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Chen XR, Cui YZ, Li BZ, Yuan YJ. Genome engineering on size reduction and complexity simplification: A review. J Adv Res 2023:S2090-1232(23)00198-4. [PMID: 37442424 DOI: 10.1016/j.jare.2023.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/25/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Genome simplification is an important topic in the field of life sciences that has attracted attention from its conception to the present day. It can help uncover the essential components of the genome and, in turn, shed light on the underlying operating principles of complex biological systems. This has made it a central focus of both basic and applied research in the life sciences. With the recent advancements in related technologies and our increasing knowledge of the genome, now is an opportune time to delve into this topic. AIM of Review: Our review investigates the progress of genome simplification from two perspectives: genome size reduction and complexity simplification. In addition, we provide insights into the future development trends of genome simplification. Key Scientific Concepts of Review: Reducing genome size requires eliminating non-essential elements as much as possible. This process has been facilitated by advances in genome manipulation and synthesis techniques. However, we still need a better and clearer understanding of living systems to reduce genome complexity. As there is a lack of quantitative and clearly defined standards for this task, we have opted to approach the topic from various perspectives and present our findings accordingly.
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Affiliation(s)
- Xiang-Rong Chen
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - You-Zhi Cui
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
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2
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Luithle N, de Bos JU, Hovius R, Maslennikova D, Lewis RT, Ungricht R, Fierz B, Kutay U. Torsin ATPases influence chromatin interaction of the Torsin regulator LAP1. eLife 2020; 9:63614. [PMID: 33320087 PMCID: PMC7773337 DOI: 10.7554/elife.63614] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/15/2020] [Indexed: 12/28/2022] Open
Abstract
The inner nuclear membrane is functionalized by diverse transmembrane proteins that associate with nuclear lamins and/or chromatin. When cells enter mitosis, membrane-chromatin contacts must be broken to allow for proper chromosome segregation; yet how this occurs remains ill-understood. Unexpectedly, we observed that an imbalance in the levels of the lamina-associated polypeptide 1 (LAP1), an activator of ER-resident Torsin AAA+-ATPases, causes a failure in membrane removal from mitotic chromatin, accompanied by chromosome segregation errors and changes in post-mitotic nuclear morphology. These defects are dependent on a hitherto unknown chromatin-binding region of LAP1 that we have delineated. LAP1-induced NE abnormalities are efficiently suppressed by expression of wild-type but not ATPase-deficient Torsins. Furthermore, a dominant-negative Torsin induces chromosome segregation defects in a LAP1-dependent manner. These results indicate that association of LAP1 with chromatin in the nucleus can be modulated by Torsins in the perinuclear space, shedding new light on the LAP1-Torsin interplay.
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Affiliation(s)
- Naemi Luithle
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Jelmi Uit de Bos
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Ruud Hovius
- Institute of Chemical Sciences and Engineering - ISIC, EPFL, Lausanne, Switzerland
| | - Daria Maslennikova
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Renard Tm Lewis
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Rosemarie Ungricht
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Beat Fierz
- Institute of Chemical Sciences and Engineering - ISIC, EPFL, Lausanne, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
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Finardi A, Massari LF, Visintin R. Anaphase Bridges: Not All Natural Fibers Are Healthy. Genes (Basel) 2020; 11:genes11080902. [PMID: 32784550 PMCID: PMC7464157 DOI: 10.3390/genes11080902] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
At each round of cell division, the DNA must be correctly duplicated and distributed between the two daughter cells to maintain genome identity. In order to achieve proper chromosome replication and segregation, sister chromatids must be recognized as such and kept together until their separation. This process of cohesion is mainly achieved through proteinaceous linkages of cohesin complexes, which are loaded on the sister chromatids as they are generated during S phase. Cohesion between sister chromatids must be fully removed at anaphase to allow chromosome segregation. Other (non-proteinaceous) sources of cohesion between sister chromatids consist of DNA linkages or sister chromatid intertwines. DNA linkages are a natural consequence of DNA replication, but must be timely resolved before chromosome segregation to avoid the arising of DNA lesions and genome instability, a hallmark of cancer development. As complete resolution of sister chromatid intertwines only occurs during chromosome segregation, it is not clear whether DNA linkages that persist in mitosis are simply an unwanted leftover or whether they have a functional role. In this review, we provide an overview of DNA linkages between sister chromatids, from their origin to their resolution, and we discuss the consequences of a failure in their detection and processing and speculate on their potential role.
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Affiliation(s)
- Alice Finardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
| | - Lucia F. Massari
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK;
| | - Rosella Visintin
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
- Correspondence: ; Tel.: +39-02-5748-9859; Fax: +39-02-9437-5991
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4
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Di Stefano M, Di Giovanni F, Pozharskaia V, Gomar-Alba M, Baù D, Carey LB, Marti-Renom MA, Mendoza M. Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast. Genetics 2020; 214:651-667. [PMID: 31907200 PMCID: PMC7054015 DOI: 10.1534/genetics.119.302978] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/01/2020] [Indexed: 12/03/2022] Open
Abstract
The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.
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Affiliation(s)
- Marco Di Stefano
- CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Francesca Di Giovanni
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Vasilisa Pozharskaia
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Davide Baù
- CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Lucas B Carey
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871 Beijing, China
- Peking-Tsinghua Center for the Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871 Beijing, China
| | - Marc A Marti-Renom
- CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- ICREA, 08010 Barcelona, Spain
| | - Manuel Mendoza
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
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5
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Lee JH, Berger JM. Cell Cycle-Dependent Control and Roles of DNA Topoisomerase II. Genes (Basel) 2019; 10:E859. [PMID: 31671531 DOI: 10.3390/genes10110859] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
Type II topoisomerases are ubiquitous enzymes in all branches of life that can alter DNA superhelicity and unlink double-stranded DNA segments during processes such as replication and transcription. In cells, type II topoisomerases are particularly useful for their ability to disentangle newly-replicated sister chromosomes. Growing lines of evidence indicate that eukaryotic topoisomerase II (topo II) activity is monitored and regulated throughout the cell cycle. Here, we discuss the various roles of topo II throughout the cell cycle, as well as mechanisms that have been found to govern and/or respond to topo II function and dysfunction. Knowledge of how topo II activity is controlled during cell cycle progression is important for understanding how its misregulation can contribute to genetic instability and how modulatory pathways may be exploited to advance chemotherapeutic development.
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Abstract
Mitosis in metazoans involves detachment of chromosomes from the nuclear envelope (NE) and NE breakdown, whereas yeasts maintain the nuclear structure throughout mitosis. It remains unknown how chromosome attachment to the NE might affect chromosome movement in yeast. By using a rapamycin-induced dimerization system to tether a specific locus of the chromosome to the NE, I found that the tethering delays the separation and causes missegregation of the region distal to the tethered site. The phenotypes are exacerbated by mutations in kinetochore components and Aurora B kinase Ipl1. The chromosome region proximal to the centromere is less affected by the tether, but it exhibits excessive oscillation before segregation. Furthermore, the tether impacts full extension of the mitotic spindle, causing abrupt shrinkage or bending of the spindle in shortened anaphase. The study supports detachment of chromosomes from the NE being required for faithful chromosome segregation in yeast and segregation of tethered chromosomes being dependent on a fully functional mitotic apparatus.
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Affiliation(s)
- Rey-Huei Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
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7
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Abstract
The nucleolus is a membraneless organelle of the nucleus and the site of rRNA synthesis, maturation, and assembly into preribosomal particles. The nucleolus, organized around arrays of rRNA genes (rDNA), dissolves during prophase of mitosis in metazoans, when rDNA transcription ceases, and reforms in telophase, when rDNA transcription resumes. No such dissolution and reformation cycle exists in budding yeast, and the precise course of nucleolar segregation remains unclear. By quantitative live-cell imaging, we observed that the yeast nucleolus is reorganized in its protein composition during mitosis. Daughter cells received equal shares of preinitiation factors, which bind the RNA polymerase I promoter and the rDNA binding barrier protein Fob1, but only about one-third of RNA polymerase I and the processing factors Nop56 and Nsr1. The distribution bias was diminished in nonpolar chromosome segregation events observable in dyn1 mutants. Unequal distribution, however, was enhanced by defects in RNA polymerase I, suggesting that rDNA transcription supports nucleolar segregation. Indeed, quantification of pre-rRNA levels indicated ongoing rDNA transcription in yeast mitosis. These data, together with photobleaching experiments to measure nucleolar protein dynamics in anaphase, consolidate a model that explains the differential partitioning of nucleolar components in budding yeast mitosis.
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Affiliation(s)
- Philipp Girke
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
| | - Wolfgang Seufert
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
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Champion L, Pawar S, Luithle N, Ungricht R, Kutay U. Dissociation of membrane-chromatin contacts is required for proper chromosome segregation in mitosis. Mol Biol Cell 2018; 30:427-440. [PMID: 30586323 PMCID: PMC6594442 DOI: 10.1091/mbc.e18-10-0609] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The nuclear envelope (NE) aids in organizing the interphase genome by tethering chromatin to the nuclear periphery. During mitotic entry, NE–chromatin contacts are broken. Here, we report on the consequences of impaired NE removal from chromatin for cell division of human cells. Using a membrane–chromatin tether that cannot be dissociated when cells enter mitosis, we show that a failure in breaking membrane–chromatin interactions impairs mitotic chromatin organization, chromosome segregation and cytokinesis, and induces an aberrant NE morphology in postmitotic cells. In contrast, chromosome segregation and cell division proceed successfully when membrane attachment to chromatin is induced during metaphase, after chromosomes have been singularized and aligned at the metaphase plate. These results indicate that the separation of membranes and chromatin is critical during prometaphase to allow for proper chromosome compaction and segregation. We propose that one cause of these defects is the multivalency of membrane–chromatin interactions.
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Affiliation(s)
- Lysie Champion
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Sumit Pawar
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Naemi Luithle
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Rosemarie Ungricht
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
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9
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Chi H, Wang X, Shao Y, Qin Y, Deng Z, Wang L, Chen S. Engineering and modification of microbial chassis for systems and synthetic biology. Synth Syst Biotechnol 2019; 4:25-33. [PMID: 30560208 DOI: 10.1016/j.synbio.2018.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/14/2018] [Accepted: 12/05/2018] [Indexed: 12/14/2022] Open
Abstract
Engineering and modifying synthetic microbial chassis is one of the best ways not only to unravel the fundamental principles of life but also to enhance applications in the health, medicine, agricultural, veterinary, and food industries. The two primary strategies for constructing a microbial chassis are the top-down approach (genome reduction) and the bottom-up approach (genome synthesis). Research programs on this topic have been funded in several countries. The ‘Minimum genome factory’ (MGF) project was launched in 2001 in Japan with the goal of constructing microorganisms with smaller genomes for industrial use. One of the best examples of the results of this project is E. coli MGF-01, which has a reduced-genome size and exhibits better growth and higher threonine production characteristics than the parental strain [1]. The ‘cell factory’ project was carried out from 1998 to 2002 in the Fifth Framework Program of the EU (European Union), which tried to comprehensively understand microorganisms used in the application field. One of the outstanding results of this project was the elucidation of proteins secreted by Bacillus subtilis, which was summarized as the ‘secretome’ [2]. The GTL (Genomes to Life) program began in 2002 in the United States. In this program, researchers aimed to create artificial cells both in silico and in vitro, such as the successful design and synthesis of a minimal bacterial genome by John Craig Venter's group [3]. This review provides an update on recent advances in engineering, modification and application of synthetic microbial chassis, with particular emphasis on the value of learning about chassis as a way to better understand life and improve applications.
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Jiang S, Dai J. Inevitability or contingency: how many chromosomes do we really need? Sci China Life Sci 2019; 62:140-3. [PMID: 30519879 DOI: 10.1007/s11427-018-9425-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
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Luo J, Sun X, Cormack BP, Boeke JD. Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast. Nature 2018; 560:392-396. [PMID: 30069047 DOI: 10.1038/s41586-018-0374-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 06/25/2018] [Indexed: 11/09/2022]
Abstract
Extant species have wildly different numbers of chromosomes, even among taxa with relatively similar genome sizes (for example, insects)1,2. This is likely to reflect accidents of genome history, such as telomere-telomere fusions and genome duplication events3-5. Humans have 23 pairs of chromosomes, whereas other apes have 24. One human chromosome is a fusion product of the ancestral state6. This raises the question: how well can species tolerate a change in chromosome numbers without substantial changes to genome content? Many tools are used in chromosome engineering in Saccharomyces cerevisiae7-10, but CRISPR-Cas9-mediated genome editing facilitates the most aggressive engineering strategies. Here we successfully fused yeast chromosomes using CRISPR-Cas9, generating a near-isogenic series of strains with progressively fewer chromosomes ranging from sixteen to two. A strain carrying only two chromosomes of about six megabases each exhibited modest transcriptomic changes and grew without major defects. When we crossed a sixteen-chromosome strain with strains with fewer chromosomes, we noted two trends. As the number of chromosomes dropped below sixteen, spore viability decreased markedly, reaching less than 10% for twelve chromosomes. As the number of chromosomes decreased further, yeast sporulation was arrested: a cross between a sixteen-chromosome strain and an eight-chromosome strain showed greatly reduced full tetrad formation and less than 1% sporulation, from which no viable spores could be recovered. However, homotypic crosses between pairs of strains with eight, four or two chromosomes produced excellent sporulation and spore viability. These results indicate that eight chromosome-chromosome fusion events suffice to isolate strains reproductively. Overall, budding yeast tolerates a reduction in chromosome number unexpectedly well, providing a striking example of the robustness of genomes to change.
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Affiliation(s)
- Jingchuan Luo
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.,Department of Molecular Biology & Genetics, JHU School of Medicine, Baltimore, MD, USA
| | - Xiaoji Sun
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Brendan P Cormack
- Department of Molecular Biology & Genetics, JHU School of Medicine, Baltimore, MD, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
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12
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Callaway E. Entire yeast genome squeezed into one lone chromosome. Nature 2018. [DOI: 10.1038/d41586-018-05857-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Pommier Y, Sun Y, Huang SYN, Nitiss JL. Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat Rev Mol Cell Biol 2016; 17:703-721. [DOI: 10.1038/nrm.2016.111] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Abstract
PICH is an SNF2-family DNA translocase that appears to play a role specifically in mitosis. Characterization of PICH in human cells led to the initial discovery of "ultra-fine DNA bridges" (UFBs) that connect the 2 segregating DNA masses in the anaphase of mitosis. These bridge structures, which arise from specific regions of the genome, are a normal feature of anaphase but had escaped detection previously because they do not stain with commonly used DNA dyes. Nevertheless, UFBs are important for genome maintenance because defects in UFB resolution can lead to cytokinesis failure. We reported recently that PICH stimulates the unlinking (decatenation) of entangled DNA by Topoisomerase IIα (Topo IIα), and is important for the resolution of UFBs. We also demonstrated that PICH and Topo IIα co-localize at the rDNA (rDNA). In this Extra View article, we discuss the mitotic roles of PICH and explore further the role of PICH in the timely segregation of the rDNA locus.
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Affiliation(s)
- Christian F Nielsen
- a Center for Chromosome Stability , Department of Cellular and Molecular Medicine , University of Copenhagen , Copenhagen , Denmark.,b Chromosome Research, Murdoch Children's Research Institute, Royal Children's Hospital , Parkville , VIC , Australia
| | - Ian D Hickson
- a Center for Chromosome Stability , Department of Cellular and Molecular Medicine , University of Copenhagen , Copenhagen , Denmark
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15
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Afonso O, Figueiredo AC, Maiato H. Late mitotic functions of Aurora kinases. Chromosoma 2017; 126:93-103. [DOI: 10.1007/s00412-016-0594-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 10/21/2022]
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Kruitwagen T, Denoth-Lippuner A, Wilkins BJ, Neumann H, Barral Y. Axial contraction and short-range compaction of chromatin synergistically promote mitotic chromosome condensation. eLife 2015; 4:e1039. [PMID: 26615018 PMCID: PMC4755758 DOI: 10.7554/elife.10396] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/27/2015] [Indexed: 11/16/2022] Open
Abstract
The segregation of eukaryotic chromosomes during mitosis requires their extensive folding into units of manageable size for the mitotic spindle. Here, we report on how phosphorylation at serine 10 of histone H3 (H3 S10) contributes to this process. Using a fluorescence-based assay to study local compaction of the chromatin fiber in living yeast cells, we show that chromosome condensation entails two temporally and mechanistically distinct processes. Initially, nucleosome-nucleosome interaction triggered by H3 S10 phosphorylation and deacetylation of histone H4 promote short-range compaction of chromatin during early anaphase. Independently, condensin mediates the axial contraction of chromosome arms, a process peaking later in anaphase. Whereas defects in chromatin compaction have no observable effect on axial contraction and condensin inactivation does not affect short-range chromatin compaction, inactivation of both pathways causes synergistic defects in chromosome segregation and cell viability. Furthermore, both pathways rely at least partially on the deacetylase Hst2, suggesting that this protein helps coordinating chromatin compaction and axial contraction to properly shape mitotic chromosomes. DOI:http://dx.doi.org/10.7554/eLife.10396.001 DNA in humans, yeast and other eukaryotic organisms is packaged in structures called chromosomes. When a cell divides these chromosomes are copied and then the matching pairs are separated so that each daughter cell has a full set of its genome. To enable these events to take place, the DNA must become more tightly packed so that the chromosomes become rigid units with projections called arms. Any failure in this chromosome “condensation” leads to the loss of chromosomes during cell division. Within a chromosome, sections of DNA are wrapped around groups of proteins to make a series of linked units called nucleosomes, which resemble beads on a string. These units and other scaffold proteins together make a structure called chromatin and establish the overall shape of the chromosome. However, it is not exactly clear how the nucleosomes and scaffold proteins are rearranged during condensation. Kruitwagen et al. used microscopy to study chromosome condensation in budding yeast. The experiments reveal that condensation involves two separate processes. First, modifications to the nucleosomes result in these units becoming more tightly packed in a process called short-range compaction. Second, a group of proteins called condensin is responsible for rearranging the compacted chromatin to enforce higher-order structure on the arms of the condensed chromosome (long-range contraction). Further experiments suggest that an enzyme called Hst2 may help to co-ordinate these processes to ensure that chromosomes adopt the right shape before the cell divides. For example, Hst2 ensures that longer chromosomes condense more than shorter ones. A future challenge will be to find out whether chromosome condensation works in a similar way in humans and other large eukaryotes, which form much larger chromosomes with more complicated structures than yeast. DOI:http://dx.doi.org/10.7554/eLife.10396.002
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Affiliation(s)
- Tom Kruitwagen
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Annina Denoth-Lippuner
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Bryan J Wilkins
- Free Floater (Junior) Research Group "Applied Synthetic Biology," Institute for Microbiology and Genetics, Georg- August University Göttingen, Göttingen, Germany
| | - Heinz Neumann
- Free Floater (Junior) Research Group "Applied Synthetic Biology," Institute for Microbiology and Genetics, Georg- August University Göttingen, Göttingen, Germany
| | - Yves Barral
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
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Machín F, Quevedo O, Ramos-Pérez C, García-Luis J. Cdc14 phosphatase: warning, no delay allowed for chromosome segregation! Curr Genet 2015; 62:7-13. [PMID: 26116076 PMCID: PMC4723626 DOI: 10.1007/s00294-015-0502-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/15/2015] [Indexed: 01/08/2023]
Abstract
Cycling events in nature start and end to restart again and again. In the cell cycle, whose purpose is to become two where there was only one, cyclin-dependent kinases (CDKs) are the beginning and, therefore, phosphatases must play a role in the ending. Since CDKs are drivers of the cell cycle and cancer cells uncontrollably divide, much attention has been put into knocking down CDK activity. However, much less is known on the consequences of interfering with the phosphatases that put an end to the cell cycle. We have addressed in recent years the consequences of transiently inactivating the only master cell cycle phosphatase in the model yeast Saccharomyces cerevisiae, Cdc14. Transient inactivation is expected to better mimic the pharmacological action of drugs. Interestingly, we have found that yeast cells tolerate badly a relatively brief inactivation of Cdc14 when cells are already committed into anaphase, the first cell cycle stage where this phosphatase plays important roles. First, we noticed that the segregation of distal regions in the chromosome arm that carries the ribosomal DNA array was irreversibly impaired, leading to an anaphase bridge (AB). Next, we found that this AB could eventually be severed by cytokinesis and led to two different types of genetically compromised daughter cells. All these previous studies were done in haploid cells. We have now recently expanded this analysis to diploid cells and used the advantage of making hybrid diploids to study chromosome rearrangements and changes in the ploidy of the surviving progeny. We have found that the consequences for the genome integrity were far more dramatic than originally envisioned.
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Affiliation(s)
- Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de la Candelaria, Ctra del Rosario 145, 38010, Santa Cruz de Tenerife, Spain.
| | - Oliver Quevedo
- Unidad de Investigación, Hospital Universitario Nuestra Señora de la Candelaria, Ctra del Rosario 145, 38010, Santa Cruz de Tenerife, Spain.,Center for Chromosome Stability and Department of Biology, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Cristina Ramos-Pérez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de la Candelaria, Ctra del Rosario 145, 38010, Santa Cruz de Tenerife, Spain
| | - Jonay García-Luis
- Unidad de Investigación, Hospital Universitario Nuestra Señora de la Candelaria, Ctra del Rosario 145, 38010, Santa Cruz de Tenerife, Spain.,Cell Cycle Group, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN, UK
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Reyes C, Serrurier C, Gauthier T, Gachet Y, Tournier S. Aurora B prevents chromosome arm separation defects by promoting telomere dispersion and disjunction. ACTA ACUST UNITED AC 2015; 208:713-27. [PMID: 25778919 PMCID: PMC4362453 DOI: 10.1083/jcb.201407016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The segregation of centromeres and telomeres at mitosis is coordinated at multiple levels to prevent the formation of aneuploid cells, a phenotype frequently observed in cancer. Mitotic instability arises from chromosome segregation defects, giving rise to chromatin bridges at anaphase. Most of these defects are corrected before anaphase onset by a mechanism involving Aurora B kinase, a key regulator of mitosis in a wide range of organisms. Here, we describe a new role for Aurora B in telomere dispersion and disjunction during fission yeast mitosis. Telomere dispersion initiates in metaphase, whereas disjunction takes place in anaphase. Dispersion is promoted by the dissociation of Swi6/HP1 and cohesin Rad21 from telomeres, whereas disjunction occurs at anaphase after the phosphorylation of condensin subunit Cnd2. Strikingly, we demonstrate that deletion of Ccq1, a telomeric shelterin component, rescued cell death after Aurora inhibition by promoting the loading of condensin on chromosome arms. Our findings reveal an essential role for telomeres in chromosome arm segregation.
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Affiliation(s)
- Céline Reyes
- Laboratoire de biologie cellulaire et moléculaire du contrôle de la prolifération, Université de Toulouse, F-31062 Toulouse, France Centre National de la Recherche Scientifique, LBCMCP-UMR5088, F-31062 Toulouse, France
| | - Céline Serrurier
- Laboratoire de biologie cellulaire et moléculaire du contrôle de la prolifération, Université de Toulouse, F-31062 Toulouse, France Centre National de la Recherche Scientifique, LBCMCP-UMR5088, F-31062 Toulouse, France
| | - Tiphaine Gauthier
- Laboratoire de biologie cellulaire et moléculaire du contrôle de la prolifération, Université de Toulouse, F-31062 Toulouse, France Centre National de la Recherche Scientifique, LBCMCP-UMR5088, F-31062 Toulouse, France
| | - Yannick Gachet
- Laboratoire de biologie cellulaire et moléculaire du contrôle de la prolifération, Université de Toulouse, F-31062 Toulouse, France Centre National de la Recherche Scientifique, LBCMCP-UMR5088, F-31062 Toulouse, France
| | - Sylvie Tournier
- Laboratoire de biologie cellulaire et moléculaire du contrôle de la prolifération, Université de Toulouse, F-31062 Toulouse, France Centre National de la Recherche Scientifique, LBCMCP-UMR5088, F-31062 Toulouse, France
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Leslie M. Topoisomerase II has to work late. J Biophys Biochem Cytol 2014. [PMCID: PMC4164950 DOI: 10.1083/jcb.2066if] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chromatid-untangling enzyme takes longer than expected to complete job.
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