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Roisné-Hamelin F, Marcand S. All roads lead to MRN regulation at telomeres: different paths to one solution. Nat Struct Mol Biol 2023; 30:1242-1243. [PMID: 37653240 DOI: 10.1038/s41594-023-01077-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Affiliation(s)
- Florian Roisné-Hamelin
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Stéphane Marcand
- Université Paris-Saclay, Université Paris-Cité, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France.
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Maloisel L, Ma E, Phipps J, Deshayes A, Mattarocci S, Marcand S, Dubrana K, Coïc E. Rad51 filaments assembled in the absence of the complex formed by the Rad51 paralogs Rad55 and Rad57 are outcompeted by translesion DNA polymerases on UV-induced ssDNA gaps. PLoS Genet 2023; 19:e1010639. [PMID: 36749784 PMCID: PMC9937489 DOI: 10.1371/journal.pgen.1010639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 02/17/2023] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
The bypass of DNA lesions that block replicative polymerases during DNA replication relies on DNA damage tolerance pathways. The error-prone translesion synthesis (TLS) pathway depends on specialized DNA polymerases that incorporate nucleotides in front of base lesions, potentially inducing mutagenesis. Two error-free pathways can bypass the lesions: the template switching pathway, which uses the sister chromatid as a template, and the homologous recombination pathway (HR), which also can use the homologous chromosome as template. The balance between error-prone and error-free pathways controls the mutagenesis level. Therefore, it is crucial to precisely characterize factors that influence the pathway choice to better understand genetic stability at replication forks. In yeast, the complex formed by the Rad51 paralogs Rad55 and Rad57 promotes HR and template-switching at stalled replication forks. At DNA double-strand breaks (DSBs), this complex promotes Rad51 filament formation and stability, notably by counteracting the Srs2 anti-recombinase. To explore the role of the Rad55-Rad57 complex in error-free pathways, we monitored the genetic interactions between Rad55-Rad57, the translesion polymerases Polζ or Polη, and Srs2 following UV radiation that induces mostly single-strand DNA gaps. We found that the Rad55-Rad57 complex was involved in three ways. First, it protects Rad51 filaments from Srs2, as it does at DSBs. Second, it promotes Rad51 filament stability independently of Srs2. Finally, we observed that UV-induced HR is almost abolished in Rad55-Rad57 deficient cells, and is partially restored upon Polζ or Polη depletion. Hence, we propose that the Rad55-Rad57 complex is essential to promote Rad51 filament stability on single-strand DNA gaps, notably to counteract the error-prone TLS polymerases and mutagenesis.
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Affiliation(s)
- Laurent Maloisel
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
- * E-mail: (LM); (EC)
| | - Emilie Ma
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Jamie Phipps
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Alice Deshayes
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Stefano Mattarocci
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Stéphane Marcand
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Karine Dubrana
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Eric Coïc
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
- * E-mail: (LM); (EC)
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Bordelet H, Costa R, Brocas C, Dépagne J, Veaute X, Busso D, Batté A, Guérois R, Marcand S, Dubrana K. Sir3 heterochromatin protein promotes non-homologous end joining by direct inhibition of Sae2. EMBO J 2022; 41:e108813. [PMID: 34817085 PMCID: PMC8724767 DOI: 10.15252/embj.2021108813] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 01/07/2023] Open
Abstract
Heterochromatin is a conserved feature of eukaryotic chromosomes, with central roles in gene expression regulation and maintenance of genome stability. How heterochromatin proteins regulate DNA repair remains poorly described. In the yeast Saccharomyces cerevisiae, the silent information regulator (SIR) complex assembles heterochromatin-like chromatin at sub-telomeric chromosomal regions. SIR-mediated repressive chromatin limits DNA double-strand break (DSB) resection, thus protecting damaged chromosome ends during homologous recombination (HR). As resection initiation represents the crossroads between repair by non-homologous end joining (NHEJ) or HR, we asked whether SIR-mediated heterochromatin regulates NHEJ. We show that SIRs promote NHEJ through two pathways, one depending on repressive chromatin assembly, and the other relying on Sir3 in a manner that is independent of its heterochromatin-promoting function. Via physical interaction with the Sae2 protein, Sir3 impairs Sae2-dependent functions of the MRX (Mre11-Rad50-Xrs2) complex, thereby limiting Mre11-mediated resection, delaying MRX removal from DSB ends, and promoting NHEJ.
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Affiliation(s)
- Hélène Bordelet
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
- Régulation spatiale des génomes, Institut Pasteur, CNRS UMR3525ParisFrance
| | - Rafaël Costa
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Clémentine Brocas
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Jordane Dépagne
- CIGEx platform. Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Xavier Veaute
- CIGEx platform. Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Didier Busso
- CIGEx platform. Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Amandine Batté
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
- Center for Integrative GenomicsBâtiment GénopodeUniversity of LausanneLausanneSwitzerland
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell (I2BC)CEA, CNRS, Université Paris‐Sud, Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Stéphane Marcand
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
| | - Karine Dubrana
- Université de Paris and Université Paris‐Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et RadiationsFontenay‐aux‐RosesFrance
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Pobiega S, Alibert O, Marcand S. A new assay capturing chromosome fusions shows a protection trade-off at telomeres and NHEJ vulnerability to low-density ionizing radiation. Nucleic Acids Res 2021; 49:6817-6831. [PMID: 34125900 PMCID: PMC8266670 DOI: 10.1093/nar/gkab502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/31/2021] [Accepted: 05/27/2021] [Indexed: 11/14/2022] Open
Abstract
Chromosome fusions threaten genome integrity and promote cancer by engaging catastrophic mutational processes, namely chromosome breakage-fusion-bridge cycles and chromothripsis. Chromosome fusions are frequent in cells incurring telomere dysfunctions or those exposed to DNA breakage. Their occurrence and therefore their contribution to genome instability in unchallenged cells is unknown. To address this issue, we constructed a genetic assay able to capture and quantify rare chromosome fusions in budding yeast. This chromosome fusion capture (CFC) assay relies on the controlled inactivation of one centromere to rescue unstable dicentric chromosome fusions. It is sensitive enough to quantify the basal rate of end-to-end chromosome fusions occurring in wild-type cells. These fusions depend on canonical nonhomologous end joining (NHEJ). Our results show that chromosome end protection results from a trade-off at telomeres between positive effectors (Rif2, Sir4, telomerase) and a negative effector partially antagonizing them (Rif1). The CFC assay also captures NHEJ-dependent chromosome fusions induced by ionizing radiation. It provides evidence for chromosomal rearrangements stemming from a single photon-matter interaction.
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Affiliation(s)
- Sabrina Pobiega
- Université de Paris and Université Paris-Saclay, Inserm, CEA IBFJ/iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, 92265 Fontenay-au-Roses, France
| | | | - Stéphane Marcand
- To whom correspondence should be addressed. Tel: +33 1 46 54 82 33;
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Roisné-Hamelin F, Pobiega S, Jézéquel K, Miron S, Dépagne J, Veaute X, Busso D, Du MHL, Callebaut I, Charbonnier JB, Cuniasse P, Zinn-Justin S, Marcand S. Mechanism of MRX inhibition by Rif2 at telomeres. Nat Commun 2021; 12:2763. [PMID: 33980827 PMCID: PMC8115599 DOI: 10.1038/s41467-021-23035-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Specific proteins present at telomeres ensure chromosome end stability, in large part through unknown mechanisms. In this work, we address how the Saccharomyces cerevisiae ORC-related Rif2 protein protects telomere. We show that the small N-terminal Rif2 BAT motif (Blocks Addition of Telomeres) previously known to limit telomere elongation and Tel1 activity is also sufficient to block NHEJ and 5' end resection. The BAT motif inhibits the ability of the Mre11-Rad50-Xrs2 complex (MRX) to capture DNA ends. It acts through a direct contact with Rad50 ATP-binding Head domains. Through genetic approaches guided by structural predictions, we identify residues at the surface of Rad50 that are essential for the interaction with Rif2 and its inhibition. Finally, a docking model predicts how BAT binding could specifically destabilise the DNA-bound state of the MRX complex. From these results, we propose that when an MRX complex approaches a telomere, the Rif2 BAT motif binds MRX Head in its ATP-bound resting state. This antagonises MRX transition to its DNA-bound state, and favours a rapid return to the ATP-bound state. Unable to stably capture the telomere end, the MRX complex cannot proceed with the subsequent steps of NHEJ, Tel1-activation and 5' resection.
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Affiliation(s)
- Florian Roisné-Hamelin
- Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Sabrina Pobiega
- Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Kévin Jézéquel
- Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Simona Miron
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jordane Dépagne
- CIGEx, Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Xavier Veaute
- CIGEx, Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Didier Busso
- CIGEx, Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Marie-Hélène Le Du
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Jean-Baptiste Charbonnier
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Philippe Cuniasse
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sophie Zinn-Justin
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphane Marcand
- Université de Paris, Université Paris-Saclay, Inserm, CEA, Institut de Biologie François Jacob, iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France.
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Guérin TM, Béneut C, Barinova N, López V, Lazar-Stefanita L, Deshayes A, Thierry A, Koszul R, Dubrana K, Marcand S. Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis. Mol Cell 2019; 75:131-144.e3. [PMID: 31204167 DOI: 10.1016/j.molcel.2019.05.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/12/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
In Saccharomyces cerevisiae, dicentric chromosomes stemming from telomere fusions preferentially break at the fusion. This process restores a normal karyotype and protects chromosomes from the detrimental consequences of accidental fusions. Here, we address the molecular basis of this rescue pathway. We observe that tandem arrays tightly bound by the telomere factor Rap1 or a heterologous high-affinity DNA binding factor are sufficient to establish breakage hotspots, mimicking telomere fusions within dicentrics. We also show that condensins generate forces sufficient to rapidly refold dicentrics prior to breakage by cytokinesis and are essential to the preferential breakage at telomere fusions. Thus, the rescue of fused telomeres results from a condensin- and Rap1-driven chromosome folding that favors fusion entrapment where abscission takes place. Because a close spacing between the DNA-bound Rap1 molecules is essential to this process, Rap1 may act by stalling condensins.
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Affiliation(s)
- Thomas M Guérin
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Claire Béneut
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Natalja Barinova
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Virginia López
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Alice Deshayes
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Karine Dubrana
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Stéphane Marcand
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France.
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Faure G, Jézéquel K, Roisné-Hamelin F, Bitard-Feildel T, Lamiable A, Marcand S, Callebaut I. Discovery and Evolution of New Domains in Yeast Heterochromatin Factor Sir4 and Its Partner Esc1. Genome Biol Evol 2019; 11:572-585. [PMID: 30668669 PMCID: PMC6394760 DOI: 10.1093/gbe/evz010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2019] [Indexed: 12/22/2022] Open
Abstract
Sir4 is a core component of heterochromatin found in yeasts of the Saccharomycetaceae family, whose general hallmark is to harbor a three-loci mating-type system with two silent loci. However, a large part of the Sir4 amino acid sequences has remained unexplored, belonging to the dark proteome. Here, we analyzed the phylogenetic profile of yet undescribed foldable regions present in Sir4 as well as in Esc1, an Sir4-interacting perinuclear anchoring protein. Within Sir4, we identified a new conserved motif (TOC) adjacent to the N-terminal KU-binding motif. We also found that the Esc1-interacting region of Sir4 is a Dbf4-related H-BRCT domain, only present in species possessing the HO endonuclease and in Kluveryomyces lactis. In addition, we found new motifs within Esc1 including a motif (Esc1-F) that is unique to species where Sir4 possesses an H-BRCT domain. Mutagenesis of conserved amino acids of the Sir4 H-BRCT domain, known to play a critical role in the Dbf4 function, shows that the function of this domain is separable from the essential role of Sir4 in transcriptional silencing and the protection from HO-induced cutting in Saccharomyces cerevisiae. In the more distant methylotrophic clade of yeasts, which often harbor a two-loci mating-type system with one silent locus, we also found a yet undescribed H-BRCT domain in a distinct protein, the ISWI2 chromatin-remodeling factor subunit Itc1. This study provides new insights on yeast heterochromatin evolution and emphasizes the interest of using sensitive methods of sequence analysis for identifying hitherto ignored functional regions within the dark proteome.
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Affiliation(s)
- Guilhem Faure
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Kévin Jézéquel
- Institut de Biologie François Jacob, IRCM/SIGRR/LTR, INSERM U1274, Université Paris-Saclay, CEA Paris-Saclay, Paris, France.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Florian Roisné-Hamelin
- Institut de Biologie François Jacob, IRCM/SIGRR/LTR, INSERM U1274, Université Paris-Saclay, CEA Paris-Saclay, Paris, France.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Tristan Bitard-Feildel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Alexis Lamiable
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Stéphane Marcand
- Institut de Biologie François Jacob, IRCM/SIGRR/LTR, INSERM U1274, Université Paris-Saclay, CEA Paris-Saclay, Paris, France.,Sorbonne Université, UMR CNRS 7238, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France.,Sorbonne Université, UMR CNRS 7238, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
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Lopez V, Barinova N, Onishi M, Pobiega S, Pringle JR, Dubrana K, Marcand S. Cytokinesis breaks dicentric chromosomes preferentially at pericentromeric regions and telomere fusions. Genes Dev 2015; 29:322-36. [PMID: 25644606 PMCID: PMC4318148 DOI: 10.1101/gad.254664.114] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Dicentric chromosomes are unstable products of erroneous DNA repair events that can lead to further genome rearrangements and extended gene copy number variations. Lopez et al. find that dicentrics without internal telomere sequences preferentially break at pericentromeric regions. In all cases, cleavage does not occur in anaphase but instead requires cytokinesis. Dicentrics cause the spindle pole bodies and centromeres to relocate to the bud neck during cytokinesis, explaining how cytokinesis can sever dicentrics near centromeres. Dicentric chromosomes are unstable products of erroneous DNA repair events that can lead to further genome rearrangements and extended gene copy number variations. During mitosis, they form anaphase bridges, resulting in chromosome breakage by an unknown mechanism. In budding yeast, dicentrics generated by telomere fusion break at the fusion, a process that restores the parental karyotype and protects cells from rare accidental telomere fusion. Here, we observed that dicentrics lacking telomere fusion preferentially break within a 25- to 30-kb-long region next to the centromeres. In all cases, dicentric breakage requires anaphase exit, ruling out stretching by the elongated mitotic spindle as the cause of breakage. Instead, breakage requires cytokinesis. In the presence of dicentrics, the cytokinetic septa pinch the nucleus, suggesting that dicentrics are severed after actomyosin ring contraction. At this time, centromeres and spindle pole bodies relocate to the bud neck, explaining how cytokinesis can sever dicentrics near centromeres.
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Affiliation(s)
- Virginia Lopez
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - Natalja Barinova
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - Masayuki Onishi
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Sabrina Pobiega
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - John R Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Karine Dubrana
- UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France; Laboratoire Instabilité Génétique et Organisation Nucléaire, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France
| | - Stéphane Marcand
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France;
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9
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Abstract
The telomeres of eukaryotes are stable open double-strand ends that coexist with nonhomologous end joining (NHEJ), the repair pathway that directly ligates DNA ends generated by double-strand breaks. Since a single end-joining event between 2 telomeres generates a circular chromosome or an unstable dicentric chromosome, NHEJ must be prevented from acting on telomeres. Multiple mechanisms mediated by telomere factors act in synergy to achieve this inhibition.
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Affiliation(s)
- Stéphane Marcand
- CEA; DSV/IRCM/SIGRR/LTR; Fontenay-aux-roses; France; INSERM UMR 967; Fontenay-aux-roses; France
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10
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Lescasse R, Pobiega S, Callebaut I, Marcand S. End-joining inhibition at telomeres requires the translocase and polySUMO-dependent ubiquitin ligase Uls1. EMBO J 2013; 32:805-15. [PMID: 23417015 DOI: 10.1038/emboj.2013.24] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 01/21/2013] [Indexed: 11/09/2022] Open
Abstract
In eukaryotes, permanent inhibition of the non-homologous end joining (NHEJ) repair pathway at telomeres ensures that chromosome ends do not fuse. In budding yeast, binding of Rap1 to telomere repeats establishes NHEJ inhibition. Here, we show that the Uls1 protein is required for the maintenance of NHEJ inhibition at telomeres. Uls1 protein is a non-essential Swi2/Snf2-related translocase and a Small Ubiquitin-related Modifier (SUMO)-Targeted Ubiquitin Ligase (STUbL) with unknown targets. Loss of Uls1 results in telomere-telomere fusions. Uls1 requirement is alleviated by the absence of poly-SUMO chains and by rap1 alleles lacking SUMOylation sites. Furthermore, Uls1 limits the accumulation of Rap1 poly-SUMO conjugates. We propose that one of Uls1 functions is to clear non-functional poly-SUMOylated Rap1 molecules from telomeres to ensure the continuous efficiency of NHEJ inhibition. Since Uls1 is the only known STUbL with a translocase activity, it can be the general molecular sweeper for the clearance of poly-SUMOylated proteins on DNA in eukaryotes.
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Affiliation(s)
- Rachel Lescasse
- CEA, Direction des sciences du vivant/Institut de radiobiologie cellulaire et moléculaire/Service instabilité génétique réparation recombinaison/Laboratoire télomère et réparation du chromosome, Fontenay-aux-roses, France
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11
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Abstract
Nonhomologous end-joining (NHEJ) inhibition at telomeres ensures that native chromosome ends do not fuse together. But the occurrence and consequences of rare telomere fusions are not well understood. It is notably unclear whether a telomere fusion could be processed to restore telomere ends. Here we address the behavior of individual dicentrics formed by telomere fusion in the yeast Saccharomyces cerevisiae. Our approach was to first stabilize and amplify fusions between two chromosomes by temporarily inactivating one centromere. Next we analyzed dicentric breakage following centromere reactivation. Unexpectedly, dicentrics often break at the telomere fusions during progression through mitosis, a process that restores the parental chromosomes. This unforeseen result suggests a rescue pathway able to process telomere fusions and to back up NHEJ inhibition at telomeres.
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Affiliation(s)
- Sabrina Pobiega
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Service Instabilité Génétique Réparation et Recombinaison, Laboratoire Télmère et Réparation du Chromosome, Fontenay-aux-roses 92260, France
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12
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Abstract
The nonhomologous end-joining (NHEJ) repair pathway is inhibited at telomeres, preventing chromosome fusion. In budding yeast Saccharomyces cerevisiae, the Rap1 protein directly binds the telomere sequences and is required for NHEJ inhibition. Here we show that the Rap1 C-terminal domain establishes two parallel inhibitory pathways through the proteins Rif2 and Sir4. In addition, the central domain of Rap1 inhibits NHEJ independently of Rif2 and Sir4. Thus, Rap1 establishes several independent pathways to prevent telomere fusions. We discuss a possible mechanism that would explain Rif2 multifunctionality at telomeres and the recent evolutionary origin of Rif2 from an origin recognition complex (ORC) subunit.
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Affiliation(s)
- Stéphane Marcand
- Centre National de la Recherche Scientifque UMR 217, Institut de Radiobiologie Cellulaire et Moléculaire, CEA/Fontenay, 92265 Fontenay-aux-roses cedex, France.
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13
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Abstract
In yeast, the nonhomologous end joining pathway (NHEJ) mobilizes the DNA polymerase Pol4 to repair DNA double-strand breaks when gap filling is required prior to ligation. Using telomere-telomere fusions caused by loss of the telomeric protein Rap1 and double-strand break repair on transformed DNA as assays for NHEJ between fully uncohesive ends, we show that Pol4 is able to extend a 3'-end whose last bases are mismatched, i.e., mispaired or unpaired, to the template strand.
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Affiliation(s)
- Benjamin Pardo
- Laboratoire de Radiobiologie de l'ADN, Service de Radiobiologie Moléculaire et Cellulaire, UMR217 du CNRS, CEA/Fontenay, Fontenay-aux-Roses, France
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14
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Abstract
Telomeres protect chromosomes from end-to-end fusions. In yeast Saccharomyces cerevisiae, the protein Rap1 directly binds telomeric DNA. Here, we use a new conditional allele of RAP1 and show that Rap1 loss results in frequent fusions between telomeres. Analysis of the fusion point with restriction enzymes indicates that fusions occur between telomeres of near wild-type length. Telomere fusions are not observed in cells lacking factors required for nonhomologous end joining (NHEJ), including Lig4 (ligase IV), KU and the Mre11 complex. SAE2 and TEL1 do not affect the frequency of fusions. Together, these results show that Rap1 is essential to block NHEJ between telomeres. Since the presence of Rap1 at telomeres has been conserved through evolution, the establishment of NHEJ suppression by Rap1 could be universal.
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Affiliation(s)
- Benjamin Pardo
- Laboratoire de Radiobiologie de l'ADN, Service de Radiobiologie Moléculaire et Cellulaire, CEA/Fontenay, Fontenay aux Roses, France
- Laboratoire du Contrôle du Cycle Cellulaire, Service de Biochimie et de Génétique Moléculaire, CEA/Saclay, Gif sur Yvette, France
| | - Stéphane Marcand
- Laboratoire de Radiobiologie de l'ADN, Service de Radiobiologie Moléculaire et Cellulaire, CEA/Fontenay, Fontenay aux Roses, France
- Laboratoire du Contrôle du Cycle Cellulaire, Service de Biochimie et de Génétique Moléculaire, CEA/Saclay, Gif sur Yvette, France
- CEA/Far, UMR217-DSV/DRR/SRMC Laboratoire de Radiobiologie de l'ADN, 92265 Fontenay aux Roses Cedex, France. Tel.: +33 1 46 54 82 33; Fax: +33 1 46 54 91 80; E-mail:
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15
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Abstract
The stability of DNA ends generated by the HO endonuclease in yeast is surprisingly high with a half-life of more than an hour. This transient stability is unaffected by mutations that abolish nonhomologous end joining (NHEJ). The unprocessed ends interact with Yku70p and Yku80p, two proteins required for NHEJ, but not significantly with Rad52p, a protein involved in homologous recombination (HR). Repair of a double-strand break by NHEJ is unaffected by the possibility of HR, although the use of HR is increased in NHEJ-defective cells. Partial in vitro 5' strand processing suppresses NHEJ but not HR. These results show that NHEJ precedes HR temporally, and that the availability of substrate dictates the particular pathway used. We propose that transient stability of DNA ends is a foundation for the permanent stability of telomeres.
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Affiliation(s)
- Marie Frank-Vaillant
- Laboratoire du Cycle Cellulaire, Service de Biochimie et de Génétique Moléculaire, CEA/Saclay, 91191 Gif sur Yvette Cedex, France
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16
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Abstract
In the yeast Saccharomyces cerevisiae, DNA double strand break (DSB) repair by nonhomologous end-joining (NHEJ) requires the DNA end-binding heterodimer Yku70p-Yku80p and the ligase Dnl4p associated with its cofactor Lif1p. NHEJ efficiency is down-regulated in MATa/MATalpha cells relative to MATa or MATalpha cells, but the mechanism of this mating type regulation is unknown. Here we report the identification of Lif2p, a S. cerevisiae protein that interacts with Lif1p in a two-hybrid system. Disruption of LIF2 abolishes the capacity of cells to repair DSBs by end-joining to the same extent than lif1 and dnl4 mutants. In MATa/MATalpha cells, Lif2p steady-state level is strongly repressed when other factors involved in NHEJ are unaffected. Increasing the dosage of the Lif2p protein can suppress the NHEJ defect in a/alpha cells. Together, these results indicate that NHEJ regulation by mating type is achieved, at least in part, by a regulation of Lif2p activity.
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Affiliation(s)
- M Frank-Vaillant
- Laboratoire du cycle cellulaire, Service de biochimie et de génétique moléculaire, CEA/Saclay, 91191 Gif sur Yvette cedex, France
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17
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Abstract
Telomere elongation by telomerase balances the progressive shortening of chromosome ends due to the succession of replication cycles [1] [2]. Telomerase activity is regulated in vivo at its site of action by the telomere itself. In yeast and human cells, the mean telomere length is maintained at a constant value through a cis-inhibition of telomerase by factors specifically bound to the telomeric DNA [3] [4] [5] [6] [7]. Here, we address an unexplored aspect of telomerase regulation by testing the link between telomere dynamics and cell cycle progression in the budding yeast Saccharomyces cerevisiae. We followed the elongation of an abnormally shortened telomere and observed that, like telomere shortening in the absence of telomerase, telomere elongation is linked to the succession of cell divisions. In cells progressing synchronously through the cell cycle, telomere elongation coincided with the time of telomere replication. On a minichromosome, a replication defect partially suppressed telomere elongation, suggesting a coupling between in vivo telomerase activity and conventional DNA replication.
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Affiliation(s)
- S Marcand
- CEA/Saclay, Laboratoire de Biologie Moléculaire et Cellulaire, UMR5665 CNRS/ENSL, Service de Biochimie et de Génétique Moléculaire, Ecole Normale Supérieure de Lyon, France.
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18
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Abstract
In yeast, the constant length of telomeric DNA results from a negative regulation of telomerase by the telomere itself. Here we follow the return to equilibrium of an abnormally shortened telomere. We observe that telomere elongation is restricted to a few base pairs per generation and that its rate decreases progressively with increasing telomere length. In contrast, in the absence of telomerase or in the presence of an over-elongated telomere, the degradation rate linked to the succession of generations appears to be constant, i.e. independent of telomere length. Together, these results indicate that telomerase is gradually inhibited at its site of action by the elongating telomere. The implications of this finding for the dynamics of telomere length regulation are discussed in this study.
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Affiliation(s)
- S Marcand
- Laboratoire de Biologie Moléculaire et Cellulaire, Ecole Normale Supérieure de Lyon, UMR8510 CNRS/ENSL, 69364 Lyon Cedex 07, France
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19
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Abstract
Telomere length in the yeast Saccharomyces cerevisiae is under stringent genetic control such that a narrow length distribution of TG1-3 repeats is observed. Previous studies have shown that Rap1p, which binds to the double-stranded telomeric repeats, plays a role in regulating repeat length: point mutations in the Rap1p C-terminus often result in a higher average telomere length and deletion of this region causes extreme telomere elongation. We have investigated further the role of Rap1p in this process. Our results suggest that telomere length is regulated by a negative feedback mechanism that can sense the number of Rap1p molecules bound at the chromosome end. This length regulatory mechanism requires two other proteins, Rif1p and Rif2p, that interact with each other and with the Rap1p C-terminus. Although the same C-terminal domain of Rap1p is also involved in the initiation of telomere position effect (telomeric transcriptional silencing), this Rap1p function appears to be separate from, and indeed antagonistic to, its role in telomere length regulation.
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Affiliation(s)
- S Marcand
- Department of Microbiology, College of Physicians & Surgeons of Columbia University, NY 10032, USA
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20
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Abstract
In budding yeast, the DNA-binding protein Rap1p orchestrates a negative feedback on regulation of telomere length and the organization of a heterochromatin-like telomeric compartment. Recent studies have led to the identification of functionally related telomeric proteins from fission yeast and mammals. These advances underline the key role played by the proteins that bind to the duplex part of telomeric DNA and reveal an important structural diversity among telomeric proteins.
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21
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Abstract
In the yeast Saccharomyces cerevisiae, telomere elongation is negatively regulated by the telomere repeat-binding protein Rap1p, such that a narrow length distribution of telomere repeat tracts is observed. This length regulation was shown to function independently of the orientation of the telomere repeats. The number of repeats at an individual telomere was reduced when hybrid proteins containing the Rap1p carboxyl terminus were targeted there by a heterologous DNA-binding domain. The extent of this telomere tract shortening was proportional to the number of targeted molecules, consistent with a feedback mechanism of telomere length regulation that can discriminate the precise number of Rap1p molecules bound to the chromosome end.
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Affiliation(s)
- S Marcand
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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22
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Marcand S, Brun B, Ancelin K, Gilson E. Les télomères : du normal au pathologique. Med Sci (Paris) 1997. [DOI: 10.4267/10608/543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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23
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Abstract
Recent findings indicate that heterochromatin serves as a molecular sink for factors involved in chromatin-mediated repression of gene expression; long-range interactions that position a euchromatic gene near a heterochromatin domain influence its susceptibility to transcriptional silencing.
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Affiliation(s)
- S Marcand
- Laboratoire de Biologie Moléculaire et Cellulaire, l'Ecole Normale Supérieure de Lyon, UMR49 CNRS/ENS, France
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24
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Maillet L, Boscheron C, Gotta M, Marcand S, Gilson E, Gasser SM. Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev 1996; 10:1796-811. [PMID: 8698239 DOI: 10.1101/gad.10.14.1796] [Citation(s) in RCA: 230] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Transcriptional repression at the silent mating-type loci in yeast requires the targeting of silent information regulator (Sir) proteins through specific interactions formed at cis-acting silencer elements. We show here that a reporter gene flanked by two functional silencers is not repressed when integrated at >200 kb from a telomere. Repression is restored by creation of a new telomere 13 kb from the integrated reporter or by elevated expression of SIR1, SIR3, and/or SIR4. Coupled expression represses in an additive manner, suggesting that all three factors are in limiting concentrations. When overexpressed, Sir3 and Sir4 are dispersed throughout the nucleoplasm, in contrast to wild-type cells where they are clustered in a limited number of foci together with telomeres. Efficient silencer function thus seems to require either proximity to a pool of concentrated Sir proteins, that is, proximity to telomeres, or delocalization of the silencing factors.
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Affiliation(s)
- L Maillet
- Laboratoire de Biologie Moléculaire et Cellulaire de l'Ecole Normale Supérieure de Lyon, France
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25
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Marcand S, Buck SW, Moretti P, Gilson E, Shore D. Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap 1 protein. Genes Dev 1996; 10:1297-309. [PMID: 8647429 DOI: 10.1101/gad.10.11.1297] [Citation(s) in RCA: 143] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Rap1p binds to silencer elements and telomeric repeats in yeast, where it appears to initiate silencing by recruiting Sir3p and Sir4p to the chromosome through interactions with its carboxy-terminal domain. Sir3p and Sir4p interact in vitro with histones H3 and H4 and are likely to be structural components of silent chromatin. We show that targeting of these Sir proteins to the chromosome is sufficient to initiate stable silencing either at a silent mating-type locus lacking a functional silencer element or at a telomere in a strain in which the Rap1p carboxy-terminal silencing domain has been deleted. Silencing by Sir protein targeting can also be initiated at a telomere-proximal site (ADH4), but is much weaker at an internal chromosomal locus (LYS2). Strikingly, deletion of the Rap1p silencing domain, which abolishes telomeric silencing, improves targeted silencing at LYS2 by both Sir3p and Sir4p, while weakening the silencing activity of these proteins at or near a telomere. This effect may result from the release of Sir proteins from the telomeres, thus increasing their effective concentration at other chromosomal sites. We suggest that telomeres and Rap1p serve a regulatory role in sequestering Sir proteins at telomeres, controlling silencing at other loci in trans and preventing indiscriminate gene silencing throughout the genome.
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Affiliation(s)
- S Marcand
- Department of Microbiology, College of Physicians and Surgeons of Columbia University, New York, New York 10032, USA
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Boscheron C, Maillet L, Marcand S, Tsai-Pflugfelder M, Gasser SM, Gilson E. Cooperation at a distance between silencers and proto-silencers at the yeast HML locus. EMBO J 1996; 15:2184-95. [PMID: 8641284 PMCID: PMC450142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Transcriptional repression at the silent yeast mating type loci is achieved through the formation of a particular nucleoprotein complex at specific cis-acting elements called silencers. This complex in turn appears to initiate the spreading of a histone binding protein complex into the surrounding chromatin, which restricts accessibility of the region to the transcription machinery. We have investigated long-range, cooperative effects between silencers by studying the repression of a reporter gene integrated at the HML locus flanked by various combinations of wild-type and mutated silencer sequences. Two silencers can cooperate over >4000 bp to repress transcription efficiently. More importantly, a single binding site for either the repressor activator protein 1 (Rap1), the autonomous replicating sequence (ARS) binding factor 1 (Abf1) or the origin recognition complex (ORC) can enhance the action of a distant silencer without acting as a silencer on its own. Functional cooperativity is demonstrated using a quantitative assay for repression, and varies with the affinity of the binding sites used. Since the repression mechanism is Sir dependent, the Rap1, ORC and/or Abf1 proteins bound to distant DNA elements may interact to create an interface of sufficiently high affinity such that Sir-containing complexes bind, nucleating the silent chromatin state.
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Boscheron C, Maillet L, Marcand S, Tsai-Pflugfelder M, Gasser SM, Gilson E. Cooperation at a distance between silencers and proto-silencers at the yeast HML locus. EMBO J 1996. [DOI: 10.1002/j.1460-2075.1996.tb00572.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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