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Arcangioli B, Gangloff S. The Fission Yeast Mating-Type Switching Motto: "One-for-Two" and "Two-for-One". Microbiol Mol Biol Rev 2023; 87:e0000821. [PMID: 36629411 PMCID: PMC10029342 DOI: 10.1128/mmbr.00008-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Schizosaccharomyces pombe is an ascomycete fungus that divides by medial fission; it is thus commonly referred to as fission yeast, as opposed to the distantly related budding yeast Saccharomyces cerevisiae. The reproductive lifestyle of S. pombe relies on an efficient genetic sex determination system generating a 1:1 sex ratio and using alternating haploid/diploid phases in response to environmental conditions. In this review, we address how one haploid cell manages to generate two sister cells with opposite mating types, a prerequisite to conjugation and meiosis. This mating-type switching process depends on two highly efficient consecutive asymmetric cell divisions that rely on DNA replication, repair, and recombination as well as the structure and components of heterochromatin. We pay special attention to the intimate interplay between the genetic and epigenetic partners involved in this process to underscore the importance of basic research and its profound implication for a better understanding of chromatin biology.
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Affiliation(s)
- Benoît Arcangioli
- Genome Dynamics Unit, Genomes and Genetics Department, Pasteur Institute, Paris, France
| | - Serge Gangloff
- Genome Dynamics Unit, Genomes and Genetics Department, Pasteur Institute, Paris, France
- UMR3525, Genetics of Genomes, CNRS-Pasteur Institute, Paris, France
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2
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Williams JS, Kunkel TA. Ribonucleotide Incorporation by Eukaryotic B-family Replicases and Its Implications for Genome Stability. Annu Rev Biochem 2022; 91:133-155. [PMID: 35287470 DOI: 10.1146/annurev-biochem-032620-110354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our current view of how DNA-based genomes are efficiently and accurately replicated continues to evolve as new details emerge on the presence of ribonucleotides in DNA. Ribonucleotides are incorporated during eukaryotic DNA replication at rates that make them the most common noncanonical nucleotide placed into the nuclear genome, they are efficiently repaired, and their removal impacts genome integrity. This review focuses on three aspects of this subject: the incorporation of ribonucleotides into the eukaryotic nuclear genome during replication by B-family DNA replicases, how these ribonucleotides are removed, and the consequences of their presence or removal for genome stability and disease. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jessica S Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA;
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA;
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3
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Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
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4
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RNA insertion in DNA as the imprint moiety: the fission yeast paradigm. Curr Genet 2019; 65:1301-1306. [PMID: 31076844 DOI: 10.1007/s00294-019-00991-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 10/26/2022]
Abstract
This review elaborates on the findings of a new report which possibly resolves the biochemical nature of a novel type of DNA imprint as ribonucleotide and the mechanism of its formation during cell differentiation in fission yeast. The process of mating-type switching in fission yeast, Schizosaccharomyces pombe, displays characteristics of a typical mammalian stem cell lineage, wherein a cell divides to produce an identical cell and a differentiated cell after every two cell divisions. This developmental asymmetry has been ascribed to play a role in generation of a DNA strand-specific imprint at the mat1 locus during lagging strand synthesis and its segregation to one of the two daughter cells by the process of asymmetric, semi-conservative DNA replication. The nature of this imprint and mechanisms of its generation have been a subject of research and debate. A recent report by Singh et al. (Nucleic Acids Res 47:3422-3433. https://doi.org/10.1093/nar/gkz092 , 2019) provides compelling evidence in support of a ribonucleotide as the imprint moiety within the mat1 DNA and demonstrates the role of Mcm10/Cdc23, an important, evolutionarily conserved component of DNA replication machinery in eukaryotes, in installing the imprint through a non-canonical primase activity and interaction with DNA Polα and Swi1. The high degree of conservation of DNA replication machinery, especially the presence of the T7 gene 4 helicase/primase domain in the mammalian orthologs of Mcm10 suggests that similar mechanisms of DNA imprinting may play a role during cell differentiation in metazoans.
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5
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Díaz-Talavera A, Calvo PA, González-Acosta D, Díaz M, Sastre-Moreno G, Blanco-Franco L, Guerra S, Martínez-Jiménez MI, Méndez J, Blanco L. A cancer-associated point mutation disables the steric gate of human PrimPol. Sci Rep 2019; 9:1121. [PMID: 30718533 PMCID: PMC6362072 DOI: 10.1038/s41598-018-37439-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/03/2018] [Indexed: 11/30/2022] Open
Abstract
PrimPol is a human primase/polymerase specialized in re-starting stalled forks by repriming beyond lesions such as pyrimidine dimers, and replication-perturbing structures including G-quadruplexes and R-loops. Unlike most conventional primases, PrimPol proficiently discriminates against ribonucleotides (NTPs), being able to start synthesis using deoxynucleotides (dNTPs), yet the structural basis and physiological implications for this discrimination are not understood. In silico analyses based on the three-dimensional structure of human PrimPol and related enzymes enabled us to predict a single residue, Tyr100, as the main effector of sugar discrimination in human PrimPol and a change of Tyr100 to histidine to boost the efficiency of NTP incorporation. We show here that the Y100H mutation profoundly stimulates NTP incorporation by human PrimPol, with an efficiency similar to that for dNTP incorporation during both primase and polymerase reactions in vitro. As expected from the higher cellular concentration of NTPs relative to dNTPs, Y100H expression in mouse embryonic fibroblasts and U2OS osteosarcoma cells caused enhanced resistance to hydroxyurea, which decreases the dNTP pool levels in S-phase. Remarkably, the Y100H PrimPol mutation has been identified in cancer, suggesting that this mutation could be selected to promote survival at early stages of tumorigenesis, which is characterized by depleted dNTP pools.
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Affiliation(s)
- Alberto Díaz-Talavera
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Patricia A Calvo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Daniel González-Acosta
- Centro Nacional de Investigaciones Oncológicas (CNIO), c/Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Marcos Díaz
- Centro Nacional de Investigaciones Oncológicas (CNIO), c/Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Guillermo Sastre-Moreno
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Luis Blanco-Franco
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Susana Guerra
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Maria I Martínez-Jiménez
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Juan Méndez
- Centro Nacional de Investigaciones Oncológicas (CNIO), c/Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Luis Blanco
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain.
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Raimondi C, Jagla B, Proux C, Waxin H, Gangloff S, Arcangioli B. Molecular signature of the imprintosome complex at the mating-type locus in fission yeast. MICROBIAL CELL 2018; 5:169-183. [PMID: 29610759 PMCID: PMC5878685 DOI: 10.15698/mic2018.04.623] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genetic and molecular studies have indicated that an epigenetic imprint at mat1, the sexual locus of fission yeast, initiates mating type switching. The polar DNA replication of mat1 generates an imprint on the Watson strand. The process by which the imprint is formed and maintained through the cell cycle remains unclear. To understand better the mechanism of imprint formation and stability, we characterized the recruitment of early players of mating type switching at the mat1 region. We found that the switch activating protein 1 (Sap1) is preferentially recruited inside the mat1M allele on a sequence (SS13) that enhances the imprint. The lysine specific demethylases, Lsd1/2, that control the replication fork pause at MPS1 and the formation of the imprint are specifically drafted inside of mat1, regardless of the allele. The CENP-B homolog, Abp1, is highly enriched next to mat1 but it is not required in the process. Additionally, we established the computational signature of the imprint. Using this signature, we show that both sides of the imprinted molecule are bound by Lsd1/2 and Sap1, suggesting a nucleoprotein protective structure defined as imprintosome.
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Affiliation(s)
- Célia Raimondi
- Genomes and Genetics department, Genome Dynamics Unit, UMR 3525 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, Paris, France. Sorbonne Universités, Université Pierre et Marie Curie, Institut de Formation Doctorale, 75252 Paris Cedex 05, France
| | - Bernd Jagla
- Center for Human Immunology, CRT & Hub de Bioinformatique et Biostatistiques, C3BI, Institut Pasteur, 25-28 rue du Docteur Roux, Paris, France
| | - Caroline Proux
- Genomes and Genetics department, Plate-forme Transcriptome & Epigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Institut Pasteur, 25-28 rue du Docteur Roux, Paris, France
| | - Hervé Waxin
- Enseignement, Institut Pasteur, 25-28 rue du Docteur Roux, Paris, France
| | - Serge Gangloff
- Genomes and Genetics department, Genome Dynamics Unit, UMR 3525 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, Paris, France. Sorbonne Universités, Université Pierre et Marie Curie, Institut de Formation Doctorale, 75252 Paris Cedex 05, France
| | - Benoit Arcangioli
- Genomes and Genetics department, Genome Dynamics Unit, UMR 3525 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, Paris, France. Sorbonne Universités, Université Pierre et Marie Curie, Institut de Formation Doctorale, 75252 Paris Cedex 05, France
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7
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Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC. Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu. Nucleic Acids Res 2017; 45:9138-9148. [PMID: 28911097 PMCID: PMC5587726 DOI: 10.1093/nar/gkx527] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 06/23/2017] [Indexed: 02/02/2023] Open
Abstract
While most DNA polymerases discriminate against ribonucleotide triphosphate (rNTP) incorporation very effectively, the Family X member DNA polymerase μ (Pol μ) incorporates rNTPs almost as efficiently as deoxyribonucleotides. To gain insight into how this occurs, here we have used X-ray crystallography to describe the structures of pre- and post-catalytic complexes of Pol μ with a ribonucleotide bound at the active site. These structures reveal that Pol μ binds and incorporates a rNTP with normal active site geometry and no distortion of the DNA substrate or nucleotide. Moreover, a comparison of rNTP incorporation kinetics by wildtype and mutant Pol μ indicates that rNTP accommodation involves synergistic interactions with multiple active site residues not found in polymerases with greater discrimination. Together, the results are consistent with the hypothesis that rNTP incorporation by Pol μ is advantageous in gap-filling synthesis during DNA double strand break repair by nonhomologous end joining, particularly in nonreplicating cells containing very low deoxyribonucleotide concentrations.
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Affiliation(s)
- Andrea F Moon
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - John M Pryor
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dale A Ramsden
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Katarzyna Bebenek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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8
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Williams JS, Lujan SA, Kunkel TA. Processing ribonucleotides incorporated during eukaryotic DNA replication. Nat Rev Mol Cell Biol 2016; 17:350-63. [PMID: 27093943 PMCID: PMC5445644 DOI: 10.1038/nrm.2016.37] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The information encoded in DNA is influenced by the presence of non-canonical nucleotides, the most frequent of which are ribonucleotides. In this Review, we discuss recent discoveries about ribonucleotide incorporation into DNA during replication by the three major eukaryotic replicases, DNA polymerases α, δ and ε. The presence of ribonucleotides in DNA causes short deletion mutations and may result in the generation of single- and double-strand DNA breaks, leading to genome instability. We describe how these ribonucleotides are removed from DNA through ribonucleotide excision repair and by topoisomerase I. We discuss the biological consequences and the physiological roles of ribonucleotides in DNA, and consider how deficiencies in their removal from DNA may be important in the aetiology of disease.
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Affiliation(s)
- Jessica S. Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
| | - Scott A. Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
| | - Thomas A. Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
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9
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Zech J, Godfrey EL, Masai H, Hartsuiker E, Dalgaard JZ. The DNA-Binding Domain of S. pombe Mrc1 (Claspin) Acts to Enhance Stalling at Replication Barriers. PLoS One 2015. [PMID: 26201080 PMCID: PMC4511789 DOI: 10.1371/journal.pone.0132595] [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: 11/19/2022] Open
Abstract
During S-phase replication forks can stall at specific genetic loci. At some loci, the stalling events depend on the replisome components Schizosaccharomyces pombe Swi1 (Saccharomyces cerevisiae Tof1) and Swi3 (S. cerevisiae Csm3) as well as factors that bind DNA in a site-specific manner. Using a new genetic screen we identified Mrc1 (S. cerevisiae Mrc1/metazoan Claspin) as a replisome component involved in replication stalling. Mrc1 is known to form a sub-complex with Swi1 and Swi3 within the replisome and is required for the intra-S phase checkpoint activation. This discovery is surprising as several studies show that S. cerevisiae Mrc1 is not required for replication barrier activity. In contrast, we show that deletion of S. pombe mrc1 leads to an approximately three-fold reduction in barrier activity at several barriers and that Mrc1’s role in replication fork stalling is independent of its role in checkpoint activation. Instead, S. pombe Mrc1 mediated fork stalling requires the presence of a functional copy of its phylogenetically conserved DNA binding domain. Interestingly, this domain is on the sequence level absent from S. cerevisiae Mrc1. Our study indicates that direct interactions between the eukaryotic replisome and the DNA are important for site-specific replication stalling.
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Affiliation(s)
- Juergen Zech
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, CV47AL Coventry, United Kingdom
- * E-mail: (JZ); (JZD)
| | - Emma Louise Godfrey
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, CV47AL Coventry, United Kingdom
| | - Hisao Masai
- Genome Dynamics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156–8613, Japan
| | - Edgar Hartsuiker
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Wales, LI57 2UW, United Kingdom
| | - Jacob Zeuthen Dalgaard
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, CV47AL Coventry, United Kingdom
- * E-mail: (JZ); (JZD)
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10
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Jinks-Robertson S, Klein HL. Ribonucleotides in DNA: hidden in plain sight. Nat Struct Mol Biol 2015; 22:176-8. [PMID: 25736085 DOI: 10.1038/nsmb.2981] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Hannah L Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
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11
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Vaisman A, Woodgate R. Redundancy in ribonucleotide excision repair: Competition, compensation, and cooperation. DNA Repair (Amst) 2015; 29:74-82. [PMID: 25753809 DOI: 10.1016/j.dnarep.2015.02.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 02/07/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
Abstract
The survival of all living organisms is determined by their ability to reproduce, which in turn depends on accurate duplication of chromosomal DNA. In order to ensure the integrity of genome duplication, DNA polymerases are equipped with stringent mechanisms by which they select and insert correctly paired nucleotides with a deoxyribose sugar ring. However, this process is never 100% accurate. To fix occasional mistakes, cells have evolved highly sophisticated and often redundant mechanisms. A good example is mismatch repair (MMR), which corrects the majority of mispaired bases and which has been extensively studied for many years. On the contrary, pathways leading to the replacement of nucleotides with an incorrect sugar that is embedded in chromosomal DNA have only recently attracted significant attention. This review describes progress made during the last few years in understanding such pathways in both prokaryotes and eukaryotes. Genetic studies in Escherichia coli and Saccharomyces cerevisiae demonstrated that MMR has the capacity to replace errant ribonucleotides, but only when the base is mispaired. In contrast, the major evolutionarily conserved ribonucleotide repair pathway initiated by the ribonuclease activity of type 2 Rnase H has broad specificity. In yeast, this pathway also requires the concerted action of Fen1 and pol δ, while in bacteria it can be successfully completed by DNA polymerase I. Besides these main players, all organisms contain alternative enzymes able to accomplish the same tasks, although with differing efficiency and fidelity. Studies in bacteria have very recently demonstrated that isolated rNMPs can be removed from genomic DNA by error-free nucleotide excision repair (NER), while studies in yeast suggest the involvement of topoisomerase 1 in alternative mutagenic ribonucleotide processing. This review summarizes the most recent progress in understanding the ribonucleotide repair mechanisms in prokaryotes and eukaryotes.
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Affiliation(s)
- Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA.
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12
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Klar AJS, Ishikawa K, Moore S. A Unique DNA Recombination Mechanism of the Mating/Cell-type Switching of Fission Yeasts: a Review. Microbiol Spectr 2014; 2:10.1128/microbiolspec.MDNA3-0003-2014. [PMID: 26104357 PMCID: PMC7687047 DOI: 10.1128/microbiolspec.mdna3-0003-2014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Indexed: 12/29/2022] Open
Abstract
Cells of the highly diverged Schizosaccharomyces (S.) pombe and S. japonicus fission yeasts exist in one of two sex/mating types, called P (for plus) or M (for minus), specified by which allele, M or P, resides at mat1. The fission yeasts have evolved an elegant mechanism for switching P or M information at mat1 by a programmed DNA recombination event with a copy of one of the two silent mating-type genes residing nearby in the genome. The switching process is highly cell-cycle and generation dependent such that only one of four grandchildren of a cell switches mating type. Extensive studies of fission yeast established the natural DNA strand chirality at the mat1 locus as the primary basis of asymmetric cell division. The asymmetry results from a unique site- and strand-specific epigenetic "imprint" at mat1 installed in one of the two chromatids during DNA replication. The imprint is inherited by one daughter cell, maintained for one cell cycle, and is then used for initiating recombination during mat1 replication in the following cell cycle. This mechanism of cell-type switching is considered to be unique to these two organisms, but determining the operation of such a mechanism in other organisms has not been possible for technical reasons. This review summarizes recent exciting developments in the understanding of mating-type switching in fission yeasts and extends these observations to suggest how such a DNA strand-based epigenetic mechanism of cellular differentiation could also operate in diploid organisms.
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Affiliation(s)
- Amar J S Klar
- National Cancer Institute at Frederick, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702-1201
| | - Ken Ishikawa
- National Cancer Institute at Frederick, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702-1201
| | - Sharon Moore
- National Cancer Institute at Frederick, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702-1201
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13
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Potenski CJ, Klein HL. How the misincorporation of ribonucleotides into genomic DNA can be both harmful and helpful to cells. Nucleic Acids Res 2014; 42:10226-34. [PMID: 25159610 PMCID: PMC4176331 DOI: 10.1093/nar/gku773] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Ribonucleotides are misincorporated into replicating DNA due to the similarity of deoxyribonucleotides and ribonucleotides, the high concentration of ribonucleotides in the nucleus and the imperfect accuracy of replicative DNA polymerases in choosing the base with the correct sugar. Embedded ribonucleotides change certain properties of the DNA and can interfere with normal DNA transactions. Therefore, misincorporated ribonucleotides are targeted by the cell for removal. Failure to remove ribonucleotides from DNA results in an increase in genome instability, a phenomenon that has been characterized in various systems using multiple assays. Recently, however, another side to ribonucleotide misincorporation has emerged, where there is evidence for a functional role of misinserted ribonucleotides in DNA, leading to beneficial consequences for the cell. This review examines examples of both positive and negative effects of genomic ribonucleotide misincorporation in various organisms, aiming to highlight the diversity and the utility of this common replication variation.
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Affiliation(s)
- Catherine J Potenski
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Hannah L Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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14
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Singh J. Role of DNA replication in establishment and propagation of epigenetic states of chromatin. Semin Cell Dev Biol 2014; 30:131-43. [PMID: 24794003 DOI: 10.1016/j.semcdb.2014.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
DNA replication is the fundamental process of duplication of the genetic information that is vital for survival of all living cells. The basic mechanistic steps of replication initiation, elongation and termination are conserved among bacteria, lower eukaryotes, like yeast and metazoans. However, the details of the mechanisms are different. Furthermore, there is a close coordination between chromatin assembly pathways and various components of replication machinery whereby DNA replication is coupled to "chromatin replication" during cell cycle. Thereby, various epigenetic modifications associated with different states of gene expression in differentiated cells and the related chromatin structures are faithfully propagated during the cell division through tight coupling with the DNA replication machinery. Several examples are found in lower eukaryotes like budding yeast and fission yeast with close parallels in metazoans.
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Affiliation(s)
- Jagmohan Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India.
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Abstract
While primordial life is thought to have been RNA-based (Cech, Cold Spring Harbor Perspect. Biol. 4 (2012) a006742), all living organisms store genetic information in DNA, which is chemically more stable. Distinctions between the RNA and DNA worlds and our views of "DNA" synthesis continue to evolve as new details emerge on the incorporation, repair and biological effects of ribonucleotides in DNA genomes of organisms from bacteria through humans.
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Affiliation(s)
- Jessica S Williams
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
| | - Thomas A Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States.
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16
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Holmes A, Roseaulin L, Schurra C, Waxin H, Lambert S, Zaratiegui M, Martienssen RA, Arcangioli B. Lsd1 and lsd2 control programmed replication fork pauses and imprinting in fission yeast. Cell Rep 2012; 2:1513-20. [PMID: 23260662 DOI: 10.1016/j.celrep.2012.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 06/09/2012] [Accepted: 10/15/2012] [Indexed: 01/09/2023] Open
Abstract
In the fission yeast Schizosaccharomyces pombe, a chromosomal imprinting event controls the asymmetric pattern of mating-type switching. The orientation of DNA replication at the mating-type locus is instrumental in this process. However, the factors leading to imprinting are not fully identified and the mechanism is poorly understood. Here, we show that the replication fork pause at the mat1 locus (MPS1), essential for imprint formation, depends on the lysine-specific demethylase Lsd1. We demonstrate that either Lsd1 or Lsd2 amine oxidase activity is required for these processes, working upstream of the imprinting factors Swi1 and Swi3 (homologs of mammalian Timeless and Tipin, respectively). We also show that the Lsd1/2 complex controls the replication fork terminators, within the rDNA repeats. These findings reveal a role for the Lsd1/2 demethylases in controlling polar replication fork progression, imprint formation, and subsequent asymmetric cell divisions.
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Affiliation(s)
- Allyson Holmes
- Institut Pasteur, Dynamic of the Genome Unit, Department of Genomes and Genetic, UMR3525, Paris, France
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17
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Abstract
A key question in developmental biology addresses the mechanism of asymmetric cell division. Asymmetry is crucial for generating cellular diversity required for development in multicellular organisms. As one of the potential mechanisms, chromosomally borne epigenetic difference between sister cells that changes mating/cell type has been demonstrated only in the Schizosaccharomyces pombe fission yeast. For technical reasons, it is nearly impossible to determine the existence of such a mechanism operating during embryonic development of multicellular organisms. Our work addresses whether such an epigenetic mechanism causes asymmetric cell division in the recently sequenced fission yeast, S. japonicus (with 36% GC content), which is highly diverged from the well-studied S. pombe species (with 44% GC content). We find that the genomic location and DNA sequences of the mating-type loci of S. japonicus differ vastly from those of the S. pombe species. Remarkably however, similar to S. pombe, the S. japonicus cells switch cell/mating type after undergoing two consecutive cycles of asymmetric cell divisions: only one among four “granddaughter” cells switches. The DNA-strand–specific epigenetic imprint at the mating-type locus1 initiates the recombination event, which is required for cellular differentiation. Therefore the S. pombe and S. japonicus mating systems provide the first two examples in which the intrinsic chirality of double helical structure of DNA forms the primary determinant of asymmetric cell division. Our results show that this unique strand-specific imprinting/segregation epigenetic mechanism for asymmetric cell division is evolutionary conserved. Motivated by these findings, we speculate that DNA-strand–specific epigenetic mechanisms might have evolved to dictate asymmetric cell division in diploid, higher eukaryotes as well.
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18
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Koulintchenko M, Vengrova S, Eydmann T, Arumugam P, Dalgaard JZ. DNA polymerase α (swi7) and the flap endonuclease Fen1 (rad2) act together in the S-phase alkylation damage response in S. pombe. PLoS One 2012; 7:e47091. [PMID: 23071723 PMCID: PMC3469492 DOI: 10.1371/journal.pone.0047091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/07/2012] [Indexed: 11/30/2022] Open
Abstract
Polymerase α is an essential enzyme mainly mediating Okazaki fragment synthesis during lagging strand replication. A specific point mutation in Schizosaccharomyces pombe polymerase α named swi7-1, abolishes imprinting required for mating-type switching. Here we investigate whether this mutation confers any genome-wide defects. We show that the swi7-1 mutation renders cells hypersensitive to the DNA damaging agents methyl methansulfonate (MMS), hydroxyurea (HU) and UV and incapacitates activation of the intra-S checkpoint in response to DNA damage. In addition we show that, in the swi7-1 background, cells are characterized by an elevated level of repair foci and recombination, indicative of increased genetic instability. Furthermore, we detect novel Swi1-, -Swi3- and Pol α- dependent alkylation damage repair intermediates with mobility on 2D-gel that suggests presence of single-stranded regions. Genetic interaction studies showed that the flap endonuclease Fen1 works in the same pathway as Pol α in terms of alkylation damage response. Fen1 was also required for formation of alkylation- damage specific repair intermediates. We propose a model to explain how Pol α, Swi1, Swi3 and Fen1 might act together to detect and repair alkylation damage during S-phase.
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Affiliation(s)
- Milana Koulintchenko
- Division of Biomedical Cell Biology, Warwick Medical School, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Sonya Vengrova
- Division of Biomedical Cell Biology, Warwick Medical School, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Trevor Eydmann
- Division of Biomedical Cell Biology, Warwick Medical School, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Prakash Arumugam
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Jacob Z. Dalgaard
- Division of Biomedical Cell Biology, Warwick Medical School, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
- * E-mail:
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19
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Dalgaard JZ. Causes and consequences of ribonucleotide incorporation into nuclear DNA. Trends Genet 2012; 28:592-7. [PMID: 22951139 DOI: 10.1016/j.tig.2012.07.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 07/12/2012] [Accepted: 07/31/2012] [Indexed: 12/01/2022]
Abstract
Intuitively one would not expect that ribonucleotides are incorporated into nuclear DNA beyond their role in priming Okazaki fragments, nor that such incorporation would be functional. However, several recent studies have shown that not only are ribonucleotides present in the nuclear DNA, but that they can be incorporated by at least two different mechanisms: random 'mis'-incorporation of ribonucleotides, which occurs at a surprisingly high frequency; and site-specific incorporation at a stalled fork. Importantly, in the latter case, the ribonucleotides have been shown to have a biological function - acting to initiate a replication-coupled recombination event mediating a cell type change. Traditionally, it has been thought that 'random' ribonucleotide incorporation causes genetic instability, but new evidence suggests there may be a fine balance between mechanisms preventing and incorporating ribonucleotides into genomic DNA. Indeed, genomic ribonucleotides might have diverse roles affecting genetic stability, DNA damage repair, heterochromatin formation, cellular differentiation, and development.
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Affiliation(s)
- Jacob Z Dalgaard
- Division of Biomedical Cell Biology, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK.
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20
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Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C. Comparative functional genomics of the fission yeasts. Science 2011; 332:930-6. [PMID: 21511999 PMCID: PMC3131103 DOI: 10.1126/science.1203357] [Citation(s) in RCA: 387] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The fission yeast clade--comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus--occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.
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MESH Headings
- Centromere/genetics
- Centromere/physiology
- Centromere/ultrastructure
- DNA Transposable Elements
- Evolution, Molecular
- Gene Expression Profiling
- Gene Expression Regulation, Fungal
- Genes, Mating Type, Fungal
- Genome, Fungal
- Genomics
- Glucose/metabolism
- Meiosis
- Molecular Sequence Annotation
- Molecular Sequence Data
- Phylogeny
- RNA, Antisense/genetics
- RNA, Fungal/genetics
- RNA, Small Interfering/genetics
- RNA, Untranslated/genetics
- Regulatory Elements, Transcriptional
- Schizosaccharomyces/genetics
- Schizosaccharomyces/growth & development
- Schizosaccharomyces/metabolism
- Schizosaccharomyces pombe Proteins/genetics
- Schizosaccharomyces pombe Proteins/metabolism
- Sequence Analysis, DNA
- Species Specificity
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- Nicholas Rhind
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester MA 01605 USA
| | - Zehua Chen
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Moran Yassour
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge MA 02142 USA
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA 02139 USA
- School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
| | - Dawn A Thompson
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge MA 02142 USA
| | - Brian J Haas
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Naomi Habib
- School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, The Hebrew University, Jerusalem 91120 Israel
| | - Ilan Wapinski
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge MA 02142 USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Alpert 536, Boston, MA 02115 USA
| | - Sushmita Roy
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge MA 02142 USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar St. 32-D510, Cambridge, MA 02139 USA
| | - Michael F. Lin
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar St. 32-D510, Cambridge, MA 02139 USA
| | - David I Heiman
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Sarah K Young
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Kanji Furuya
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan
| | - Yabin Guo
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892 USA
| | - Alison Pidoux
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.34 Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Huei Mei Chen
- Department of Molecular Genetics and Microbiology, Life Science, room 130, State University of New York, Stony Brook, NY 11794 USA
| | - Barbara Robbertse
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 USA
| | | | - Keita Aoki
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan
| | - Elizabeth H. Bayne
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.34 Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Aaron M Berlin
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | | | - Edward Dobbs
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.34 Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Livio Dukaj
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester MA 01605 USA
| | - Lin Fan
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | | | - Courtney French
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, The Hebrew University, Jerusalem 91120 Israel
| | - Sharvari Gujja
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Klavs Hansen
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY 11724 USA
| | - Dan Keifenheim
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester MA 01605 USA
| | - Joshua Z. Levin
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Rebecca A. Mosher
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Carolin A. Müller
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Jenna Pfiffner
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Margaret Priest
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Carsten Russ
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Agata Smialowska
- Karolinska Institute, Center for Biosciences, Dept of Biosciences and Nutrition, Stockholm, Sweden
- Department of Life Sciences, Sodertorn Hogskola, Huddinge, Sweden
| | - Peter Swoboda
- Karolinska Institute, Center for Biosciences, Dept of Biosciences and Nutrition, Stockholm, Sweden
| | - Sean M Sykes
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Matthew Vaughn
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY 11724 USA
| | - Sonya Vengrova
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Ryan Yoder
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 USA
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
| | - Robin Allshire
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.34 Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - David Baulcombe
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Bruce W. Birren
- Broad Institute of MIT and Harvard, 301 Binney St., Cambridge MA 02141 USA
| | - William Brown
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Karl Ekwall
- Karolinska Institute, Center for Biosciences, Dept of Biosciences and Nutrition, Stockholm, Sweden
- Department of Life Sciences, Sodertorn Hogskola, Huddinge, Sweden
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge MA 02142 USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar St. 32-D510, Cambridge, MA 02139 USA
| | - Janet Leatherwood
- Department of Molecular Genetics and Microbiology, Life Science, room 130, State University of New York, Stony Brook, NY 11794 USA
| | - Henry Levin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892 USA
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, The Hebrew University, Jerusalem 91120 Israel
| | - Rob Martienssen
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY 11724 USA
| | - Conrad A. Nieduszynski
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 USA
| | - Nir Friedman
- School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Jacob Z. Dalgaard
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Peter Baumann
- Stowers Institute for Medical Research, Kansas City MO USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical School, Kansas City KS USA
- Howard Hughes Medical Institute
| | - Hironori Niki
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan
| | - Aviv Regev
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge MA 02142 USA
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA 02139 USA
- Howard Hughes Medical Institute
| | - Chad Nusbaum
- Broad Institute of MIT and Harvard, 320 Charles St., Cambridge MA 02141 USA
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