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Roles of G4-DNA and G4-RNA in Class Switch Recombination and Additional Regulations in B-Lymphocytes. Molecules 2023; 28:molecules28031159. [PMID: 36770824 PMCID: PMC9921937 DOI: 10.3390/molecules28031159] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Mature B cells notably diversify immunoglobulin (Ig) production through class switch recombination (CSR), allowing the junction of distant "switch" (S) regions. CSR is initiated by activation-induced deaminase (AID), which targets cytosines adequately exposed within single-stranded DNA of transcribed targeted S regions, with a specific affinity for WRCY motifs. In mammals, G-rich sequences are additionally present in S regions, forming canonical G-quadruplexes (G4s) DNA structures, which favor CSR. Small molecules interacting with G4-DNA (G4 ligands), proved able to regulate CSR in B lymphocytes, either positively (such as for nucleoside diphosphate kinase isoforms) or negatively (such as for RHPS4). G4-DNA is also implicated in the control of transcription, and due to their impact on both CSR and transcriptional regulation, G4-rich sequences likely play a role in the natural history of B cell malignancies. Since G4-DNA stands at multiple locations in the genome, notably within oncogene promoters, it remains to be clarified how it can more specifically promote legitimate CSR in physiology, rather than pathogenic translocation. The specific regulatory role of G4 structures in transcribed DNA and/or in corresponding transcripts and recombination hereby appears as a major issue for understanding immune responses and lymphomagenesis.
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2
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Bruzeau C, Cook-Moreau J, Pinaud E, Le Noir S. Contribution of Immunoglobulin Enhancers to B Cell Nuclear Organization. Front Immunol 2022; 13:877930. [PMID: 35812441 PMCID: PMC9263370 DOI: 10.3389/fimmu.2022.877930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/26/2022] [Indexed: 11/19/2022] Open
Abstract
B cells undergo genetic rearrangements at immunoglobulin gene (Ig) loci during B cell maturation. First V(D)J recombination occurs during early B cell stages followed by class switch recombination (CSR) and somatic hypermutation (SHM) which occur during mature B cell stages. Given that RAG1/2 induces DNA double strand breaks (DSBs) during V(D)J recombination and AID (Activation-Induced Deaminase) leads to DNA modifications (mutations during SHM or DNA DSBs during CSR), it is mandatory that IgH rearrangements be tightly regulated to avoid any mutations or translocations within oncogenes. Ig loci contain various cis-regulatory elements that are involved in germline transcription, chromatin modifications or RAG/AID recruitment. Ig cis-regulatory elements are increasingly recognized as being involved in nuclear positioning, heterochromatin addressing and chromosome loop regulation. In this review, we examined multiple data showing the critical interest of studying Ig gene regulation at the whole nucleus scale. In this context, we highlighted the essential function of Ig gene regulatory elements that now have to be considered as nuclear organizers in B lymphocytes.
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3
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Thomson E, Dawson R, H’ng CH, Adikusuma F, Piltz S, Thomas PQ. The Nestin neural enhancer is essential for normal levels of endogenous Nestin in neuroprogenitors but is not required for embryo development. PLoS One 2021; 16:e0258538. [PMID: 34739481 PMCID: PMC8570527 DOI: 10.1371/journal.pone.0258538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/29/2021] [Indexed: 11/23/2022] Open
Abstract
Enhancers are vitally important during embryonic development to control the spatial and temporal expression of genes. Recently, large scale genome projects have identified a vast number of putative developmental regulatory elements. However, the proportion of these that have been functionally assessed is relatively low. While enhancers have traditionally been studied using reporter assays, this approach does not characterise their contribution to endogenous gene expression. We have studied the murine Nestin (Nes) intron 2 enhancer, which is widely used to direct exogenous gene expression within neural progenitor cells in cultured cells and in vivo. We generated CRISPR deletions of the enhancer region in mice and assessed their impact on Nes expression during embryonic development. Loss of the Nes neural enhancer significantly reduced Nes expression in the developing CNS by as much as 82%. By assessing NES protein localization, we also show that this enhancer region contains repressor element(s) that inhibit Nes expression within the vasculature. Previous reports have stated that Nes is an essential gene, and its loss causes embryonic lethality. We also generated 2 independent Nes null lines and show that both develop without any obvious phenotypic effects. Finally, through crossing of null and enhancer deletion mice we provide evidence of trans-chromosomal interaction of the Nes enhancer and promoter.
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Affiliation(s)
- Ella Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Ruby Dawson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Chee Ho H’ng
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Fatwa Adikusuma
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Biomedicine, University of Adelaide, Adelaide, SA, Australia
- South Australian Genome Editing Facility, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
| | - Sandra Piltz
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- South Australian Genome Editing Facility, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
| | - Paul Q. Thomas
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Biomedicine, University of Adelaide, Adelaide, SA, Australia
- South Australian Genome Editing Facility, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
- * E-mail:
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4
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Dauba A, Khamlichi AA. Long-Range Control of Class Switch Recombination by Transcriptional Regulatory Elements. Front Immunol 2021; 12:738216. [PMID: 34594340 PMCID: PMC8477019 DOI: 10.3389/fimmu.2021.738216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/17/2021] [Indexed: 01/18/2023] Open
Abstract
Immunoglobulin class switch recombination (CSR) plays a crucial role in adaptive immune responses through a change of the effector functions of antibodies and is triggered by T-cell-dependent as well as T-cell-independent antigens. Signals generated following encounter with each type of antigen direct CSR to different isotypes. At the genomic level, CSR occurs between highly repetitive switch sequences located upstream of the constant gene exons of the immunoglobulin heavy chain locus. Transcription of switch sequences is mandatory for CSR and is induced in a stimulation-dependent manner. Switch transcription takes place within dynamic chromatin domains and is regulated by long-range regulatory elements which promote alignment of partner switch regions in CSR centers. Here, we review recent work and models that account for the function of long-range transcriptional regulatory elements and the chromatin-based mechanisms involved in the control of CSR.
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Affiliation(s)
- Audrey Dauba
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
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5
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Bruzeau C, Moreau J, Le Noir S, Pinaud E. Panorama of stepwise involvement of the IgH 3' regulatory region in murine B cells. Adv Immunol 2021; 149:95-114. [PMID: 33993921 DOI: 10.1016/bs.ai.2021.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Among the multiple events leading to immunoglobulin (Ig) expression in B cells, stepwise activation of the Ig heavy chain locus (IgH) is of critical importance. Transcription regulation of the complex IgH locus has always been an interesting viewpoint to unravel the multiple and complex events required for IgH expression. First, regulatory germline transcripts (GLT) assist DNA remodeling events such as VDJ recombination, class switch recombination (CSR) and somatic hypermutation (SHM). Second, productive spliced transcripts restrict heavy chain protein expression associated either with the surface receptor of developing B cells or secreted in large amounts in plasma cells. One main transcriptional regulator for IgH lies at its 3' extremity and includes both a set of enhancers grouped in a large 3' regulatory region (3'RR) and a cluster of 3'CTCF-binding elements (3'CBEs). In this focused review, we will preferentially refer to evidence reported for the murine endogenous IgH locus, whether it is wt or carries deletions or insertions within the IgH 3' boundary and associated regulatory region.
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Affiliation(s)
- Charlotte Bruzeau
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France
| | - Jeanne Moreau
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France
| | - Sandrine Le Noir
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France
| | - Eric Pinaud
- CNRS, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, Limoges, France; INSERM, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 1262, Limoges, France; Université de Limoges, Contrôle de la Réponse Immune B et des Lymphoproliférations, UMR 7276, UMR 1262, Limoges, France.
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IgH 3' regulatory region increases ectopic class switch recombination. PLoS Genet 2021; 17:e1009288. [PMID: 33556079 PMCID: PMC7869978 DOI: 10.1371/journal.pgen.1009288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
DNA lesions inflicted by activation-induced deaminase (AID) instrumentally initiate the processes reshaping immunoglobulin genes in mature B-cells, from local somatic hypermutation (SHM) to junctions of distant breaks during class switch recombination (CSR). It remains incompletely understood how these divergent outcomes of AID attacks are differentially and temporally focused, with CSR strictly occurring in the Ig heavy chain (IgH) locus while SHM concentrates on rearranged V(D)J regions in the IgH and Ig light chain loci. In the IgH locus, disruption of either the 3’Regulatory Region (3’RR) super-enhancer or of switch (S) regions preceding constant genes, profoundly affects CSR. Reciprocally, we now examined if these elements are sufficient to induce CSR in a synthetic locus based on the Igκ locus backbone. Addition of a surrogate “core 3’RR” (c3’RR) and of a pair of transcribed and spliced Switch regions, together with a reporter system for “κ-CSR” yielded a switchable Igκ locus. While the c3’RR stimulated SHM at S regions, it also lowered the local SHM threshold necessary for switch recombination to occur. The 3’RR thus both helps recruit AID to initiate DNA lesions, but then also promotes their resolution through long-distance synapses and recombination following double-strand breaks. Class switching allows B lymphocytes to replace expression of immunoglobin M with that of immunoglobulins G, A or E. The genetic support of class switching, is a unique and large deletion uniquely occuring within the immunoglobulin heavy chain (IgH) locus. This recombination is triggered after DNA lesions inflicted by the activation-induced deaminase (AID) enzyme. In immunoglobulin light chain loci, AID only stimulates somatic hypermutation. In such a non-IgH locus, we now show that the IgH 3’ superenhancer can promote junctions between distant DNA breaks and ectopic class switch recombination. This study identifies the minimal elements necessary for class-switch recombination to occur instead of hypermutation in a locus targeted by AID, i.e. transcribed (and spliced) target sites for AID in so-called S regions, and the 3’IgH superenhancer which both helps recruit AID for DNA lesions, and helps repair these lesions through distant gene synapsis and recombination.
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Laffleur B, Lim J, Zhang W, Chen Y, Pefanis E, Bizarro J, Batista CR, Wu L, Economides AN, Wang J, Basu U. Noncoding RNA processing by DIS3 regulates chromosomal architecture and somatic hypermutation in B cells. Nat Genet 2021; 53:230-242. [PMID: 33526923 PMCID: PMC8011275 DOI: 10.1038/s41588-020-00772-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Noncoding RNAs are exquisitely titrated by the cellular RNA surveillance machinery for regulating diverse biological processes. The RNA exosome, the predominant 3' RNA exoribonuclease in mammalian cells, is composed of nine core and two catalytic subunits. Here, we developed a mouse model with a conditional allele to study the RNA exosome catalytic subunit DIS3. In DIS3-deficient B cells, integrity of the immunoglobulin heavy chain (Igh) locus in its topologically associating domain is affected, with accumulation of DNA-associated RNAs flanking CTCF-binding elements, decreased CTCF binding to CTCF-binding elements and disorganized cohesin localization. DIS3-deficient B cells also accumulate activation-induced cytidine deaminase-mediated asymmetric nicks, altering somatic hypermutation patterns and increasing microhomology-mediated end-joining DNA repair. Altered mutation patterns and Igh architectural defects in DIS3-deficient B cells lead to decreased class-switch recombination but increased chromosomal translocations. Our observations of DIS3-mediated architectural regulation at the Igh locus are reflected genome wide, thus providing evidence that noncoding RNA processing is an important mechanism for controlling genome organization.
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Affiliation(s)
- Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pharmacy, School of Pharmacy, Jeonbuk National University, Jeonju, South Korea
| | - Wanwei Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Yiyun Chen
- Division of Life Science, Department of Chemical and Biological Engineering, Center for Systems Biology and Human Health, and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Evangelos Pefanis
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Jonathan Bizarro
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Carolina R Batista
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lijing Wu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | | | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, Center for Systems Biology and Human Health, and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
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Dalloul I, Boyer F, Dalloul Z, Pignarre A, Caron G, Fest T, Chatonnet F, Delaloy C, Durandy A, Jeannet R, Lereclus E, Boutouil H, Aldigier JC, Péron S, Le Noir S, Cook-Moreau J, Cogné M. Locus suicide recombination actively occurs on the functionally rearranged IgH allele in B-cells from inflamed human lymphoid tissues. PLoS Genet 2019; 15:e1007721. [PMID: 31199803 PMCID: PMC6594652 DOI: 10.1371/journal.pgen.1007721] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 06/26/2019] [Accepted: 05/14/2019] [Indexed: 12/24/2022] Open
Abstract
B-cell activation yields abundant cell death in parallel to clonal amplification and remodeling of immunoglobulin (Ig) genes by activation-induced deaminase (AID). AID promotes affinity maturation of Ig variable regions and class switch recombination (CSR) in mature B lymphocytes. In the IgH locus, these processes are under control of the 3' regulatory region (3'RR) super-enhancer, a region demonstrated in the mouse to be both transcribed and itself targeted by AID-mediated recombination. Alternatively to CSR, IgH deletions joining Sμ to "like-switch" DNA repeats that flank the 3' super-enhancer can thus accomplish so-called "locus suicide recombination" (LSR) in mouse B-cells. Using an optimized LSR-seq high throughput method, we now show that AID-mediated LSR is evolutionarily conserved and also actively occurs in humans, providing an activation-induced cell death pathway in multiple conditions of B-cell activation. LSR either focuses on the functional IgH allele or is bi-allelic, and its signature is mainly detected when LSR is ongoing while it vanishes from fully differentiated plasma cells or from "resting" blood memory B-cells. Highly diversified breakpoints are distributed either within the upstream (3'RR1) or downstream (3'RR2) copies of the IgH 3' super-enhancer and all conditions activating CSR in vitro also seem to trigger LSR although TLR ligation appeared the most efficient. Molecular analysis of breakpoints and junctions confirms that LSR is AID-dependent and reveals junctional sequences somehow similar to CSR junctions but with increased usage of microhomologies.
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Affiliation(s)
- Iman Dalloul
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - François Boyer
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Zeinab Dalloul
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | | | - Gersende Caron
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | - Thierry Fest
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | | | - Céline Delaloy
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | | | - Robin Jeannet
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Emilie Lereclus
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Hend Boutouil
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | | | - Sophie Péron
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Sandrine Le Noir
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Jeanne Cook-Moreau
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
- MC and JCM co-directed this work
- * E-mail: (MC); (JCM)
| | - Michel Cogné
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
- MC and JCM co-directed this work
- * E-mail: (MC); (JCM)
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Cianci R, D'Addabbo P, Gambassi G, Lolli S, Serone E, Rizzi A, Pitocco D, Pandolfi F, Frezza D. Association between IgH enhancer hs1.2 and type 1 diabetes. Acta Diabetol 2018; 55:443-448. [PMID: 29441414 DOI: 10.1007/s00592-018-1103-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/10/2018] [Indexed: 01/25/2023]
Abstract
AIM To investigate the association of alleles of the 3' immunoglobulin heavy-chain regulatory region 1 (3'RR-1) enhancer hs1.2 in patients with type 1 diabetes (T1D). METHODS Eighty-one patients with T1D [among which 12 had concomitant coeliac disease (CD) and 25 an autoimmune thyroid disease (AITD)] were compared to 248 healthy individuals. All subjects were recruited from the same geographical area. Blood samples were collected from all patients and a nested PCR was performed to amplify the core of the 3'RR-1 and detect the alleles of the hs1.2 enhancer. RESULTS Allele distribution in healthy individuals was significantly different when compared to that of patients with T1D (p < 0.01). Even greater differences were detected comparing allele distribution of patients with T1D alone versus those with concomitant CD, but not versus those with concomitant AITD. The frequency of *2 allele is increased by 23% in patients with T1D and CD. CONCLUSIONS The present study establishes that the multiallelic hs1.2 enhancer of the 3'RR-1 is associated with T1D, with higher frequency when there is co-occurrence of CD. This evidence has been previously observed in other immune diseases.
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Affiliation(s)
- Rossella Cianci
- Institute of Internal Medicine, Catholic University, Largo A. Gemelli, 8, 00168, Rome, Italy
| | - Pietro D'Addabbo
- Department of Biology, University of Bari, Via Orabona, 4, 70125, Bari, Italy
| | - Giovanni Gambassi
- Institute of Internal Medicine, Catholic University, Largo A. Gemelli, 8, 00168, Rome, Italy
| | - Serena Lolli
- Department of Biology Enrico Calef, Tor Vergata University, Viale della Ricerca Scientifica, 1, 00133, Rome, Italy
| | - Eliseo Serone
- Department of Biology Enrico Calef, Tor Vergata University, Viale della Ricerca Scientifica, 1, 00133, Rome, Italy
| | - Alessandro Rizzi
- Institute of Internal Medicine, Catholic University, Largo A. Gemelli, 8, 00168, Rome, Italy
| | - Dario Pitocco
- Institute of Internal Medicine, Catholic University, Largo A. Gemelli, 8, 00168, Rome, Italy
| | - Franco Pandolfi
- Institute of Internal Medicine, Catholic University, Largo A. Gemelli, 8, 00168, Rome, Italy
| | - Domenico Frezza
- Department of Biology Enrico Calef, Tor Vergata University, Viale della Ricerca Scientifica, 1, 00133, Rome, Italy.
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Le Noir S, Boyer F, Lecardeur S, Brousse M, Oruc Z, Cook-Moreau J, Denizot Y, Cogné M. Functional anatomy of the immunoglobulin heavy chain 3΄ super-enhancer needs not only core enhancer elements but also their unique DNA context. Nucleic Acids Res 2017; 45:5829-5837. [PMID: 28369649 PMCID: PMC5449612 DOI: 10.1093/nar/gkx203] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/22/2017] [Indexed: 01/04/2023] Open
Abstract
Cis-regulatory elements feature clustered sites for transcription factors, defining core enhancers and have inter-species homology. The mouse IgH 3΄ regulatory region (3'RR), a major B-cell super-enhancer, consists of four of such core enhancers, scattered throughout more than 25 kb of packaging 'junk DNA', the sequence of which is not conserved but follows a unique palindromic architecture which is conserved in all mammalian species. The 3'RR promotes long-range interactions and potential IgH loops with upstream promoters, controlling class switch recombination (CSR) and somatic hypermutation (SHM). It was thus of interest to determine whether this functional architecture also involves the specific functional structure of the super-enhancer itself, potentially promoted by its symmetric DNA shell. Since many transgenic 3'RR models simply linked core enhancers without this shell, it was also important to compare such a 'core 3'RR' (c3'RR) with the intact full-length super-enhancer in an actual endogenous IgH context. Packaging DNA between 3'RR core enhancers proved in fact to be necessary for optimal SHM, CSR and IgH locus expression in plasma cells. This reveals that packaging DNA can matter in the functional anatomy of a super-enhancer, and that precise evaluation of such elements requires full consideration of their global architecture.
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Affiliation(s)
- Sandrine Le Noir
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - François Boyer
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Sandrine Lecardeur
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Mylène Brousse
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Zeliha Oruc
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Jeanne Cook-Moreau
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Yves Denizot
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France
| | - Michel Cogné
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, 2 rue du Dr. Descottes, 87025 Limoges, France.,Institut Universitaire de France, Paris, France
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11
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Ko JY, Oh S, Yoo KH. Functional Enhancers As Master Regulators of Tissue-Specific Gene Regulation and Cancer Development. Mol Cells 2017; 40:169-177. [PMID: 28359147 PMCID: PMC5386954 DOI: 10.14348/molcells.2017.0033] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 12/30/2022] Open
Abstract
Tissue-specific transcription is critical for normal development, and abnormalities causing undesirable gene expression may lead to diseases such as cancer. Such highly organized transcription is controlled by enhancers with specific DNA sequences recognized by transcription factors. Enhancers are associated with chromatin modifications that are distinct epigenetic features in a tissue-specific manner. Recently, super-enhancers comprising enhancer clusters co-occupied by lineage-specific factors have been identified in diverse cell types such as adipocytes, hair follicle stem cells, and mammary epithelial cells. In addition, noncoding RNAs, named eRNAs, are synthesized at super-enhancer regions before their target genes are transcribed. Many functional studies revealed that super-enhancers and eRNAs are essential for the regulation of tissue-specific gene expression. In this review, we summarize recent findings concerning enhancer function in tissue-specific gene regulation and cancer development.
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Affiliation(s)
- Je Yeong Ko
- Molecular Medicine Laboratory, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310,
Korea
| | - Sumin Oh
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310,
Korea
| | - Kyung Hyun Yoo
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310,
Korea
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