1
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Padmanaban S, Lambacher NJ, Tesmer VM, Zhang J, Shibuya H, Nandakumar J. Caenorhabditis elegans telomere-binding proteins TEBP-1 and TEBP-2 adapt the Myb module to dimerize and bind telomeric DNA. Proc Natl Acad Sci U S A 2024; 121:e2316651121. [PMID: 38588418 PMCID: PMC11032478 DOI: 10.1073/pnas.2316651121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/17/2024] [Indexed: 04/10/2024] Open
Abstract
Protecting chromosome ends from misrecognition as double-stranded (ds) DNA breaks is fundamental to eukaryotic viability. The protein complex shelterin prevents a DNA damage response at mammalian telomeres. Mammalian shelterin proteins TRF1 and TRF2 and their homologs in yeast and protozoa protect telomeric dsDNA. N-terminal homodimerization and C-terminal Myb-domain-mediated dsDNA binding are two structural hallmarks of end protection by TRF homologs. Yet our understanding of how Caenorhabditis elegans protects its telomeric dsDNA is limited. Recently identified C. elegans proteins TEBP-1 (also called DTN-1) and TEBP-2 (also called DTN-2) are functional homologs of TRF proteins, but how they bind DNA and whether or how they dimerize is not known. TEBP-1 and TEBP-2 harbor three Myb-containing domains (MCDs) and no obvious dimerization domain. We demonstrate biochemically that only the third MCD binds DNA. We solve the X-ray crystal structure of TEBP-2 MCD3 with telomeric dsDNA to reveal the structural mechanism of telomeric dsDNA protection in C. elegans. Mutagenesis of the DNA-binding site of TEBP-1 and TEBP-2 compromises DNA binding in vitro, and increases DNA damage signaling, lengthens telomeres, and decreases brood size in vivo. Via an X-ray crystal structure, biochemical validation of the dimerization interface, and SEC-MALS analysis, we demonstrate that MCD1 and MCD2 form a composite dimerization module that facilitates not only TEBP-1 and TEBP-2 homodimerization but also heterodimerization. These findings provide fundamental insights into C. elegans telomeric dsDNA protection and highlight how different eukaryotes have evolved distinct strategies to solve the chromosome end protection problem.
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Affiliation(s)
- Shilpa Padmanaban
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI48109
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Nils J. Lambacher
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden41390
| | - Valerie M. Tesmer
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI48109
| | - Jingjing Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden41390
| | - Hiroki Shibuya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden41390
- Laboratory for Gametogenesis, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI48109
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2
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Casari E, Gnugnoli M, Rinaldi C, Pizzul P, Colombo CV, Bonetti D, Longhese MP. To Fix or Not to Fix: Maintenance of Chromosome Ends Versus Repair of DNA Double-Strand Breaks. Cells 2022; 11:cells11203224. [PMID: 36291091 PMCID: PMC9601279 DOI: 10.3390/cells11203224] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 02/08/2023] Open
Abstract
Early work by Muller and McClintock discovered that the physical ends of linear chromosomes, named telomeres, possess an inherent ability to escape unwarranted fusions. Since then, extensive research has shown that this special feature relies on specialized proteins and structural properties that confer identity to the chromosome ends, thus allowing cells to distinguish them from intrachromosomal DNA double-strand breaks. Due to the inability of conventional DNA replication to fully replicate the chromosome ends and the downregulation of telomerase in most somatic human tissues, telomeres shorten as cells divide and lose this protective capacity. Telomere attrition causes the activation of the DNA damage checkpoint that leads to a cell-cycle arrest and the entering of cells into a nondividing state, called replicative senescence, that acts as a barrier against tumorigenesis. However, downregulation of the checkpoint overcomes this barrier and leads to further genomic instability that, if coupled with re-stabilization of telomeres, can drive tumorigenesis. This review focuses on the key experiments that have been performed in the model organism Saccharomyces cerevisiae to uncover the mechanisms that protect the chromosome ends from eliciting a DNA damage response, the conservation of these pathways in mammals, as well as the consequences of their loss in human cancer.
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3
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Michael AK, Thomä NH. Reading the chromatinized genome. Cell 2021; 184:3599-3611. [PMID: 34146479 DOI: 10.1016/j.cell.2021.05.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
Eukaryotic DNA-binding proteins operate in the context of chromatin, where nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around a histone core, thereby rendering a large fraction of the DNA surface inaccessible to DNA-binding proteins. Nevertheless, first responders in DNA repair and sequence-specific transcription factors bind DNA target sites obstructed by chromatin. While early studies examined protein binding to histone-free DNA, it is only now beginning to emerge how DNA sequences are interrogated on nucleosomes. These readout strategies range from the release of nucleosomal DNA from histones, to rotational/translation register shifts of the DNA motif, and nucleosome-specific DNA binding modes that differ from those observed on naked DNA. Since DNA motif engagement on nucleosomes strongly depends on position and orientation, we argue that motif location and nucleosome positioning co-determine protein access to DNA in transcription and DNA repair.
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Affiliation(s)
- Alicia K Michael
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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4
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Galli M, Frigerio C, Longhese MP, Clerici M. The regulation of the DNA damage response at telomeres: focus on kinases. Biochem Soc Trans 2021; 49:933-943. [PMID: 33769480 DOI: 10.1042/bst20200856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/17/2022]
Abstract
The natural ends of linear chromosomes resemble those of accidental double-strand breaks (DSBs). DSBs induce a multifaceted cellular response that promotes the repair of lesions and slows down cell cycle progression. This response is not elicited at chromosome ends, which are organized in nucleoprotein structures called telomeres. Besides counteracting DSB response through specialized telomere-binding proteins, telomeres also prevent chromosome shortening. Despite of the different fate of telomeres and DSBs, many proteins involved in the DSB response also localize at telomeres and participate in telomere homeostasis. In particular, the DSB master regulators Tel1/ATM and Mec1/ATR contribute to telomere length maintenance and arrest cell cycle progression when chromosome ends shorten, thus promoting a tumor-suppressive process known as replicative senescence. During senescence, the actions of both these apical kinases and telomere-binding proteins allow checkpoint activation while bulk DNA repair activities at telomeres are still inhibited. Checkpoint-mediated cell cycle arrest also prevents further telomere erosion and deprotection that would favor chromosome rearrangements, which are known to increase cancer-associated genome instability. This review summarizes recent insights into functions and regulation of Tel1/ATM and Mec1/ATR at telomeres both in the presence and in the absence of telomerase, focusing mainly on discoveries in budding yeast.
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Affiliation(s)
- Michela Galli
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Chiara Frigerio
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
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5
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Bonetti D, Rinaldi C, Vertemara J, Notaro M, Pizzul P, Tisi R, Zampella G, Longhese MP. DNA binding modes influence Rap1 activity in the regulation of telomere length and MRX functions at DNA ends. Nucleic Acids Res 2020; 48:2424-2441. [PMID: 31879780 PMCID: PMC7049697 DOI: 10.1093/nar/gkz1203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 12/09/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023] Open
Abstract
The cellular response to DNA double-strand breaks (DSBs) is initiated by the Mre11–Rad50–Xrs2 (MRX) complex that has structural and catalytic functions. MRX association at DSBs is counteracted by Rif2, which is known to interact with Rap1 that binds telomeric DNA through two tandem Myb-like domains. Whether and how Rap1 acts at DSBs is unknown. Here we show that Rif2 inhibits MRX association to DSBs in a manner dependent on Rap1, which binds to DSBs and promotes Rif2 association to them. Rap1 in turn can negatively regulate MRX function at DNA ends also independently of Rif2. In fact, a characterization of Rap1 mutant variants shows that Rap1 binding to DNA through both Myb-like domains results in formation of Rap1-DNA complexes that control MRX functions at both DSBs and telomeres primarily through Rif2. By contrast, Rap1 binding to DNA through a single Myb-like domain results in formation of high stoichiometry complexes that act at DNA ends mostly in a Rif2-independent manner. Altogether these findings indicate that the DNA binding modes of Rap1 influence its functional properties, thus highlighting the structural plasticity of this protein.
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Affiliation(s)
- Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Carlo Rinaldi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Jacopo Vertemara
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Marco Notaro
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Paolo Pizzul
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Renata Tisi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Giuseppe Zampella
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
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6
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Mivelaz M, Cao AM, Kubik S, Zencir S, Hovius R, Boichenko I, Stachowicz AM, Kurat CF, Shore D, Fierz B. Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor. Mol Cell 2019; 77:488-500.e9. [PMID: 31761495 PMCID: PMC7005674 DOI: 10.1016/j.molcel.2019.10.025] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/09/2019] [Accepted: 10/16/2019] [Indexed: 02/03/2023]
Abstract
Pioneer transcription factors (pTFs) bind to target sites within compact chromatin, initiating chromatin remodeling and controlling the recruitment of downstream factors. The mechanisms by which pTFs overcome the chromatin barrier are not well understood. Here, we reveal, using single-molecule fluorescence, how the yeast transcription factor Rap1 invades and remodels chromatin. Using a reconstituted chromatin system replicating yeast promoter architecture, we demonstrate that Rap1 can bind nucleosomal DNA within a chromatin fiber but with shortened dwell times compared to naked DNA. Moreover, we show that Rap1 binding opens chromatin fiber structure by inhibiting inter-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to displace promoter nucleosomes, paving the way for long-lived bound states on newly exposed DNA. Together, our results provide a mechanistic view of how Rap1 gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression. The yeast transcription factor Rap1 can invade compact chromatin Rap1 directly opens chromatin structure by preventing nucleosome stacking Stable Rap1 binding requires collaboration with RSC to shift promoter nucleosomes
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Affiliation(s)
- Maxime Mivelaz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Anne-Marinette Cao
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Sevil Zencir
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Ruud Hovius
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Iuliia Boichenko
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Anna Maria Stachowicz
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Christoph F Kurat
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Beat Fierz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland.
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7
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Hailemariam S, De Bona P, Galletto R, Hohl M, Petrini JH, Burgers PM. The telomere-binding protein Rif2 and ATP-bound Rad50 have opposing roles in the activation of yeast Tel1 ATM kinase. J Biol Chem 2019; 294:18846-18852. [PMID: 31640985 DOI: 10.1074/jbc.ra119.011077] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/11/2019] [Indexed: 11/06/2022] Open
Abstract
Saccharomyces cerevisiae Tel1 is the ortholog of human ATM kinase and initiates a cell cycle checkpoint in response to dsDNA breaks (DSBs). Tel1ATM kinase is activated synergistically by naked dsDNA and the Mre11-Rad50-Xrs2NBS1 complex (MRX). A multisubunit protein complex, which is related to human shelterin, protects telomeres from being recognized as DSBs, thereby preventing a Tel1ATM checkpoint response. However, at very short telomeres, Tel1ATM can be recruited and activated by the MRX complex, resulting in telomere elongation. Conversely, at long telomeres, Rap1-interacting-factor 2 (Rif2) is instrumental in suppressing Tel1 activity. Here, using an in vitro reconstituted Tel1 kinase activation assay, we show that Rif2 inhibits MRX-dependent Tel1 kinase activity. Rif2 discharges the ATP-bound form of Rad50, which is essential for all MRX-dependent activities. This conclusion is further strengthened by experiments with a Rad50 allosteric ATPase mutant that maps outside the conserved ATP binding pocket. We propose a model in which Rif2 attenuates Tel1 activity at telomeres by acting directly on Rad50 and discharging its activated ATP-bound state, thereby rendering the MRX complex incompetent for Tel1 activation. These findings expand our understanding of the mechanism by which Rif2 controls telomere length.
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Affiliation(s)
- Sarem Hailemariam
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110
| | - Paolo De Bona
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110.
| | - Marcel Hohl
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - John H Petrini
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110.
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8
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Singh SP, Kukshal V, De Bona P, Antony E, Galletto R. The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers. Nucleic Acids Res 2019; 46:7193-7205. [PMID: 29931186 PMCID: PMC6101547 DOI: 10.1093/nar/gky530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/04/2018] [Indexed: 01/29/2023] Open
Abstract
Rim1 is the mitochondrial single-stranded DNA binding protein in Saccharomyces cerevisiae and functions to coordinate replication and maintenance of mtDNA. Rim1 can form homo-tetramers in solution and this species has been assumed to be solely responsible for ssDNA binding. We solved structures of tetrameric Rim1 in two crystals forms which differ in the relative orientation of the dimers within the tetramer. In testing whether the different arrangement of the dimers was due to formation of unstable tetramers, we discovered that while Rim1 forms tetramers at high protein concentration, it dissociates into a smaller oligomeric species at low protein concentrations. A single point mutation at the dimer-dimer interface generates stable dimers and provides support for a dimer-tetramer oligomerization model. The presence of Rim1 dimers in solution becomes evident in DNA binding studies using short ssDNA substrates. However, binding of the first Rim1 dimer is followed by binding of a second dimer, whose affinity depends on the length of the ssDNA. We propose a model where binding of DNA to a dimer of Rim1 induces tetramerization, modulated by the ability of the second dimer to interact with ssDNA.
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Affiliation(s)
- Saurabh P Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Vandna Kukshal
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Paolo De Bona
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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9
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Challal D, Barucco M, Kubik S, Feuerbach F, Candelli T, Geoffroy H, Benaksas C, Shore D, Libri D. General Regulatory Factors Control the Fidelity of Transcription by Restricting Non-coding and Ectopic Initiation. Mol Cell 2019; 72:955-969.e7. [PMID: 30576657 DOI: 10.1016/j.molcel.2018.11.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/29/2018] [Accepted: 11/29/2018] [Indexed: 10/27/2022]
Abstract
The fidelity of transcription initiation is essential for accurate gene expression, but the determinants of start site selection are not fully understood. Rap1 and other general regulatory factors (GRFs) control the expression of many genes in yeast. We show that depletion of these factors induces widespread ectopic transcription initiation within promoters. This generates many novel non-coding RNAs and transcript isoforms with diverse stability, drastically altering the coding potential of the transcriptome. Ectopic transcription initiation strongly correlates with altered nucleosome positioning. We provide evidence that Rap1 can suppress ectopic initiation by a "place-holder" mechanism whereby it physically occludes inappropriate sites for pre-initiation complex formation. These results reveal an essential role for GRFs in the fidelity of transcription initiation and in the suppression of pervasive transcription, profoundly redefining current models for their function. They have important implications for the mechanism of transcription initiation and the control of gene expression.
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Affiliation(s)
- Drice Challal
- Institut Jacques Monod, Centre National de la Recherche Scientifique, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France; Université Paris Saclay, Ecole doctorale Structure et Dynamique des Systèmes Vivants, 91190 Gif sur Yvette, France
| | - Mara Barucco
- Institut Jacques Monod, Centre National de la Recherche Scientifique, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGe3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Frank Feuerbach
- Institut Pasteur, Centre National de la Recherche Scientifique, UMR3525 Paris, France
| | - Tito Candelli
- Princess Máxima Center for Pediatric Oncology, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Hélène Geoffroy
- Institut Jacques Monod, Centre National de la Recherche Scientifique, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Chaima Benaksas
- Institut Jacques Monod, Centre National de la Recherche Scientifique, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGe3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Domenico Libri
- Institut Jacques Monod, Centre National de la Recherche Scientifique, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France.
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10
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Červenák F, Juríková K, Sepšiová R, Neboháčová M, Nosek J, Tomáška L. Double-stranded telomeric DNA binding proteins: Diversity matters. Cell Cycle 2017; 16:1568-1577. [PMID: 28749196 DOI: 10.1080/15384101.2017.1356511] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Telomeric sequences constitute only a small fraction of the whole genome yet they are crucial for ensuring genomic stability. This function is in large part mediated by protein complexes recruited to telomeric sequences by specific telomere-binding proteins (TBPs). Although the principal tasks of nuclear telomeres are the same in all eukaryotes, TBPs in various taxa exhibit a surprising diversity indicating their distinct evolutionary origin. This diversity is especially pronounced in ascomycetous yeasts where they must have co-evolved with rapidly diversifying sequences of telomeric repeats. In this article we (i) provide a historical overview of the discoveries leading to the current list of TBPs binding to double-stranded (ds) regions of telomeres, (ii) describe examples of dsTBPs highlighting their diversity in even closely related species, and (iii) speculate about possible evolutionary trajectories leading to a long list of various dsTBPs fulfilling the same general role(s) in their own unique ways.
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Affiliation(s)
- Filip Červenák
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Katarína Juríková
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Regina Sepšiová
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Martina Neboháčová
- b Department of Biochemistry , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Jozef Nosek
- b Department of Biochemistry , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - L'ubomír Tomáška
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
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11
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Feldmann EA, De Bona P, Galletto R. The wrapping loop and Rap1 C-terminal (RCT) domain of yeast Rap1 modulate access to different DNA binding modes. J Biol Chem 2015; 290:11455-66. [PMID: 25805496 DOI: 10.1074/jbc.m115.637678] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Indexed: 11/06/2022] Open
Abstract
Budding yeast Rap1 is a specific double-stranded DNA-binding protein involved in repression and activation of gene transcription and in the establishment of the nucleoprotein complex formed at telomeres. The DNA-binding domain (DBD) of Rap1 forms a high affinity complex with DNA where both Myb-like domains bind to the recognition site. However, we recently showed that the DBD can also access an alternative, lower affinity DNA-binding mode where a single Myb-like domain binds. This results in Rap1-DNA complexes with stoichiometry higher than previously anticipated. In this work, we show that the ability of the DBD to form higher stoichiometry complexes on DNA is maintained also in larger Rap1 constructs. This indicates that transition between at least two DNA-binding modes is a general property of the protein and not a specific feature of the DBD in isolation. The transition between binding modes is modulated by the C-terminal wrapping loop within the DBD, consistent with the proposed model in which the transient opening of this region allows a switch between binding modes. Finally, we provide evidence that the Rap1 C terminus interacts with the DNA-binding domain, suggesting a complex network of interactions that couples changes in conformation of the protein to the binding of its DNA recognition sequence.
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Affiliation(s)
- Erik A Feldmann
- From the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Paolo De Bona
- From the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Roberto Galletto
- From the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110
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12
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Alternative arrangements of telomeric recognition sites regulate the binding mode of the DNA-binding domain of yeast Rap1. Biophys Chem 2015; 198:1-8. [PMID: 25637888 DOI: 10.1016/j.bpc.2015.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/02/2015] [Accepted: 01/02/2015] [Indexed: 01/17/2023]
Abstract
The function of yeast Rap1 as an activator in transcription, a repressor at silencer elements, and as a major component of the shelterin-like complex at telomeres requires the known high-affinity and specific interaction of the DNA-binding domain (DBD) with its recognition sequences. In addition to a high-affinity one-to-one complex with its DNA recognition site, Rap1(DBD) also forms lower affinity complexes with higher stoichiometries on DNA. We proposed that this originates from the ability of Rap1(DBD) to access at least two DNA-binding modes. In this work, we show that Rap1(DBD) binds in multiple binding modes to recognition sequences that contain different spacer lengths between the hemi-sites. We also provide evidence that in the singly-ligated complex Rap1(DBD) binds quite differently to these sequences. Rap1(DBD) also binds to a single half-site but does so using the alternative DNA-binding mode where only a single Myb-like domain interacts with DNA. We found that all arrangements of Rap1 sites tested are represented within the telomeric sequence and our data suggest that at telomeres Rap1 might form a nucleoprotein complex with a heterogeneous distribution of bound states.
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