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Heuzé J, Kemiha S, Barthe A, Vilarrubias AT, Aouadi E, Aiello U, Libri D, Lin Y, Lengronne A, Poli J, Pasero P. RNase H2 degrades toxic RNA:DNA hybrids behind stalled forks to promote replication restart. EMBO J 2023; 42:e113104. [PMID: 37855233 PMCID: PMC10690446 DOI: 10.15252/embj.2022113104] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/20/2022] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
R-loops represent a major source of replication stress, but the mechanism by which these structures impede fork progression remains unclear. To address this question, we monitored fork progression, arrest, and restart in Saccharomyces cerevisiae cells lacking RNase H1 and H2, two enzymes responsible for degrading RNA:DNA hybrids. We found that while RNase H-deficient cells could replicate their chromosomes normally under unchallenged growth conditions, their replication was impaired when exposed to hydroxyurea (HU) or methyl methanesulfonate (MMS). Treated cells exhibited increased levels of RNA:DNA hybrids at stalled forks and were unable to generate RPA-coated single-stranded (ssDNA), an important postreplicative intermediate in resuming replication. Similar impairments in nascent DNA resection and ssDNA formation at HU-arrested forks were observed in human cells lacking RNase H2. However, fork resection was fully restored by addition of triptolide, an inhibitor of transcription that induces RNA polymerase degradation. Taken together, these data indicate that RNA:DNA hybrids not only act as barriers to replication forks, but also interfere with postreplicative fork repair mechanisms if not promptly degraded by RNase H.
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Affiliation(s)
- Jonathan Heuzé
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Samira Kemiha
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Antoine Barthe
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Alba Torán Vilarrubias
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Elyès Aouadi
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Umberto Aiello
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Domenico Libri
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- Present address:
Institut de Génétique Moléculaire de MontpellierUniversité de Montpellier, CNRSMontpellierFrance
| | - Yea‐Lih Lin
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Armelle Lengronne
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Jérôme Poli
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Philippe Pasero
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
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2
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Heuzé J, Lin YL, Lengronne A, Poli J, Pasero P. Impact of R-loops on oncogene-induced replication stress in cancer cells. C R Biol 2023; 346:95-105. [PMID: 37779381 DOI: 10.5802/crbiol.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 10/03/2023]
Abstract
Replication stress is an alteration in the progression of replication forks caused by a variety of events of endogenous or exogenous origin. In precancerous lesions, this stress is exacerbated by the deregulation of oncogenic pathways, which notably disrupts the coordination between replication and transcription, and leads to genetic instability and cancer development. It is now well established that transcription can interfere with genome replication in different ways, such as head-on collisions between polymerases, accumulation of positive DNA supercoils or formation of R-loops. These structures form during transcription when nascent RNA reanneals with DNA behind the RNA polymerase, forming a stable DNA:RNA hybrid. In this review, we discuss how these different cotranscriptional processes disrupt the progression of replication forks and how they contribute to genetic instability in cancer cells.
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3
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Hurst V, Challa K, Jonas F, Forey R, Sack R, Seebacher J, Schmid CD, Barkai N, Shimada K, Gasser SM, Poli J. A regulatory phosphorylation site on Mec1 controls chromatin occupancy of RNA polymerases during replication stress. EMBO J 2021; 40:e108439. [PMID: 34569643 PMCID: PMC8561635 DOI: 10.15252/embj.2021108439] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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] [Received: 04/08/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 01/16/2023] Open
Abstract
Upon replication stress, budding yeast checkpoint kinase Mec1ATR triggers the downregulation of transcription, thereby reducing the level of RNA polymerase (RNAP) on chromatin to facilitate replication fork progression. Here, we identify a hydroxyurea-induced phosphorylation site on Mec1, Mec1-S1991, that contributes to the eviction of RNAPII and RNAPIII during replication stress. The expression of the non-phosphorylatable mec1-S1991A mutant reduces replication fork progression genome-wide and compromises survival on hydroxyurea. This defect can be suppressed by destabilizing chromatin-bound RNAPII through a TAP fusion to its Rpb3 subunit, suggesting that lethality in mec1-S1991A mutants arises from replication-transcription conflicts. Coincident with a failure to repress gene expression on hydroxyurea in mec1-S1991A cells, highly transcribed genes such as GAL1 remain bound at nuclear pores. Consistently, we find that nuclear pore proteins and factors controlling RNAPII and RNAPIII are phosphorylated in a Mec1-dependent manner on hydroxyurea. Moreover, we show that Mec1 kinase also contributes to reduced RNAPII occupancy on chromatin during an unperturbed S phase by promoting degradation of the Rpb1 subunit.
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Affiliation(s)
- Verena Hurst
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Kiran Challa
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Felix Jonas
- Departments of Molecular Genetics and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Ragna Sack
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Christoph D Schmid
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Naama Barkai
- Departments of Molecular Genetics and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
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4
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Kemiha S, Poli J, Lin YL, Lengronne A, Pasero P. Toxic R-loops: Cause or consequence of replication stress? DNA Repair (Amst) 2021; 107:103199. [PMID: 34399314 DOI: 10.1016/j.dnarep.2021.103199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 01/08/2023]
Abstract
Transcription-replication conflicts (TRCs) represent a potential source of endogenous replication stress (RS) and genomic instability in eukaryotic cells but the mechanisms that underlie this instability remain poorly understood. Part of the problem could come from non-B DNA structures called R-loops, which are formed of a RNA:DNA hybrid and a displaced ssDNA loop. In this review, we discuss different scenarios in which R-loops directly or indirectly interfere with DNA replication. We also present other types of TRCs that may not depend on R-loops to impede fork progression. Finally, we discuss alternative models in which toxic RNA:DNA hybrids form at stalled forks as a consequence - but not a cause - of replication stress and interfere with replication resumption.
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Affiliation(s)
- Samira Kemiha
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Jérôme Poli
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Yea-Lih Lin
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France.
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5
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Da Mota M, Cau J, Mateos-Langerak J, Lengronne A, Pasero P, Poli J. 3D positioning of tagged DNA loci by widefield and super-resolution fluorescence imaging of fixed yeast nuclei. STAR Protoc 2021; 2:100525. [PMID: 34027483 DOI: 10.1016/j.xpro.2021.100525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 11/19/2022] Open
Abstract
This protocol describes how to culture, image, and determine the nuclear position of a fluorescently tagged DNA locus in the 3D nucleoplasm of fixed Saccharomyces cerevisiae cells. Here, we propose a manual scoring method based on widefield images and an automated method based on 3D-SIM images. Yeast culture conditions have to be followed meticulously to get the best biological response in a given environment. For complete details on the use and execution of this protocol, please refer to Forey et al. (2020).
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Affiliation(s)
- Mégane Da Mota
- Institut de Génétique Humaine, CNRS, Université de Montpellier, 34396 Montpellier, France
| | - Julien Cau
- Institut de Génétique Humaine, CNRS, Université de Montpellier, 34396 Montpellier, France
| | - Julio Mateos-Langerak
- Institut de Génétique Humaine, CNRS, Université de Montpellier, 34396 Montpellier, France
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, 34396 Montpellier, France
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, 34396 Montpellier, France
| | - Jérôme Poli
- Institut de Génétique Humaine, CNRS, Université de Montpellier, 34396 Montpellier, France
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6
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Forey R, Barthe A, Tittel-Elmer M, Wery M, Barrault MB, Ducrot C, Seeber A, Krietenstein N, Szachnowski U, Skrzypczak M, Ginalski K, Rowicka M, Cobb JA, Rando OJ, Soutourina J, Werner M, Dubrana K, Gasser SM, Morillon A, Pasero P, Lengronne A, Poli J. A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization. Mol Cell 2020; 81:183-197.e6. [PMID: 33278361 DOI: 10.1016/j.molcel.2020.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/09/2023]
Abstract
Mre11-Rad50-Xrs2 (MRX) is a highly conserved complex with key roles in various aspects of DNA repair. Here, we report a new function for MRX in limiting transcription in budding yeast. We show that MRX interacts physically and colocalizes on chromatin with the transcriptional co-regulator Mediator. MRX restricts transcription of coding and noncoding DNA by a mechanism that does not require the nuclease activity of Mre11. MRX is required to tether transcriptionally active loci to the nuclear pore complex (NPC), and it also promotes large-scale gene-NPC interactions. Moreover, MRX-mediated chromatin anchoring to the NPC contributes to chromosome folding and helps to control gene expression. Together, these findings indicate that MRX has a role in transcription and chromosome organization that is distinct from its known function in DNA repair.
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Affiliation(s)
- Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France
| | - Mireille Tittel-Elmer
- Departments of Biochemistry and Molecular Biology and Oncology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Maxime Wery
- Institut Curie, PSL Research University, CNRS UMR 3244, ncRNA, Epigenetic and Genome Fluidity, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Marie-Bénédicte Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Cécile Ducrot
- Institute of Molecular and Cellular Radiobiology, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA)/Direction de la Recherche Fondamentale (DRF), 92260 Fontenay-aux-Roses Cedex, France
| | - Andrew Seeber
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA; University of Basel and Friedrich Miescher Institute for Biomedical Research, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Nils Krietenstein
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ugo Szachnowski
- Institut Curie, PSL Research University, CNRS UMR 3244, ncRNA, Epigenetic and Genome Fluidity, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Jennifer A Cobb
- Departments of Biochemistry and Molecular Biology and Oncology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Michel Werner
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Karine Dubrana
- Institute of Molecular and Cellular Radiobiology, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA)/Direction de la Recherche Fondamentale (DRF), 92260 Fontenay-aux-Roses Cedex, France
| | - Susan M Gasser
- University of Basel and Friedrich Miescher Institute for Biomedical Research, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Antonin Morillon
- Institut Curie, PSL Research University, CNRS UMR 3244, ncRNA, Epigenetic and Genome Fluidity, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France.
| | - Jérôme Poli
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France; University of Basel and Friedrich Miescher Institute for Biomedical Research, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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Poli J, Gasser SM, Papamichos-Chronakis M. The INO80 remodeller in transcription, replication and repair. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0290. [PMID: 28847827 DOI: 10.1098/rstb.2016.0290] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2017] [Indexed: 02/06/2023] Open
Abstract
The accessibility of eukaryotic genomes to the action of enzymes involved in transcription, replication and repair is maintained despite the organization of DNA into nucleosomes. This access is often regulated by the action of ATP-dependent nucleosome remodellers. The INO80 class of nucleosome remodellers has unique structural features and it is implicated in a diverse array of functions, including transcriptional regulation, DNA replication and DNA repair. Underlying these diverse functions is the catalytic activity of the main ATPase subunit, which in the context of a multisubunit complex can shift nucleosomes and carry out histone dimer exchange. In vitro studies showed that INO80 promotes replication fork progression on a chromatin template, while in vivo it was shown to facilitate replication fork restart after stalling and to help evict RNA polymerase II at transcribed genes following the collision of a replication fork with transcription. More recent work in yeast implicates INO80 in the general eviction and degradation of nucleosomes following high doses of oxidative DNA damage. Beyond these replication and repair functions, INO80 was shown to repress inappropriate transcription at promoters in the opposite direction to the coding sequence. Here we discuss the ways in which INO80's diverse functions help maintain genome integrity.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Montpellier and Centre de Recherche en Biologie Cellulaire (CRBM), UMR5237, CNRS, Montpellier 34095, Cedex 5, France
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland .,Faculty of Natural Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Manolis Papamichos-Chronakis
- Institute for Cell and Molecular Biosciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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8
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Seeber A, Hegnauer AM, Hustedt N, Deshpande I, Poli J, Eglinger J, Pasero P, Gut H, Shinohara M, Hopfner KP, Shimada K, Gasser SM. RPA Mediates Recruitment of MRX to Forks and Double-Strand Breaks to Hold Sister Chromatids Together. Mol Cell 2016; 64:951-966. [PMID: 27889450 DOI: 10.1016/j.molcel.2016.10.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/29/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
Abstract
The Mre11-Rad50-Xrs2 (MRX) complex is related to SMC complexes that form rings capable of holding two distinct DNA strands together. MRX functions at stalled replication forks and double-strand breaks (DSBs). A mutation in the N-terminal OB fold of the 70 kDa subunit of yeast replication protein A, rfa1-t11, abrogates MRX recruitment to both types of DNA damage. The rfa1 mutation is functionally epistatic with loss of any of the MRX subunits for survival of replication fork stress or DSB recovery, although it does not compromise end-resection. High-resolution imaging shows that either the rfa1-t11 or the rad50Δ mutation lets stalled replication forks collapse and allows the separation not only of opposing ends but of sister chromatids at breaks. Given that cohesin loss does not provoke visible sister separation as long as the RPA-MRX contacts are intact, we conclude that MRX also serves as a structural linchpin holding sister chromatids together at breaks.
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Affiliation(s)
- Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Anna Maria Hegnauer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Nicole Hustedt
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Ishan Deshpande
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Jan Eglinger
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Philippe Pasero
- Institute of Human Genetics, CNRS UPR 1142, 34090 Montpellier, France
| | - Heinz Gut
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Miki Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | | | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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Rivard MJ, Emrich JG, Poli J. SU-F-T-03: Radiobiological Evaluation of a Directional Brachytherapy Device Surgically Implanted Following EBRT. Med Phys 2016. [DOI: 10.1118/1.4956138] [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: 11/07/2022] Open
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10
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Poli J, Gerhold CB, Tosi A, Hustedt N, Seeber A, Sack R, Herzog F, Pasero P, Shimada K, Hopfner KP, Gasser SM. Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress. Genes Dev 2016; 30:337-54. [PMID: 26798134 PMCID: PMC4743062 DOI: 10.1101/gad.273813.115] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [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] [Received: 10/21/2015] [Accepted: 12/21/2015] [Indexed: 12/11/2022]
Abstract
Poli et al. present genetic and proteomic analyses from budding yeast that uncover links between the DNA replication checkpoint sensor Mec1–Ddc2 (ATR–ATRIP), the chromatin remodeling complex INO80C, and the transcription complex PAF1C. A subset of chromatin-bound RNAPII is degraded in a manner dependent on Mec1, INO80, and PAF1 complexes in cells exposed to hydroxyurea. Little is known about how cells ensure DNA replication in the face of RNA polymerase II (RNAPII)-mediated transcription, especially under conditions of replicative stress. Here we present genetic and proteomic analyses from budding yeast that uncover links between the DNA replication checkpoint sensor Mec1–Ddc2 (ATR–ATRIP), the chromatin remodeling complex INO80C (INO80 complex), and the transcription complex PAF1C (PAF1 complex). We found that a subset of chromatin-bound RNAPII is degraded in a manner dependent on Mec1, INO80, and PAF1 complexes in cells exposed to hydroxyurea (HU). On HU, Mec1 triggers the efficient removal of PAF1C and RNAPII from transcribed genes near early firing origins. Failure to evict RNAPII correlates inversely with recovery from replication stress: paf1Δ cells, like ino80 and mec1 mutants, fail to restart forks efficiently after stalling. Our data reveal unexpected synergies between INO80C, Mec1, and PAF1C in the maintenance of genome integrity and suggest a mechanism of RNAPII degradation that reduces transcription–replication fork collision.
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Affiliation(s)
- Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | | | - Alessandro Tosi
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Nicole Hustedt
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Ragna Sack
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Franz Herzog
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Philippe Pasero
- UPR 1142, Institut de Génétique Humaine, Centre National de la Recherche Scientifique, 30396 Montpellier, France
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Karl-Peter Hopfner
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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11
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Abstract
In recent years, an increasing number of studies have shown that prokaryotes and eukaryotes are armed with sophisticated mechanisms to restart stalled or collapsed replication forks. Although these processes are better understood in bacteria, major breakthroughs have also been made to explain how fork restart mechanisms operate in eukaryotic cells. In particular, repriming on the leading strand and fork regression are now established as critical for the maintenance and recovery of stalled forks in both systems. Despite the lack of conservation between the factors involved, these mechanisms are strikingly similar in eukaryotes and prokaryotes. However, they differ in that fork restart occurs in the context of chromatin in eukaryotes and is controlled by multiple regulatory pathways.
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Affiliation(s)
- Joseph T P Yeeles
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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Martin-Yken H, Ribaud V, Poli J, Hoareau-Aveilla C, Spichal M, Beaufort S, Tilloy V, Delerue T, Capp JP, Parrou JL. 10th Francophone Yeast Meeting 'Levures, Modèles & Outils'. Res Microbiol 2012; 163:309-15. [PMID: 22705268 DOI: 10.1016/j.resmic.2012.05.007] [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: 11/15/2022]
Affiliation(s)
- Hélène Martin-Yken
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, INSA, CNRS UMR5504, INRA UMR792, Université de Toulouse, INSA, UPS, INP, 135 avenue de Rangueil, 31077 Toulouse cedex 4, France
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Bianco JN, Poli J, Saksouk J, Bacal J, Silva MJ, Yoshida K, Lin YL, Tourrière H, Lengronne A, Pasero P. Analysis of DNA replication profiles in budding yeast and mammalian cells using DNA combing. Methods 2012; 57:149-57. [PMID: 22579803 DOI: 10.1016/j.ymeth.2012.04.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 04/11/2012] [Accepted: 04/14/2012] [Indexed: 11/17/2022] Open
Abstract
DNA combing is a powerful method developed by Bensimon and colleagues to stretch DNA molecules on silanized glass coverslips. This technique provides a unique way to monitor the activation of replication origins and the progression of replication forks at the level of single DNA molecules, after incorporation of thymidine analogs, such as 5-bromo-2'-deoxyuridine (BrdU), 5-iodo-2'-deoxyuridine (IdU) and 5-chloro-2'-deoxyuridine (CldU) in newly-synthesized DNA. Unlike microarray-based approaches, this assay gives access to the variability of replication profiles in individual cells. It can also be used to monitor the effect of DNA lesions on fork progression, arrest and restart. In this review, we propose standard DNA combing methods to analyze DNA replication in budding yeast and in human cells. We also show that 5-ethynyl-2'-deoxyuridine (EdU) can be used as a good alternative to BrdU for DNA combing analysis, as unlike halogenated nucleotides, it can be detected without prior denaturation of DNA.
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Affiliation(s)
- Julien N Bianco
- Institute of Human Genetics, CNRS UPR 1142, Montpellier F-34396, France
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Sherr D, Poli J, Mehta R, Wernicke G, Nori D. Kinetics of Prostate Specific Antigen Decline Following Treatment of Localized Prostate Cancer with External Beam Radiotherapy: The Impact of Dose Escalation. Int J Radiat Oncol Biol Phys 2008. [DOI: 10.1016/j.ijrobp.2008.06.1140] [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: 11/15/2022]
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Reddy N, Sood B, Mazur A, Osian A, Sampath S, Ravi A, Poli J, Nori D. SU-FF-T-65: Comparison of Dose to Rectum and Bladder with 3DCRT and IMRT Plans for the Treatment of Prostate. Med Phys 2005. [DOI: 10.1118/1.1997736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Abstract
ERPs were recorded while subjects were reading short familiar metaphors (e.g., Those fighters are lions), unfamiliar metaphors (Those apprentices are lions), or literal control sentences (Those animals are lions) presented in isolation or preceded by either an irrelevant or relevant context (e.g., They are not idiotic: ...." vs. "They are not cowardly: Those fighters are lions"). The terminal word of metaphors elicited larger N400 components than did the terminal word of literal sentences (Experiment 1) suggesting that the (incongruous) literal meaning of metaphors was indeed accessed at some point during comprehension. The analysis of the 600-1000 and 1000-1400 latency bands (Late Positive Components) revealed no significant difference between metaphors and literal sentences. The manipulation of metaphor difficulty (Experiments 2 and 3) also failed to reveal any late effect specifically linked to metaphorical processing. Finally, an effect of the preceding sentence context was found in Experiments 3 and 4, as early as 300 ms following the terminal word onset. Overall, these results support a context-dependent account of metaphor comprehension stating that when contextually relevant, the metaphorical meaning is the only one accessed.
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Affiliation(s)
- J Pynte
- Centre de Recherche en Psychologie Cognitive, CNRS, Aix-en-Provence, France
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Marty M, Mauchauffe M, Poli J, Larsen CJ. [Isolation of ribonucleic acids rich in polyadenylic acid by unesterified cellulose column chromatography]. Biochimie 1974; 56:659-65. [PMID: 4375493 DOI: 10.1016/s0300-9084(74)80036-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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