1
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Parsons AM, Su K, Daniels M, Bouma GJ, Vanden Heuvel GB, Larson ED. Human PKD1 sequences form R-loop structures in vitro. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001058. [PMID: 38371318 PMCID: PMC10873753 DOI: 10.17912/micropub.biology.001058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/08/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024]
Abstract
Autosomal dominant polycystic kidney disease results from the loss of the PKD1 gene product, polycystin 1. Regulatory mechanisms are unresolved, but an apparent G/C sequence bias in the gene is consistent with co-transcriptional R-loop formation. R-loops regulate gene expression and stability, and they form when newly synthesized RNA extensively pairs with the template DNA to displace the non-template strand. In this study, we tested two human PKD1 sequences for co-transcriptional R-loop formation in vitro. We observed RNase H-sensitive R-loop formation in intron 1 and 22 sequences, but only in one transcriptional orientation. Therefore, R-loops may participate in PKD1 expression or stability.
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Affiliation(s)
- Agata M Parsons
- Biomedical Sciences, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, United States
| | - Kemin Su
- Investigative Medicine, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, United States
| | - Maya Daniels
- Biomedical Sciences, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, United States
| | - Gerrit J Bouma
- Biomedical Sciences, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, United States
| | - Gregory B Vanden Heuvel
- Biomedical Sciences, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, United States
| | - Erik D Larson
- Biomedical Sciences, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, United States
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2
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The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
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3
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Gómez-González B, Aguilera A. Origin matters: spontaneous DNA-RNA hybrids do not form in trans as a source of genome instability. Curr Genet 2020; 67:93-97. [PMID: 33095299 DOI: 10.1007/s00294-020-01117-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 12/30/2022]
Abstract
Multiple exogenous and endogenous genotoxic agents threaten the integrity of the genome, but one major source of spontaneous DNA damage is the formation of unscheduled DNA-RNA hybrids. These can be genetically detected by their ability to induce recombination. The origin of spontaneous hybrids has been mainly attributed to the nascent RNA formed co-transcriptionally in cis invading its own DNA template. However, it was unclear whether hybrids could also be spontaneously generated by RNA produced in a different locus (in trans). Using new genetic systems in the yeast Saccharomyces cerevisiae, we recently tested whether hybrids could be formed in trans and compromise genome integrity. Whereas we detected recombinogenic DNA-RNA hybrids in cis and in a Rad51-independent manner, we found no evidence for recombinogenic DNA-RNA hybrids to be formed with RNAs produced in trans. Here, we further discuss the implications in the field for the origin of genetic instability and the threats coming from RNAs.
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Affiliation(s)
- Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC, Seville, Spain. .,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain.
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4
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Vannutelli A, Belhamiti S, Garant JM, Ouangraoua A, Perreault JP. Where are G-quadruplexes located in the human transcriptome? NAR Genom Bioinform 2020; 2:lqaa035. [PMID: 33575590 PMCID: PMC7671396 DOI: 10.1093/nargab/lqaa035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/28/2020] [Accepted: 05/05/2020] [Indexed: 12/23/2022] Open
Abstract
It has been demonstrated that RNA G-quadruplexes (G4) are structural motifs present in transcriptomes and play important regulatory roles in several post-transcriptional mechanisms. However, the full picture of RNA G4 locations and the extent of their implication remain elusive. Solely computational prediction analysis of the whole transcriptome may reveal all potential G4, since experimental identifications are always limited to specific conditions or specific cell lines. The present study reports the first in-depth computational prediction of potential G4 region across the complete human transcriptome. Although using a relatively stringent approach based on three prediction scores that accounts for the composition of G4 sequences, the composition of their neighboring sequences, and the various forms of G4, over 1.1 million of potential G4 (pG4) were predicted. The abundance of G4 was computationally confirmed in both 5' and 3'UTR as well as splicing junction of mRNA, appreciate for the first time in the long ncRNA, while almost absent of most of the small ncRNA families. The present results constitute an important step toward a full understanding of the roles of G4 in post-transcriptional mechanisms.
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Affiliation(s)
- Anaïs Vannutelli
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC J1K 2R1, Canada
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Sarah Belhamiti
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC J1K 2R1, Canada
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Jean-Michel Garant
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Aida Ouangraoua
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC J1K 2R1, Canada
| | - Jean-Pierre Perreault
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada
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5
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Yewdell WT, Chaudhuri J. A transcriptional serenAID: the role of noncoding RNAs in class switch recombination. Int Immunol 2018; 29:183-196. [PMID: 28535205 DOI: 10.1093/intimm/dxx027] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 05/22/2017] [Indexed: 12/31/2022] Open
Abstract
During an immune response, activated B cells may undergo class switch recombination (CSR), a molecular rearrangement that allows B cells to switch from expressing IgM and IgD to a secondary antibody heavy chain isotype such as IgG, IgA or IgE. Secondary antibody isotypes provide the adaptive immune system with distinct effector functions to optimally combat various pathogens. CSR occurs between repetitive DNA elements within the immunoglobulin heavy chain (Igh) locus, termed switch (S) regions and requires the DNA-modifying enzyme activation-induced cytidine deaminase (AID). AID-mediated DNA deamination within S regions initiates the formation of DNA double-strand breaks, which serve as biochemical beacons for downstream DNA repair pathways that coordinate the ligation of DNA breaks. Myriad factors contribute to optimal AID targeting; however, many of these factors also localize to genomic regions outside of the Igh locus. Thus, a current challenge is to explain the specific targeting of AID to the Igh locus. Recent studies have implicated noncoding RNAs in CSR, suggesting a provocative mechanism that incorporates Igh-specific factors to enable precise AID targeting. Here, we chronologically recount the rich history of noncoding RNAs functioning in CSR to provide a comprehensive context for recent and future discoveries. We present a model for the RNA-guided targeting of AID that attempts to integrate historical and recent findings, and highlight potential caveats. Lastly, we discuss testable hypotheses ripe for current experimentation, and explore promising ideas for future investigations.
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Affiliation(s)
- William T Yewdell
- Immunology Program, Memorial Sloan Kettering Cancer, New York, NY 10065, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
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6
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Related Mechanisms of Antibody Somatic Hypermutation and Class Switch Recombination. Microbiol Spectr 2016; 3:MDNA3-0037-2014. [PMID: 26104555 DOI: 10.1128/microbiolspec.mdna3-0037-2014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The primary antibody repertoire is generated by mechanisms involving the assembly of the exons that encode the antigen-binding variable regions of immunoglobulin heavy (IgH) and light (IgL) chains during the early development of B lymphocytes. After antigen-dependent activation, mature B lymphocytes can further alter their IgH and IgL variable region exons by the process of somatic hypermutation (SHM), which allows the selection of B cells in which SHMs resulted in the production of antibodies with increased antigen affinity. In addition, during antigen-dependent activation, B cells can also change the constant region of their IgH chain through a DNA double-strand-break (DSB) dependent process referred to as IgH class switch recombination (CSR), which generates B cell progeny that produce antibodies with different IgH constant region effector functions that are best suited for a elimination of a particular pathogen or in a particular setting. Both the mutations that underlie SHM and the DSBs that underlie CSR are initiated in target genes by activation-induced cytidine deaminase (AID). This review describes in depth the processes of SHM and CSR with a focus on mechanisms that direct AID cytidine deamination in activated B cells and mechanisms that promote the differential outcomes of such cytidine deamination.
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7
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Hamperl S, Cimprich KA. The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. DNA Repair (Amst) 2014; 19:84-94. [PMID: 24746923 PMCID: PMC4051866 DOI: 10.1016/j.dnarep.2014.03.023] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accurate DNA replication and DNA repair are crucial for the maintenance of genome stability, and it is generally accepted that failure of these processes is a major source of DNA damage in cells. Intriguingly, recent evidence suggests that DNA damage is more likely to occur at genomic loci with high transcriptional activity. Furthermore, loss of certain RNA processing factors in eukaryotic cells is associated with increased formation of co-transcriptional RNA:DNA hybrid structures known as R-loops, resulting in double-strand breaks (DSBs) and DNA damage. However, the molecular mechanisms by which R-loop structures ultimately lead to DNA breaks and genome instability is not well understood. In this review, we summarize the current knowledge about the formation, recognition and processing of RNA:DNA hybrids, and discuss possible mechanisms by which these structures contribute to DNA damage and genome instability in the cell.
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Affiliation(s)
- Stephan Hamperl
- Department of Chemical, Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Karlene A Cimprich
- Department of Chemical, Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
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8
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Matthews AJ, Zheng S, DiMenna LJ, Chaudhuri J. Regulation of immunoglobulin class-switch recombination: choreography of noncoding transcription, targeted DNA deamination, and long-range DNA repair. Adv Immunol 2014; 122:1-57. [PMID: 24507154 PMCID: PMC4150736 DOI: 10.1016/b978-0-12-800267-4.00001-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default Cμ constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as "Ch genes", e.g., Cγ, Cɛ, or Cα). The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction. CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor Sμ and acceptor S regions. CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining. In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs. Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations. Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming.
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Affiliation(s)
- Allysia J Matthews
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Simin Zheng
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Lauren J DiMenna
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA.
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9
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Collie GW, Parkinson GN. The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem Soc Rev 2011; 40:5867-92. [PMID: 21789296 DOI: 10.1039/c1cs15067g] [Citation(s) in RCA: 461] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The intriguing structural diversity in folded topologies available to guanine-rich nucleic acid repeat sequences have made four-stranded G-quadruplex structures the focus of both basic and applied research, from cancer biology and novel therapeutics through to nanoelectronics. Distributed widely in the human genome as targets for regulating gene expression and chromosomal maintenance, they offer unique avenues for future cancer drug development. In particular, the recent advances in chemical and structural biology have enabled the construction of bespoke selective DNA based aptamers to be used as novel therapeutic agents and access to detailed structural models for structure based drug discovery. In this critical review, we will explore the important underlying characteristics of G-quadruplexes that make them functional, stable, and predictable nanoscaffolds. We will review the current structural database of folding topologies, molecular interfaces and novel interaction surfaces, with a consideration to their future exploitation in drug discovery, molecular biology, supermolecular assembly and aptamer design. In recent years the number of potential applications for G-quadruplex motifs has rapidly grown, so in this review we aim to explore the many future challenges and highlight where possible successes may lie. We will highlight the similarities and differences between DNA and RNA folded G-quadruplexes in terms of stability, distribution, and exploitability as small molecule targets. Finally, we will provide a detailed review of basic G-quadruplex geometry, experimental tools used, and a critical evaluation of the application of high-resolution structural biology and its ability to provide meaningful and valid models for future applications (255 references).
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Affiliation(s)
- Gavin W Collie
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, UK WC1N 1AX
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10
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Haddad D, Oruc Z, Puget N, Laviolette-Malirat N, Philippe M, Carrion C, Le Bert M, Khamlichi AA. Sense transcription through the S region is essential for immunoglobulin class switch recombination. EMBO J 2011; 30:1608-20. [PMID: 21378751 DOI: 10.1038/emboj.2011.56] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 02/07/2011] [Indexed: 11/10/2022] Open
Abstract
Class switch recombination (CSR) occurs between highly repetitive sequences called switch (S) regions and is initiated by activation-induced cytidine deaminase (AID). CSR is preceded by a bidirectional transcription of S regions but the relative importance of sense and antisense transcription for CSR in vivo is unknown. We generated three mouse lines in which we attempted a premature termination of transcriptional elongation by inserting bidirectional transcription terminators upstream of Sμ, upstream of Sγ3 or downstream of Sγ3 sequences. The data show, at least for Sγ3, that sense transcriptional elongation across S region is absolutely required for CSR whereas its antisense counterpart is largely dispensable, strongly suggesting that sense transcription is sufficient for AID targeting to both DNA strands.
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Affiliation(s)
- Dania Haddad
- CNRS UMR 5089-IPBS (Institut de Pharmacologie et de Biologie Structurale) and Université Paul Sabatier III, Equipe 'Instabilité génétique et régulation transcriptionnelle', Toulouse Cedex, France
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11
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Mizuta R. Transcribed Guanine-rich RNA Aggregates on Template DNA and Changes Its Conformation. CHEM LETT 2010. [DOI: 10.1246/cl.2010.1088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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12
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Teng G, Papavasiliou FN. Long noncoding RNAs: implications for antigen receptor diversification. Adv Immunol 2009; 104:25-50. [PMID: 20457115 DOI: 10.1016/s0065-2776(08)04002-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Noncoding RNAs (ncRNAs), both small and large, have recently risen to prominence as surprisingly versatile regulators of gene expression. In fact, eukaryotic transcriptomes are rife with RNAs that do not code for protein, though the majority of these species remains wholly uncharacterized. The functional diversity among the mere handful of validated ncRNAs hints at the vast regulatory potential of these silent biomolecules. Though the act of noncoding transcription and the resultant ncRNAs do not directly produce proteins, they represent powerful means of gene control. Here we survey the accumulating literature on the myriad functions of long ncRNAs and emphasize one curious case of noncoding transcription at antigen receptor loci in lymphocytes.
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Affiliation(s)
- Grace Teng
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
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13
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Neaves KJ, Huppert JL, Henderson RM, Edwardson JM. Direct visualization of G-quadruplexes in DNA using atomic force microscopy. Nucleic Acids Res 2009; 37:6269-75. [PMID: 19696072 PMCID: PMC2764456 DOI: 10.1093/nar/gkp679] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/14/2009] [Accepted: 08/01/2009] [Indexed: 12/11/2022] Open
Abstract
The formation of G-quadruplexes in G-rich regions of DNA is believed to affect DNA transcription and replication. However, it is currently unclear how this formation occurs in the presence of a complementary strand. We have used atomic force microscopy (AFM) to image stable RNA/DNA hybrid loops generated by transcription of the plasmid pPH600, which contains a 604-bp fragment of the murine immunoglobulin Sgamma3 switch region. We show that the non-RNA-containing portion folds into G-quadruplexes, consistent with computational predictions. We also show that hybrid formation prevents further transcription from occurring, implying a regulatory role. After in vitro transcription, almost all (93%) of the plasmids had an asymmetric loop, a large asymmetric blob or a spur-like projection at the appropriate position on the DNA contour. The loops disappeared following treatment of the transcribed plasmid with RNase H, which removes mRNA hybridized with the template strand. Replacement of K+ in the transcription buffer with either Na+ or Li+ caused a reduction in the percentage of plasmids containing loops, blobs or spurs, consistent with the known effects of monovalent cations on G-quadruplex stability. The minimal sample preparation required for AFM imaging has permitted direct observation of the structural changes resulting from G-quadruplex formation.
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Affiliation(s)
- Kelly J. Neaves
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD and Physics of Medicine, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Julian L. Huppert
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD and Physics of Medicine, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Robert M. Henderson
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD and Physics of Medicine, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - J. Michael Edwardson
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD and Physics of Medicine, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
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14
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Gottipati P, Helleday T. Transcription-associated recombination in eukaryotes: link between transcription, replication and recombination. Mutagenesis 2009; 24:203-10. [PMID: 19139058 DOI: 10.1093/mutage/gen072] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Homologous recombination (HR) is an important DNA repair pathway and is essential for cellular survival. It plays a major role in repairing replication-associated lesions and is functionally connected to replication. Transcription is another cellular process, which has emerged to have a connection with HR. Transcription enhances HR, which is a ubiquitous phenomenon referred to as transcription-associated recombination (TAR). Recent evidence suggests that TAR plays a role in inducing genetic instability, for example in the THO mutants (Tho2, Hpr1, Mft1 and Thp2) in yeast or during the development of the immune system leading to genetic diversity in mammals. On the other hand, evidence also suggests that TAR may play a role in preventing genetic instability in many different ways, one of which is by rescuing replication during transcription. Hence, TAR is a double-edged sword and plays a role in both preventing and inducing genetic instability. In spite of the interesting nature of TAR, the mechanism behind TAR has remained elusive. Recent advances in the area, however, suggest a link between TAR and replication and show specific genetic requirements for TAR that differ from regular HR. In this review, we aim to present the available evidence for TAR in both lower and higher eukaryotes and discuss its possible mechanisms, with emphasis on its connection with replication.
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Affiliation(s)
- Ponnari Gottipati
- Gray Institute for Radiation Oncology and Biology, University of Oxford, Oxford, UK
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15
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Canugovi C, Samaranayake M, Bhagwat AS. Transcriptional pausing and stalling causes multiple clustered mutations by human activation-induced deaminase. FASEB J 2008; 23:34-44. [PMID: 18772346 DOI: 10.1096/fj.08-115352] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Transcription of the rearranged immunoglobulin gene and expression of the enzyme activation-induced deaminase (AID) are essential for somatic hypermutations of this gene during antibody maturation. While AID acts as a single-strand DNA-cytosine deaminase creating U . G mispairs that lead to mutations, the role played by transcription in this process is less clear. We have used in vitro transcription of the kan gene by the T7 RNA polymerase (RNAP) in the presence of AID and a genetic reversion assay for kanamycin-resistance to investigate the causes of multiple clustered mutations (MCMs) during somatic hypermutations. We find that, depending on transcription conditions, AID can cause single-base substitutions or MCMs. When wild-type RNAP is used for transcription at physiologically relevant concentrations of ribonucleoside triphosphates (NTPs), few MCMs are found. In contrast, slowing the rate of elongation by reducing the NTP concentration or using a mutant RNAP increases several-fold the percent of revertants containing MCMs. Arresting the elongation complexes by a quick removal of NTPs leads to formation of RNA-DNA hybrids (R-loops). Treatment of these structures with AID results in a high percentage of Kan(R) revertants with MCMs. Furthermore, selecting for transcription elongation complexes stalled near the codon that suffers mutations during acquisition of kanamycin-resistance results in an overwhelming majority of revertants with MCMs. These results show that if RNAP II pauses or stalls during transcription of immunoglobulin gene, AID is likely to promote MCMs. As changes in physiological conditions such as occurrence of certain DNA primary or secondary structures or DNA adducts are known to cause transcriptional pausing and stalling in mammalian cells, this process may cause MCMs during somatic hypermutation.
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Affiliation(s)
- Chandrika Canugovi
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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16
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Huppert JL. Thermodynamic prediction of RNA–DNA duplex-forming regions in the human genome. MOLECULAR BIOSYSTEMS 2008; 4:686-91. [DOI: 10.1039/b800354h] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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17
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Oruc Z, Boumédiène A, Le Bert M, Khamlichi AA. Replacement of Igamma3 germ-line promoter by Igamma1 inhibits class-switch recombination to IgG3. Proc Natl Acad Sci U S A 2007; 104:20484-9. [PMID: 18077389 PMCID: PMC2154457 DOI: 10.1073/pnas.0608364104] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Indexed: 11/18/2022] Open
Abstract
Class-switch recombination (CSR) enables IgM-producing B cells to switch to the production of IgG, IgE, and IgA. The process requires germ-line (GL) transcription that initiates from promoters upstream of switch (S) sequences and is regulated by the 3' regulatory region (3'RR) located downstream of the Ig heavy chain (IgH) locus. How the 3'RR effect its long-range activation is presently unclear. We generated a mouse line in which Igamma3 GL promoter was replaced by Igamma1. We found that GL transcription could initiate from the inserted Igamma1 promoter and was induced by increased concentrations of IL-4 and that the transcripts were normally spliced. However, when compared with GL transcripts derived from the endogenous Igamma1 promoter in the same stimulation conditions, those from the inserted Igamma1 promoter were less abundant. CSR to Cgamma3 was abrogated both in vivo and in vitro. The results strongly suggest that the endogenous Igamma1 promoter insulates the inserted Igamma1 from the long-range activating effect of the 3'RR. The implications of our findings are discussed in light of the prominent models of long-distance activation in complex loci.
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Affiliation(s)
- Zeliha Oruc
- Université Paul Sabatier, III, Centre National de la Recherche Scientifique, Unite Mixte de Recherche 5089-IPBS, Equipe "Instabilité génétique et régulation transcriptionnelle," 205 Route de Narbonne, 31077 Toulouse Cedex, France
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18
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Abstract
Accurate and complete replication of the genome in every cell division is a prerequisite of genomic stability. Thus, both prokaryotic and eukaryotic replication forks are extremely precise and robust molecular machines that have evolved to be up to the task. However, it has recently become clear that the replication fork is more of a hurdler than a runner: it must overcome various obstacles present on its way. Such obstacles can be called natural impediments to DNA replication, as opposed to external and genetic factors. Natural impediments to DNA replication are particular DNA binding proteins, unusual secondary structures in DNA, and transcription complexes that occasionally (in eukaryotes) or constantly (in prokaryotes) operate on replicating templates. This review describes the mechanisms and consequences of replication stalling at various natural impediments, with an emphasis on the role of replication stalling in genomic instability.
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Affiliation(s)
- Ekaterina V. Mirkin
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Sergei M. Mirkin
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60607
- Corresponding author. Present address: Department of Biology, Tufts University, Medford, MA 02155. Phone: (617) 627-4794. Fax: (617) 627-3805. E-mail:
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19
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Chaudhuri J, Basu U, Zarrin A, Yan C, Franco S, Perlot T, Vuong B, Wang J, Phan RT, Datta A, Manis J, Alt FW. Evolution of the Immunoglobulin Heavy Chain Class Switch Recombination Mechanism. Adv Immunol 2007; 94:157-214. [PMID: 17560275 DOI: 10.1016/s0065-2776(06)94006-1] [Citation(s) in RCA: 195] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
To mount an optimum immune response, mature B lymphocytes can change the class of expressed antibody from IgM to IgG, IgA, or IgE through a recombination/deletion process termed immunoglobulin heavy chain (IgH) class switch recombination (CSR). CSR requires the activation-induced cytidine deaminase (AID), which has been shown to employ single-stranded DNA as a substrate in vitro. IgH CSR occurs within and requires large, repetitive sequences, termed S regions, which are parts of germ line transcription units (termed "C(H) genes") that are composed of promoters, S regions, and individual IgH constant region exons. CSR requires and is directed by germ line transcription of participating C(H) genes prior to CSR. AID deamination of cytidines in S regions appears to lead to S region double-stranded breaks (DSBs) required to initiate CSR. Joining of two broken S regions to complete CSR exploits the activities of general DNA DSB repair mechanisms. In this chapter, we discuss our current knowledge of the function of S regions, germ line transcription, AID, and DNA repair in CSR. We present a model for CSR in which transcription through S regions provides DNA substrates on which AID can generate DSB-inducing lesions. We also discuss how phosphorylation of AID may mediate interactions with cofactors that facilitate access to transcribed S regions during CSR and transcribed variable regions during the related process of somatic hypermutation (SHM). Finally, in the context of this CSR model, we further discuss current findings that suggest synapsis and joining of S region DSBs during CSR have evolved to exploit general mechanisms that function to join widely separated chromosomal DSBs.
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Affiliation(s)
- Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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20
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Eddy J, Maizels N. Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res 2006; 34:3887-96. [PMID: 16914419 PMCID: PMC1557811 DOI: 10.1093/nar/gkl529] [Citation(s) in RCA: 391] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
G-rich genomic regions can form G4 DNA upon transcription or replication. We have quantified the potential for G4 DNA formation (G4P) of the 16 654 genes in the human RefSeq database, and then correlated gene function with G4P. We have found that very low and very high G4P correlates with specific functional classes of genes. Notably, tumor suppressor genes have very low G4P and proto-oncogenes have very high G4P. G4P of these genes is evenly distributed between exons and introns, and it does not reflect enrichment for CpG islands or local chromosomal environment. These results show that genomic structure undergoes selection based on gene function. Selection based on G4P could promote genomic stability (or instability) of specific classes of genes; or reflect mechanisms for global regulation of gene expression.
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Affiliation(s)
- Johanna Eddy
- Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine1959 NE Pacific Street, Seattle, WA 98195-7650, USA
| | - Nancy Maizels
- Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine1959 NE Pacific Street, Seattle, WA 98195-7650, USA
- Department of Immunology, University of Washington School of Medicine1959 NE Pacific Street, Seattle, WA 98195-7650, USA
- Department of Biochemistry, University of Washington School of Medicine1959 NE Pacific Street, Seattle, WA 98195-7650, USA
- To whom correspondence should be addressed. Tel: +1 206 221 6876; Fax: +1 206 221 6781;
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21
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Longerich S, Basu U, Alt F, Storb U. AID in somatic hypermutation and class switch recombination. Curr Opin Immunol 2006; 18:164-74. [PMID: 16464563 DOI: 10.1016/j.coi.2006.01.008] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Accepted: 01/27/2006] [Indexed: 01/15/2023]
Abstract
Somatic hypermutation and class-switch-recombination are initiated by the deamination of deoxycytosine in DNA by activation-induced-deaminase, AID. Recently, there has been much research into how AID targets double-stranded DNA in sub-regions of Ig genes, the involvement of co-factors and posttranslational modifications in this process, the co-option of DNA 'repair' mechanisms and AID evolution.
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Affiliation(s)
- Simonne Longerich
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 E. 58(th) Street, Chicago, IL 60615, USA
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22
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Dudley DD, Chaudhuri J, Bassing CH, Alt FW. Mechanism and control of V(D)J recombination versus class switch recombination: similarities and differences. Adv Immunol 2006; 86:43-112. [PMID: 15705419 DOI: 10.1016/s0065-2776(04)86002-4] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
V(D)J recombination is the process by which the variable region exons encoding the antigen recognition sites of receptors expressed on B and T lymphocytes are generated during early development via somatic assembly of component gene segments. In response to antigen, somatic hypermutation (SHM) and class switch recombination (CSR) induce further modifications of immunoglobulin genes in B cells. CSR changes the IgH constant region for an alternate set that confers distinct antibody effector functions. SHM introduces mutations, at a high rate, into variable region exons, ultimately allowing affinity maturation. All of these genomic alteration processes require tight regulatory control mechanisms, both to ensure development of a normal immune system and to prevent potentially oncogenic processes, such as translocations, caused by errors in the recombination/mutation processes. In this regard, transcription of substrate sequences plays a significant role in target specificity, and transcription is mechanistically coupled to CSR and SHM. However, there are many mechanistic differences in these reactions. V(D)J recombination proceeds via precise DNA cleavage initiated by the RAG proteins at short conserved signal sequences, whereas CSR and SHM are initiated over large target regions via activation-induced cytidine deaminase (AID)-mediated DNA deamination of transcribed target DNA. Yet, new evidence suggests that AID cofactors may help provide an additional layer of specificity for both SHM and CSR. Whereas repair of RAG-induced double-strand breaks (DSBs) involves the general nonhomologous end-joining DNA repair pathway, and CSR also depends on at least some of these factors, CSR requires induction of certain general DSB response factors, whereas V(D)J recombination does not. In this review, we compare and contrast V(D)J recombination and CSR, with particular emphasis on the role of the initiating enzymes and DNA repair proteins in these processes.
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Affiliation(s)
- Darryll D Dudley
- Howard Hughes Medical Institute, The Children's Hospital Boston, CBR Institute for Biomedical Research, and Harvard Medical School, Boston, MA 02115, USA
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23
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Abstract
Three processes alter genomic sequence and structure at the immunoglobulin genes of B lymphocytes: gene conversion, somatic hypermutation, and class switch recombination. Though the molecular signatures of these processes differ, they occur by a shared pathway which is induced by targeted DNA deamination by a B cell-specific factor, activation induced cytidine deaminase (AID). Ubiquitous factors critical for DNA repair carry out all downstream steps, creating mutations and deletions in genomic DNA. This review focuses on the genetic and biochemical mechanisms of diversification of immunoglobulin genes.
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Affiliation(s)
- Nancy Maizels
- Department of Immunology, University of Washington Medical School, Seattle, Washington 98195-7650, USA.
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24
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Mizuta R, Mizuta M, Kitamura D. Guanine is indispensable for immunoglobulin switch region RNA-DNA hybrid formation. Microscopy (Oxf) 2005; 54:403-8. [PMID: 16143700 DOI: 10.1093/jmicro/dfi058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
It is suggested that the formation of the switch (S) region RNA-DNA hybrid and the subsequent generation of higher-order chromatin structures including R-loop initiate a class switch recombination of the immunoglobulin gene. The primary factor of this recombination is the S-region derived noncoding RNA. However, the biochemical character of this guanine-rich (G-rich) transcript is poorly understood. The present study was performed to analyze the structure of this G-rich RNA using atomic force microscope (AFM). The in vitro transcribed S-region RNA was spread on a mica plate, air-dried and observed by non-contact mode AFM in air. The G-rich transcripts tend to aggregate on the template DNA and to generate a higher-order RNA-DNA complex. However, the transcripts that incorporated guanine analogues as substitutes for guanine neither aggregated nor generated higher-order structures. Incorporation of guanine analogues in transcribed RNA partially disrupts hydrogen bonds related to guanine, such as Watson-Crick GC-base pair and Hoogsteen bond GG-base pair. Thus, aggregation of S-region RNA and generation of the higher-order RNA-DNA complex are attributed to hydrogen bonds of guanine.
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Affiliation(s)
- Ryushin Mizuta
- Research Institute for Biological Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan.
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25
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Watanabe M, Nomura K, Ohyama A, Ishikawa R, Komiya Y, Hosaka K, Yamauchi E, Taniguchi H, Sasakawa N, Kumakura K, Ushiki T, Sato O, Ikebe M, Igarashi M. Myosin-Va regulates exocytosis through the submicromolar Ca2+-dependent binding of syntaxin-1A. Mol Biol Cell 2005; 16:4519-30. [PMID: 16030255 PMCID: PMC1237061 DOI: 10.1091/mbc.e05-03-0252] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Myosin-Va is an actin-based processive motor that conveys intracellular cargoes. Synaptic vesicles are one of the most important cargoes for myosin-Va, but the role of mammalian myosin-Va in secretion is less clear than for its yeast homologue, Myo2p. In the current studies, we show that myosin-Va on synaptic vesicles interacts with syntaxin-1A, a t-SNARE involved in exocytosis, at or above 0.3 microM Ca2+. Interference with formation of the syntaxin-1A-myosin-Va complex reduces the exocytotic frequency in chromaffin cells. Surprisingly, the syntaxin-1A-binding site was not in the tail of myosin-Va but rather in the neck, a region that contains calmodulin-binding IQ-motifs. Furthermore, we found that syntaxin-1A binding by myosin-Va in the presence of Ca2+ depends on the release of calmodulin from the myosin-Va neck, allowing syntaxin-1A to occupy the vacant IQ-motif. Using an anti-myosin-Va neck antibody, which blocks this binding, we demonstrated that the step most important for the antibody's inhibitory activity is the late sustained phase, which is involved in supplying readily releasable vesicles. Our results demonstrate that the interaction between myosin-Va and syntaxin-1A is involved in exocytosis and suggest that the myosin-Va neck contributes not only to the large step size but also to the regulation of exocytosis by Ca2+.
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Affiliation(s)
- Michitoshi Watanabe
- Division of Molecular and Cellular Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata 951-8510, Japan
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26
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27
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Min IM, Selsing E. Antibody class switch recombination: roles for switch sequences and mismatch repair proteins. Adv Immunol 2005; 87:297-328. [PMID: 16102577 DOI: 10.1016/s0065-2776(05)87008-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mechanisms and targeting of antibody class switch DNA recombination are reviewed. Particular emphasis is on the roles for the DNA sequences comprising switch (S) regions, including the S-region tandem repeats, and on the roles of proteins that are involved in both DNA mismatch repair and in class switch recombination.
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Affiliation(s)
- Irene M Min
- Genetics Program, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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28
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Duquette ML, Handa P, Vincent JA, Taylor AF, Maizels N. Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. Genes Dev 2004; 18:1618-29. [PMID: 15231739 PMCID: PMC443523 DOI: 10.1101/gad.1200804] [Citation(s) in RCA: 411] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We show that intracellular transcription of G-rich regions produces novel DNA structures, visible by electron microscopy as large (150-500 bp) loops. These G-loops are formed cotranscriptionally, and they contain G4 DNA on one strand and a stable RNA/DNA hybrid on the other. G-loop formation requires a G-rich nontemplate strand and reflects the unusual stability of the rG/dC base pair. G-loops and G4 DNA form efficiently within plasmid genomes transcribed in vitro or in Escherichia coli. These results establish that G4 DNA can form in vivo, a finding with implications for stability and maintenance of all G-rich genomic regions.
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Affiliation(s)
- Michelle L Duquette
- Department of Genetics, Yale University School of Medicine, New Haven, Conneticut 06520, USA
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29
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Chaudhuri J, Alt FW. Class-switch recombination: interplay of transcription, DNA deamination and DNA repair. Nat Rev Immunol 2004; 4:541-52. [PMID: 15229473 DOI: 10.1038/nri1395] [Citation(s) in RCA: 431] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jayanta Chaudhuri
- Howard Hughes Medical Institute, Center for Blood Research and Department of Genetics, Harvard University Medical School, Boston, Massachusetts 02115, USA
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30
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Khamlichi AA, Glaudet F, Oruc Z, Denis V, Le Bert M, Cogné M. Immunoglobulin class-switch recombination in mice devoid of any Sμ tandem repeat. Blood 2004; 103:3828-36. [PMID: 14962903 DOI: 10.1182/blood-2003-10-3470] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AbstractImmunoglobulin heavy-chain class-switch recombination (CSR) occurs between highly repetitive switch sequences located upstream of the constant region genes. However, the role of these sequences remains unclear. Mutant mice were generated in which most of the Iμ-Cμ intron was deleted, including all the repeats. Late B-cell development was characterized by a severe impairment, but not a complete block, in class switching to all isotypes despite normal germ line transcription. Sequence analysis of the Iμ-Cμ intron in in vitro activated–mutant splenocytes did not reveal any significant increase in activation-induced cytidine deaminase (AID)–induced somatic mutations. Analysis of switch junctions showed that, in the absence of any Sμ repeat, the Iμ exon was readily used as a substrate for CSR. In contrast to the sequence alterations downstream of the switch junctions, very few, if any, mutations were found upstream of the junction sites. Our data suggest that the core Eμ enhancer could be the boundary for CSR-associated somatic mutations. We propose that the core Eμ enhancer plays a central role in the temporal dissociation of somatic hypermutation from class switching.
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31
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Zeng X, Negrete GA, Kasmer C, Yang WW, Gearhart PJ. Absence of DNA polymerase eta reveals targeting of C mutations on the nontranscribed strand in immunoglobulin switch regions. ACTA ACUST UNITED AC 2004; 199:917-24. [PMID: 15051760 PMCID: PMC2211872 DOI: 10.1084/jem.20032022] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Activation-induced cytosine deaminase preferentially deaminates C in DNA on the nontranscribed strand in vitro, which theoretically should produce a large increase in mutations of C during hypermutation of immunoglobulin genes. However, a bias for C mutations has not been observed among the mutations in variable genes. Therefore, we examined mutations in the mu and gamma switch regions, which can form stable secondary structures, to look for C mutations. To further simplify the pattern, mutations were studied in the absence of DNA polymerase (pol) eta, which may produce substitutions of nucleotides downstream of C. DNA from lymphocytes of patients with xeroderma pigmentosum variant (XP-V) disease, whose polymerase eta is defective, had the same frequency of switching to all four gamma isotypes and hypermutation in mu-gamma switch sites (0.5% mutations per basepair) as control subjects. There were fewer mutations of A and T bases in the XP-V clones, similar to variable gene mutations from these patients, which confirms that polymerase eta produces substitutions opposite A and T. Most importantly, the absence of polymerase eta revealed an increase in C mutations on the nontranscribed strand. This data shows for the first time that C is preferentially mutated in vivo and pol eta generates hypermutation in the mu and gamma switch regions.
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Affiliation(s)
- Xianmin Zeng
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
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32
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Huertas P, Aguilera A. Cotranscriptionally Formed DNA:RNA Hybrids Mediate Transcription Elongation Impairment and Transcription-Associated Recombination. Mol Cell 2003; 12:711-21. [PMID: 14527416 DOI: 10.1016/j.molcel.2003.08.010] [Citation(s) in RCA: 563] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Genetic instability, a phenomenon relevant for developmentally regulated processes, cancer, and inherited disorders, can be induced by transcription. However, the mechanisms of transcription-associated genetic instability are not yet understood. Analysis of S. cerevisiae mutants of THO/TREX, a conserved eukaryotic protein complex functioning at the interface of transcription and mRNA metabolism, has provided evidence that transcription elongation impairment can cause hyperrecombination. Here we show, using hpr1Delta mutants, that the nascent mRNA can diminish transcription elongation efficiency and promote recombination. If during transcription the nascent mRNA is self-cleaved by a hammerhead ribozyme, the transcription-defect and hyperrecombination phenotypes of hpr1Delta cells are suppressed. Abolishment of hyperrecombination by overexpression of RNase H1 and molecular detection of DNA:RNA hybrids indicate that these are formed cotranscriptionally in hpr1Delta cells. These data support a model to explain the connection between recombination, transcription, and mRNA metabolism and provide a new perspective to understanding transcription-associated recombination.
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Affiliation(s)
- Pablo Huertas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avenida Reina, Mercedes 6, 41012 Seville, Spain
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33
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Ta VT, Nagaoka H, Catalan N, Durandy A, Fischer A, Imai K, Nonoyama S, Tashiro J, Ikegawa M, Ito S, Kinoshita K, Muramatsu M, Honjo T. AID mutant analyses indicate requirement for class-switch-specific cofactors. Nat Immunol 2003; 4:843-8. [PMID: 12910268 DOI: 10.1038/ni964] [Citation(s) in RCA: 263] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2003] [Accepted: 07/15/2003] [Indexed: 01/20/2023]
Abstract
Activation-induced cytidine deaminase (AID) is the essential and sole B cell-specific factor required for class-switch recombination (CSR) and somatic hypermutation (SHM). However, it is not known how AID differentially regulates these two independent events. Involvement of several cofactors interacting with AID has been indicated by scattered distribution of loss-of-function point mutations and evolutionary conservation of the entire 198-amino-acid protein. Here, we report that human AID mutant proteins with insertions, replacements or truncations in the C-terminal region retained strong SHM activity but almost completely lost CSR activity. These results indicate that AID requires interaction with a cofactor(s) specific to CSR.
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Affiliation(s)
- Van-Thanh Ta
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
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34
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Abstract
The immune defense against extracellular pathogens is largely dependent on antibody production. Class switch recombination and somatic hypermutation shape the secondary antibody repertoire in peripheral lymphoid tissue. In the past few years, a series of primary immune deficiencies characterized by defects in these processes and collectively referred to as hyper-IgM syndromes, have been described. Careful investigation of these rare "experiments of nature" has enabled to identify novel genes and molecular events that drive terminal B-cell differentiation. Abnormalities in these genes are likely involved also in lymphoid tumorigenesis and autoimmunity.
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35
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Shinkura R, Tian M, Smith M, Chua K, Fujiwara Y, Alt FW. The influence of transcriptional orientation on endogenous switch region function. Nat Immunol 2003; 4:435-41. [PMID: 12679811 DOI: 10.1038/ni918] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2003] [Accepted: 02/19/2003] [Indexed: 11/09/2022]
Abstract
Immunoglobulin heavy chain (IgH) class switch recombination (CSR) takes place between large switch (S) regions that precede exons of the constant region. The precise functions of the S region are controversial, although transcription of the S region targets CSR. We have tested the effects of deletion, inversion and replacement of the endogenous 12-kilobase S(gamma1) region on CSR in vivo. Here we show that S(gamma1) is required for CSR, that CSR is effected by a 1-kilobase sequence that generates a G-rich transcript, and that inversion of S(gamma1) or the G-rich sequence decreases CSR. We conclude that S(gamma1) function is dependent on orientation and lacks an absolute requirement for common S region motifs. We propose that single-stranded DNA stabilized by transcription-dependent, higher order structures is a primary substrate of CSR.
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Affiliation(s)
- Reiko Shinkura
- Howard Hughes Medical Institute, The Children's Hospital, The Center for Blood Research, and Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA
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36
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Chaudhuri J, Tian M, Khuong C, Chua K, Pinaud E, Alt FW. Transcription-targeted DNA deamination by the AID antibody diversification enzyme. Nature 2003; 422:726-30. [PMID: 12692563 DOI: 10.1038/nature01574] [Citation(s) in RCA: 575] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2003] [Accepted: 03/24/2003] [Indexed: 11/09/2022]
Abstract
Activation-induced cytidine deaminase (AID), which is specific to B lymphocytes, is required for class switch recombination (CSR)--a process mediating isotype switching of immunoglobulin--and somatic hypermutation--the introduction of many point mutations into the immunoglobulin variable region genes. It has been suggested that AID may function as an RNA-editing enzyme or as a cytidine deaminase on DNA. However, the precise enzymatic activity of AID has not been assessed in previous studies. Similarly, although transcription of the target immunoglobulin locus sequences is required for both CSR and somatic hypermutation, the precise role of transcription has remained speculative. Here we use two different assays to demonstrate that AID can deaminate specifically cytidines on single-stranded (ss)DNA but not double-stranded (ds)DNA substrates in vitro. However, dsDNA can be deaminated by AID in vitro when the reaction is coupled to transcription. Moreover, a synthetic dsDNA sequence, which targets CSR in vivo in a manner dependent on transcriptional orientation, was deaminated by AID in vitro with the same transcriptional-orientation-dependence as observed for endogenous CSR. We conclude that transcription targets the DNA deamination activity of AID to dsDNA by generating secondary structures that provide ssDNA substrates.
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Affiliation(s)
- Jayanta Chaudhuri
- Howard Hughes Medical Institute, The Children's Hospital, The Center for Blood Research, and Department of Genetics, Harvard University Medical School, Boston, Massachusetts 02115, USA
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