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Tremblay R, Mehrjoo Y, Ahmed O, Simoneau A, McQuaid ME, Affar EB, Nislow C, Giaever G, Wurtele H. Persistent Acetylation of Histone H3 Lysine 56 Compromises the Activity of DNA Replication Origins. Mol Cell Biol 2023; 43:566-595. [PMID: 37811746 PMCID: PMC10791153 DOI: 10.1080/10985549.2023.2259739] [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: 10/21/2022] [Accepted: 08/09/2023] [Indexed: 10/10/2023] Open
Abstract
In Saccharomyces cerevisiae, newly synthesized histones H3 are acetylated on lysine 56 (H3 K56ac) by the Rtt109 acetyltransferase prior to their deposition on nascent DNA behind replication forks. Two deacetylases of the sirtuin family, Hst3 and Hst4, remove H3 K56ac from chromatin after S phase. hst3Δ hst4Δ cells present constitutive H3 K56ac, which sensitizes cells to replicative stress via unclear mechanisms. A chemogenomic screen revealed that DBF4 heterozygosity sensitizes cells to NAM-induced inhibition of sirtuins. DBF4 and CDC7 encode subunits of the Dbf4-dependent kinase (DDK), which activates origins of DNA replication during S phase. We show that (i) cells harboring the dbf4-1 or cdc7-4 hypomorphic alleles are sensitized to NAM, and that (ii) the sirtuins Sir2, Hst1, Hst3, and Hst4 promote DNA replication in cdc7-4 cells. We further demonstrate that Rif1, an inhibitor of DDK-dependent activation of origins, causes DNA damage and replication defects in NAM-treated cells and hst3Δ hst4Δ mutants. cdc7-4 hst3Δ hst4Δ cells are shown to display delayed initiation of DNA replication, which is not due to intra-S checkpoint activation but requires Rtt109-dependent H3 K56ac. Our results suggest that constitutive H3 K56ac sensitizes cells to replicative stress in part by negatively influencing the activation of origins of DNA replication.
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Affiliation(s)
- Roch Tremblay
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Yosra Mehrjoo
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Oumaima Ahmed
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Antoine Simoneau
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Mary E. McQuaid
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Department of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Department of Medicine, Université de Montréal, Montreal, Québec, Canada
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Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun 2021; 12:6003. [PMID: 34650064 PMCID: PMC8516963 DOI: 10.1038/s41467-021-26077-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.
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Affiliation(s)
- Dayana E. Salas-Leiva
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada ,grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Eelco C. Tromer
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom ,grid.4830.f0000 0004 0407 1981Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Bruce A. Curtis
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Jon Jerlström-Hultqvist
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Martin Kolisko
- grid.418095.10000 0001 1015 3316Institute of Parasitology, Biology Centre, Czech Acad. Sci, České Budějovice, Czech Republic
| | - Zhenzhen Yi
- grid.263785.d0000 0004 0368 7397Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Joan S. Salas-Leiva
- grid.466575.30000 0001 1835 194XCONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136 Chihuahua, Chih. México
| | - Lucie Gallot-Lavallée
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Shelby K. Williams
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Geert J. P. L. Kops
- grid.7692.a0000000090126352Oncode Institute, Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - John M. Archibald
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Alastair G. B. Simpson
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Andrew J. Roger
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
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The Amazing Acrobat: Yeast's Histone H3K56 Juggles Several Important Roles While Maintaining Perfect Balance. Genes (Basel) 2021; 12:genes12030342. [PMID: 33668997 PMCID: PMC7996553 DOI: 10.3390/genes12030342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 01/16/2023] Open
Abstract
Acetylation on lysine 56 of histone H3 of the yeast Saccharomyces cerevisiae has been implicated in many cellular processes that affect genome stability. Despite being the object of much research, the complete scope of the roles played by K56 acetylation is not fully understood even today. The acetylation is put in place at the S-phase of the cell cycle, in order to flag newly synthesized histones that are incorporated during DNA replication. The signal is removed by two redundant deacetylases, Hst3 and Hst4, at the entry to G2/M phase. Its crucial location, at the entry and exit points of the DNA into and out of the nucleosome, makes this a central modification, and dictates that if acetylation and deacetylation are not well concerted and executed in a timely fashion, severe genomic instability arises. In this review, we explore the wealth of information available on the many roles played by H3K56 acetylation and the deacetylases Hst3 and Hst4 in DNA replication and repair.
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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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Damasceno JD, Marques CA, Black J, Briggs E, McCulloch R. Read, Write, Adapt: Challenges and Opportunities during Kinetoplastid Genome Replication. Trends Genet 2020; 37:21-34. [PMID: 32993968 PMCID: PMC9213392 DOI: 10.1016/j.tig.2020.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022]
Abstract
The genomes of all organisms are read throughout their growth and development, generating new copies during cell division and encoding the cellular activities dictated by the genome’s content. However, genomes are not invariant information stores but are purposefully altered in minor and major ways, adapting cellular behaviour and driving evolution. Kinetoplastids are eukaryotic microbes that display a wide range of such read–write genome activities, in many cases affecting critical aspects of their biology, such as host adaptation. Here we discuss the range of read–write genome changes found in two well-studied kinetoplastid parasites, Trypanosoma brucei and Leishmania, focusing on recent work that suggests such adaptive genome variation is linked to novel strategies the parasites use to replicate their unconventional genomes. Polycistronic transcription dominates and shapes kinetoplastid genomes, inevitably leading to clashes with DNA replication. By harnessing the resultant DNA damage for adaptation, kinetoplastids have huge potential for dynamic read–write genome variation. Major origins of DNA replication are confined to the boundaries of polycistronic transcription units in the Trypanosoma brucei and Leishmania genomes, putatively limiting DNA damage. Subtelomeres may lack this arrangement, generating read–write hotspots. In T. brucei, early replication of the highly transcribed subtelomeric variant surface glycoprotein (VSG) expression site may ensure replication-transcription clashes within this site to trigger DNA recombination, an event critical for antigenic variation. Leishmania genomes show extensive aneuploidy and copy number variation. Notably, DNA replication requires recombination factors and relies on post-S phase replication of subtelomeres. Evolution of compartmentalised DNA replication programmes underpin important aspects of genome biology in kinetoplastids, illustrating the consolidation of genome maintenance strategies to promote genome plasticity.
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Affiliation(s)
- Jeziel D Damasceno
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK.
| | - Catarina A Marques
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Jennifer Black
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Emma Briggs
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK; Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK.
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Damasceno JD, Marques CA, Beraldi D, Crouch K, Lapsley C, Obonaga R, Tosi LR, McCulloch R. Genome duplication in Leishmania major relies on persistent subtelomeric DNA replication. eLife 2020; 9:58030. [PMID: 32897188 PMCID: PMC7511235 DOI: 10.7554/elife.58030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022] Open
Abstract
DNA replication is needed to duplicate a cell’s genome in S phase and segregate it during cell division. Previous work in Leishmania detected DNA replication initiation at just a single region in each chromosome, an organisation predicted to be insufficient for complete genome duplication within S phase. Here, we show that acetylated histone H3 (AcH3), base J and a kinetochore factor co-localise in each chromosome at only a single locus, which corresponds with previously mapped DNA replication initiation regions and is demarcated by localised G/T skew and G4 patterns. In addition, we describe previously undetected subtelomeric DNA replication in G2/M and G1-phase-enriched cells. Finally, we show that subtelomeric DNA replication, unlike chromosome-internal DNA replication, is sensitive to hydroxyurea and dependent on 9-1-1 activity. These findings indicate that Leishmania’s genome duplication programme employs subtelomeric DNA replication initiation, possibly extending beyond S phase, to support predominantly chromosome-internal DNA replication initiation within S phase.
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Affiliation(s)
- Jeziel Dener Damasceno
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Catarina A Marques
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Dario Beraldi
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Kathryn Crouch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Craig Lapsley
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Ricardo Obonaga
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz Ro Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
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Petty EL, Pillus L. Cell cycle roles for GCN5 revealed through genetic suppression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194625. [PMID: 32798737 DOI: 10.1016/j.bbagrm.2020.194625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 11/17/2022]
Abstract
The conserved acetyltransferase Gcn5 is a member of several complexes in eukaryotic cells, playing roles in regulating chromatin organization, gene expression, metabolism, and cell growth and differentiation via acetylation of both nuclear and cytoplasmic proteins. Distinct functions of Gcn5 have been revealed through a combination of biochemical and genetic approaches in many in vitro studies and model organisms. In this review, we focus on the unique insights that have been gleaned from suppressor studies of gcn5 phenotypes in the budding yeast Saccharomyces cerevisiae. Such studies were fundamental in the early understanding of the balance of counteracting chromatin activities in regulating transcription. Most recently, suppressor screens have revealed roles for Gcn5 in early cell cycle (G1 to S) gene expression and regulation of chromosome segregation during mitosis. Much has been learned, but many questions remain which will be informed by focused analysis of additional genetic and physical interactions.
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Affiliation(s)
- Emily L Petty
- University of California, San Diego, Division of Biological Sciences, Section of Molecular Biology, UCSD Moores Cancer Center, United States of America.
| | - Lorraine Pillus
- University of California, San Diego, Division of Biological Sciences, Section of Molecular Biology, UCSD Moores Cancer Center, United States of America.
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Boginya A, Detroja R, Matityahu A, Frenkel-Morgenstern M, Onn I. The chromatin remodeler Chd1 regulates cohesin in budding yeast and humans. Sci Rep 2019; 9:8929. [PMID: 31222142 PMCID: PMC6586844 DOI: 10.1038/s41598-019-45263-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 06/04/2019] [Indexed: 12/24/2022] Open
Abstract
Chd1 is a chromatin remodeler that is involved in nucleosome positioning and transcription. Deletion of CHD1 is a frequent event in prostate cancer. The Structural Maintenance of Chromosome (SMC) complex cohesin mediates long-range chromatin interactions and is involved in maintaining genome stability. We provide new evidence that Chd1 is a regulator of cohesin. In the yeast S. cerevisiae, Chd1 is not essential for viability. We show that deletion of the gene leads to a defect in sister chromatid cohesion and in chromosome morphology. Chl1 is a non-essential DNA helicase that has been shown to regulate cohesin loading. Surprisingly, co-deletion of CHD1 and CHL1 results in an additive cohesion defect but partial suppression of the chromosome structure phenotype. We found that the cohesin regulator Pds5 is overexpressed when Chd1 and Chl1 are deleted. However, Pds5 expression is reduced to wild type levels when both genes are deleted. Finally, we show a correlation in the expression of CHD1 and cohesin genes in prostate cancer patients. Furthermore, we show that overexpression of cohesin subunits is correlated with the aggressiveness of the tumor. The biological roles of the interplay between Chd1, Chl1 and SMCs are discussed.
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Affiliation(s)
- Alexandra Boginya
- Chromosome Instability and Dynamics Lab. The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Rajesh Detroja
- Cancer Genomics and Biocomputing of Complex Diseases Lab. The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Avi Matityahu
- Chromosome Instability and Dynamics Lab. The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and Biocomputing of Complex Diseases Lab. The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Itay Onn
- Chromosome Instability and Dynamics Lab. The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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Petty EL, Evpak M, Pillus L. Connecting GCN5's centromeric SAGA to the mitotic tension-sensing checkpoint. Mol Biol Cell 2018; 29:2201-2212. [PMID: 29995571 PMCID: PMC6249797 DOI: 10.1091/mbc.e17-12-0701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Multiple interdependent mechanisms ensure faithful segregation of chromosomes during cell division. Among these, the spindle assembly checkpoint monitors attachment of spindle microtubules to the centromere of each chromosome, whereas the tension-sensing checkpoint monitors the opposing forces between sister chromatid centromeres for proper biorientation. We report here a new function for the deeply conserved Gcn5 acetyltransferase in the centromeric localization of Rts1, a key player in the tension-sensing checkpoint. Rts1 is a regulatory component of protein phopshatase 2A, a near universal phosphatase complex, which is recruited to centromeres by the Shugoshin (Sgo) checkpoint component under low-tension conditions to maintain sister chromatid cohesion. We report that loss of Gcn5 disrupts centromeric localization of Rts1. Increased RTS1 dosage robustly suppresses gcn5∆ cell cycle and chromosome segregation defects, including restoration of Rts1 to centromeres. Sgo1’s Rts1-binding function also plays a key role in RTS1 dosage suppression of gcn5∆ phenotypes. Notably, we have identified residues of the centromere histone H3 variant Cse4 that function in these chromosome segregation-related roles of RTS1. Together, these findings expand the understanding of the mechanistic roles of Gcn5 and Cse4 in chromosome segregation.
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Affiliation(s)
- Emily L Petty
- Division of Biological Sciences, Molecular Biology, UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA 92103
| | - Masha Evpak
- Division of Biological Sciences, Molecular Biology, UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA 92103
| | - Lorraine Pillus
- Division of Biological Sciences, Molecular Biology, UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA 92103
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Hoggard TA, Chang F, Perry KR, Subramanian S, Kenworthy J, Chueng J, Shor E, Hyland EM, Boeke JD, Weinreich M, Fox CA. Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins. PLoS Genet 2018; 14:e1007418. [PMID: 29795547 PMCID: PMC5991416 DOI: 10.1371/journal.pgen.1007418] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/06/2018] [Accepted: 05/15/2018] [Indexed: 01/23/2023] Open
Abstract
Most active DNA replication origins are found within euchromatin, while origins within heterochromatin are often inactive or inhibited. In yeast, origin activity within heterochromatin is negatively controlled by the histone H4K16 deacetylase, Sir2, and at some heterochromatic loci also by the nucleosome binding protein, Sir3. The prevailing view has been that direct functions of Sir2 and Sir3 are confined to heterochromatin. However, growth defects in yeast mutants compromised for loading the MCM helicase, such as cdc6-4, are suppressed by deletion of either SIR2 or SIR3. While these and other observations indicate that SIR2,3 can have a negative impact on at least some euchromatic origins, the genomic scale of this effect was unknown. It was also unknown whether this suppression resulted from direct functions of Sir2,3 within euchromatin, or was an indirect effect of their previously established roles within heterochromatin. Using MCM ChIP-Seq, we show that a SIR2 deletion rescued MCM complex loading at ~80% of euchromatic origins in cdc6-4 cells. Therefore, Sir2 exhibited a pervasive effect at the majority of euchromatic origins. Using MNase-H4K16ac ChIP-Seq, we show that origin-adjacent nucleosomes were depleted for H4K16 acetylation in a SIR2-dependent manner in wild type (i.e. CDC6) cells. In addition, we present evidence that both Sir2 and Sir3 bound to nucleosomes adjacent to euchromatic origins. The relative levels of each of these molecular hallmarks of yeast heterochromatin–SIR2-dependent H4K16 hypoacetylation, Sir2, and Sir3 –correlated with how strongly a SIR2 deletion suppressed the MCM loading defect in cdc6-4 cells. Finally, a screen for histone H3 and H4 mutants that could suppress the cdc6-4 growth defect identified amino acids that map to a surface of the nucleosome important for Sir3 binding. We conclude that heterochromatin proteins directly modify the local chromatin environment of euchromatic DNA replication origins. When a cell divides, it must copy or “replicate” its DNA. DNA replication starts at chromosomal regions called origins when a collection of replication proteins gains local access to unwind the two DNA strands. Chromosomal DNA is packaged into a protein-DNA complex called chromatin and there are two major structurally and functionally distinct types. Euchromatin allows DNA replication proteins to access origin DNA, while heterochromatin inhibits their access. The prevalent view has been that the heterochromatin proteins required to inhibit origins are confined to heterochromatin. In this study, the conserved heterochromatin proteins, Sir2 and Sir3, were shown to both physically and functionally associate with the majority of origins in euchromatin. This observation raises important questions about the chromosomal targets of heterochromatin proteins, and how and why the majority of origins exist within a potentially repressive chromatin structure.
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Affiliation(s)
- Timothy A. Hoggard
- Department of Biomolecular Chemistry, School of Medicine and Public Health, Madison, WI, United States of America
| | - FuJung Chang
- Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute, Grand Rapids, MI, United States of America
| | - Kelsey Rae Perry
- Department of Biomolecular Chemistry, School of Medicine and Public Health, Madison, WI, United States of America
- Integrated Program in Biochemistry, School of Medicine and Public Health and College of Agricultural Sciences, University of Wisconsin, Madison, WI, United States of America
| | - Sandya Subramanian
- Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute, Grand Rapids, MI, United States of America
| | - Jessica Kenworthy
- Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute, Grand Rapids, MI, United States of America
| | - Julie Chueng
- Integrated Program in Biochemistry, School of Medicine and Public Health and College of Agricultural Sciences, University of Wisconsin, Madison, WI, United States of America
| | - Erika Shor
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Edel M. Hyland
- School of Biological Sciences, Medical Biology Center, Queen’s University, Belfast, United Kingdom
| | - Jef D. Boeke
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics and NYU Langone Health, New York, NY, United States of America
| | - Michael Weinreich
- Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute, Grand Rapids, MI, United States of America
- * E-mail: (MW); (CAF)
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, Madison, WI, United States of America
- Integrated Program in Biochemistry, School of Medicine and Public Health and College of Agricultural Sciences, University of Wisconsin, Madison, WI, United States of America
- * E-mail: (MW); (CAF)
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11
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Müller CA, Nieduszynski CA. DNA replication timing influences gene expression level. J Cell Biol 2017; 216:1907-1914. [PMID: 28539386 PMCID: PMC5496624 DOI: 10.1083/jcb.201701061] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/06/2017] [Accepted: 04/19/2017] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic genomes are replicated in a reproducible temporal order whose physiological significance is poorly understood. Müller and Nieduszynski compare the temporal order of genome replication in phylogenetically diverse yeast species and identify genes for which conserved replication timing contributes to maximal expression. Eukaryotic genomes are replicated in a reproducible temporal order; however, the physiological significance is poorly understood. We compared replication timing in divergent yeast species and identified genomic features with conserved replication times. Histone genes were among the earliest replicating loci in all species. We specifically delayed the replication of HTA1-HTB1 and discovered that this halved the expression of these histone genes. Finally, we showed that histone and cell cycle genes in general are exempt from Rtt109-dependent dosage compensation, suggesting the existence of pathways excluding specific loci from dosage compensation mechanisms. Thus, we have uncovered one of the first physiological requirements for regulated replication time and demonstrated a direct link between replication timing and gene expression.
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Affiliation(s)
- Carolin A Müller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, England, UK
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12
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Hang L, Zhao X. The Rtt107 BRCT scaffold and its partner modification enzymes collaborate to promote replication. Nucleus 2016; 7:346-51. [PMID: 27385431 DOI: 10.1080/19491034.2016.1201624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Faithful duplication of the entire genome during each cell cycle is key for genome maintenance. Each stage of DNA replication, including initiation, progression, and termination, is tightly regulated. Some of these regulations enable replisomes to overcome tens of thousands of template obstacles that block DNA synthesis. Previous studies have identified a large number of proteins that are dedicated to this mission, including protein modification enzymes and scaffold proteins. Protein modification enzymes can bestow fast and reversible changes on many substrates, and thus are ideal for coordinating multiple events needed to promptly overcome replication impediments. Scaffold proteins can support specific protein-protein interactions that enable protein complex formation, protein recruitment, and partner enzyme functions. Taken together with previous studies, our recent work elucidates that a group of modification and scaffold proteins form several complexes to aid replication progression and are particularly important for synthesizing large replicons. Additionally, our work reveals that the intrinsic plasticity of the replication initiation program can be used to compensate for deficient replication progression. (1).
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Affiliation(s)
- Lisa Hang
- a Molecular Biology Program, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
| | - Xiaolan Zhao
- a Molecular Biology Program, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
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13
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Hang LE, Peng J, Tan W, Szakal B, Menolfi D, Sheng Z, Lobachev K, Branzei D, Feng W, Zhao X. Rtt107 Is a Multi-functional Scaffold Supporting Replication Progression with Partner SUMO and Ubiquitin Ligases. Mol Cell 2015; 60:268-79. [PMID: 26439300 DOI: 10.1016/j.molcel.2015.08.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 07/15/2015] [Accepted: 08/25/2015] [Indexed: 11/17/2022]
Abstract
Elucidating the individual and collaborative functions of genome maintenance factors is critical for understanding how genome duplication is achieved. Here, we investigate a conserved scaffold in budding yeast, Rtt107, and its three partners: a SUMO E3 complex, a ubiquitin E3 complex, and Slx4. Biochemical and genetic findings show that Rtt107 interacts separately with these partners and contributes to their individual functions, including a role in replisome sumoylation. We also provide evidence that Rtt107 associates with replisome components, and both itself and its associated E3s are important for replicating regions far from initiation sites. Corroborating these results, replication defects due to Rtt107 loss and genotoxic sensitivities in mutants of Rtt107 and its associated E3s are rescued by increasing replication initiation events through mutating two master repressors of late origins, Mrc1 and Mec1. These findings suggest that Rtt107 functions as a multi-functional platform to support replication progression with its partner E3 enzymes.
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Affiliation(s)
- Lisa E Hang
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jie Peng
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Wei Tan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Barnabas Szakal
- IFOM, The FIRC (Fondazione Italiana per la Ricerca sul Cancro) of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Demis Menolfi
- IFOM, The FIRC (Fondazione Italiana per la Ricerca sul Cancro) of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Ziwei Sheng
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kirill Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Dana Branzei
- IFOM, The FIRC (Fondazione Italiana per la Ricerca sul Cancro) of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Wenyi Feng
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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14
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Irene C, Theis JF, Gresham D, Soteropoulos P, Newlon CS. Hst3p, a histone deacetylase, promotes maintenance of Saccharomyces cerevisiae chromosome III lacking efficient replication origins. Mol Genet Genomics 2015; 291:271-83. [PMID: 26319649 PMCID: PMC4729790 DOI: 10.1007/s00438-015-1105-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/12/2015] [Indexed: 01/15/2023]
Abstract
Long gaps between active replication origins probably occur frequently during chromosome replication, but little is known about how cells cope with them. To address this issue, we deleted replication origins from S. cerevisiae chromosome III to create chromosomes with long interorigin gaps and identified mutations that destabilize them [originless fragment maintenance (Ofm) mutations]. ofm6-1 is an allele of HST3, a sirtuin that deacetylates histone H3K56Ac. Hst3p and Hst4p are closely related, but hst4Δ does not cause an Ofm phenotype. Expressing HST4 under the control of the HST3 promoter suppressed the Ofm phenotype of hst3Δ, indicating Hst4p, when expressed at the appropriate levels and/or at the correct time, can fully substitute for Hst3p in maintenance of ORIΔ chromosomes. H3K56Ac is the Hst3p substrate critical for chromosome maintenance. H3K56Ac-containing nucleosomes are preferentially assembled into chromatin behind replication forks. Deletion of the H3K56 acetylase and downstream chromatin assembly factors suppressed the Ofm phenotype of hst3, indicating that persistence of H3K56Ac-containing chromatin is deleterious for the maintenance of ORIΔ chromosomes, and experiments with synchronous cultures showed that it is replication of H3K56Ac-containing chromatin that causes chromosome loss. This work shows that while normal chromosomes can tolerate hyperacetylation of H3K56Ac, deacetylation of histone H3K56Ac by Hst3p is required for stable maintenance of a chromosome with a long interorigin gap. The Ofm phenotype is the first report of a chromosome instability phenotype of an hst3 single mutant.
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Affiliation(s)
- Carmela Irene
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, ICPH, 225 Warren St., Newark, NJ, 07101-1701, USA
| | - James F Theis
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, ICPH, 225 Warren St., Newark, NJ, 07101-1701, USA
| | - David Gresham
- Department of Biology, Center for Genomics and System Biology, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Patricia Soteropoulos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, ICPH, 225 Warren St., Newark, NJ, 07101-1701, USA
| | - Carol S Newlon
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, ICPH, 225 Warren St., Newark, NJ, 07101-1701, USA.
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15
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Musiałek MW, Rybaczek D. Behavior of replication origins in Eukaryota - spatio-temporal dynamics of licensing and firing. Cell Cycle 2015; 14:2251-64. [PMID: 26030591 DOI: 10.1080/15384101.2015.1056421] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Although every organism shares some common features of replication, this process varies greatly among eukaryotic species. Current data show that mathematical models of the organization of origins based on possibility theory may be applied (and remain accurate) in every model organism i.e. from yeast to humans. The major differences lie within the dynamics of origin firing and the regulation mechanisms that have evolved to meet new challenges throughout the evolution of the organism. This article elaborates on the relations between chromatin structure, organization of origins, their firing times and the impact that these features can have on genome stability, showing both differences and parallels inside the eukaryotic domain.
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Key Words
- APC, anaphase promoting complex
- ARS, autonomously replicating sequences
- ATR, ataxia telangiectasia mutated and Rad3-related kinase
- C-Frag, chromosome fragmentation
- CDK, cyclin-dependent kinase
- CDT, C-terminus domain
- CEN, centromere
- CFSs, chromosome fragile sites
- CIN, chromosome instability
- CMG, Cdc45-MCM-GINS complex
- Cdc45, cell division control protein 45
- Cdc6, cell division control protein 6
- Cdt1, chromatin licensing and DNA replication factor 1
- Chk1, checkpoint kinase 1
- Clb2, G2/mitotic-specific cyclin Clb2
- DCR, Ddb1-Cu14a-Roc1 complex
- DDK, Dbf-4-dependent kinase
- DSBs, double strand breaks
- Dbf4, protein Dbf4 homolog A
- Dfp1, Hsk1-Dfp1 kinase complex regulatory subunit Dfp1
- Dpb11, DNA replication regulator Dpb11
- E2F, E2F transcription factor
- EL, early to late origins transition
- ETG1, E2F target gene 1/replisome factor
- Fkh, fork head domain protein
- GCN5, histone acetyltransferase GCN5
- GINS, go-ichi-ni-san
- LE, late to early origins transition
- MCM2–7, minichromosome maintenance helicase complex
- NDT, N-terminus domain
- ORC, origin recognition complex
- ORCA, origin recognition complex subunit A
- PCC, premature chromosome condensation
- PCNA, proliferating cell nuclear antigen
- RO, replication origin
- RPD3, histone deacetylase 3
- RTC, replication timing control
- Rif1, replication timing regulatory factor 1
- SCF, Skp1-Cullin-F-Box ligase
- SIR, sulfite reductase
- Sld2, replication regulator Sld2
- Sld3, replication regulator Sld3
- Swi6, chromatin-associated protein swi6
- Taz1, telomere length regulator taz1
- YKU70, yeast Ku protein.
- dormant origins
- mathematical models of replication
- ori, origin
- origin competence
- origin efficiency
- origin firing
- origin licensing
- p53, tumor suppressor protein p53
- replication timing
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Affiliation(s)
- Marcelina W Musiałek
- a Department of Cytophysiology ; Institute of Experimental Biology; Faculty of Biology and Environmental Protection; University of Łódź ; Łódź , Poland
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16
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Covo S, Chiou E, Gordenin DA, Resnick MA. Suppression of allelic recombination and aneuploidy by cohesin is independent of Chk1 in Saccharomyces cerevisiae. PLoS One 2014; 9:e113435. [PMID: 25551702 PMCID: PMC4281242 DOI: 10.1371/journal.pone.0113435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/23/2014] [Indexed: 12/16/2022] Open
Abstract
Sister chromatid cohesion (SCC), which is established during DNA replication, ensures genome stability. Establishment of SCC is inhibited in G2. However, this inhibition is relived and SCC is established as a response to DNA damage, a process known as Damage Induced Cohesion (DIC). In yeast, Chk1, which is a kinase that functions in DNA damage signal transduction, is considered an activator of SCC through DIC. Nonetheless, here we show that, unlike SCC mutations, loss of CHK1 did not increase spontaneous or damage-induced allelic recombination or aneuploidy. We suggest that Chk1 has a redundant role in the control of DIC or that DIC is redundant for maintaining genome stability.
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Affiliation(s)
- Shay Covo
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Eric Chiou
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Dmitry A. Gordenin
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Michael A. Resnick
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
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17
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Bogenschutz NL, Rodriguez J, Tsukiyama T. Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome. PLoS One 2014; 9:e114545. [PMID: 25486280 PMCID: PMC4259332 DOI: 10.1371/journal.pone.0114545] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 11/11/2014] [Indexed: 12/18/2022] Open
Abstract
Eukaryotic DNA replication initiates from multiple sites on each chromosome called replication origins (origins). In the budding yeast Saccharomyces cerevisiae, origins are defined at discrete sites. Regular spacing and diverse firing characteristics of origins are thought to be required for efficient completion of replication, especially in the presence of replication stress. However, a S. cerevisiae chromosome III harboring multiple origin deletions has been reported to replicate relatively normally, and yet how an origin-deficient chromosome could accomplish successful replication remains unknown. To address this issue, we deleted seven well-characterized origins from chromosome VI, and found that these deletions do not cause gross growth defects even in the presence of replication inhibitors. We demonstrated that the origin deletions do cause a strong decrease in the binding of the origin recognition complex. Unexpectedly, replication profiling of this chromosome showed that DNA replication initiates from non-canonical loci around deleted origins in yeast. These results suggest that replication initiation can be unexpectedly flexible in this organism.
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Affiliation(s)
- Naomi L. Bogenschutz
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jairo Rodriguez
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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18
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Alver RC, Chadha GS, Blow JJ. The contribution of dormant origins to genome stability: from cell biology to human genetics. DNA Repair (Amst) 2014; 19:182-9. [PMID: 24767947 PMCID: PMC4065331 DOI: 10.1016/j.dnarep.2014.03.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The ability of a eukaryotic cell to precisely and accurately replicate its DNA is crucial to maintain genome stability. Here we describe our current understanding of the process by which origins are licensed for DNA replication and review recent work suggesting that fork stalling has exerted a strong selective pressure on the positioning of licensed origins. In light of this, we discuss the complex and disparate phenotypes observed in mouse models and humans patients that arise due to defects in replication licensing proteins.
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Affiliation(s)
- Robert C Alver
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Gaganmeet Singh Chadha
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - J Julian Blow
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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19
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Ayuda-Durán P, Devesa F, Gomes F, Sequeira-Mendes J, Avila-Zarza C, Gómez M, Calzada A. The CDK regulators Cdh1 and Sic1 promote efficient usage of DNA replication origins to prevent chromosomal instability at a chromosome arm. Nucleic Acids Res 2014; 42:7057-68. [PMID: 24753426 PMCID: PMC4066753 DOI: 10.1093/nar/gku313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Robustness and completion of DNA replication rely on redundant DNA replication origins. Reduced efficiency of origin licensing is proposed to contribute to chromosome instability in CDK-deregulated cell cycles, a frequent alteration in oncogenesis. However, the mechanism by which this instability occurs is largely unknown. Current models suggest that limited origin numbers would reduce fork density favouring chromosome rearrangements, but experimental support in CDK-deregulated cells is lacking. We have investigated the pattern of origin firing efficiency in budding yeast cells lacking the CDK regulators Cdh1 and Sic1. We show that each regulator is required for efficient origin activity, and that both cooperate non-redundantly. Notably, origins are differentially sensitive to CDK deregulation. Origin sensitivity is independent on normal origin efficiency, firing timing or chromosomal location. Interestingly, at a chromosome arm, there is a shortage of origin firing involving active and dormant origins, and the extent of shortage correlates with the severity of CDK deregulation and chromosome instability. We therefore propose that CDK deregulation in G1 phase compromises origin redundancy by decreasing the number of active and dormant origins, leading to origin shortage and increased chromosome instability.
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Affiliation(s)
- Pilar Ayuda-Durán
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología CNB-CSIC, Darwin 3, Madrid 28049, Spain
| | - Fernando Devesa
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología CNB-CSIC, Darwin 3, Madrid 28049, Spain
| | - Fábia Gomes
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología CNB-CSIC, Darwin 3, Madrid 28049, Spain
| | - Joana Sequeira-Mendes
- Centro de Biología Molecular Severo Ochoa CBMSO-CSIC/UAM, Nicolás Cabrera 1, Madrid 28049, Spain
| | | | - María Gómez
- Centro de Biología Molecular Severo Ochoa CBMSO-CSIC/UAM, Nicolás Cabrera 1, Madrid 28049, Spain
| | - Arturo Calzada
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología CNB-CSIC, Darwin 3, Madrid 28049, Spain
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20
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Newman TJ, Mamun MA, Nieduszynski CA, Blow JJ. Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts. Nucleic Acids Res 2013; 41:9705-18. [PMID: 23963700 PMCID: PMC3834809 DOI: 10.1093/nar/gkt728] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/24/2013] [Accepted: 07/25/2013] [Indexed: 01/21/2023] Open
Abstract
During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication is maximized if replication origins are evenly spaced, the largest inter-origin distances are minimized, and the end-most origins are positioned close to chromosome ends. We show that origin positions in the yeast Saccharomyces cerevisiae genome conform to all three predictions thereby maximizing the probability of complete replication if replication forks stall. Origin positions in four other yeasts-Kluyveromyces lactis, Lachancea kluyveri, Lachancea waltii and Schizosaccharomyces pombe-also conform to these predictions. Equating failure rates at chromosome ends with those in chromosome interiors gives a mean per nucleotide fork stall rate of ∼5 × 10(-8), which is consistent with experimental estimates. Using this value in our theoretical predictions gives replication failure rates that are consistent with data from replication origin knockout experiments. Our theory also predicts that significantly larger genomes, such as those of mammals, will experience a much greater probability of replication failure genome-wide, and therefore will likely require additional compensatory mechanisms.
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Affiliation(s)
- Timothy J. Newman
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Mohammed A. Mamun
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Conrad A. Nieduszynski
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
| | - J. Julian Blow
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
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21
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Hoggard T, Shor E, Müller CA, Nieduszynski CA, Fox CA. A Link between ORC-origin binding mechanisms and origin activation time revealed in budding yeast. PLoS Genet 2013; 9:e1003798. [PMID: 24068963 PMCID: PMC3772097 DOI: 10.1371/journal.pgen.1003798] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 07/30/2013] [Indexed: 01/19/2023] Open
Abstract
Eukaryotic DNA replication origins are selected in G1-phase when the origin recognition complex (ORC) binds chromosomal positions and triggers molecular events culminating in the initiation of DNA replication (a.k.a. origin firing) during S-phase. Each chromosome uses multiple origins for its duplication, and each origin fires at a characteristic time during S-phase, creating a cell-type specific genome replication pattern relevant to differentiation and genome stability. It is unclear whether ORC-origin interactions are relevant to origin activation time. We applied a novel genome-wide strategy to classify origins in the model eukaryote Saccharomyces cerevisiae based on the types of molecular interactions used for ORC-origin binding. Specifically, origins were classified as DNA-dependent when the strength of ORC-origin binding in vivo could be explained by the affinity of ORC for origin DNA in vitro, and, conversely, as ‘chromatin-dependent’ when the ORC-DNA interaction in vitro was insufficient to explain the strength of ORC-origin binding in vivo. These two origin classes differed in terms of nucleosome architecture and dependence on origin-flanking sequences in plasmid replication assays, consistent with local features of chromatin promoting ORC binding at ‘chromatin-dependent’ origins. Finally, the ‘chromatin-dependent’ class was enriched for origins that fire early in S-phase, while the DNA-dependent class was enriched for later firing origins. Conversely, the latest firing origins showed a positive association with the ORC-origin DNA paradigm for normal levels of ORC binding, whereas the earliest firing origins did not. These data reveal a novel association between ORC-origin binding mechanisms and the regulation of origin activation time. Cell division requires the duplication of chromosomes, protein-DNA complexes harboring genetic information. Specific chromosomal positions, origins, initiate this duplication. Multiple origins are required for accurate, efficient duplication—an insufficient number leads to mistakes in the genetic material and pathologies such as cancer. Origins are chosen when the origin recognition complex (ORC) binds to them. The molecular interactions controlling this binding remain unclear. Understanding these interactions will lead to new ways to control cell division, which could aid in treatments of disease. Experiments were performed in the eukaryotic microbe budding yeast to define the types of molecular interactions ORC uses to bind origins. Yeasts are useful for these studies because chromosome duplication and structure are well conserved from yeast to humans. While ORC-DNA interactions were important, interactions between ORC and chromosomal proteins played a role. In addition, different origins relied on different types of molecular interactions with ORC. Finally, ORC-protein interactions but not ORC-DNA interactions were associated with enhanced origin function during chromosome-duplication, revealing an unanticipated link between the types of molecular interactions ORC uses to select an origin and the ultimate function of that origin. These results have implications for interfering with ORC-origin interactions to control cell division.
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Affiliation(s)
- Timothy Hoggard
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Program in Cellular and Molecular Biology, College of Agriculture and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Erika Shor
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Carolin A. Müller
- Centre for Genetics and Genomics, University of Nottingham Queen's Medical Centre, Nottingham, United Kingdom
| | - Conrad A. Nieduszynski
- Centre for Genetics and Genomics, University of Nottingham Queen's Medical Centre, Nottingham, United Kingdom
- * E-mail: (CAN); (CAF)
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Program in Cellular and Molecular Biology, College of Agriculture and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (CAN); (CAF)
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22
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Thorpe PH, Dittmar JC, Rothstein R. ScreenTroll: a searchable database to compare genome-wide yeast screens. Database (Oxford) 2012; 2012:bas022. [PMID: 22522342 PMCID: PMC3330810 DOI: 10.1093/database/bas022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Systematic biological screens typically identify many genes or proteins that are implicated in a specific phenotype. However, deriving mechanistic insight from these screens typically involves focusing upon one or a few genes within the set in order to elucidate their precise role in producing the phenotype. To find these critical genes, researchers use a variety of tools to query the set of genes to uncover underlying common genetic or physical interactions or common functional annotations (e.g. gene ontology terms). Not only it is necessary to find previous screens containing genes in common with the new set, but also useful to easily access the individual manuscript or study that classified those genes. Unfortunately, no tool currently exists to facilitate this task. We have developed a web-based tool (ScreenTroll) that queries one or more genes against a database of systematic yeast screens. The software determines which genome-wide yeast screens also identified the queried gene(s) and the resulting screens are listed in an order based on the extent of the overlap between the queried gene(s) and the open reading frames (ORFs) characterized in each individual yeast screen. In a separate list, the corresponding ORFs that are found in both the queried set of genes and each individual genome-wide screen are displayed along with links to the relevant manuscript via NIH's PubMed database. ScreenTroll is useful for comparing a list of ORFs with genes identified in a wide array of published genome-wide screens. This comparison informs users whether any of their queried ORFs overlaps a previous study in the ScreenTroll database. By listing the manuscript of the published screen, users can read more about the phenotype associated with that study. Together, this information provides insight into the function of the queried genes and helps the user focus on a subset of them.
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Affiliation(s)
- Peter H. Thorpe
- Department of Genetics & Development, Columbia University Medical Center, 701 West 168th Street, NY 10032, USA, Division of Stem Cell Biology & Developmental Genetics, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, NW7 1AA, UK and Department of Biological Sciences, Columbia University, NY 10027, USA
| | - John C. Dittmar
- Department of Genetics & Development, Columbia University Medical Center, 701 West 168th Street, NY 10032, USA, Division of Stem Cell Biology & Developmental Genetics, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, NW7 1AA, UK and Department of Biological Sciences, Columbia University, NY 10027, USA
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Medical Center, 701 West 168th Street, NY 10032, USA, Division of Stem Cell Biology & Developmental Genetics, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, NW7 1AA, UK and Department of Biological Sciences, Columbia University, NY 10027, USA
- *Corresponding author: Tel: +1 212 305 1733; Fax: +1 212 923 2090;
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Carr AM, Paek AL, Weinert T. DNA replication: failures and inverted fusions. Semin Cell Dev Biol 2011; 22:866-74. [PMID: 22020070 DOI: 10.1016/j.semcdb.2011.10.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 10/12/2011] [Indexed: 11/16/2022]
Abstract
DNA replication normally follows the rules passed down from Watson and Crick: the chromosome duplicates as dictated by its antiparallel strands, base-pairing and leading and lagging strand differences. Real-life replication is more complicated, fraught with perils posed by chromosome damage for one, and by transcription of genes and by other perils that disrupt progress of the DNA replication machinery. Understanding the replication fork, including DNA structures, associated replisome and its regulators, is key to understanding how cells overcome perils and minimize error. Replication fork error leads to genome rearrangements and, potentially, cell death. Interest in the replication fork and its errors has recently gained added interest by the results of deep sequencing studies of human genomes. Several pathologies are associated with sometimes-bizarre genome rearrangements suggestive of elaborate replication fork failures. To try and understand the links between the replication fork, its failure and genome rearrangements, we discuss here phases of fork behavior (stall, collapse, restart and fork failures leading to rearrangements) and analyze two examples of instability from our own studies; one in fission yeast and the other in budding yeast.
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Affiliation(s)
- Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, Sussex, UK.
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