1
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Fajri N, Petryk N. Monitoring and quantifying replication fork dynamics with high-throughput methods. Commun Biol 2024; 7:729. [PMID: 38877080 PMCID: PMC11178896 DOI: 10.1038/s42003-024-06412-1] [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: 12/07/2023] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
Before each cell division, eukaryotic cells must replicate their chromosomes to ensure the accurate transmission of genetic information. Chromosome replication involves more than just DNA duplication; it also includes chromatin assembly, inheritance of epigenetic marks, and faithful resumption of all genomic functions after replication. Recent progress in quantitative technologies has revolutionized our understanding of the complexity and dynamics of DNA replication forks at both molecular and genomic scales. Here, we highlight the pivotal role of these novel methods in uncovering the principles and mechanisms of chromosome replication. These technologies have illuminated the regulation of genome replication programs, quantified the impact of DNA replication on genomic mutations and evolutionary processes, and elucidated the mechanisms of replication-coupled chromatin assembly and epigenome maintenance.
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Affiliation(s)
- Nora Fajri
- UMR9019 - CNRS, Intégrité du Génome et Cancers, Université Paris-Saclay, Gustave Roussy, Villejuif, France, 114 rue Edouard Vaillant, 94805, Villejuif, France
| | - Nataliya Petryk
- UMR9019 - CNRS, Intégrité du Génome et Cancers, Université Paris-Saclay, Gustave Roussy, Villejuif, France, 114 rue Edouard Vaillant, 94805, Villejuif, France.
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2
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Padayachy L, Ntallis SG, Halazonetis TD. RECQL4 is not critical for firing of human DNA replication origins. Sci Rep 2024; 14:7708. [PMID: 38565932 PMCID: PMC10987555 DOI: 10.1038/s41598-024-58404-0] [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: 12/25/2023] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
Human RECQL4, a member of the RecQ helicase family, plays a role in maintaining genomic stability, but its precise function remains unclear. The N-terminus of RECQL4 has similarity to Sld2, a protein required for the firing of DNA replication origins in budding yeast. Consistent with this sequence similarity, the Xenopus laevis homolog of RECQL4 has been implicated in initiating DNA replication in egg extracts. To determine whether human RECQL4 is required for firing of DNA replication origins, we generated cells in which both RECQL4 alleles were targeted, resulting in either lack of protein expression (knock-out; KO) or expression of a full-length, mutant protein lacking helicase activity (helicase-dead; HD). Interestingly, both the RECQL4 KO and HD cells were viable and exhibited essentially identical origin firing profiles as the parental cells. Analysis of the rate of fork progression revealed increased rates in the RECQL4 KO cells, which might be indicative of decreased origin firing efficiency. Our results are consistent with human RECQL4 having a less critical role in firing of DNA replication origins, than its budding yeast homolog Sld2.
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Affiliation(s)
- Laura Padayachy
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Sotirios G Ntallis
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland.
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3
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Yang Z, Mogre S, He R, Berdan EL, Ho Sui S, Hill S. The ORFIUS complex regulates ORC2 localization at replication origins. NAR Cancer 2024; 6:zcae003. [PMID: 38288445 PMCID: PMC10823580 DOI: 10.1093/narcan/zcae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 12/18/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024] Open
Abstract
High-grade serous ovarian cancer (HGSC) is a lethal malignancy with elevated replication stress (RS) levels and defective RS and RS-associated DNA damage responses. Here we demonstrate that the bromodomain-containing protein BRD1 is a RS suppressing protein that forms a replication origin regulatory complex with the histone acetyltransferase HBO1, the BRCA1 tumor suppressor, and BARD1, ORigin FIring Under Stress (ORFIUS). BRD1 and HBO1 promote eventual origin firing by supporting localization of the origin licensing protein ORC2 at origins. In the absence of BRD1 and/or HBO1, both origin firing and nuclei with ORC2 foci are reduced. BRCA1 regulates BRD1, HBO1, and ORC2 localization at replication origins. In the absence of BRCA1, both origin firing and nuclei with BRD1, HBO1, and ORC2 foci are increased. In normal and non-HGSC ovarian cancer cells, the ORFIUS complex responds to ATR and CDC7 origin regulatory signaling and disengages from origins during RS. In BRCA1-mutant and sporadic HGSC cells, BRD1, HBO1, and ORC2 remain associated with replication origins, and unresponsive to RS, DNA damage, or origin regulatory kinase inhibition. ORFIUS complex dysregulation may promote HGSC cell survival by allowing for upregulated origin firing and cell cycle progression despite accumulating DNA damage, and may be a RS target.
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Affiliation(s)
- Zelei Yang
- Department of Medical Oncology and Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Saie Mogre
- Department of Medical Oncology and Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Department of Medical Oncology and Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Emma L Berdan
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shannan J Ho Sui
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sarah J Hill
- Department of Medical Oncology and Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
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4
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Day M, Tetik B, Parlak M, Almeida-Hernández Y, Räschle M, Kaschani F, Siegert H, Marko A, Sanchez-Garcia E, Kaiser M, Barker IA, Pearl LH, Oliver AW, Boos D. TopBP1 utilises a bipartite GINS binding mode to support genome replication. Nat Commun 2024; 15:1797. [PMID: 38413589 PMCID: PMC10899662 DOI: 10.1038/s41467-024-45946-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Activation of the replicative Mcm2-7 helicase by loading GINS and Cdc45 is crucial for replication origin firing, and as such for faithful genetic inheritance. Our biochemical and structural studies demonstrate that the helicase activator GINS interacts with TopBP1 through two separate binding surfaces, the first involving a stretch of highly conserved amino acids in the TopBP1-GINI region, the second a surface on TopBP1-BRCT4. The two surfaces bind to opposite ends of the A domain of the GINS subunit Psf1. Mutation analysis reveals that either surface is individually able to support TopBP1-GINS interaction, albeit with reduced affinity. Consistently, either surface is sufficient for replication origin firing in Xenopus egg extracts and becomes essential in the absence of the other. The TopBP1-GINS interaction appears sterically incompatible with simultaneous binding of DNA polymerase epsilon (Polε) to GINS when bound to Mcm2-7-Cdc45, although TopBP1-BRCT4 and the Polε subunit PolE2 show only partial competitivity in binding to Psf1. Our TopBP1-GINS model improves the understanding of the recently characterised metazoan pre-loading complex. It further predicts the coordination of three molecular origin firing processes, DNA polymerase epsilon arrival, TopBP1 ejection and GINS integration into Mcm2-7-Cdc45.
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Affiliation(s)
- Matthew Day
- School of Biological and Behavioural Sciences, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK.
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Bilal Tetik
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Milena Parlak
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Yasser Almeida-Hernández
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Räschle
- Molecular Genetics, Technical University Kaiserslautern, Paul-Ehrlich Straße 24, 67663, Kaiserslautern, Germany
| | - Farnusch Kaschani
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Heike Siegert
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Anika Marko
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Kaiser
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Isabel A Barker
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW1E 6BT, UK.
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Dominik Boos
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany.
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5
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Foss EJ, Lichauco C, Gatbonton-Schwager T, Gonske SJ, Lofts B, Lao U, Bedalov A. Identification of 1600 replication origins in S. cerevisiae. eLife 2024; 12:RP88087. [PMID: 38315095 PMCID: PMC10945306 DOI: 10.7554/elife.88087] [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] [Indexed: 02/07/2024] Open
Abstract
There are approximately 500 known origins of replication in the yeast genome, and the process by which DNA replication initiates at these locations is well understood. In particular, these sites are made competent to initiate replication by loading of the Mcm replicative helicase prior to the start of S phase; thus, 'a site that binds Mcm in G1' might be considered to provide an operational definition of a replication origin. By fusing a subunit of Mcm to micrococcal nuclease, we previously showed that known origins are typically bound by a single Mcm double hexamer, loaded adjacent to the ARS consensus sequence (ACS). Here, we extend this analysis from known origins to the entire genome, identifying candidate Mcm binding sites whose signal intensity varies over at least three orders of magnitude. Published data quantifying single-stranded DNA (ssDNA) during S phase revealed replication initiation among the most abundant 1600 of these sites, with replication activity decreasing with Mcm abundance and disappearing at the limit of detection of ssDNA. Three other hallmarks of replication origins were apparent among the most abundant 5500 sites. Specifically, these sites: (1) appeared in intergenic nucleosome-free regions flanked on one or both sides by well-positioned nucleosomes; (2) were flanked by ACSs; and (3) exhibited a pattern of GC skew characteristic of replication initiation. We conclude that, if sites at which Mcm double hexamers are loaded can function as replication origins, then DNA replication origins are at least threefold more abundant than previously assumed, and we suggest that replication may occasionally initiate in essentially every intergenic region. These results shed light on recent reports that as many as 15% of replication events initiate outside of known origins, and this broader distribution of replication origins suggest that S phase in yeast may be less distinct from that in humans than widely assumed.
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Affiliation(s)
- Eric J Foss
- Clinical Research Division, Fred Hutch Cancer CenterSeattleUnited States
| | - Carmina Lichauco
- Clinical Research Division, Fred Hutch Cancer CenterSeattleUnited States
| | | | - Sara J Gonske
- Clinical Research Division, Fred Hutch Cancer CenterSeattleUnited States
| | - Brandon Lofts
- Clinical Research Division, Fred Hutch Cancer CenterSeattleUnited States
| | - Uyen Lao
- Clinical Research Division, Fred Hutch Cancer CenterSeattleUnited States
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutch Cancer CenterSeattleUnited States
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6
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Spegg V, Altmeyer M. Genome maintenance meets mechanobiology. Chromosoma 2024; 133:15-36. [PMID: 37581649 PMCID: PMC10904543 DOI: 10.1007/s00412-023-00807-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023]
Abstract
Genome stability is key for healthy cells in healthy organisms, and deregulated maintenance of genome integrity is a hallmark of aging and of age-associated diseases including cancer and neurodegeneration. To maintain a stable genome, genome surveillance and repair pathways are closely intertwined with cell cycle regulation and with DNA transactions that occur during transcription and DNA replication. Coordination of these processes across different time and length scales involves dynamic changes of chromatin topology, clustering of fragile genomic regions and repair factors into nuclear repair centers, mobilization of the nuclear cytoskeleton, and activation of cell cycle checkpoints. Here, we provide a general overview of cell cycle regulation and of the processes involved in genome duplication in human cells, followed by an introduction to replication stress and to the cellular responses elicited by perturbed DNA synthesis. We discuss fragile genomic regions that experience high levels of replication stress, with a particular focus on telomere fragility caused by replication stress at the ends of linear chromosomes. Using alternative lengthening of telomeres (ALT) in cancer cells and ALT-associated PML bodies (APBs) as examples of replication stress-associated clustered DNA damage, we discuss compartmentalization of DNA repair reactions and the role of protein properties implicated in phase separation. Finally, we highlight emerging connections between DNA repair and mechanobiology and discuss how biomolecular condensates, components of the nuclear cytoskeleton, and interfaces between membrane-bound organelles and membraneless macromolecular condensates may cooperate to coordinate genome maintenance in space and time.
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Affiliation(s)
- Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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7
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Foss EJ, Lichauco C, Gatbonton-Schwager T, Gonske SJ, Lofts B, Lao U, Bedalov A. Identification of 1600 replication origins in S. cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536402. [PMID: 38014147 PMCID: PMC10680564 DOI: 10.1101/2023.04.11.536402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
There are approximately 500 known origins of replication in the yeast genome, and the process by which DNA replication initiates at these locations is well understood. In particular, these sites are made competent to initiate replication by loading of the Mcm replicative helicase prior to the start of S phase; thus, "a site to which MCM is bound in G1" might be considered to provide an operational definition of a replication origin. By fusing a subunit of Mcm to micrococcal nuclease, a technique referred to as "Chromatin Endogenous Cleavage", we previously showed that known origins are typically bound by a single Mcm double hexamer, loaded adjacent to the ARS consensus sequence (ACS). Here we extend this analysis from known origins to the entire genome, identifying candidate Mcm binding sites whose signal intensity varies over at least 3 orders of magnitude. Published data quantifying the production of ssDNA during S phase showed clear evidence of replication initiation among the most abundant 1600 of these sites, with replication activity decreasing in concert with Mcm abundance and disappearing at the limit of detection of ssDNA. Three other hallmarks of replication origins were apparent among the most abundant 5,500 sites. Specifically, these sites (1) appeared in intergenic nucleosome-free regions that were flanked on one or both sides by well-positioned nucleosomes; (2) were flanked by ACSs; and (3) exhibited a pattern of GC skew characteristic of replication initiation. Furthermore, the high resolution of this technique allowed us to demonstrate a strong bias for detecting Mcm double-hexamers downstream rather than upstream of the ACS, which is consistent with the directionality of Mcm loading by Orc that has been observed in vitro. We conclude that, if sites at which Mcm double-hexamers are loaded can function as replication origins, then DNA replication origins are at least 3-fold more abundant than previously assumed, and we suggest that replication may occasionally initiate in essentially every intergenic region. These results shed light on recent reports that as many as 15% of replication events initiate outside of known origins, and this broader distribution of replication origins suggest that S phase in yeast may be less distinct from that in humans than is widely assumed.
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Affiliation(s)
- Eric J Foss
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, WA 98109
| | - Carmina Lichauco
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, WA 98109
| | | | - Sara J Gonske
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, WA 98109
| | - Brandon Lofts
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, WA 98109
| | - Uyen Lao
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, WA 98109
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, WA 98109
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8
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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] [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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9
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Haccard O, Ciardo D, Narrissamprakash H, Bronchain O, Kumagai A, Dunphy WG, Goldar A, Marheineke K. Rif1 restrains the rate of replication origin firing in Xenopus laevis. Commun Biol 2023; 6:788. [PMID: 37516798 PMCID: PMC10387115 DOI: 10.1038/s42003-023-05172-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023] Open
Abstract
Metazoan genomes are duplicated by the coordinated activation of clusters of replication origins at different times during S phase, but the underlying mechanisms of this temporal program remain unclear during early development. Rif1, a key replication timing factor, inhibits origin firing by recruiting protein phosphatase 1 (PP1) to chromatin counteracting S phase kinases. We have previously described that Rif1 depletion accelerates early Xenopus laevis embryonic cell cycles. Here, we find that in the absence of Rif1, patterns of replication foci change along with the acceleration of replication cluster activation. However, initiations increase only moderately inside active clusters. Our numerical simulations suggest that the absence of Rif1 compresses the temporal program towards more homogeneity and increases the availability of limiting initiation factors. We experimentally demonstrate that Rif1 depletion increases the chromatin-binding of the S phase kinase Cdc7/Drf1, the firing factors Treslin, MTBP, Cdc45, RecQL4, and the phosphorylation of both Treslin and MTBP. We show that Rif1 globally, but not locally, restrains the replication program in early embryos, possibly by inhibiting or excluding replication factors from chromatin.
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Affiliation(s)
- Olivier Haccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Diletta Ciardo
- Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Hemalatha Narrissamprakash
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Odile Bronchain
- Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, CERTO-Retina France, 91400, Saclay, France
| | - Akiko Kumagai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - William G Dunphy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Kathrin Marheineke
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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10
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Hernández‐Carralero E, Cabrera E, Rodríguez-Torres G, Hernández-Reyes Y, Singh A, Santa-María C, Fernández-Justel J, Janssens R, Marteijn J, Evert B, Mailand N, Gómez M, Ramadan K, Smits VJ, Freire R. ATXN3 controls DNA replication and transcription by regulating chromatin structure. Nucleic Acids Res 2023; 51:5396-5413. [PMID: 36971114 PMCID: PMC10287915 DOI: 10.1093/nar/gkad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 02/10/2023] [Accepted: 03/14/2023] [Indexed: 11/18/2023] Open
Abstract
The deubiquitinating enzyme Ataxin-3 (ATXN3) contains a polyglutamine (PolyQ) region, the expansion of which causes spinocerebellar ataxia type-3 (SCA3). ATXN3 has multiple functions, such as regulating transcription or controlling genomic stability after DNA damage. Here we report the role of ATXN3 in chromatin organization during unperturbed conditions, in a catalytic-independent manner. The lack of ATXN3 leads to abnormalities in nuclear and nucleolar morphology, alters DNA replication timing and increases transcription. Additionally, indicators of more open chromatin, such as increased mobility of histone H1, changes in epigenetic marks and higher sensitivity to micrococcal nuclease digestion were detected in the absence of ATXN3. Interestingly, the effects observed in cells lacking ATXN3 are epistatic to the inhibition or lack of the histone deacetylase 3 (HDAC3), an interaction partner of ATXN3. The absence of ATXN3 decreases the recruitment of endogenous HDAC3 to the chromatin, as well as the HDAC3 nuclear/cytoplasm ratio after HDAC3 overexpression, suggesting that ATXN3 controls the subcellular localization of HDAC3. Importantly, the overexpression of a PolyQ-expanded version of ATXN3 behaves as a null mutant, altering DNA replication parameters, epigenetic marks and the subcellular distribution of HDAC3, giving new insights into the molecular basis of the disease.
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Affiliation(s)
- Esperanza Hernández‐Carralero
- Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
- Escuela de Doctorado y Estudios de Posgrado, Universidad de la Laguna, Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Centro de Investigaciones Biomédicas de Canarias, Facultad de Medicina, Campus Ciencias de la Salud, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Elisa Cabrera
- Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
| | - Gara Rodríguez-Torres
- Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
- Escuela de Doctorado y Estudios de Posgrado, Universidad de la Laguna, Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Centro de Investigaciones Biomédicas de Canarias, Facultad de Medicina, Campus Ciencias de la Salud, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Yeray Hernández-Reyes
- Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
- Escuela de Doctorado y Estudios de Posgrado, Universidad de la Laguna, Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Centro de Investigaciones Biomédicas de Canarias, Facultad de Medicina, Campus Ciencias de la Salud, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Abhay N Singh
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Cristina Santa-María
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain
| | - José Miguel Fernández-Justel
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bernd O Evert
- Department of Neurology, University Hospital Bonn, Bonn, Germany
| | - Niels Mailand
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - María Gómez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain
| | - Kristijan Ramadan
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Veronique A J Smits
- Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Centro de Investigaciones Biomédicas de Canarias, Facultad de Medicina, Campus Ciencias de la Salud, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Centro de Investigaciones Biomédicas de Canarias, Facultad de Medicina, Campus Ciencias de la Salud, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
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11
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Brison O, Gnan S, Azar D, Koundrioukoff S, Melendez-Garcia R, Kim SJ, Schmidt M, El-Hilali S, Jaszczyszyn Y, Lachages AM, Thermes C, Chen CL, Debatisse M. Mistimed origin licensing and activation stabilize common fragile sites under tight DNA-replication checkpoint activation. Nat Struct Mol Biol 2023; 30:539-550. [PMID: 37024657 DOI: 10.1038/s41594-023-00949-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/28/2023] [Indexed: 04/08/2023]
Abstract
Genome integrity requires replication to be completed before chromosome segregation. The DNA-replication checkpoint (DRC) contributes to this coordination by inhibiting CDK1, which delays mitotic onset. Under-replication of common fragile sites (CFSs), however, escapes surveillance, resulting in mitotic chromosome breaks. Here we asked whether loose DRC activation induced by modest stresses commonly used to destabilize CFSs could explain this leakage. We found that tightening DRC activation or CDK1 inhibition stabilizes CFSs in human cells. Repli-Seq and molecular combing analyses showed a burst of replication initiations implemented in mid S-phase across a subset of late-replicating sequences, including CFSs, while the bulk genome was unaffected. CFS rescue and extra-initiations required CDC6 and CDT1 availability in S-phase, implying that CDK1 inhibition permits mistimed origin licensing and firing. In addition to delaying mitotic onset, tight DRC activation therefore supports replication completion of late origin-poor domains at risk of under-replication, two complementary roles preserving genome stability.
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Affiliation(s)
- Olivier Brison
- CNRS UMR 9019, Gustave Roussy Institute, Villejuif, France
- Paris-Saclay University, Gif-sur-Yvette, France
| | - Stefano Gnan
- Curie Institute, PSL Research University, CNRS UMR 3244, Paris, France
- Sorbonne University, Paris, France
| | - Dana Azar
- Curie Institute, PSL Research University, CNRS UMR 3244, Paris, France
- Sorbonne University, Paris, France
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Beirut, Lebanon
| | - Stéphane Koundrioukoff
- CNRS UMR 9019, Gustave Roussy Institute, Villejuif, France
- Sorbonne University, Paris, France
| | - Rodrigo Melendez-Garcia
- CNRS UMR 9019, Gustave Roussy Institute, Villejuif, France
- Paris-Saclay University, Gif-sur-Yvette, France
| | - Su-Jung Kim
- CNRS UMR 9019, Gustave Roussy Institute, Villejuif, France
- Paris-Saclay University, Gif-sur-Yvette, France
| | - Mélanie Schmidt
- CNRS UMR 9019, Gustave Roussy Institute, Villejuif, France
- Paris-Saclay University, Gif-sur-Yvette, France
| | - Sami El-Hilali
- Curie Institute, PSL Research University, CNRS UMR 3244, Paris, France
- Sorbonne University, Paris, France
- Villefranche sur mer Developmental Biology Laboratory, CNRS UMR7009, Villefranche-sur-Mer, France
| | - Yan Jaszczyszyn
- Paris-Saclay University, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198CNRS, CEA, Paris-Sud University, Gif-sur-Yvette, France
| | - Anne-Marie Lachages
- Curie Institute, PSL Research University, CNRS UMR 3244, Paris, France
- UTCBS, CNRS UMR 8258/ INSERM U 1267, Sorbonne-Paris-Cité University, Paris, France
| | - Claude Thermes
- Paris-Saclay University, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198CNRS, CEA, Paris-Sud University, Gif-sur-Yvette, France
| | - Chun-Long Chen
- Curie Institute, PSL Research University, CNRS UMR 3244, Paris, France
- Sorbonne University, Paris, France
| | - Michelle Debatisse
- CNRS UMR 9019, Gustave Roussy Institute, Villejuif, France.
- Sorbonne University, Paris, France.
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12
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Birtwistle MR. Modeling the Dynamics of Eukaryotic DNA Synthesis in Remembrance of Tunde Ogunnaike. Ind Eng Chem Res 2023. [DOI: 10.1021/acs.iecr.2c02856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- Marc R. Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina29631, United States
- Department of Bioengineering, Clemson University, Clemson, South Carolina29631, United States
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13
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Dephosphorylation of the pre-initiation complex is critical for origin firing. Mol Cell 2023; 83:12-25.e10. [PMID: 36543171 DOI: 10.1016/j.molcel.2022.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 08/13/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
In eukaryotes, cyclin-dependent kinase (CDK) ensures that the genome is duplicated exactly once by inhibiting helicase loading factors before activating origin firing. CDK activates origin firing by phosphorylating two substrates, Sld2 and Sld3, forming a transient and limiting intermediate-the pre-initiation complex (pre-IC). Here, we show in the budding yeast Saccharomyces cerevisiae that the CDK phosphorylations of Sld3 and Sld2 are rapidly turned over during S phase by the PP2A and PP4 phosphatases. PP2ARts1 targets Sld3 specifically through an Rts1-interaction motif, and this targeted dephosphorylation is important for origin firing genome-wide, for formation of the pre-IC at origins and for ensuring that Sld3 is dephosphorylated in G1 phase. PP2ARts1 promotes replication in vitro, and we show that targeted Sld3 dephosphorylation is critical for viability. Together, these studies demonstrate that phosphatases enforce the correct ordering of replication factor phosphorylation and in addition to kinases are also key drivers of replication initiation.
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14
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Lee SY, Kim JJ, Miller KM. Single-Cell Analysis of Histone Acetylation Dynamics at Replication Forks Using PLA and SIRF. Methods Mol Biol 2023; 2589:345-360. [PMID: 36255636 DOI: 10.1007/978-1-0716-2788-4_23] [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] [Indexed: 06/16/2023]
Abstract
Genome integrity is constantly challenged by various processes including DNA damage, structured DNA, transcription, and DNA-protein crosslinks. During DNA replication, active replication forks that encounter these obstacles can result in their stalling and collapse. Accurate DNA replication requires the ability of forks to navigate these threats, which is aided by DNA repair proteins. Histone acetylation participates in this process through an ability to signal and recruit proteins to regions of replicating DNA. For example, the histone acetyltransferase PCAF promotes the recruitment of the DNA repair factors MRE11 and EXO1 to stalled forks by acetylating histone H4 at lysine 8 (H4K8ac). These highly dynamic processes can be detected and analyzed using a modified proximity ligation assay (PLA) method, known as SIRF (in situ protein interactions with nascent DNA replication forks). This single-cell assay combines PLA with EdU-coupled Click-iT chemistry reactions and fluorescence microscopy to detect these interactions at sites of replicating DNA. Here we provide a detailed protocol utilizing SIRF that detects the HAT PCAF and histone acetylation at replication forks. This technique provides a robust methodology to determine protein recruitment and modifications at the replication fork with single-cell resolution.
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Affiliation(s)
- Seo Yun Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jae Jin Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Republic of Korea.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
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15
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Böhly N, Schmidt AK, Zhang X, Slusarenko BO, Hennecke M, Kschischo M, Bastians H. Increased replication origin firing links replication stress to whole chromosomal instability in human cancer. Cell Rep 2022; 41:111836. [PMID: 36516748 DOI: 10.1016/j.celrep.2022.111836] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 09/12/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and comprises structural CIN (S-CIN) and numerical or whole chromosomal CIN (W-CIN). Recent work indicated that replication stress (RS), known to contribute to S-CIN, also affects mitotic chromosome segregation, possibly explaining the common co-existence of S-CIN and W-CIN in human cancer. Here, we show that RS-induced increased origin firing is sufficient to trigger W-CIN in human cancer cells. We discovered that overexpression of origin firing genes, including GINS1 and CDC45, correlates with W-CIN in human cancer specimens and causes W-CIN in otherwise chromosomally stable human cells. Furthermore, modulation of the ATR-CDK1-RIF1 axis increases the number of firing origins and leads to W-CIN. Importantly, chromosome missegregation upon additional origin firing is mediated by increased mitotic microtubule growth rates, a mitotic defect prevalent in chromosomally unstable cancer cells. Thus, our study identifies increased replication origin firing as a cancer-relevant trigger for chromosomal instability.
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Affiliation(s)
- Nicolas Böhly
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Ann-Kathrin Schmidt
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Xiaoxiao Zhang
- University of Applied Sciences Koblenz, Department of Mathematics and Technology, 53424 Remagen, Germany; Technical University of Munich, Department of Informatics, 81675 Munich, Germany
| | - Benjamin O Slusarenko
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Magdalena Hennecke
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Maik Kschischo
- University of Applied Sciences Koblenz, Department of Mathematics and Technology, 53424 Remagen, Germany
| | - Holger Bastians
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany.
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16
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Rhind N. DNA replication timing: Biochemical mechanisms and biological significance. Bioessays 2022; 44:e2200097. [PMID: 36125226 PMCID: PMC9783711 DOI: 10.1002/bies.202200097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 12/27/2022]
Abstract
The regulation of DNA replication is a fascinating biological problem both from a mechanistic angle-How is replication timing regulated?-and from an evolutionary one-Why is replication timing regulated? Recent work has provided significant insight into the first question. Detailed biochemical understanding of the mechanism and regulation of replication initiation has made possible robust hypotheses for how replication timing is regulated. Moreover, technical progress, including high-throughput, single-molecule mapping of replication initiation and single-cell assays of replication timing, has allowed for direct testing of these hypotheses in mammalian cells. This work has consolidated the conclusion that differential replication timing is a consequence of the varying probability of replication origin initiation. The second question is more difficult to directly address experimentally. Nonetheless, plausible hypotheses can be made and one-that replication timing contributes to the regulation of chromatin structure-has received new experimental support.
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Affiliation(s)
- Nicholas Rhind
- Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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17
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Clarke TL, Mostoslavsky R. DNA repair as a shared hallmark in cancer and ageing. Mol Oncol 2022; 16:3352-3379. [PMID: 35834102 PMCID: PMC9490147 DOI: 10.1002/1878-0261.13285] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/23/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
Increasing evidence demonstrates that DNA damage and genome instability play a crucial role in ageing. Mammalian cells have developed a wide range of complex and well‐orchestrated DNA repair pathways to respond to and resolve many different types of DNA lesions that occur from exogenous and endogenous sources. Defects in these repair pathways lead to accelerated or premature ageing syndromes and increase the likelihood of cancer development. Understanding the fundamental mechanisms of DNA repair will help develop novel strategies to treat ageing‐related diseases. Here, we revisit the processes involved in DNA damage repair and how these can contribute to diseases, including ageing and cancer. We also review recent mechanistic insights into DNA repair and discuss how these insights are being used to develop novel therapeutic strategies for treating human disease. We discuss the use of PARP inhibitors in the clinic for the treatment of breast and ovarian cancer and the challenges associated with acquired drug resistance. Finally, we discuss how DNA repair pathway‐targeted therapeutics are moving beyond PARP inhibition in the search for ever more innovative and efficacious cancer therapies.
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Affiliation(s)
- Thomas L Clarke
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
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18
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Impact of Chromosomal Context on Origin Selection and the Replication Program. Genes (Basel) 2022; 13:genes13071244. [PMID: 35886027 PMCID: PMC9318681 DOI: 10.3390/genes13071244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/28/2022] [Accepted: 07/08/2022] [Indexed: 02/01/2023] Open
Abstract
Eukaryotic DNA replication is regulated by conserved mechanisms that bring about a spatial and temporal organization in which distinct genomic domains are copied at characteristic times during S phase. Although this replication program has been closely linked with genome architecture, we still do not understand key aspects of how chromosomal context modulates the activity of replication origins. To address this question, we have exploited models that combine engineered genomic rearrangements with the unique replication programs of post-quiescence and pre-meiotic S phases. Our results demonstrate that large-scale inversions surprisingly do not affect cell proliferation and meiotic progression, despite inducing a restructuring of replication domains on each rearranged chromosome. Remarkably, these alterations in the organization of DNA replication are entirely due to changes in the positions of existing origins along the chromosome, as their efficiencies remain virtually unaffected genome wide. However, we identified striking alterations in origin firing proximal to the fusion points of each inversion, suggesting that the immediate chromosomal neighborhood of an origin is a crucial determinant of its activity. Interestingly, the impact of genome reorganization on replication initiation is highly comparable in the post-quiescent and pre-meiotic S phases, despite the differences in DNA metabolism in these two physiological states. Our findings therefore shed new light on how origin selection and the replication program are governed by chromosomal architecture.
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19
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Zaffar E, Ferreira P, Sanchez-Pulido L, Boos D. The Role of MTBP as a Replication Origin Firing Factor. BIOLOGY 2022; 11:biology11060827. [PMID: 35741348 PMCID: PMC9219753 DOI: 10.3390/biology11060827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 12/12/2022]
Abstract
The initiation step of replication at replication origins determines when and where in the genome replication machines, replisomes, are generated. Tight control of replication initiation helps facilitate the two main tasks of genome replication, to duplicate the genome accurately and exactly once each cell division cycle. The regulation of replication initiation must ensure that initiation occurs during the S phase specifically, that no origin fires more than once per cell cycle, that enough origins fire to avoid non-replicated gaps, and that the right origins fire at the right time but only in favorable circumstances. Despite its importance for genetic homeostasis only the main molecular processes of eukaryotic replication initiation and its cellular regulation are understood. The MTBP protein (Mdm2-binding protein) is so far the last core replication initiation factor identified in metazoan cells. MTBP is the orthologue of yeast Sld7. It is essential for origin firing, the maturation of pre-replicative complexes (pre-RCs) into replisomes, and is emerging as a regulation focus targeted by kinases and by regulated degradation. We present recent insight into the structure and cellular function of the MTBP protein in light of recent structural and biochemical studies revealing critical molecular details of the eukaryotic origin firing reaction. How the roles of MTBP in replication and other cellular processes are mutually connected and are related to MTBP's contribution to tumorigenesis remains largely unclear.
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Affiliation(s)
- Eman Zaffar
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany; (E.Z.); (P.F.)
| | - Pedro Ferreira
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany; (E.Z.); (P.F.)
| | - Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, IGC, University of Edinburgh, Edinburgh EH9 3JR, UK;
| | - Dominik Boos
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany; (E.Z.); (P.F.)
- Correspondence: ; Tel.: +49-201-183-4132
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20
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Kelly RL, Huehls AM, Venkatachalam A, Huntoon CJ, Machida YJ, Karnitz LM. Intra-S phase checkpoint kinase Chk1 dissociates replication proteins Treslin and TopBP1 through multiple mechanisms during replication stress. J Biol Chem 2022; 298:101777. [PMID: 35231445 PMCID: PMC8965152 DOI: 10.1016/j.jbc.2022.101777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 02/17/2022] [Accepted: 02/19/2022] [Indexed: 11/17/2022] Open
Abstract
Replication stress impedes DNA polymerase progression causing activation of the ataxia telangiectasia and Rad3-related signaling pathway, which promotes the intra-S phase checkpoint activity through phosphorylation of checkpoint kinase 1 (Chk1). Chk1 suppresses replication origin firing, in part, by disrupting the interaction between the preinitiation complex components Treslin and TopBP1, an interaction that is mediated by TopBP1 BRCT domain-binding to two cyclin-dependent kinase (CDK) phosphorylation sites, T968 and S1000, in Treslin. Two nonexclusive models for how Chk1 regulates the Treslin–TopBP1 interaction have been proposed in the literature: in one model, these proteins dissociate due to a Chk1-induced decrease in CDK activity that reduces phosphorylation of the Treslin sites that bind TopBP1 and in the second model, Chk1 directly phosphorylates Treslin, resulting in dissociation of TopBP1. However, these models have not been formally examined. We show here that Treslin T968 phosphorylation was decreased in a Chk1-dependent manner, while Treslin S1000 phosphorylation was unchanged, demonstrating that T968 and S1000 are differentially regulated. However, CDK2-mediated phosphorylation alone did not fully account for Chk1 regulation of the Treslin–TopBP1 interaction. We also identified additional Chk1 phosphorylation sites on Treslin that contributed to disruption of the Treslin–TopBP1 interaction, including S1114. Finally, we showed that both of the proposed mechanisms regulate origin firing in cancer cell line models undergoing replication stress, with the relative roles of each mechanism varying among cell lines. This study demonstrates that Chk1 regulates Treslin through multiple mechanisms to promote efficient dissociation of Treslin and TopBP1 and furthers our understanding of Treslin regulation during the intra-S phase checkpoint.
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Affiliation(s)
- Rebecca L Kelly
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Amelia M Huehls
- Division of Oncology Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Annapoorna Venkatachalam
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Yuichi J Machida
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA; Division of Oncology Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Larry M Karnitz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA; Division of Oncology Research, Mayo Clinic, Rochester, Minnesota, USA.
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21
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Yeast Stn1 promotes MCM to circumvent Rad53 control of the S phase checkpoint. Curr Genet 2022; 68:165-179. [PMID: 35150303 PMCID: PMC8976814 DOI: 10.1007/s00294-022-01228-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 11/17/2022]
Abstract
Treating yeast cells with the replication inhibitor hydroxyurea activates the S phase checkpoint kinase Rad53, eliciting responses that block DNA replication origin firing, stabilize replication forks, and prevent premature extension of the mitotic spindle. We previously found overproduction of Stn1, a subunit of the telomere-binding Cdc13–Stn1–Ten1 complex, circumvents Rad53 checkpoint functions in hydroxyurea, inducing late origin firing and premature spindle extension even though Rad53 is activated normally. Here, we show Stn1 overproduction acts through remarkably similar pathways compared to loss of RAD53, converging on the MCM complex that initiates origin firing and forms the catalytic core of the replicative DNA helicase. First, mutations affecting Mcm2 and Mcm5 block the ability of Stn1 overproduction to disrupt the S phase checkpoint. Second, loss of function stn1 mutations compensate rad53 S phase checkpoint defects. Third Stn1 overproduction suppresses a mutation in Mcm7. Fourth, stn1 mutants accumulate single-stranded DNA at non-telomeric genome locations, imposing a requirement for post-replication DNA repair. We discuss these interactions in terms of a model in which Stn1 acts as an accessory replication factor that facilitates MCM activation at ORIs and potentially also maintains MCM activity at replication forks advancing through challenging templates.
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22
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The yeast Dbf4 Zn 2+ finger domain suppresses single-stranded DNA at replication forks initiated from a subset of origins. Curr Genet 2022; 68:253-265. [PMID: 35147742 PMCID: PMC8976809 DOI: 10.1007/s00294-022-01230-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/23/2021] [Accepted: 01/06/2022] [Indexed: 11/25/2022]
Abstract
Dbf4 is the cyclin-like subunit for the Dbf4-dependent protein kinase (DDK), required for activating the replicative helicase at DNA replication origin that fire during S phase. Dbf4 also functions as an adaptor, targeting the DDK to different groups of origins and substrates. Here we report a genome-wide analysis of origin firing in a budding yeast mutant, dbf4-zn, lacking the Zn2+ finger domain within the C-terminus of Dbf4. At one group of origins, which we call dromedaries, we observe an unanticipated DNA replication phenotype: accumulation of single-stranded DNA spanning ± 5kbp from the center of the origins. A similar accumulation of single-stranded DNA at origins occurs more globally in pri1-m4 mutants defective for the catalytic subunit of DNA primase and rad53 mutants defective for the S phase checkpoint following DNA replication stress. We propose the Dbf4 Zn2+ finger suppresses single-stranded gaps at replication forks emanating from dromedary origins. Certain origins may impose an elevated requirement for the DDK to fully initiate DNA synthesis following origin activation. Alternatively, dbf4-zn may be defective for stabilizing/restarting replication forks emanating from dromedary origins during replication stress.
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23
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Ferreira P, Sanchez-Pulido L, Marko A, Ponting CP, Boos D. Refining the domain architecture model of the replication origin firing factor Treslin/TICRR. Life Sci Alliance 2022; 5:5/5/e202101088. [PMID: 35091422 PMCID: PMC8807876 DOI: 10.26508/lsa.202101088] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/24/2022] Open
Abstract
Faithful genome duplication requires appropriately controlled replication origin firing. The metazoan origin firing regulation hub Treslin/TICRR and its yeast orthologue Sld3 share the Sld3-Treslin domain and the adjacent TopBP1/Dpb11 interaction domain. We report a revised domain architecture model of Treslin/TICRR. Protein sequence analyses uncovered a conserved Ku70-homologous β-barrel fold in the Treslin/TICRR middle domain (M domain) and in Sld3. Thus, the Sld3-homologous Treslin/TICRR core comprises its three central domains, M domain, Sld3-Treslin domain, and TopBP1/Dpb11 interaction domain, flanked by non-conserved terminal domains, the CIT (conserved in Treslins) and the C terminus. The CIT includes a von Willebrand factor type A domain. Unexpectedly, MTBP, Treslin/TICRR, and Ku70/80 share the same N-terminal domain architecture, von Willebrand factor type A and Ku70-like β-barrels, suggesting a common ancestry. Binding experiments using mutants and the Sld3-Sld7 dimer structure suggest that the Treslin/Sld3 and MTBP/Sld7 β-barrels engage in homotypic interactions, reminiscent of Ku70-Ku80 dimerization. Cells expressing Treslin/TICRR domain mutants indicate that all Sld3-core domains and the non-conserved terminal domains fulfil important functions during origin firing in human cells. Thus, metazoa-specific and widely conserved molecular processes cooperate during metazoan origin firing.
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Affiliation(s)
- Pedro Ferreira
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Anika Marko
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Chris P Ponting
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Dominik Boos
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
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24
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Wootton J, Soutoglou E. Chromatin and Nuclear Dynamics in the Maintenance of Replication Fork Integrity. Front Genet 2022; 12:773426. [PMID: 34970302 PMCID: PMC8712883 DOI: 10.3389/fgene.2021.773426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Replication of the eukaryotic genome is a highly regulated process and stringent control is required to maintain genome integrity. In this review, we will discuss the many aspects of the chromatin and nuclear environment that play key roles in the regulation of both unperturbed and stressed replication. Firstly, the higher order organisation of the genome into A and B compartments, topologically associated domains (TADs) and sub-nuclear compartments has major implications in the control of replication timing. In addition, the local chromatin environment defined by non-canonical histone variants, histone post-translational modifications (PTMs) and enrichment of factors such as heterochromatin protein 1 (HP1) plays multiple roles in normal S phase progression and during the repair of replicative damage. Lastly, we will cover how the spatial organisation of stalled replication forks facilitates the resolution of replication stress.
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Affiliation(s)
- Jack Wootton
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Evi Soutoglou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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25
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Blasiak J, Szczepańska J, Sobczuk A, Fila M, Pawlowska E. RIF1 Links Replication Timing with Fork Reactivation and DNA Double-Strand Break Repair. Int J Mol Sci 2021; 22:11440. [PMID: 34768871 PMCID: PMC8583789 DOI: 10.3390/ijms222111440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Replication timing (RT) is a cellular program to coordinate initiation of DNA replication in all origins within the genome. RIF1 (replication timing regulatory factor 1) is a master regulator of RT in human cells. This role of RIF1 is associated with binding G4-quadruplexes and changes in 3D chromatin that may suppress origin activation over a long distance. Many effects of RIF1 in fork reactivation and DNA double-strand (DSB) repair (DSBR) are underlined by its interaction with TP53BP1 (tumor protein p53 binding protein). In G1, RIF1 acts antagonistically to BRCA1 (BRCA1 DNA repair associated), suppressing end resection and homologous recombination repair (HRR) and promoting non-homologous end joining (NHEJ), contributing to DSBR pathway choice. RIF1 is an important element of intra-S-checkpoints to recover damaged replication fork with the involvement of HRR. High-resolution microscopic studies show that RIF1 cooperates with TP53BP1 to preserve 3D structure and epigenetic markers of genomic loci disrupted by DSBs. Apart from TP53BP1, RIF1 interact with many other proteins, including proteins involved in DNA damage response, cell cycle regulation, and chromatin remodeling. As impaired RT, DSBR and fork reactivation are associated with genomic instability, a hallmark of malignant transformation, RIF1 has a diagnostic, prognostic, and therapeutic potential in cancer. Further studies may reveal other aspects of common regulation of RT, DSBR, and fork reactivation by RIF1.
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Affiliation(s)
- Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Joanna Szczepańska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland;
| | - Anna Sobczuk
- Department of Gynaecology and Obstetrics, Medical University of Lodz, 93-338 Lodz, Poland;
| | - Michal Fila
- Department of Developmental Neurology and Epileptology, Polish Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland;
| | - Elzbieta Pawlowska
- Department of Orthodontics, Medical University of Lodz, 92-217 Lodz, Poland;
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26
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Jo U, Murai Y, Takebe N, Thomas A, Pommier Y. Precision Oncology with Drugs Targeting the Replication Stress, ATR, and Schlafen 11. Cancers (Basel) 2021; 13:4601. [PMID: 34572827 PMCID: PMC8465591 DOI: 10.3390/cancers13184601] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022] Open
Abstract
Precision medicine aims to implement strategies based on the molecular features of tumors and optimized drug delivery to improve cancer diagnosis and treatment. DNA replication is a logical approach because it can be targeted by a broad range of anticancer drugs that are both clinically approved and in development. These drugs increase deleterious replication stress (RepStress); however, how to selectively target and identify the tumors with specific molecular characteristics are unmet clinical needs. Here, we provide background information on the molecular processes of DNA replication and its checkpoints, and discuss how to target replication, checkpoint, and repair pathways with ATR inhibitors and exploit Schlafen 11 (SLFN11) as a predictive biomarker.
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Affiliation(s)
- Ukhyun Jo
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
| | - Yasuhisa Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Naoko Takebe
- Developmental Therapeutics Branch and Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, MD 20892-4264, USA;
| | - Anish Thomas
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
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27
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Li Y, Xue B, Zhang M, Zhang L, Hou Y, Qin Y, Long H, Su QP, Wang Y, Guan X, Jin Y, Cao Y, Li G, Sun Y. Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency. Genome Biol 2021; 22:206. [PMID: 34253239 PMCID: PMC8276456 DOI: 10.1186/s13059-021-02424-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/30/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined. RESULTS We apply dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We find that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase. Intriguingly, while both high-efficiency and low-efficiency origins are distributed homogeneously in the TAD during the G1 phase, high-efficiency origins relocate to the TAD periphery before the S phase. Origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observe that the replication machinery protein PCNA forms immobile clusters around TADs at the G1/S transition, explaining why origins at the TAD periphery are preferentially fired. CONCLUSION Our work reveals a new origin selection mechanism that the replication efficiency of origins is determined by their physical distribution in the chromatin domain, which undergoes a transcription-dependent structural re-organization process. Our model explains the complex links between replication origin efficiency and many genetic and epigenetic signatures that mark active transcription. The coordination between DNA replication, transcription, and chromatin organization inside individual TADs also provides new insights into the biological functions of sub-domain chromatin structural dynamics.
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Affiliation(s)
- Yongzheng Li
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Liwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yingping Hou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yizhi Qin
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Haizhen Long
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian Peter Su
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Yao Wang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaodong Guan
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yanyan Jin
- Department of Neurobiology, Beijing Centre of Neural Regeneration and Repair, Capital Medical University, Beijing, 100101, China
| | - Yuan Cao
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.
- College of Future Technology, Peking University, Beijing, 100871, China.
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28
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Droghetti R, Agier N, Fischer G, Gherardi M, Cosentino Lagomarsino M. An evolutionary model identifies the main evolutionary biases for the evolution of genome-replication profiles. eLife 2021; 10:63542. [PMID: 34013887 PMCID: PMC8213407 DOI: 10.7554/elife.63542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Recent results comparing the temporal program of genome replication of yeast species belonging to the Lachancea clade support the scenario that the evolution of the replication timing program could be mainly driven by correlated acquisition and loss events of active replication origins. Using these results as a benchmark, we develop an evolutionary model defined as birth-death process for replication origins and use it to identify the evolutionary biases that shape the replication timing profiles. Comparing different evolutionary models with data, we find that replication origin birth and death events are mainly driven by two evolutionary pressures, the first imposes that events leading to higher double-stall probability of replication forks are penalized, while the second makes less efficient origins more prone to evolutionary loss. This analysis provides an empirically grounded predictive framework for quantitative evolutionary studies of the replication timing program.
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Affiliation(s)
- Rossana Droghetti
- Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, Milan, Italy
| | - Nicolas Agier
- Sorbonne Universitè, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Gilles Fischer
- Sorbonne Universitè, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Marco Gherardi
- Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, Milan, Italy and INFN sezione di Milano, Milan, Italy
| | - Marco Cosentino Lagomarsino
- Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, Milan, Italy and INFN sezione di Milano, Milan, Italy.,IFOM Foundation, FIRC Institute for Molecular Oncology, via Adamello 16, Milan, Italy
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29
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Petryk N, Bultmann S, Bartke T, Defossez PA. Staying true to yourself: mechanisms of DNA methylation maintenance in mammals. Nucleic Acids Res 2021; 49:3020-3032. [PMID: 33300031 PMCID: PMC8034647 DOI: 10.1093/nar/gkaa1154] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022] Open
Abstract
DNA methylation is essential to development and cellular physiology in mammals. Faulty DNA methylation is frequently observed in human diseases like cancer and neurological disorders. Molecularly, this epigenetic mark is linked to other chromatin modifications and it regulates key genomic processes, including transcription and splicing. Each round of DNA replication generates two hemi-methylated copies of the genome. These must be converted back to symmetrically methylated DNA before the next S-phase, or the mark will fade away; therefore the maintenance of DNA methylation is essential. Mechanistically, the maintenance of this epigenetic modification takes place during and after DNA replication, and occurs within the very dynamic context of chromatin re-assembly. Here, we review recent discoveries and unresolved questions regarding the mechanisms, dynamics and fidelity of DNA methylation maintenance in mammals. We also discuss how it could be regulated in normal development and misregulated in disease.
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Affiliation(s)
- Nataliya Petryk
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, F-75013 Paris, France
| | - Sebastian Bultmann
- Department of Biology II, Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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30
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Kirstein N, Buschle A, Wu X, Krebs S, Blum H, Kremmer E, Vorberg IM, Hammerschmidt W, Lacroix L, Hyrien O, Audit B, Schepers A. Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones. eLife 2021; 10:62161. [PMID: 33683199 PMCID: PMC7993996 DOI: 10.7554/elife.62161] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 03/05/2021] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic DNA replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors Orc2, Orc3, Mcm3, and Mcm7 with gene expression, replication timing, and fork directionality profiles obtained by RNA-seq, Repli-seq, and OK-seq. Both, the origin recognition complex (ORC) and the minichromosome maintenance complex (MCM) are significantly and homogeneously depleted from transcribed genes, enriched at gene promoters, and more abundant in early- than in late-replicating domains. Surprisingly, after controlling these variables, no difference in ORC/MCM density is detected between initiation zones, termination zones, unidirectionally replicating regions, and randomly replicating regions. Therefore, ORC/MCM density correlates with replication timing but does not solely regulate the probability of replication initiation. Interestingly, H4K20me3, a histone modification proposed to facilitate late origin licensing, was enriched in late-replicating initiation zones and gene deserts of stochastic replication fork direction. We discuss potential mechanisms specifying when and where replication initiates in human cells.
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Affiliation(s)
- Nina Kirstein
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Munich, Germany
| | - Alexander Buschle
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health and German Center for Infection Research (DZIF), Munich, Germany
| | - Xia Wu
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians Universität (LMU) München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians Universität (LMU) München, Munich, Germany
| | - Elisabeth Kremmer
- Institute for Molecular Immunology, Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Ina M Vorberg
- German Center for Neurodegenerative Diseases (DZNE e.V.), Bonn, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health and German Center for Infection Research (DZIF), Munich, Germany
| | - Laurent Lacroix
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Benjamin Audit
- Univ Lyon, ENS de Lyon, Univ. Claude Bernard, CNRS, Laboratoire de Physique, 69342 Lyon, France
| | - Aloys Schepers
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Munich, Germany
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31
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Dukaj L, Rhind N. The capacity of origins to load MCM establishes replication timing patterns. PLoS Genet 2021; 17:e1009467. [PMID: 33764973 PMCID: PMC8023499 DOI: 10.1371/journal.pgen.1009467] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/06/2021] [Accepted: 03/04/2021] [Indexed: 11/24/2022] Open
Abstract
Loading of the MCM replicative helicase at origins of replication is a highly regulated process that precedes DNA replication in all eukaryotes. The stoichiometry of MCM loaded at origins has been proposed to be a key determinant of when those origins initiate replication during S phase. Nevertheless, the genome-wide regulation of MCM loading stoichiometry and its direct effect on replication timing remain unclear. In order to investigate why some origins load more MCM than others, we perturbed MCM levels in budding yeast cells and, for the first time, directly measured MCM levels and replication timing in the same experiment. Reduction of MCM levels through degradation of Mcm4, one of the six obligate components of the MCM complex, slowed progression through S phase and increased sensitivity to replication stress. Reduction of MCM levels also led to differential loading at origins during G1, revealing origins that are sensitive to reductions in MCM and others that are not. Sensitive origins loaded less MCM under normal conditions and correlated with a weak ability to recruit the origin recognition complex (ORC). Moreover, reduction of MCM loading at specific origins of replication led to a delay in their replication during S phase. In contrast, overexpression of MCM had no effects on cell cycle progression, relative MCM levels at origins, or replication timing, suggesting that, under optimal growth conditions, cellular MCM levels are not limiting for MCM loading. Our results support a model in which the loading capacity of origins is the primary determinant of MCM stoichiometry in wild-type cells, but that stoichiometry is controlled by origins' ability to recruit ORC and compete for MCM when MCM becomes limiting.
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Affiliation(s)
- Livio Dukaj
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, Massachusetts, United States of America
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, Massachusetts, United States of America
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32
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A novel role for Dun1 in the regulation of origin firing upon hyper-acetylation of H3K56. PLoS Genet 2021; 17:e1009391. [PMID: 33600490 PMCID: PMC7924802 DOI: 10.1371/journal.pgen.1009391] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 03/02/2021] [Accepted: 02/01/2021] [Indexed: 01/27/2023] Open
Abstract
During DNA replication newly synthesized histones are incorporated into the chromatin of the replicating sister chromatids. In the yeast Saccharomyces cerevisiae new histone H3 molecules are acetylated at lysine 56. This modification is carefully regulated during the cell cycle, and any disruption of this process is a source of genomic instability. Here we show that the protein kinase Dun1 is necessary in order to maintain viability in the absence of the histone deacetylases Hst3 and Hst4, which remove the acetyl moiety from histone H3. This lethality is not due to the well-characterized role of Dun1 in upregulating dNTPs, but rather because Dun1 is needed in order to counteract the checkpoint kinase Rad53 (human CHK2) that represses the activity of late firing origins. Deletion of CTF18, encoding the large subunit of an alternative RFC-like complex (RLC), but not of components of the Elg1 or Rad24 RLCs, is enough to overcome the dependency of cells with hyper-acetylated histones on Dun1. We show that the detrimental function of Ctf18 depends on its interaction with the leading strand polymerase, Polε. Our results thus show that the main problem of cells with hyper-acetylated histones is the regulation of their temporal and replication programs, and uncover novel functions for the Dun1 protein kinase and the Ctf18 clamp loader. Within the cell’s nucleus the DNA is wrapped around proteins called histones. Upon DNA replication, newly synthesized H3 histones are acetylated at lysine 56. This acetylation is significant for the cell because when it is not removed in a timely manner it leads to genomic instability. We have investigated the source of this instability and discovered that the kinase Dun1, usually implicated in the regulation of dNTPs, the building blocks of DNA, has a novel, dNTP-independent, essential role when histones are hyper-acetylated. The essential role of Dun1 is in the regulation of the temporal program of DNA replication. Thus, our results uncover what the main defect is in cells unable to regulate the acetylation of histones, while revealing new functions for well-characterized proteins with roles in genome stability maintenance.
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33
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Gaggioli V, Kieninger MR, Klucnika A, Butler R, Zegerman P. Identification of the critical replication targets of CDK reveals direct regulation of replication initiation factors by the embryo polarity machinery in C. elegans. PLoS Genet 2020; 16:e1008948. [PMID: 33320862 PMCID: PMC7771872 DOI: 10.1371/journal.pgen.1008948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 12/29/2020] [Accepted: 11/02/2020] [Indexed: 12/26/2022] Open
Abstract
During metazoan development, the cell cycle is remodelled to coordinate proliferation with differentiation. Developmental cues cause dramatic changes in the number and timing of replication initiation events, but the mechanisms and physiological importance of such changes are poorly understood. Cyclin-dependent kinases (CDKs) are important for regulating S-phase length in many metazoa, and here we show in the nematode Caenorhabditis elegans that an essential function of CDKs during early embryogenesis is to regulate the interactions between three replication initiation factors SLD-3, SLD-2 and MUS-101 (Dpb11/TopBP1). Mutations that bypass the requirement for CDKs to generate interactions between these factors is partly sufficient for viability in the absence of Cyclin E, demonstrating that this is a critical embryonic function of this Cyclin. Both SLD-2 and SLD-3 are asymmetrically localised in the early embryo and the levels of these proteins inversely correlate with S-phase length. We also show that SLD-2 asymmetry is determined by direct interaction with the polarity protein PKC-3. This study explains an essential function of CDKs for replication initiation in a metazoan and provides the first direct molecular mechanism through which polarization of the embryo is coordinated with DNA replication initiation factors. How and when a cell divides changes as the cell assumes different fates. How these changes in cell division are brought about are poorly understood, but are critical to ensure that cells do not over-proliferate leading to cancer. The nematode C. elegans is an excellent system to study the role of cell cycle changes during animal development. Here we show that two factors SLD-2 and SLD-3 are critical to control the decision to begin genome duplication. We show that these factors are differently distributed to different cell lineages in the early embryo, which may be a key event in determining the cell cycle rate in these cells. For the first time we show that, PKC-3, a key component of the machinery that determines the front (anterior) from the back (posterior) of the embryo directly controls SLD-2 distribution, which might explain how the polarisation of the embryo causes changes in the proliferation of different cell lineages. As PKC-3 is frequently mutated in human cancers, how this factor controls cell proliferation may be important to understand tumour progression.
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Affiliation(s)
- Vincent Gaggioli
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
| | - Manuela R. Kieninger
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
| | - Anna Klucnika
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, United Kingdom
| | - Richard Butler
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
| | - Philip Zegerman
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, United Kingdom
- * E-mail:
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34
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Strobino M, Wenda JM, Padayachy L, Steiner FA. Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans. Genome Res 2020; 30:1740-1751. [PMID: 33172964 PMCID: PMC7706726 DOI: 10.1101/gr.260794.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Histone H3.3 is a replication-independent variant of histone H3 with important roles in development, differentiation, and fertility. Here, we show that loss of H3.3 results in replication defects in Caenorhabditis elegans embryos at elevated temperatures. To characterize these defects, we adapt methods to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the genome is replicated from early and late firing origins and is partitioned into domains of early and late replication. We find that under temperature stress conditions, additional replication origins become activated. Moreover, loss of H3.3 results in altered replication fork progression around origins, which is particularly evident at stress-activated origins. These replication defects are accompanied by replication checkpoint activation, a delayed cell cycle, and increased lethality in checkpoint-compromised embryos. Our comprehensive analysis of DNA replication in C. elegans reveals the genomic location of replication origins and the dynamics of their firing, and uncovers a role of H3.3 in the regulation of replication origins under stress conditions.
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Affiliation(s)
- Maude Strobino
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Joanna M Wenda
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Laura Padayachy
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
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35
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Ding Q, Koren A. Positive and Negative Regulation of DNA Replication Initiation. Trends Genet 2020; 36:868-879. [PMID: 32739030 PMCID: PMC7572746 DOI: 10.1016/j.tig.2020.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
Genomic DNA is replicated every cell cycle by the programmed activation of replication origins at specific times and chromosomal locations. The factors that define the locations of replication origins and their typical activation times in eukaryotic cells are poorly understood. Previous studies highlighted the role of activating factors and epigenetic modifications in regulating replication initiation. Here, we review the role that repressive pathways - and their alleviation - play in establishing the genomic landscape of replication initiation. Several factors mediate this repression, in particular, factors associated with inactive chromatin. Repression can support organized, yet stochastic, replication initiation, and its absence could explain instances of rapid and random replication or re-replication.
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Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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Hsieh YYP, Makrantoni V, Robertson D, Marston AL, Murray AW. Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis. PLoS Biol 2020; 18:e3000635. [PMID: 32155147 PMCID: PMC7138332 DOI: 10.1371/journal.pbio.3000635] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/07/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
The role of proteins often changes during evolution, but we do not know how cells adapt when a protein is asked to participate in a different biological function. We forced the budding yeast, Saccharomyces cerevisiae, to use the meiosis-specific kleisin, recombination 8 (Rec8), during the mitotic cell cycle, instead of its paralog, Scc1. This perturbation impairs sister chromosome linkage, advances the timing of genome replication, and reduces reproductive fitness by 45%. We evolved 15 parallel populations for 1,750 generations, substantially increasing their fitness, and analyzed the genotypes and phenotypes of the evolved cells. Only one population contained a mutation in Rec8, but many populations had mutations in the transcriptional mediator complex, cohesin-related genes, and cell cycle regulators that induce S phase. These mutations improve sister chromosome cohesion and delay genome replication in Rec8-expressing cells. We conclude that changes in known and novel partners allow cells to use an existing protein to participate in new biological functions.
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Affiliation(s)
- Yu-Ying Phoebe Hsieh
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Vasso Makrantoni
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel Robertson
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Adèle L. Marston
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew W. Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
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