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Zhang A, Friedman LJ, Gelles J, Bell SP. Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545300. [PMID: 37398123 PMCID: PMC10312730 DOI: 10.1101/2023.06.16.545300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
During origin licensing, the eukaryotic replicative helicase Mcm2-7 forms head-to-head double hexamers to prime origins for bidirectional replication. Recent single-molecule and structural studies revealed that one molecule of the helicase loader ORC can sequentially load two Mcm2-7 hexamers to ensure proper head-to-head helicase alignment. To perform this task, ORC must release from its initial high-affinity DNA binding site and "flip" to bind a weaker, inverted DNA site. However, the mechanism of this binding-site switch remains unclear. In this study, we used single-molecule Förster resonance energy transfer (sm-FRET) to study the changing interactions between DNA and ORC or Mcm2-7. We found that the loss of DNA bending that occurs during DNA deposition into the Mcm2-7 central channel increases the rate of ORC dissociation from DNA. Further studies revealed temporally-controlled DNA sliding of helicase-loading intermediates, and that the first sliding complex includes ORC, Mcm2-7, and Cdt1. We demonstrate that sequential events of DNA unbending, Cdc6 release, and sliding lead to a stepwise decrease in ORC stability on DNA, facilitating ORC dissociation from its strong binding site during site switching. In addition, the controlled sliding we observed provides insight into how ORC accesses secondary DNA binding sites at different locations relative to the initial binding site. Our study highlights the importance of dynamic protein-DNA interactions in the loading of two oppositely-oriented Mcm2-7 helicases to ensure bidirectional DNA replication. Significance Statement Bidirectional DNA replication, in which two replication forks travel in opposite directions from each origin of replication, is required for complete genome duplication. To prepare for this event, two copies of the Mcm2-7 replicative helicase are loaded at each origin in opposite orientations. Using single-molecule assays, we studied the sequence of changing protein-DNA interactions involved in this process. These stepwise changes gradually reduce the DNA-binding strength of ORC, the primary DNA binding protein involved in this event. This reduced affinity promotes ORC dissociation and rebinding in the opposite orientation on the DNA, facilitating the sequential assembly of two Mcm2-7 molecules in opposite orientations. Our findings identify a coordinated series of events that drive proper DNA replication initiation.
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Affiliation(s)
- Annie Zhang
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Larry J. Friedman
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Stephen P Bell
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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2
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Hu Y, Stillman B. Origins of DNA replication in eukaryotes. Mol Cell 2023; 83:352-372. [PMID: 36640769 PMCID: PMC9898300 DOI: 10.1016/j.molcel.2022.12.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Errors occurring during DNA replication can result in inaccurate replication, incomplete replication, or re-replication, resulting in genome instability that can lead to diseases such as cancer or disorders such as autism. A great deal of progress has been made toward understanding the entire process of DNA replication in eukaryotes, including the mechanism of initiation and its control. This review focuses on the current understanding of how the origin recognition complex (ORC) contributes to determining the location of replication initiation in the multiple chromosomes within eukaryotic cells, as well as methods for mapping the location and temporal patterning of DNA replication. Origin specification and configuration vary substantially between eukaryotic species and in some cases co-evolved with gene-silencing mechanisms. We discuss the possibility that centromeres and origins of DNA replication were originally derived from a common element and later separated during evolution.
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Affiliation(s)
- Yixin Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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3
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Cluett TJ, Akman G, Reyes A, Kazak L, Mitchell A, Wood SR, Spinazzola A, Spelbrink JN, Holt IJ. Transcript availability dictates the balance between strand-asynchronous and strand-coupled mitochondrial DNA replication. Nucleic Acids Res 2019; 46:10771-10781. [PMID: 30239839 PMCID: PMC6237803 DOI: 10.1093/nar/gky852] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 09/12/2018] [Indexed: 11/15/2022] Open
Abstract
Mammalian mitochondria operate multiple mechanisms of DNA replication. In many cells and tissues a strand-asynchronous mechanism predominates over coupled leading and lagging-strand DNA synthesis. However, little is known of the factors that control or influence the different mechanisms of replication, and the idea that strand-asynchronous replication entails transient incorporation of transcripts (aka bootlaces) is controversial. A firm prediction of the bootlace model is that it depends on mitochondrial transcripts. Here, we show that elevated expression of Twinkle DNA helicase in human mitochondria induces bidirectional, coupled leading and lagging-strand DNA synthesis, at the expense of strand-asynchronous replication; and this switch is accompanied by decreases in the steady-state level of some mitochondrial transcripts. However, in the so-called minor arc of mitochondrial DNA where transcript levels remain high, the strand-asynchronous replication mechanism is instated. Hence, replication switches to a strand-coupled mechanism only where transcripts are scarce, thereby establishing a direct correlation between transcript availability and the mechanism of replication. Thus, these findings support a critical role of mitochondrial transcripts in the strand-asynchronous mechanism of mitochondrial DNA replication; and, as a corollary, mitochondrial RNA availability and RNA/DNA hybrid formation offer means of regulating the mechanisms of DNA replication in the organelle.
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Affiliation(s)
- Tricia J Cluett
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | | | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | - Lawrence Kazak
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | - Alice Mitchell
- Department of Clinical Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London NW3 2PF, UK
| | - Stuart R Wood
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | - Antonella Spinazzola
- Department of Clinical Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London NW3 2PF, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
| | - Johannes N Spelbrink
- Department of Pediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Geert Grooteplein 10, 6500 HB, Nijmegen, The Netherlands
| | - Ian J Holt
- Department of Clinical Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London NW3 2PF, UK.,Biodonostia Health Research Institute, 20014 San Sebastián, Spain and IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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4
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Singh VK, Kumar V, Krishnamachari A. Prediction of replication sites in Saccharomyces cerevisiae genome using DNA segment properties: Multi-view ensemble learning (MEL) approach. Biosystems 2018; 163:59-69. [DOI: 10.1016/j.biosystems.2017.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/27/2017] [Accepted: 12/07/2017] [Indexed: 10/18/2022]
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5
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6
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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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7
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Origin replication complex binding, nucleosome depletion patterns, and a primary sequence motif can predict origins of replication in a genome with epigenetic centromeres. mBio 2014; 5:e01703-14. [PMID: 25182328 PMCID: PMC4173791 DOI: 10.1128/mbio.01703-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Origins of DNA replication are key genetic elements, yet their identification remains elusive in most organisms. In previous work, we found that centromeres contain origins of replication (ORIs) that are determined epigenetically in the pathogenic yeast Candida albicans. In this study, we used origin recognition complex (ORC) binding and nucleosome occupancy patterns in Saccharomyces cerevisiae and Kluyveromyces lactis to train a machine learning algorithm to predict the position of active arm (noncentromeric) origins in the C. albicans genome. The model identified bona fide active origins as determined by the presence of replication intermediates on nondenaturing two-dimensional (2D) gels. Importantly, these origins function at their native chromosomal loci and also as autonomously replicating sequences (ARSs) on a linear plasmid. A “mini-ARS screen” identified at least one and often two ARS regions of ≥100 bp within each bona fide origin. Furthermore, a 15-bp AC-rich consensus motif was associated with the predicted origins and conferred autonomous replicating activity to the mini-ARSs. Thus, while centromeres and the origins associated with them are epigenetic, arm origins are dependent upon critical DNA features, such as a binding site for ORC and a propensity for nucleosome exclusion. DNA replication machinery is highly conserved, yet the definition of exactly what specifies a replication origin differs in different species. Here, we utilized computational genomics to predict origin locations in Candida albicans by combining locations of binding sites for the conserved origin replication complex, necessary for replication initiation, together with chromatin organization patterns. We identified predicted sequences that exhibited bona fide origin function and developed a linear plasmid assay to delimit the DNA fragments necessary for origin function. Additionally, we found that a short AC-rich motif, which is enriched in predicted origins, is required for origin function. Thus, we demonstrated a new machine learning paradigm for identification of potential origins from a genome with no prior information. Furthermore, this work suggests that C. albicans has two different types of origins: “hard-wired” arm origins that rely upon specific sequence motifs and “epigenetic” centromeric origins that are recruited to kinetochores in a sequence-independent manner.
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Janbon G, Ormerod KL, Paulet D, Byrnes EJ, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EWL, Coppée JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet 2014; 10:e1004261. [PMID: 24743168 PMCID: PMC3990503 DOI: 10.1371/journal.pgen.1004261] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 02/07/2014] [Indexed: 02/07/2023] Open
Abstract
Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence. Cryptococcus neoformans var. grubii is a major human pathogen responsible for deadly meningoencephalitis in immunocompromised patients. Here, we report the sequencing and annotation of its genome. Evidence for extensive intron splicing, antisense transcription, non-coding RNAs, and alternative polyadenylation indicates the potential for highly intricate regulation of gene expression in this opportunistic pathogen. In addition, detailed molecular, genetic, and genomic studies were performed to characterize structural features of the genome, including centromeres and origins of replication. Finally, the phenotypic and genome re-sequencing analysis of a collection of isolates of the reference H99 strain resulting from laboratory passage revealed that microevolutionary processes during in vitro culturing of pathogenic fungi can impact virulence.
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Affiliation(s)
- Guilhem Janbon
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
- * E-mail: (GJ); (JH); (CAC); (FSD)
| | - Kate L. Ormerod
- University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Damien Paulet
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France
| | - Edmond J. Byrnes
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Vikas Yadav
- Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India
| | - Gautam Chatterjee
- Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India
| | | | - Chung-Chau Hon
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Département Biologie Cellulaire et Infection, Paris, France
| | - R. Blake Billmyre
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | | | - Yong-Sun Bahn
- Yonsei University, Center for Fungal Pathogenesis, Department of Biotechnology, Seoul, Republic of Korea
| | - Weidong Chen
- Rutgers New Jersey Medical School, Department of Microbiology and Molecular Genetics, Newark, New Jersey, United States of America
| | - Yuan Chen
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Eve W. L. Chow
- University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Jean-Yves Coppée
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France
| | - Anna Floyd-Averette
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | | | - Kimberly J. Gerik
- Washington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America
| | - Jonathan Goldberg
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sara Gonzalez-Hilarion
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Sharvari Gujja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Joyce L. Hamlin
- University of Virginia, Department of Biochemistry and Molecular Genetics, Charlottesville, Virginia, United States of America
| | - Yen-Ping Hsueh
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- California Institute of Technology, Division of Biology, Pasadena, California, United States of America
| | - Giuseppe Ianiri
- University of Missouri-Kansas City, School of Biological Sciences, Division of Cell Biology and Biophysics, Kansas City, Missouri, United States of America
| | - Steven Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Chinnappa D. Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Lukasz Kozubowski
- Clemson University, Department of Genetics and Biochemistry, Clemson, South Carolina, United States of America
| | - Woei Lam
- Washington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America
| | - Marco Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Larry D. Mesner
- University of Virginia, Department of Biochemistry and Molecular Genetics, Charlottesville, Virginia, United States of America
| | - Piotr A. Mieczkowski
- University of North Carolina, Department of Genetics, Chapel Hill, North Carolina, United States of America
| | - Frédérique Moyrand
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Kirsten Nielsen
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- University of Minnesota, Microbiology Department, Minneapolis, Minnesota, United States of America
| | - Caroline Proux
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France
| | | | - Jacqueline E. Schein
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Sheng Sun
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Carolin Wollschlaeger
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Ian A. Wood
- University of Queensland, School of Mathematics and Physics, Brisbane, Queensland, Australia
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Carol S. Newlon
- Rutgers New Jersey Medical School, Department of Microbiology and Molecular Genetics, Newark, New Jersey, United States of America
| | - John R. Perfect
- Duke University Medical Center, Duke Department of Medicine and Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Jennifer K. Lodge
- Washington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America
| | - Alexander Idnurm
- University of Missouri-Kansas City, School of Biological Sciences, Division of Cell Biology and Biophysics, Kansas City, Missouri, United States of America
| | - Jason E. Stajich
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- University of California, Department of Plant Pathology & Microbiology, Riverside, California, United States of America
| | - James W. Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, Vancouver, British Columbia, Canada
| | - Kaustuv Sanyal
- Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India
| | - Joseph Heitman
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- * E-mail: (GJ); (JH); (CAC); (FSD)
| | - James A. Fraser
- University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (GJ); (JH); (CAC); (FSD)
| | - Fred S. Dietrich
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- * E-mail: (GJ); (JH); (CAC); (FSD)
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9
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Müller CA, Hawkins M, Retkute R, Malla S, Wilson R, Blythe MJ, Nakato R, Komata M, Shirahige K, de Moura AP, Nieduszynski CA. The dynamics of genome replication using deep sequencing. Nucleic Acids Res 2014; 42:e3. [PMID: 24089142 PMCID: PMC3874191 DOI: 10.1093/nar/gkt878] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 09/03/2013] [Accepted: 09/07/2013] [Indexed: 11/12/2022] Open
Abstract
Eukaryotic genomes are replicated from multiple DNA replication origins. We present complementary deep sequencing approaches to measure origin location and activity in Saccharomyces cerevisiae. Measuring the increase in DNA copy number during a synchronous S-phase allowed the precise determination of genome replication. To map origin locations, replication forks were stalled close to their initiation sites; therefore, copy number enrichment was limited to origins. Replication timing profiles were generated from asynchronous cultures using fluorescence-activated cell sorting. Applying this technique we show that the replication profiles of haploid and diploid cells are indistinguishable, indicating that both cell types use the same cohort of origins with the same activities. Finally, increasing sequencing depth allowed the direct measure of replication dynamics from an exponentially growing culture. This is the first time this approach, called marker frequency analysis, has been successfully applied to a eukaryote. These data provide a high-resolution resource and methodological framework for studying genome biology.
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Affiliation(s)
- Carolin A. Müller
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
| | - Michelle Hawkins
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
| | - Renata Retkute
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
| | - Sunir Malla
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
| | - Ray Wilson
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
| | - Martin J. Blythe
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
| | - Ryuichiro Nakato
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
| | - Makiko Komata
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
| | - Katsuhiko Shirahige
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
| | - Alessandro P.S. de Moura
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
| | - Conrad A. Nieduszynski
- School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Deep Seq, The University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan and Institute for Complex Systems and Mathematical Biology, The University of Aberdeen, Aberdeen, AB24 3UE UK
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10
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Yoshida K, Poveda A, Pasero P. Time to be versatile: regulation of the replication timing program in budding yeast. J Mol Biol 2013; 425:4696-705. [PMID: 24076190 DOI: 10.1016/j.jmb.2013.09.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 01/24/2023]
Abstract
Eukaryotic replication origins are activated at different times during the S phase of the cell cycle, following a temporal program that is stably transmitted to daughter cells. Although the mechanisms that control initiation at the level of individual origins are now well understood, much less is known on how cells coordinate replication at hundreds of origins distributed on the chromosomes. In this review, we discuss recent advances shedding new light on how this complex process is regulated in the budding yeast Saccharomyces cerevisiae. The picture that emerges from these studies is that replication timing is regulated in cis by mechanisms modulating the chromatin structure and the subnuclear organization of origins. These mechanisms do not affect the licensing of replication origins but determine their ability to compete for limiting initiation factors, which are recycled from early to late origins throughout the length of the S phase.
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Affiliation(s)
- Kazumasa Yoshida
- Institute of Human Genetics, CNRS UPR 1142, 141 rue de la Cardonille, Equipe Labellisée Ligue Contre le Cancer, 34396 Montpellier cedex 5, France; Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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11
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Abstract
The origin recognition complex (ORC) was first discovered in the baker's yeast in 1992. Identification of ORC opened up a path for subsequent molecular level investigations on how eukaryotic cells initiate and control genome duplication each cell cycle. Twenty years after the first biochemical isolation, ORC is now taking on a three-dimensional shape, although a very blurry shape at the moment, thanks to the recent electron microscopy and image reconstruction efforts. In this chapter, we outline the current biochemical knowledge about ORC from several eukaryotic systems, with emphasis on the most recent structural and biochemical studies. Despite many species-specific properties, an emerging consensus is that ORC is an ATP-dependent machine that recruits other key proteins to form pre-replicative complexes (pre-RCs) at many origins of DNA replication, enabling the subsequent initiation of DNA replication in S phase.
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Affiliation(s)
- Huilin Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA, And, Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA, , Tel: 631-344-2931, Fax: 631-344-3407
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, , Tel: 516-367-8383
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12
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Martin MM, Ryan M, Kim R, Zakas AL, Fu H, Lin CM, Reinhold WC, Davis SR, Bilke S, Liu H, Doroshow JH, Reimers MA, Valenzuela MS, Pommier Y, Meltzer PS, Aladjem MI. Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res 2011; 21:1822-32. [PMID: 21813623 DOI: 10.1101/gr.124644.111] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This report investigates the mechanisms by which mammalian cells coordinate DNA replication with transcription and chromatin assembly. In yeast, DNA replication initiates within nucleosome-free regions, but studies in mammalian cells have not revealed a similar relationship. Here, we have used genome-wide massively parallel sequencing to map replication initiation events, thereby creating a database of all replication initiation sites within nonrepetitive DNA in two human cell lines. Mining this database revealed that genomic regions transcribed at moderate levels were generally associated with high replication initiation frequency. In genomic regions with high rates of transcription, very few replication initiation events were detected. High-resolution mapping of replication initiation sites showed that replication initiation events were absent from transcription start sites but were highly enriched in adjacent, downstream sequences. Methylation of CpG sequences strongly affected the location of replication initiation events, whereas histone modifications had minimal effects. These observations suggest that high levels of transcription interfere with formation of pre-replication protein complexes. Data presented here identify replication initiation sites throughout the genome, providing a foundation for further analyses of DNA-replication dynamics and cell-cycle progression.
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Affiliation(s)
- Melvenia M Martin
- Laboratory of Molecular Pharmacology, CCR, NCI, Bethesda, Maryland 20892, USA
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13
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The DNA damage response pathway contributes to the stability of chromosome III derivatives lacking efficient replicators. PLoS Genet 2010; 6:e1001227. [PMID: 21151954 PMCID: PMC2996327 DOI: 10.1371/journal.pgen.1001227] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 10/29/2010] [Indexed: 11/21/2022] Open
Abstract
In eukaryotic chromosomes, DNA replication initiates at multiple origins. Large inter-origin gaps arise when several adjacent origins fail to fire. Little is known about how cells cope with this situation. We created a derivative of Saccharomyces cerevisiae chromosome III lacking all efficient origins, the 5ORIΔ-ΔR fragment, as a model for chromosomes with large inter-origin gaps. We used this construct in a modified synthetic genetic array screen to identify genes whose products facilitate replication of long inter-origin gaps. Genes identified are enriched in components of the DNA damage and replication stress signaling pathways. Mrc1p is activated by replication stress and mediates transduction of the replication stress signal to downstream proteins; however, the response-defective mrc1AQ allele did not affect 5ORIΔ-ΔR fragment maintenance, indicating that this pathway does not contribute to its stability. Deletions of genes encoding the DNA-damage-specific mediator, Rad9p, and several components shared between the two signaling pathways preferentially destabilized the 5ORIΔ-ΔR fragment, implicating the DNA damage response pathway in its maintenance. We found unexpected differences between contributions of components of the DNA damage response pathway to maintenance of ORIΔ chromosome derivatives and their contributions to DNA repair. Of the effector kinases encoded by RAD53 and CHK1, Chk1p appears to be more important in wild-type cells for reducing chromosomal instability caused by origin depletion, while Rad53p becomes important in the absence of Chk1p. In contrast, RAD53 plays a more important role than CHK1 in cell survival and replication fork stability following treatment with DNA damaging agents and hydroxyurea. Maintenance of ORIΔ chromosomes does not depend on homologous recombination. These observations suggest that a DNA-damage-independent mechanism enhances ORIΔ chromosome stability. Thus, components of the DNA damage response pathway contribute to genome stability, not simply by detecting and responding to DNA template damage, but also by facilitating replication of large inter-origin gaps. Loss of genome integrity underlies aspects of aging and human disease. During DNA replication, two parallel signaling pathways play important roles in the maintenance of genome integrity. One pathway detects DNA damage, while the other senses replication stress. Both pathways activate responses that include arrest of cell cycle progression, giving cells time to cope with the problem. These pathways have been defined by treating cells with compounds that induce either replication stress or DNA damage, but little is known about their roles during unperturbed DNA replication. They may be important when several adjacent replication origins fail to initiate and forks from flanking origins must replicate longer regions of DNA than normal to complete replication. We have used a derivative of budding yeast chromosome III lacking all efficient replication origins to identify mutants that preferentially destabilize this chromosome fragment, which mimics a chromosome with a large inter-origin gap. We found that the DNA damage response pathway, but not the replication stress response pathway, plays an important role in maintaining this fragment. The signal recognized in this case may be replisome failure rather than forks stalled at endogenous DNA damage.
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14
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Raghuraman MK, Brewer BJ. Molecular analysis of the replication program in unicellular model organisms. Chromosome Res 2010; 18:19-34. [PMID: 20012185 DOI: 10.1007/s10577-009-9099-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Eukaryotes have long been reported to show temporal programs of replication, different portions of the genome being replicated at different times in S phase, with the added possibility of developmentally regulated changes in this pattern depending on species and cell type. Unicellular model organisms, primarily the budding yeast Saccharomyces cerevisiae, have been central to our current understanding of the mechanisms underlying the regulation of replication origins and the temporal program of replication in particular. But what exactly is a temporal program of replication, and how might it arise? In this article, we explore this question, drawing again on the wealth of experimental information in unicellular model organisms.
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Affiliation(s)
- M K Raghuraman
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA, 98133, USA.
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15
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Cotobal C, Segurado M, Antequera F. Structural diversity and dynamics of genomic replication origins in Schizosaccharomyces pombe. EMBO J 2010; 29:934-42. [PMID: 20094030 DOI: 10.1038/emboj.2009.411] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 12/21/2009] [Indexed: 11/09/2022] Open
Abstract
DNA replication origins (ORI) in Schizosaccharomyces pombe colocalize with adenine and thymine (A+T)-rich regions, and earlier analyses have established a size from 0.5 to over 3 kb for a DNA fragment to drive replication in plasmid assays. We have asked what are the requirements for ORI function in the chromosomal context. By designing artificial ORIs, we have found that A+T-rich fragments as short as 100 bp without homology to S. pombe DNA are able to initiate replication in the genome. On the other hand, functional dissection of endogenous ORIs has revealed that some of them span a few kilobases and include several modules that may be as short as 25-30 contiguous A+Ts capable of initiating replication from ectopic chromosome positions. The search for elements with these characteristics across the genome has uncovered an earlier unnoticed class of low-efficiency ORIs that fire late during S phase. These results indicate that ORI specification and dynamics varies widely in S. pombe, ranging from very short elements to large regions reminiscent of replication initiation zones in mammals.
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Affiliation(s)
- Cristina Cotobal
- Instituto de Microbiología Bioquímica, CSIC/Universidad de Salamanca, Edificio Departamental, Salamanca, Spain
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16
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Theis JF, Dershowitz A, Irene C, Maciariello C, Tobin ML, Liberi G, Tabrizifard S, Korus M, Fabiani L, Newlon CS. Identification of mutations that decrease the stability of a fragment of Saccharomyces cerevisiae chromosome III lacking efficient replicators. Genetics 2007; 177:1445-58. [PMID: 17720931 PMCID: PMC2147994 DOI: 10.1534/genetics.107.074690] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Eukaryotic chromosomes are duplicated during S phase and transmitted to progeny during mitosis with high fidelity. Chromosome duplication is controlled at the level of replication initiation, which occurs at cis-acting replicator sequences that are spaced at intervals of approximately 40 kb along the chromosomes of the budding yeast Saccharomyces cerevisiae. Surprisingly, we found that derivatives of yeast chromosome III that lack known replicators were replicated and segregated properly in at least 96% of cell divisions. To gain insight into the mechanisms that maintain these "originless" chromosome fragments, we screened for mutants defective in the maintenance of an "originless" chromosome fragment, but proficient in the maintenance of the same fragment that carries its normal complement of replicators (originless fragment maintenance mutants, or ofm). We show that three of these Ofm mutations appear to disrupt different processes involved in chromosome transmission. The OFM1-1 mutant seems to disrupt an alternative initiation mechanism, and the ofm6 mutant appears to be defective in replication fork progression. ofm14 is an allele of RAD9, which is required for the activation of the DNA damage checkpoint, suggesting that this checkpoint plays a key role in the maintenance of the "originless" fragment.
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Affiliation(s)
- James F Theis
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, New Jersey 07103, USA
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17
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Aladjem MI. Replication in context: dynamic regulation of DNA replication patterns in metazoans. Nat Rev Genet 2007; 8:588-600. [PMID: 17621316 DOI: 10.1038/nrg2143] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Replication in eukaryotes initiates from discrete genomic regions according to a strict, often tissue-specific temporal programme. However, the locations of initiation events within initiation regions vary, show sequence disparity and are affected by interactions with distal elements. Increasing evidence suggests that specification of replication sites and the timing of replication are dynamic processes that are regulated by tissue-specific and developmental cues, and are responsive to epigenetic modifications. Dynamic specification of replication patterns might serve to prevent or resolve possible spatial and/or temporal conflicts between replication, transcription and chromatin assembly, and facilitate subtle or extensive changes of gene expression during differentiation and development.
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Affiliation(s)
- Mirit I Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Building 37, Room 5056, 37 Convent Drive, Bethesda, Maryland 20892-4255, USA.
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18
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Dershowitz A, Snyder M, Sbia M, Skurnick JH, Ong LY, Newlon CS. Linear derivatives of Saccharomyces cerevisiae chromosome III can be maintained in the absence of autonomously replicating sequence elements. Mol Cell Biol 2007; 27:4652-63. [PMID: 17452442 PMCID: PMC1951491 DOI: 10.1128/mcb.01246-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Replication origins in Saccharomyces cerevisiae are spaced at intervals of approximately 40 kb. However, both measurements of replication fork rate and studies of hypomorphic alleles of genes encoding replication initiation proteins suggest the question of whether replication origins are more closely spaced than should be required. We approached this question by systematically deleting replicators from chromosome III. The first significant increase in loss rate detected for the 315-kb full-length chromosome occurred only after all five efficient chromosomal replicators in the left two-thirds of the chromosome (ARS305, ARS306, ARS307, ARS309, and ARS310) had been deleted. The removal of the inefficient replicator ARS308 from this originless region caused little or no additional increase in loss rate. Chromosome fragmentations that removed the normally inactive replicators on the left end of the chromosome or the replicators distal to ARS310 on the right arm showed that both groups of replicators contribute significantly to the maintenance of the originless chromosome. Surprisingly, a 142-kb derivative of chromosome III, lacking all sequences that function as autonomously replicating sequence elements in plasmids, replicated and segregated properly 97% of the time. Both the replication initiation protein ORC and telomeres or a linear topology were required for the maintenance of chromosome fragments lacking replicators.
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Affiliation(s)
- Ann Dershowitz
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, ICPH, 225 Warren St., Newark, NJ 07103, USA
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19
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Irene C, Maciariello C, Micheli G, Theis JF, Newlon CS, Fabiani L. DNA elements modulating the KARS12 chromosomal replicator in Kluyveromyces lactis. Mol Genet Genomics 2006; 277:287-99. [PMID: 17136349 DOI: 10.1007/s00438-006-0188-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Accepted: 10/21/2006] [Indexed: 12/24/2022]
Abstract
Eukaryotic chromosomal DNA replication is initiated by a highly conserved set of proteins that interact with cis-acting elements on chromosomes called replicators. Despite the conservation of replication initiation proteins, replicator sequences show little similarity from species to species in the small number of organisms that have been examined. Examination of replicators in other species is likely to reveal common features of replicators. We have examined a Kluyeromyces lactis replicator, KARS12, that functions as origin of DNA replication on plasmids and in the chromosome. It contains a 50-bp region with similarity to two other K. lactis replicators, KARS101 and the pKD1 replication origin. Replacement of the 50-bp sequence with an EcoRI site completely abrogated the ability of KARS12 to support plasmid and chromosomal DNA replication origin activity, demonstrating this sequence is a common feature of K. lactis replicators and is essential for function, possibly as the initiator protein binding site. Additional sequences up to 1 kb in length are required for efficient KARS12 function. Within these sequences are a binding site for a global regulator, Abf1p, and a region of bent DNA, both of which contribute to the activity of KARS12. These elements may facilitate protein binding, protein/protein interaction and/or nucleosome positioning as has been proposed for other eukaryotic origins of DNA replication.
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Affiliation(s)
- Carmela Irene
- Dipartimento di Biologia Cellulare e dello Sviluppo, Università La Sapienza, Piazzale A. Moro, 5, Roma, Italy
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20
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Bolon YT, Bielinsky AK. The spatial arrangement of ORC binding modules determines the functionality of replication origins in budding yeast. Nucleic Acids Res 2006; 34:5069-80. [PMID: 16984967 PMCID: PMC1635292 DOI: 10.1093/nar/gkl661] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
In the quest to define autonomously replicating sequences (ARSs) in eukaryotic cells, an ARS consensus sequence (ACS) has emerged for budding yeast. This ACS is recognized by the replication initiator, the origin recognition complex (ORC). However, not every match to the ACS constitutes a replication origin. Here, we investigated the requirements for ORC binding to origins that carry multiple, redundant ACSs, such as ARS603. Previous studies raised the possibility that these ACSs function as individual ORC binding sites. Detailed mutational analysis of the two ACSs in ARS603 revealed that they function in concert and give rise to an initiation pattern compatible with a single bipartite ORC binding site. Consistent with this notion, deletion of one base pair between the ACS matches abolished ORC binding at ARS603. Importantly, loss of ORC binding in vitro correlated with the loss of ARS activity in vivo. Our results argue that replication origins in yeast are in general comprised of bipartite ORC binding sites that cannot function in random alignment but must conform to a configuration that permits ORC binding. These requirements help to explain why only a limited number of ACS matches in the yeast genome qualify as ORC binding sites.
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Affiliation(s)
| | - Anja-Katrin Bielinsky
- To whom correspondence should be addressed. Tel: +1 612 624 2469; Fax: +1 612 625 2163;
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21
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Nieduszynski CA, Knox Y, Donaldson AD. Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 2006; 20:1874-9. [PMID: 16847347 PMCID: PMC1522085 DOI: 10.1101/gad.385306] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We discovered that sequences essential for replication origin function are frequently conserved in sensu stricto Saccharomyces species. Here we use analysis of phylogenetic conservation to identify replication origin sequences throughout the Saccharomyces cerevisiae genome at base pair resolution. Origin activity was confirmed for each of 228 predicted sites--representing 86% of apparent origin regions. This is the first study to determine the genome-wide location of replication origins at a resolution sufficient to identify the sequence elements bound by replication proteins. Our results demonstrate that phylogenetic conservation can be used to identify the origin sequences responsible for replicating a eukaryotic genome.
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22
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Bergero R. AT-rich sequences from the arbuscular mycorrhizal fungus Gigaspora rosea exhibit ARS function in the yeast Saccharomyces cerevisiae. Fungal Genet Biol 2006; 43:337-42. [PMID: 16504551 DOI: 10.1016/j.fgb.2006.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Revised: 12/24/2005] [Accepted: 01/09/2006] [Indexed: 11/22/2022]
Abstract
Autonomous replicating sequences are DNA elements that trigger DNA replication and are widely used in the development of episomal transformation vectors for fungi. In this paper, a genomic library from the mycorrhizal fungus Gigaspora rosea was constructed in the integrative plasmid YIp5 and screened in the budding yeast Saccharomyces cerevisiae for sequences that act as ARS and trigger plasmid replication. Two genetic elements (GrARS2, GrARS6) promoted high-rates of yeast transformation. Sequence analysis of these elements shows them to be AT-rich (72-80%) and to contain multiple near-matches to the yeast autonomous consensus sequences ACS and EACS. GrARS2 contained a putative miniature inverted-repeat transposable element (MITE) delimited by 28-bp terminal inverted repeats (TIRs). Disruption of this element and removal of one TIR increased plasmid stability several fold. The potential for palindromes to affect DNA replication is discussed.
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Affiliation(s)
- Roberta Bergero
- Crop and Soil Research Group, Scottish Agricultural College, King's Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
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23
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Abstract
Replication of DNA is essential for the propagation of life. It is somewhat surprising then that, despite the vital nature of this process, cellular organisms show a great deal of variety in the mechanisms that they employ to ensure appropriate genome duplication. This diversity is manifested along classical evolutionary lines, with distinct combinations of replicon architecture and replication proteins being found in the three domains of life: the Bacteria, the Eukarya and the Archaea. Furthermore, although there are mechanistic parallels, even within a given domain of life, the way origins of replication are defined shows remarkable variation.
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Affiliation(s)
- Nicholas P Robinson
- MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge, UK
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24
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Abstract
Eukaryotic DNA replication begins at numerous but often poorly characterized sequences called origins, which are distributed fairly regularly along chromosomes. The elusive and idiosyncratic nature of origins in higher eukaryotes is now understood as resulting from a strong epigenetic influence on their specification, which provides flexibility in origin selection and allows for tailoring the dynamics of chromosome replication to the specific needs of cells. By contrast, the factors that assemble in trans to make these origins competent for replication and the kinases that trigger initiation are well conserved. Genome-wide and single-molecule approaches are being developed to elucidate the dynamics of chromosome replication. The notion that a well-coordinated progression of replication forks is crucial for many aspects of the chromosome cycle besides simply duplication begins to be appreciated.
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Affiliation(s)
- Etienne Schwob
- Institute of Molecular Genetics, CNRS UMR5535 and University Montpellier 2, 1919, route de Mende, 34293 Montpellier, France
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25
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Chang VK, Donato JJ, Chan CS, Tye BK. Mcm1 promotes replication initiation by binding specific elements at replication origins. Mol Cell Biol 2004; 24:6514-24. [PMID: 15226450 PMCID: PMC434236 DOI: 10.1128/mcb.24.14.6514-6524.2004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Minichromosome maintenance protein 1 (Mcm1) is required for efficient replication of autonomously replicating sequence (ARS)-containing plasmids in yeast cells. Reduced DNA binding activity in the Mcm1-1 mutant protein (P97L) results in selective initiation of a subset of replication origins and causes instability of ARS-containing plasmids. This plasmid instability in the mcm1-1 mutant can be overcome for a subset of ARSs by the inclusion of flanking sequences. Previous work showed that Mcm1 binds sequences flanking the minimal functional domains of ARSs. Here, we dissected two conserved telomeric X ARSs, ARS120 (XARS6L) and ARS131a (XARS7R), that replicate with different efficiencies in the mcm1-1 mutant. We found that additional Mcm1 binding sites in the C domain of ARS120 that are missing in ARS131a are responsible for efficient replication of ARS120 in the mcm1-1 mutant. Mutating a conserved Mcm1 binding site in the C domain diminished replication efficiency in ARS120 in wild-type cells, and increasing the number of Mcm1 binding sites stimulated replication efficiency. Our results suggest that threshold occupancy of Mcm1 in the C domain of telomeric ARSs is required for efficient initiation. We propose that origin usage in Saccharomyces cerevisiae may be regulated by the occupancy of Mcm1 at replication origins.
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Affiliation(s)
- Victoria K Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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26
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Irene C, Maciariello C, Cioci F, Camilloni G, Newlon CS, Fabiani L. Identification of the sequences required for chromosomal replicator function in Kluyveromyces lactis. Mol Microbiol 2004; 51:1413-23. [PMID: 14982634 DOI: 10.1046/j.1365-2958.2003.03914.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The analysis of replication intermediates of a Kluyveromyces lactis chromosomal autonomous replicating sequence (ARS), KARS101, has shown that it is active as a chromosomal replicator. KARS101 contains a 50 bp sequence conserved in two other K. lactis ARS elements. The deletion of the conserved sequence in KARS101 completely abolished replicator activity, in both the plasmids and the chromosome. Gel shift assays indicated that this sequence binds proteins present in K. lactis nuclear extracts, and a 40 bp sequence, previously defined as the core essential for K. lactis ARS function, is required for efficient binding. Reminiscent of the origin replication complex (ORC), the binding appears to be ATP dependent. A similar pattern of protection of the core was seen with in vitro footprinting. KARS101 also functions as an ARS sequence in Saccharomyces cerevisiae. A comparative study using S. cerevisiae nuclear extracts revealed that the sequence required for binding is a dodecanucleotide related to the S. cerevisiae ARS consensus sequence and essential for S. cerevisiae ARS activity.
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Affiliation(s)
- Carmela Irene
- Dipartimento Biologia Cellulare e dello Sviluppo, Universita La Sapienza, Piazzale A Moro, 5, Rome Italy
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27
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Wang L, Lin CM, Brooks S, Cimbora D, Groudine M, Aladjem MI. The human beta-globin replication initiation region consists of two modular independent replicators. Mol Cell Biol 2004; 24:3373-86. [PMID: 15060158 PMCID: PMC381644 DOI: 10.1128/mcb.24.8.3373-3386.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have shown that mammalian cells contain replicator sequences, which can determine where DNA replication initiates. However, the specific sequences that confer replicator activity were not identified. Here we report a detailed analysis of replicator sequences that dictate initiation of DNA replication from the human beta-globin locus. This analysis suggests that the beta-globin replication initiation region contains two adjacent, redundant replicators. Each replicator was capable of initiating DNA replication independently at ectopic sites. Within each of these two replicators, we identified short, discrete, nonredundant sequences, which cooperatively determine replicator activity. Experiments with somatic cell hybrids further demonstrated that the requirements for initiation at ectopic sites were similar to the requirements for initiation within native human chromosomes. The replicator clustering and redundancy exemplified in the human beta-globin locus may account for the extreme difficulty in identifying replicator sequences in mammalian cells and suggest that mammalian replication initiation sites may be determined by cooperative sequence modules.
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Affiliation(s)
- Lixin Wang
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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28
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Affiliation(s)
- Isabelle A Lucas
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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29
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Breier AM, Chatterji S, Cozzarelli NR. Prediction of Saccharomyces cerevisiae replication origins. Genome Biol 2004; 5:R22. [PMID: 15059255 PMCID: PMC395781 DOI: 10.1186/gb-2004-5-4-r22] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Revised: 02/02/2004] [Accepted: 02/04/2004] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Autonomously replicating sequences (ARSs) function as replication origins in Saccharomyces cerevisiae. ARSs contain the 17 bp ARS consensus sequence (ACS), which binds the origin recognition complex. The yeast genome contains more than 10,000 ACS matches, but there are only a few hundred origins, and little flanking sequence similarity has been found. Thus, identification of origins by sequence alone has not been possible. RESULTS We developed an algorithm, Oriscan, to predict yeast origins using similarity to 26 characterized origins. Oriscan used 268 bp of sequence, including the T-rich ACS and a 3' A-rich region. The predictions identified the exact location of the ACS. A total of 84 of the top 100 Oriscan predictions, and 56% of the top 350, matched known ARSs or replication protein binding sites. The true accuracy was even higher because we tested 25 discrepancies, and 15 were in fact ARSs. Thus, 94% of the top 100 predictions and an estimated 70% of the top 350 were correct. We compared the predictions to corresponding sequences in related Saccharomyces species and found that the ACSs of experimentally supported predictions show significant conservation. CONCLUSIONS The high accuracy of the predictions indicates that we have defined near-sufficient conditions for ARS activity, the A-rich region is a recognizable feature of ARS elements with a probable role in replication initiation, and nucleotide sequence is a reliable predictor of yeast origins. Oriscan detected most origins in the genome, demonstrating previously unrecognized generality in yeast replication origins and significant discriminatory power in the algorithm.
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Affiliation(s)
- Adam M Breier
- Graduate Group in Biophysics, University of California-Berkeley, Berkeley, CA 94720-3204, USA
| | - Sourav Chatterji
- Department of Computer Science, University of California-Berkeley, Berkeley, CA 94720-3204, USA
| | - Nicholas R Cozzarelli
- Department of Molecular and Cellular Biology, Barker Hall, University of California-Berkeley, Berkeley, CA 94720-3204, USA
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Weinreich M, Palacios DeBeer MA, Fox CA. The activities of eukaryotic replication origins in chromatin. ACTA ACUST UNITED AC 2004; 1677:142-57. [PMID: 15020055 DOI: 10.1016/j.bbaexp.2003.11.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2003] [Accepted: 11/17/2003] [Indexed: 12/26/2022]
Abstract
DNA replication initiates at chromosomal positions called replication origins. This review will focus on the activity, regulation and roles of replication origins in Saccharomyces cerevisiae. All eukaryotic cells, including S. cerevisiae, depend on the initiation (activity) of hundreds of replication origins during a single cell cycle for the duplication of their genomes. However, not all origins are identical. For example, there is a temporal order to origin activation with some origins firing early during the S-phase and some origins firing later. Recent studies provide evidence that posttranslational chromatin modifications, heterochromatin-binding proteins and nucleosome positioning can control the efficiency and/or timing of chromosomal origin activity in yeast. Many more origins exist than are necessary for efficient replication. The availability of excess replication origins leaves individual origins free to evolve distinct forms of regulation and/or roles in chromosomes beyond their fundamental role in DNA synthesis. We propose that some origins have acquired roles in controlling chromatin structure and/or gene expression. These roles are not linked obligatorily to replication origin activity per se, but instead exploit multi-subunit replication proteins with the potential to form context-dependent protein-protein interactions.
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Affiliation(s)
- Michael Weinreich
- Laboratory of Chromosome Replication, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA.
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31
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Segurado M, de Luis A, Antequera F. Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe. EMBO Rep 2003. [PMID: 14566325 DOI: 10.1038/sj.embor.7400008] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Genome-wide analysis of replication dynamics requires the previous identification of DNA replication origins (ORIs). However, variability among the ORIs makes it difficult to predict their distribution across the genome on the basis of their sequence. We report here that ORIs in Schizosaccharomyces pombe coincide with discrete chromosomal A+T-rich islands of up to 1 kb long that are characterized by a distinctive A+T content that clearly differentiates them from the rest of the genome. Genome-wide analysis has enabled us to identify 384 of these regions, which predicts the position of most ORIs in the genome, as shown by functional replication analyses. A+T-rich islands occur at the mating locus, centromeres and subtelomeric regions at a density that is approximately fourfold higher than elsewhere in the genome, which suggests a link between the origin recognition complex (ORC) and transcriptional silencing in these regions. The absence of consensus elements in A+T-rich islands implies that different sequences can target the ORC to different ORIs.
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Affiliation(s)
- Mónica Segurado
- Instituto de Microbiología Bioquímica, CSIC/Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
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32
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Segurado M, de Luis A, Antequera F. Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe. EMBO Rep 2003; 4:1048-53. [PMID: 14566325 PMCID: PMC1326378 DOI: 10.1038/sj.embor.embor7400008] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Revised: 09/10/2003] [Accepted: 09/12/2003] [Indexed: 11/09/2022] Open
Abstract
Genome-wide analysis of replication dynamics requires the previous identification of DNA replication origins (ORIs). However, variability among the ORIs makes it difficult to predict their distribution across the genome on the basis of their sequence. We report here that ORIs in Schizosaccharomyces pombe coincide with discrete chromosomal A+T-rich islands of up to 1 kb long that are characterized by a distinctive A+T content that clearly differentiates them from the rest of the genome. Genome-wide analysis has enabled us to identify 384 of these regions, which predicts the position of most ORIs in the genome, as shown by functional replication analyses. A+T-rich islands occur at the mating locus, centromeres and subtelomeric regions at a density that is approximately fourfold higher than elsewhere in the genome, which suggests a link between the origin recognition complex (ORC) and transcriptional silencing in these regions. The absence of consensus elements in A+T-rich islands implies that different sequences can target the ORC to different ORIs.
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Affiliation(s)
- Mónica Segurado
- Instituto de Microbiología
Bioquímica, CSIC/Universidad de Salamanca, Edificio Departamental,
Campus Miguel de Unamuno, 37007 Salamanca,
Spain
| | - Alberto de Luis
- Instituto de Microbiología
Bioquímica, CSIC/Universidad de Salamanca, Edificio Departamental,
Campus Miguel de Unamuno, 37007 Salamanca,
Spain
| | - Francisco Antequera
- Instituto de Microbiología
Bioquímica, CSIC/Universidad de Salamanca, Edificio Departamental,
Campus Miguel de Unamuno, 37007 Salamanca,
Spain
- Tel: +34 923 121778; Fax: +34 923 224876;
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Chang VK, Fitch MJ, Donato JJ, Christensen TW, Merchant AM, Tye BK. Mcm1 binds replication origins. J Biol Chem 2003; 278:6093-100. [PMID: 12473677 DOI: 10.1074/jbc.m209827200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mcm1 is an essential protein required for the efficient replication of minichromosomes and the transcriptional regulation of early cell cycle genes in Saccharomyces cerevisiae. In this study, we report that Mcm1 is an abundant protein that associates globally with chromatin in a punctate pattern. We show that Mcm1 is localized at replication origins and plays an important role in the initiation of DNA synthesis at a chromosomal replication origin in vivo. Using purified Mcm1 protein, we show that Mcm1 binds cooperatively to multiple sites at autonomously replicating sequences. These results suggest that, in addition to its role as a transcription factor for the expression of replication genes, Mcm1 may influence the local structure of replication origins by direct binding.
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Affiliation(s)
- Victoria K Chang
- Department of Chemistry, Drew University, Madison, New Jersey 07940, USA
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Kong D, DePamphilis ML. Site-specific ORC binding, pre-replication complex assembly and DNA synthesis at Schizosaccharomyces pombe replication origins. EMBO J 2002; 21:5567-76. [PMID: 12374757 PMCID: PMC129078 DOI: 10.1093/emboj/cdf546] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Previous studies have shown that the Schizo saccharomyces pombe Orc4 subunit is solely responsible for in vitro binding of origin recognition complex (ORC) to specific AT-rich sites within S.pombe replication origins. Using ARS3001, a S.pombe replication origin consisting of four genetically required sites, we show that, in situ as well as in vitro, Orc4 binds strongly to the Delta3 site, weakly to the Delta6 site and not at all to the remaining sequences. In situ, the footprint over Delta3 is extended during G(1) phase, but only when Cdc18 is present and Mcm proteins are bound to chromatin. Moreover, this footprint extends into the adjacent Delta2 site, where leading strand DNA synthesis begins. Therefore, we conclude that ARS3001 consists of a single primary ORC binding site that assembles a pre-replication complex and initiates DNA synthesis, plus an additional novel origin element (Delta9) that neither binds ORC nor functions as a centromere, but does bind an as yet unidentified protein throughout the cell cycle. Schizosaccharomyces pombe may be an appropriate paradigm for the complex origins found in the metazoa.
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Affiliation(s)
- Daochun Kong
- National Institute of Child Health and Human Development, Building 6, Room 416, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892-2753, USA.
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35
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Abstract
The study of DNA replication in eukaryotic chromosomes has revealed a multitude of different regulatory levels. Nuclear and chromosomal location as well as chromatin structure may affect the activity of replication origins and their modulation during development.
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Affiliation(s)
- Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Division of Biology and Medicine, Providence, Rhode Island 02912, USA.
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36
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Poloumienko A, Dershowitz A, De J, Newlon CS. Completion of replication map of Saccharomyces cerevisiae chromosome III. Mol Biol Cell 2001; 12:3317-27. [PMID: 11694569 PMCID: PMC60257 DOI: 10.1091/mbc.12.11.3317] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In Saccharomyces cerevisiae chromosomal DNA replication initiates at intervals of approximately 40 kb and depends upon the activity of autonomously replicating sequence (ARS) elements. The identification of ARS elements and analysis of their function as chromosomal replication origins requires the use of functional assays because they are not sufficiently similar to identify by DNA sequence analysis. To complete the systematic identification of ARS elements on S. cerevisiae chromosome III, overlapping clones covering 140 kb of the right arm were tested for their ability to promote extrachromosomal maintenance of plasmids. Examination of chromosomal replication intermediates of each of the seven ARS elements identified revealed that their efficiencies of use as chromosomal replication origins varied widely, with four ARS elements active in < or = 10% of cells in the population and two ARS elements active in > or = 90% of the population. Together with our previous analysis of a 200-kb region of chromosome III, these data provide the first complete analysis of ARS elements and DNA replication origins on an entire eukaryotic chromosome.
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Affiliation(s)
- A Poloumienko
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, New Jersey 07103, USA
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37
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Abstract
Site-specific initiation of DNA replication is a conserved function in all organisms. In Escherichia coli and Saccharomyces cerevisiae, DNA replication origins are sequence specific, but in multicellular organisms, origins are not so clearly defined. In this article, I present a model of origin specification by epigenetic mechanisms that allows the establishment of stable chromatin domains, which are characterized by autonomous replication. According to this model, origins of DNA replication help to establish domains of gene expression for the generation of cell diversity.
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Affiliation(s)
- M Méchali
- Marcel Méchali is at the Institute of Human Genetics, CNRS, Genome Dynamics and Development, 141 rue de la Cardonille, 34396 Montpellier, France.
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38
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Current Awareness. Yeast 2001. [DOI: 10.1002/yea.687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Malkova A, Signon L, Schaefer CB, Naylor ML, Theis JF, Newlon CS, Haber JE. RAD51-independent break-induced replication to repair a broken chromosome depends on a distant enhancer site. Genes Dev 2001; 15:1055-60. [PMID: 11331601 PMCID: PMC312680 DOI: 10.1101/gad.875901] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Without the RAD51 strand exchange protein, Saccharomyces cerevisiae cannot repair a double-strand break (DSB) by gene conversion. However, cells can repair DSBs by recombination-dependent, break-induced replication (BIR). RAD51-independent BIR is initiated more than 13 kb from the DSB. Repair depends on a 200-bp sequence adjacent to ARS310, located approximately 34 kb centromere-proximal to the DSB, but does not depend on the origin activity of ARS310. We conclude that the ability of a recombination-induced replication fork to copy > 130 kb to the end of the chromosome depends on a special site that enhances assembly of a processive repair replication fork.
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Affiliation(s)
- A Malkova
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-9110, USA
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