immunoglobulin Repertoire. Viruses 2020; 12:v12080788. [PMID: 32717815 PMCID: PMC7472090 DOI: 10.3390/v12080788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
A common biologic property of the gammaherpesviruses Epstein–Barr Virus and Kaposi sarcoma herpesvirus is their use of B lymphocytes as a reservoir of latency in healthy individuals that can undergo oncogenic transformation later in life. Gammaherpesviruses (GHVs) employ an impressive arsenal of proteins and non-coding RNAs to reprogram lymphocytes for proliferative expansion. Within lymphoid tissues, the germinal center (GC) reaction is a hub of B cell proliferation and death. The goal of a GC is to generate and then select for a pool of immunoglobulin (Ig) genes that will provide a protective humoral adaptive immune response. B cells infected with GHVs are detected in GCs and bear the hallmark signatures of the mutagenic processes of somatic hypermutation and isotype class switching of the Ig genes. However, data also supports extrafollicular B cells as a reservoir engaged by GHVs. Next-generation sequencing technologies provide unprecedented detail of the Ig sequence that informs the natural history of infection at the single cell level. Here, we review recent reports from human and murine GHV systems that identify striking differences in the immunoglobulin repertoire of infected B cells compared to their uninfected counterparts. Implications for virus biology, GHV-associated cancers, and host immune dysfunction will be discussed.
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24
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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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25
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Chi X, Li Y, Qiu X. V(D)J recombination, somatic hypermutation and class switch recombination of immunoglobulins: mechanism and regulation. Immunology 2020; 160:233-247. [PMID: 32031242 DOI: 10.1111/imm.13176] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 12/30/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Immunoglobulins emerging from B lymphocytes and capable of recognizing almost all kinds of antigens owing to the extreme diversity of their antigen-binding portions, known as variable (V) regions, play an important role in immune responses. The exons encoding the V regions are known as V (variable), D (diversity), or J (joining) genes. V, D, J segments exist as multiple copy arrays on the chromosome. The recombination of the V(D)J gene is the key mechanism to produce antibody diversity. The recombinational process, including randomly choosing a pair of V, D, J segments, introducing double-strand breaks adjacent to each segment, deleting (or inverting in some cases) the intervening DNA and ligating the segments together, is defined as V(D)J recombination, which contributes to surprising immunoglobulin diversity in vertebrate immune systems. To enhance both the ability of immunoglobulins to recognize and bind to foreign antigens and the effector capacities of the expressed antibodies, naive B cells will undergo class switching recombination (CSR) and somatic hypermutation (SHM). However, the genetics mechanisms of V(D)J recombination, CSR and SHM are not clear. In this review, we summarize the major progress in mechanism studies of immunoglobulin V(D)J gene recombination and CSR as well as SHM, and their regulatory mechanisms.
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Affiliation(s)
- Xiying Chi
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Yue Li
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xiaoyan Qiu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
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26
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Zhao H, Li Z, Zhu Y, Hao B. A linear-amplification VDJ-seq technique for quantification of immunoglobulin and T cell receptor diversity. Genome 2019; 63:145-153. [PMID: 31825677 DOI: 10.1139/gen-2019-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The V(D)J recombination is essential for generating a highly diverse repertoire of antigen receptors expressed on T and B lymphocytes. Here, we developed a linear-amplification VDJ-seq technique for quantifying V(D)J recombination of antigen receptor genes. This technique takes advantage of linear amplification using in vitro transcription and reverse transcription to avoid bias generated by the PCR amplification of low copy number of target DNA. The unrearranged alleles are removed by in vitro cleavage with the CRISPR-Cas9 system. The linear-amplification VDJ-seq assay was applied in quantification of the Vκ-Jκ recombination of the mouse Igκ gene with Jκ capture primers. The Jκ genes were detected in 95.86% of clean reads with more than half containing the Vκ gene, indicating high specificity of capturing and amplification. We also applied this approach to quantify the usage of Jα within the Trav12 gene family of the Tcra gene.
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Affiliation(s)
- Hao Zhao
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Zhaoqiang Li
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yongchang Zhu
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Bingtao Hao
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Henan Medical Genetics Institute, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan Province, P.R. China
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27
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Shi Z, Zhang Q, Yan H, Yang Y, Wang P, Zhang Y, Deng Z, Yu M, Zhou W, Wang Q, Yang X, Mo X, Zhang C, Huang J, Dai H, Sun B, Zhao Y, Zhang L, Yang YG, Qiu X. More than one antibody of individual B cells revealed by single-cell immune profiling. Cell Discov 2019; 5:64. [PMID: 31839985 PMCID: PMC6901605 DOI: 10.1038/s41421-019-0137-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023] Open
Abstract
Antibodies have a common structure consisting of two identical heavy (H) and two identical light (L) chains. It is widely accepted that a single mature B cell produces a single antibody through restricted synthesis of only one VHDJH (encoding the H-chain variable region) and one VLJL (encoding the L-chain variable region) via recombination. Naive B cells undergo class-switch recombination (CSR) from initially producing membrane-bound IgM and IgD to expressing more effective membrane-bound IgG, IgA, or IgE when encountering antigens. To ensure the "one cell - one antibody" paradigm, only the constant region of the H chain is replaced during CSR, while the rearranged VHDJH pattern and the L chain are kept unchanged. To define those long-standing classical concepts at the single-cell transcriptome level, we applied the Chromium Single-Cell Immune Profiling Solution and Sanger sequencing to evaluate the Ig transcriptome repertoires of single B cells. Consistent with the "one cell - one antibody" rule, most of the B cells showed one V(D)J recombination pattern. Intriguingly, however, two or more VHDJH or VLJL recombination patterns of IgH chain or IgL chain were also observed in hundreds to thousands of single B cells. Moreover, each Ig class showed unique VHDJH recombination pattern in a single B-cell expressing multiple Ig classes. Together, our findings reveal an unprecedented presence of multi-Ig specificity in some single B cells, implying regulation of Ig gene rearrangement and class switching that differs from the classical mechanisms of both the "one cell - one antibody" rule and CSR.
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Affiliation(s)
- Zhan Shi
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, 100191 China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Qingyang Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408 China
| | - Huige Yan
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, 100191 China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
| | - Pingzhang Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Yixiao Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, 100191 China
| | - Zhenling Deng
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
| | - Meng Yu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, 100191 China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Wenjing Zhou
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, 100191 China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Qianqian Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, 100191 China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Xi Yang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057 China
- Department of Biomedical Science, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong China
| | - Xiaoning Mo
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Chi Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, 100191 China
| | - Jing Huang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, 100191 China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Hui Dai
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, 100191 China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Baofa Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408 China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yongliang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408 China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
| | - Liang Zhang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057 China
- Department of Biomedical Science, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408 China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
- College of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaoyan Qiu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, 100191 China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, 100191 China
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28
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Abstract
Structural maintenance of chromosomes (SMC) complexes are key organizers of chromosome architecture in all kingdoms of life. Despite seemingly divergent functions, such as chromosome segregation, chromosome maintenance, sister chromatid cohesion, and mitotic chromosome compaction, it appears that these complexes function via highly conserved mechanisms and that they represent a novel class of DNA translocases.
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Affiliation(s)
- Stanislau Yatskevich
- Laboratory of Molecular Biology, Medical Research Council, Cambridge University, Cambridge CB2 0QH, United Kingdom
| | - James Rhodes
- Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom;
| | - Kim Nasmyth
- Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom;
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29
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30
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Abstract
Vast repertoires of unique antigen receptors are created in developing lymphocytes. The antigen receptor loci contain many variable (V), diversity (D), and joining (J) gene segments that are arrayed across very large genomic expanses and are joined to form variable-region exons. This process creates the potential for an organism to respond to large numbers of different pathogens. Here, we consider the underlying molecular mechanisms that favor some V genes for recombination prior to selection of the final antigen receptor repertoire. We discuss chromatin structures that form in antigen receptor loci to permit spatial proximity among the V, D, and J gene segments and how these relate to the generation of antigen receptor diversity.
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Affiliation(s)
- Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, 60612-7344, USA
| | - Ann J Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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31
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Voss JE, Gonzalez-Martin A, Andrabi R, Fuller RP, Murrell B, McCoy LE, Porter K, Huang D, Li W, Sok D, Le K, Briney B, Chateau M, Rogers G, Hangartner L, Feeney AJ, Nemazee D, Cannon P, Burton DR. Reprogramming the antigen specificity of B cells using genome-editing technologies. eLife 2019; 8:42995. [PMID: 30648968 PMCID: PMC6355199 DOI: 10.7554/elife.42995] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/31/2018] [Indexed: 12/17/2022] Open
Abstract
We have developed a method to introduce novel paratopes into the human antibody repertoire by modifying the immunoglobulin (Ig) genes of mature B cells directly using genome editing technologies. We used CRISPR-Cas9 in a homology directed repair strategy, to replace the heavy chain (HC) variable region in B cell lines with that from an HIV broadly neutralizing antibody (bnAb), PG9. Our strategy is designed to function in cells that have undergone VDJ recombination using any combination of variable (V), diversity (D) and joining (J) genes. The modified locus expresses PG9 HC which pairs with native light chains (LCs) resulting in the cell surface expression of HIV specific B cell receptors (BCRs). Endogenous activation-induced cytidine deaminase (AID) in engineered cells allowed for Ig class switching and generated BCR variants with improved HIV neutralizing activity. Thus, BCRs engineered in this way retain the genetic flexibility normally required for affinity maturation during adaptive immune responses. Peripheral blood derived primary B cells from three different donors were edited using this strategy. Engineered cells could bind the PG9 epitope and sequenced mRNA showed PG9 HC transcribed as several different isotypes after culture with CD40 ligand and IL-4.
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Affiliation(s)
- James E Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Alicia Gonzalez-Martin
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Roberta P Fuller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, San Diego, United States.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Katelyn Porter
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Wenjuan Li
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Khoa Le
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Morgan Chateau
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Geoffrey Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Lars Hangartner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Ann J Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Paula Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, United States
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32
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Abstract
The vertebrate immune system is tasked with the challenge of responding to any pathogen the organism might encounter, and retaining memory of that pathogen in case of future infection. Recognition and memory of pathogens are encoded within the adaptive immune system and production of T and B lymphocytes with diverse antigen receptor repertoires. In B lymphocytes, diversity is generated by sequential recombination between Variable (V), Diversity (D) and Joining (J) gene segments in the immunoglobulin heavy chain gene (Igh) and subsequent V-J recombination in immunoglobulin light chain genes (Igκ followed by Igλ). However, the process by which particular V, D and J segments are selected during recombination, and stochasticity is maintained to ensure antibody repertoire diversity, is still unclear. In this review, we focus on Igκ and recent findings regarding the relationships between gene structure, the generation of diversity and allelic choice. Surprisingly, the nuclear environment in which each Igκ allele resides, including transcription factories assembled on the nuclear matrix, plays critical roles in both gene regulation and in shaping the diversity of Vκ genes accessible to recombination. These findings provide a new paradigm for understanding Igκ recombination and Vκ diversity in the context of B lymphopoiesis.
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33
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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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34
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Jain S, Ba Z, Zhang Y, Dai HQ, Alt FW. CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning. Cell 2018; 174:102-116.e14. [PMID: 29804837 PMCID: PMC6026039 DOI: 10.1016/j.cell.2018.04.035] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/07/2018] [Accepted: 04/25/2018] [Indexed: 01/06/2023]
Abstract
RAG endonuclease initiates antibody heavy chain variable region exon assembly from V, D, and J segments within a chromosomal V(D)J recombination center (RC) by cleaving between paired gene segments and flanking recombination signal sequences (RSSs). The IGCR1 control region promotes DJH intermediate formation by isolating Ds, JHs, and RCs from upstream VHs in a chromatin loop anchored by CTCF-binding elements (CBEs). How VHs access the DJHRC for VH to DJH rearrangement was unknown. We report that CBEs immediately downstream of frequently rearranged VH-RSSs increase recombination potential of their associated VH far beyond that provided by RSSs alone. This CBE activity becomes particularly striking upon IGCR1 inactivation, which allows RAG, likely via loop extrusion, to linearly scan chromatin far upstream. VH-associated CBEs stabilize interactions of D-proximal VHs first encountered by the DJHRC during linear RAG scanning and thereby promote dominant rearrangement of these VHs by an unanticipated chromatin accessibility-enhancing CBE function.
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MESH Headings
- Animals
- CCCTC-Binding Factor/metabolism
- Cell Line
- Chromatin/metabolism
- DNA, Intergenic/genetics
- DNA, Intergenic/metabolism
- DNA-Binding Proteins/deficiency
- DNA-Binding Proteins/genetics
- Homeodomain Proteins/metabolism
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Heavy Chains/metabolism
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/metabolism
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- Mutagenesis
- Protein Sorting Signals
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- V(D)J Recombination
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Suvi Jain
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Zhaoqing Ba
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yu Zhang
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hai-Qiang Dai
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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35
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Hypomorphic Rag1 mutations alter the preimmune repertoire at early stages of lymphoid development. Blood 2018; 132:281-292. [PMID: 29743177 DOI: 10.1182/blood-2017-12-820985] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/30/2018] [Indexed: 12/13/2022] Open
Abstract
Hypomorphic RAG1 mutations allowing residual T- and B-cell development have been found in patients presenting with delayed-onset combined immune deficiency with granulomas and/or autoimmunity (CID-G/AI) and abnormalities of the peripheral T- and B-cell repertoire. To examine how hypomorphic Rag1 mutations affect the earliest stages of lymphocyte development, we used CRISPR/Cas9 to generate mouse models with mutations equivalent to those found in patients with CID-G/AI. Immunological characterization showed partial development of T and B lymphocytes, with persistence of naïve cells and preserved serum immunoglobulin but impaired antibody responses and presence of autoantibodies, thereby recapitulating the phenotype seen in patients with CID-G/AI. By using high-throughput sequencing, we identified marked skewing of Igh V and Trb V gene usage in early progenitors, with a bias for productive Igh and Trb rearrangements after selection occurred and increased apoptosis of B-cell progenitors. Rearrangement at the Igk locus was impaired, and polyreactive immunoglobulin M antibodies were detected. This study provides novel insights into how hypomorphic Rag1 mutations alter the primary repertoire of T and B cells, setting the stage for immune dysregulation frequently seen in patients.
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36
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Palstra RJ, de Crignis E, Röling MD, van Staveren T, Kan TW, van Ijcken W, Mueller YM, Katsikis PD, Mahmoudi T. Allele-specific long-distance regulation dictates IL-32 isoform switching and mediates susceptibility to HIV-1. SCIENCE ADVANCES 2018; 4:e1701729. [PMID: 29507875 PMCID: PMC5833994 DOI: 10.1126/sciadv.1701729] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/19/2018] [Indexed: 06/08/2023]
Abstract
We integrated data obtained from HIV-1 genome-wide association studies with T cell-derived epigenome data and found that the noncoding intergenic variant rs4349147, which is statistically associated with HIV-1 acquisition, is located in a CD4+ T cell-specific deoxyribonuclease I hypersensitive region, suggesting regulatory potential for this variant. Deletion of the rs4349147 element in Jurkat cells strongly reduced expression of interleukin-32 (IL-32), approximately 10-kb upstream, and chromosome conformation capture assays identified a chromatin loop between rs4349147 and the IL-32 promoter validating its function as a long-distance enhancer. We generated single rs4349147-A or rs4349147-G allele clones and demonstrated that IL-32 enhancer activity and interaction with the IL-32 promoter are strongly allele dependent; rs4349147 -/A cells display reduced IL-32 expression and altered chromatin conformation as compared to rs4349147 G/- cells. Moreover, RNA sequencing demonstrated that rs4349147 G/- cells express a lower relative ratio of IL-32α to non-α isoforms than rs4349147 -/A cells and display increased expression of lymphocyte activation factors rendering them more prone to infection with HIV-1. In agreement, in primary CD4+ T cells, both treatment with recombinant IL-32γ (rIL-32γ) but not rIL-32α, and exogenous lentiviral overexpression of IL-32γ or IL-32β but not IL-32α resulted in a proinflammatory T cell cytokine environment concomitant with increased susceptibility to HIV infection. Our data demonstrate that rs4349147-G promotes transcription of non-IL-32α isoforms, generating a proinflammatory environment more conducive to HIV infection. This study provides a mechanistic link between a HIV-associated noncoding DNA variant and the expression of different IL-32 isoforms that display discrete anti-HIV properties.
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Affiliation(s)
- Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Elisa de Crignis
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Michael D. Röling
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Thomas van Staveren
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Wilfred van Ijcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Ee-671, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Yvonne M. Mueller
- Department of Immunology, Erasmus University Medical Center, Na-1218, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Peter D. Katsikis
- Department of Immunology, Erasmus University Medical Center, Na-1218, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
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Dong Y, Wu C, Zhao X, Zhang P, Zhang H, Zheng M, Li S, Jiao J, Yu X, Lv Z, Ji Y. Epigenetic modifications of the V H region after DJ H recombination in Pro-B cells. Immunology 2017; 152:218-231. [PMID: 28502113 DOI: 10.1111/imm.12758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 04/27/2017] [Accepted: 05/08/2017] [Indexed: 12/19/2022] Open
Abstract
The variable region of murine immunoglobulin heavy chain (Igh) is assembled by sequential DH -JH and VH -DJH recombination. The accessibility of the Igh locus determines the order of rearrangement. Because of the large number of VH genes and the lack of a suitable model, the epigenetic modifications of VH genes after DJH recombination have not previously been characterized. Here, we employed two v-Abl pro-B cell lines, in which the Igh locus is in germline and DJH -recombined configurations, respectively. The DJH junction displays the characteristics of a recombination centre, such as high levels of activation-associated histone modifications and recombination-activating gene protein (RAG) binding in DJH -rearranged pro-B cells, which extend the recombination centre model proposed for the germline Igh locus. The different domains of the VH region have distinct epigenetic characteristics after DJH recombination. Distal VH genes have higher levels of active histone modifications, germline transcription and Pax5 binding, and good quality recombination signal sequences. Proximal VH genes are relatively close to the DJH recombination centre, which partially compensates for the low levels of the above active epigenetic modifications. DJH recombination centre might serve as a cis-acting element to regulate the accessibility of the VH region. Furthermore, we demonstrate that RAG weakly binds to functional VH genes, which is the first detailed assessment of RAG dynamic binding to VH genes. We provide a way for VH -DJH recombination in which the VH gene is brought into close proximity with the DJH recombination centre for RAG binding by a Pax5-dependent chromosomal compaction event, and held in this position for subsequent cleavage and VH -DJH joining.
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Affiliation(s)
- Yanying Dong
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
| | - Caijun Wu
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
| | - Xiaohui Zhao
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
| | - Ping Zhang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
| | - Hua Zhang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
| | - Mingzhe Zheng
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
| | - Shichang Li
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
| | - Junna Jiao
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
| | - Xiaozhuo Yu
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
| | - Zhuangwei Lv
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
| | - Yanhong Ji
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, Shaanxi, China
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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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