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Zhu X, Kanemaki MT. Replication initiation sites and zones in the mammalian genome: Where are they located and how are they defined? DNA Repair (Amst) 2024; 141:103713. [PMID: 38959715 DOI: 10.1016/j.dnarep.2024.103713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/05/2024]
Abstract
Eukaryotic DNA replication is a tightly controlled process that occurs in two main steps, i.e., licensing and firing, which take place in the G1 and S phases of the cell cycle, respectively. In Saccharomyces cerevisiae, the budding yeast, replication origins contain consensus sequences that are recognized and bound by the licensing factor Orc1-6, which then recruits the replicative Mcm2-7 helicase. By contrast, mammalian initiation sites lack such consensus sequences, and the mammalian ORC does not exhibit sequence specificity. Studies performed over the past decades have identified replication initiation sites in the mammalian genome using sequencing-based assays, raising the question of whether replication initiation occurs at confined sites or in broad zones across the genome. Although recent reports have shown that the licensed MCMs in mammalian cells are broadly distributed, suggesting that ORC-dependent licensing may not determine the initiation sites/zones, they are predominantly located upstream of actively transcribed genes. This review compares the mechanism of replication initiation in yeast and mammalian cells, summarizes the sequencing-based technologies used for the identification of initiation sites/zones, and proposes a possible mechanism of initiation-site/zone selection in mammalian cells. Future directions and challenges in this field are also discussed.
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Affiliation(s)
- Xiaoxuan Zhu
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Shizuoka, Mishima 411-8540, Japan.
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Shizuoka, Mishima 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Shizuoka, Mishima 411-8540, Japan; Department of Biological Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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2
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Tremblay R, Mehrjoo Y, Ahmed O, Simoneau A, McQuaid ME, Affar EB, Nislow C, Giaever G, Wurtele H. Persistent Acetylation of Histone H3 Lysine 56 Compromises the Activity of DNA Replication Origins. Mol Cell Biol 2023; 43:566-595. [PMID: 37811746 PMCID: PMC10791153 DOI: 10.1080/10985549.2023.2259739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 08/09/2023] [Indexed: 10/10/2023] Open
Abstract
In Saccharomyces cerevisiae, newly synthesized histones H3 are acetylated on lysine 56 (H3 K56ac) by the Rtt109 acetyltransferase prior to their deposition on nascent DNA behind replication forks. Two deacetylases of the sirtuin family, Hst3 and Hst4, remove H3 K56ac from chromatin after S phase. hst3Δ hst4Δ cells present constitutive H3 K56ac, which sensitizes cells to replicative stress via unclear mechanisms. A chemogenomic screen revealed that DBF4 heterozygosity sensitizes cells to NAM-induced inhibition of sirtuins. DBF4 and CDC7 encode subunits of the Dbf4-dependent kinase (DDK), which activates origins of DNA replication during S phase. We show that (i) cells harboring the dbf4-1 or cdc7-4 hypomorphic alleles are sensitized to NAM, and that (ii) the sirtuins Sir2, Hst1, Hst3, and Hst4 promote DNA replication in cdc7-4 cells. We further demonstrate that Rif1, an inhibitor of DDK-dependent activation of origins, causes DNA damage and replication defects in NAM-treated cells and hst3Δ hst4Δ mutants. cdc7-4 hst3Δ hst4Δ cells are shown to display delayed initiation of DNA replication, which is not due to intra-S checkpoint activation but requires Rtt109-dependent H3 K56ac. Our results suggest that constitutive H3 K56ac sensitizes cells to replicative stress in part by negatively influencing the activation of origins of DNA replication.
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Affiliation(s)
- Roch Tremblay
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Yosra Mehrjoo
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Oumaima Ahmed
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Antoine Simoneau
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Mary E. McQuaid
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Department of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Department of Medicine, Université de Montréal, Montreal, Québec, Canada
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3
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Heuzé J, Lin YL, Lengronne A, Poli J, Pasero P. Impact of R-loops on oncogene-induced replication stress in cancer cells. C R Biol 2023; 346:95-105. [PMID: 37779381 DOI: 10.5802/crbiol.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 10/03/2023]
Abstract
Replication stress is an alteration in the progression of replication forks caused by a variety of events of endogenous or exogenous origin. In precancerous lesions, this stress is exacerbated by the deregulation of oncogenic pathways, which notably disrupts the coordination between replication and transcription, and leads to genetic instability and cancer development. It is now well established that transcription can interfere with genome replication in different ways, such as head-on collisions between polymerases, accumulation of positive DNA supercoils or formation of R-loops. These structures form during transcription when nascent RNA reanneals with DNA behind the RNA polymerase, forming a stable DNA:RNA hybrid. In this review, we discuss how these different cotranscriptional processes disrupt the progression of replication forks and how they contribute to genetic instability in cancer cells.
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Eldem V, Zararsız G, Erkan M. Global expression pattern of genes containing positively selected sites in European anchovy (Engraulis encrasicolus L.) may shed light on teleost reproduction. PLoS One 2023; 18:e0289940. [PMID: 37566603 PMCID: PMC10420382 DOI: 10.1371/journal.pone.0289940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
European anchovy is a multiple-spawning and highly fecundate pelagic fish with high economic and ecological significance. Although fecundity is influenced by nutrition, temperature and weight of spawners, high reproductive capacity is related to molecular processes in the ovary. The ovary is an essential and complex reproductive organ composed of various somatic and germ cells, which interact to facilitate the development of the ovary and functional oocytes. Revealing the ovarian transcriptome profile of highly fecundate fishes provides insights into oocyte production in teleosts. Here we use a comprehensive tissue-specific RNA sequencing which yielded 102.3 billion clean bases to analyze the transcriptional profiles of the ovary compared with other organs (liver, kidney, ovary, testis, fin, cauda and gill) and juvenile tissues of European anchovy. We conducted a comparative transcriptome and positive selection analysis of seven teleost species with varying fecundity rates to identify genes potentially involved in oogenesis and oocyte development. Of the 2,272 single copies of orthologous genes found, up to 535 genes were under positive selection in European anchovy and these genes are associated with a wide spectrum of cellular and molecular functions, with enrichments such as RNA methylation and modification, ribosome biogenesis, DNA repair, cell cycle processing and peptide/amide biosynthesis. Of the 535 positively selected genes, 55 were upregulated, and 45 were downregulated in the ovary, most of which were related to RNA and DNA transferase, developmental transcription factors, protein kinases and replication factors. Overall, our analysis of the transcriptome level in the ovarian tissue of a teleost will provide further insights into molecular processes and deepen our genetic understanding of egg production in highly fecund fish.
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Affiliation(s)
- Vahap Eldem
- Faculty of Sciences, Department of Biology, Istanbul University, Istanbul, Turkey
| | - Gökmen Zararsız
- Department of Biostatistics, Erciyes University, Kayseri, Turkey
| | - Melike Erkan
- Faculty of Sciences, Department of Biology, Istanbul University, Istanbul, Turkey
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5
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Guilz NC, Ahn YO, Seo S, Mace EM. Unwinding the Role of the CMG Helicase in Inborn Errors of Immunity. J Clin Immunol 2023; 43:847-861. [PMID: 36809597 PMCID: PMC10789183 DOI: 10.1007/s10875-023-01437-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/20/2023] [Indexed: 02/23/2023]
Abstract
Inborn errors of immunity (IEI) are a collection of diseases resulting from genetic causes that impact the immune system through multiple mechanisms. Natural killer cell deficiency (NKD) is one such IEI where natural killer (NK) cells are the main immune lineage affected. Though rare, the deficiency of several genes has been described as underlying causes of NKD, including MCM4, GINS1, MCM10 , and GINS4 , all of which are involved in the eukaryotic CMG helicase. The CMG helicase is made up of C DC45 – M CM – G INS and accessory proteins including MCM10. The CMG helicase plays a critical role in DNA replication by unwinding the double helix and enabling access of polymerases to single-stranded DNA, and thus helicase proteins are active in any proliferating cell. Replication stress, DNA damage, and cell cycle arrest are among the cellular phenotypes attributed to loss of function variants in CMG helicase proteins. Despite the ubiquitous function of the CMG helicase, NK cells have an apparent susceptibility to the deficiency of helicase proteins. This review will examine the role of the CMG helicase in inborn errors of immunity through the lens of NKD and further discuss why natural killer cells can be so strongly affected by helicase deficiency.
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Affiliation(s)
- Nicole C Guilz
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Yong-Oon Ahn
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Seungmae Seo
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA.
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6
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Williams KS, Secomb TW, El-Kareh AW. An autonomous mathematical model for the mammalian cell cycle. J Theor Biol 2023; 569:111533. [PMID: 37196820 DOI: 10.1016/j.jtbi.2023.111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 04/04/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
A mathematical model for the mammalian cell cycle is developed as a system of 13 coupled nonlinear ordinary differential equations. The variables and interactions included in the model are based on detailed consideration of available experimental data. A novel feature of the model is inclusion of cycle tasks such as origin licensing and initiation, nuclear envelope breakdown and kinetochore attachment, and their interactions with controllers (molecular complexes involved in cycle control). Other key features are that the model is autonomous, except for a dependence on external growth factors; the variables are continuous in time, without instantaneous resets at phase boundaries; mechanisms to prevent rereplication are included; and cycle progression is independent of cell size. Eight variables represent cell cycle controllers: the Cyclin D1-Cdk4/6 complex, APCCdh1, SCFβTrCP, Cdc25A, MPF, NuMA, the securin-separase complex, and separase. Five variables represent task completion, with four for the status of origins and one for kinetochore attachment. The model predicts distinct behaviors corresponding to the main phases of the cell cycle, showing that the principal features of the mammalian cell cycle, including restriction point behavior, can be accounted for in a quantitative mechanistic way based on known interactions among cycle controllers and their coupling to tasks. The model is robust to parameter changes, in that cycling is maintained over at least a five-fold range of each parameter when varied individually. The model is suitable for exploring how extracellular factors affect cell cycle progression, including responses to metabolic conditions and to anti-cancer therapies.
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Affiliation(s)
| | - Timothy W Secomb
- BIO5 Institute, University of Arizona, Tucson, AZ, USA; Department of Physiology, University of Arizona, Tucson, AZ, USA
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Hurtig F, Burgers TC, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. SCIENCE ADVANCES 2023; 9:eade5224. [PMID: 36921039 PMCID: PMC10017037 DOI: 10.1126/sciadv.ade5224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/14/2023] [Indexed: 05/13/2023]
Abstract
ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA-adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III-dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III-dependent membrane remodeling.
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Affiliation(s)
- Fredrik Hurtig
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Thomas C. Q. Burgers
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
| | - Alice Cezanne
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Xiuyun Jiang
- Laboratory of Soft Matter Physics, The Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Frank N. Mol
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
| | - Jovan Traparić
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Tim Nierhaus
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Lena Harker-Kirschneck
- University College London, Institute for the Physics of Living Systems, WC1E 6BT London, UK
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
| | - Buzz Baum
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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Tang Y, Wu W, Zheng X, Lu L, Chen X, Hao Z, Liu S, Chen Y. AT-Hook Transcription Factors Show Functions in Liriodendron chinense under Drought Stress and Somatic Embryogenesis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1353. [PMID: 36987041 PMCID: PMC10056439 DOI: 10.3390/plants12061353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
AT-hook motif nuclear localized (AHL) is a transcription factor that can directly induce plant somatic embryogenesis without adding exogenous hormones. One of its functional domains, the AT-hook motif, has a chromatin-modifying function and participates in various cellular processes, including DNA replication and repair and gene transcription leading to cell growth. Liriodendron chinense (Hemsl.) Sargent is an important ornamental and timber tree in China. However, its low drought-resistant ability further leads to a low natural growth rate of its population. Based on bioinformatics analysis, this study identified a total of 21 LcAHLs in L. chinense. To explore the expression pattern of the AHL gene family under drought and somatic embryogenesis, we performed a systematic analysis including basic characteristics, gene structure, chromosome localization, replication event, cis-acting elements and phylogenetic analyses. According to the phylogenetic tree, the 21 LcAHL genes are divided into three separate clades (Clade I, II, and III). Cis-acting element analysis indicated the involvement of the LcAHL genes in drought, cold, light, and auxin regulation. In the generated drought stress transcriptome, a total of eight LcAHL genes showed increased expression levels, with their expression peaking at 3 h and leveling off after 1 d. Nearly all LcAHL genes were highly expressed in the process of somatic embryogenesis. In this study, we performed a genome-wide analysis of the LcAHL gene family and found that LcAHLs take part in resistance to drought stress and the development of somatic embryos. These findings will provide an important theoretical basis for understanding of the LcAHL gene function.
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Affiliation(s)
- Yao Tang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Weihuang Wu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xueyan Zheng
- National Germplasm Bank of Chinese fir at Fujian Yangkou Forest Farm, Shunchang 353211, China
| | - Lu Lu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xinying Chen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Siqin Liu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Ying Chen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
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Masai H. Replicon hypothesis revisited. Biochem Biophys Res Commun 2022; 633:77-80. [DOI: 10.1016/j.bbrc.2022.09.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
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Lemay JF, St-Hilaire E, Ronato DA, Gao Y, Bélanger F, Gezzar-Dandashi S, Kimenyi Ishimwe AB, Sawchyn C, Lévesque D, McQuaid M, Boisvert FM, Mallette FA, Masson JY, Drobetsky EA, Wurtele H. A genome-wide screen identifies SCAI as a modulator of the UV-induced replicative stress response. PLoS Biol 2022; 20:e3001543. [PMID: 36215310 PMCID: PMC9584372 DOI: 10.1371/journal.pbio.3001543] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 10/20/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Helix-destabilizing DNA lesions induced by environmental mutagens such as UV light cause genomic instability by strongly blocking the progression of DNA replication forks (RFs). At blocked RF, single-stranded DNA (ssDNA) accumulates and is rapidly bound by Replication Protein A (RPA) complexes. Such stretches of RPA-ssDNA constitute platforms for recruitment/activation of critical factors that promote DNA synthesis restart. However, during periods of severe replicative stress, RPA availability may become limiting due to inordinate sequestration of this multifunctional complex on ssDNA, thereby negatively impacting multiple vital RPA-dependent processes. Here, we performed a genome-wide screen to identify factors that restrict the accumulation of RPA-ssDNA during UV-induced replicative stress. While this approach revealed some expected "hits" acting in pathways such as nucleotide excision repair, translesion DNA synthesis, and the intra-S phase checkpoint, it also identified SCAI, whose role in the replicative stress response was previously unappreciated. Upon UV exposure, SCAI knock-down caused elevated accumulation of RPA-ssDNA during S phase, accompanied by reduced cell survival and compromised RF progression. These effects were independent of the previously reported role of SCAI in 53BP1-dependent DNA double-strand break repair. We also found that SCAI is recruited to UV-damaged chromatin and that its depletion promotes nascent DNA degradation at stalled RF. Finally, we (i) provide evidence that EXO1 is the major nuclease underlying ssDNA formation and DNA replication defects in SCAI knockout cells and, consistent with this, (ii) demonstrate that SCAI inhibits EXO1 activity on a ssDNA gap in vitro. Taken together, our data establish SCAI as a novel regulator of the UV-induced replicative stress response in human cells.
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Affiliation(s)
- Jean-François Lemay
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | - Edlie St-Hilaire
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | - Daryl A. Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Québec, Canada
| | - Yuandi Gao
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Québec, Canada
| | - François Bélanger
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | - Sari Gezzar-Dandashi
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montréal, Québec, Canada
| | - Aimé Boris Kimenyi Ishimwe
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montréal, Québec, Canada
| | - Christina Sawchyn
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Dominique Lévesque
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Mary McQuaid
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | | | - Frédérick A. Mallette
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Québec, Canada
| | - Elliot A. Drobetsky
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- * E-mail: (EAD); (HW)
| | - Hugo Wurtele
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- * E-mail: (EAD); (HW)
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11
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Sun F, Zhu G, He P, Wei E, Wang R, Wang Q, Tang X, Zhang Y, Shen Z. Identification, expression and subcellular localization of Orc1 in the microsporidian Nosema bombycis. Gene X 2022; 834:146607. [PMID: 35609797 DOI: 10.1016/j.gene.2022.146607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/14/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
As a typical species of microsporidium, Nosema bombycis is the pathogen causing the pébrine disease of silkworm. Rapid proliferation of N. bombycis in host cells requires replication of genetic material. As eukaryotic origin recognition protein, origin recognition complex (ORC) plays an important role in regulating DNA replication, and Orc1 is a key subunit of the origin recognition complex. In this study, we identified the Orc1 in the microsporidian N. bombycis (NbOrc1) for the first time. The NbOrc1 gene contains a complete ORF of 987 bp in length that encodes a 328 amino acid polypeptide. Indirect immunofluorescence results showed that NbOrc1 were colocalized with Nbactin and NbSAS-6 in the nuclei of N. bombycis. Subsequently, we further identified the interaction between the NbOrc1 and Nbactin by CO-IP and Western blot. These results imply that Orc1 may be involved in the proliferation of the microsporidian N. bombycis through interacting with actin.
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Affiliation(s)
- Fuzhen Sun
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Guanyu Zhu
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Ping He
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Erjun Wei
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Runpeng Wang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Qiang Wang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericulture Research Institute of Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Xudong Tang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericulture Research Institute of Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Yiling Zhang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericulture Research Institute of Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Zhongyuan Shen
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericulture Research Institute of Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China.
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12
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A tale of topoisomerases and the knotty genetic material in the backdrop of Plasmodium biology. Biosci Rep 2022; 42:231351. [PMID: 35699968 PMCID: PMC9261774 DOI: 10.1042/bsr20212847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 05/05/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
The untangling or overwinding of genetic material is an inevitable part of DNA
replication, repair, recombination, and transcription. Topoisomerases belong to
a conserved enzyme family that amends DNA topology during various processes of
DNA metabolism. To relax the genetic material, topoisomerases transiently break
the phosphodiester bond on one or both DNA strands and remain associated with
the cleavage site by forming a covalent enzyme–DNA intermediate. This
releases torsional stress and allows the broken DNA to be re-ligated by the
enzyme. The biological function of topoisomerases ranges from the separation of
sister chromatids following DNA replication to the aiding of chromosome
condensation and segregation during mitosis. Topoisomerases are also actively
involved in meiotic recombination. The unicellular apicomplexan parasite,
Plasmodium falciparum, harbors different topoisomerase
subtypes, some of which have substantially different sequences and functions
from their human counterparts. This review highlights the biological function of
each identified Plasmodium topoisomerase along with a
comparative analysis of their orthologs in human or other model organisms. There
is also a focus on recent advancements towards the development of topoisomerase
chemical inhibitors, underscoring the druggability of unique topoisomerase
subunits that are absent in humans. Plasmodium harbors three
distinct genomes in the nucleus, apicoplast, and mitochondria, respectively, and
undergoes non-canonical cell division during the schizont stage of development.
This review emphasizes the specific developmental stages of
Plasmodium on which future topoisomerase research should
focus.
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13
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Greil C, Engelhardt M, Wäsch R. The Role of the APC/C and Its Coactivators Cdh1 and Cdc20 in Cancer Development and Therapy. Front Genet 2022; 13:941565. [PMID: 35832196 PMCID: PMC9273091 DOI: 10.3389/fgene.2022.941565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
To sustain genomic stability by correct DNA replication and mitosis, cell cycle progression is tightly controlled by the cyclic activity of cyclin-dependent kinases, their binding to cyclins in the respective phase and the regulation of cyclin levels by ubiquitin-dependent proteolysis. The spindle assembly checkpoint plays an important role at the metaphase-anaphase transition to ensure a correct separation of sister chromatids before cytokinesis and to initiate mitotic exit, as an incorrect chromosome distribution may lead to genetically unstable cells and tumorigenesis. The ubiquitin ligase anaphase-promoting complex or cyclosome (APC/C) is essential for these processes by mediating the proteasomal destruction of cyclins and other important cell cycle regulators. To this end, it interacts with the two regulatory subunits Cdh1 and Cdc20. Both play a role in tumorigenesis with Cdh1 being a tumor suppressor and Cdc20 an oncogene. In this review, we summarize the current knowledge about the APC/C-regulators Cdh1 and Cdc20 in tumorigenesis and potential targeted therapeutic approaches.
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14
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Joseph CR, Dusi S, Giannattasio M, Branzei D. Rad51-mediated replication of damaged templates relies on monoSUMOylated DDK kinase. Nat Commun 2022; 13:2480. [PMID: 35513396 PMCID: PMC9072374 DOI: 10.1038/s41467-022-30215-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/21/2022] [Indexed: 12/24/2022] Open
Abstract
DNA damage tolerance (DDT), activated by replication stress during genome replication, is mediated by translesion synthesis and homologous recombination (HR). Here we uncover that DDK kinase, essential for replication initiation, is critical for replication-associated recombination-mediated DDT. DDK relies on its multi-monoSUMOylation to facilitate HR-mediated DDT and optimal retention of Rad51 recombinase at replication damage sites. Impairment of DDK kinase activity, reduced monoSUMOylation and mutations in the putative SUMO Interacting Motifs (SIMs) of Rad51 impair replication-associated recombination and cause fork uncoupling with accumulation of large single-stranded DNA regions at fork branching points. Notably, genetic activation of salvage recombination rescues the uncoupled fork phenotype but not the recombination-dependent gap-filling defect of DDK mutants, revealing that the salvage recombination pathway operates preferentially proximal to fork junctions at stalled replication forks. Overall, we uncover that monoSUMOylated DDK acts with Rad51 in an axis that prevents replication fork uncoupling and mediates recombination-dependent gap-filling.
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Affiliation(s)
- Chinnu Rose Joseph
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| | - Sabrina Dusi
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| | - Michele Giannattasio
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
- Università degli Studi di Milano, Dipartimento di Oncologia ed Emato-Oncologia, Via S. Sofia 9/1, 20122, Milano, Italy
| | - Dana Branzei
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy.
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100, Pavia, Italy.
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15
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Limas JC, Littlejohn AN, House AM, Kedziora KM, Mouery BL, Ma B, Fleifel D, Walens A, Aleman MM, Dominguez D, Cook JG. Quantitative profiling of adaptation to cyclin E overproduction. Life Sci Alliance 2022; 5:e202201378. [PMID: 35173014 PMCID: PMC8860095 DOI: 10.26508/lsa.202201378] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 01/03/2023] Open
Abstract
Cyclin E/CDK2 drives cell cycle progression from G1 to S phase. Despite the toxicity of cyclin E overproduction in mammalian cells, the cyclin E gene is overexpressed in some cancers. To further understand how cells can tolerate high cyclin E, we characterized non-transformed epithelial cells subjected to chronic cyclin E overproduction. Cells overproducing cyclin E, but not cyclins D or A, briefly experienced truncated G1 phases followed by a transient period of DNA replication origin underlicensing, replication stress, and impaired proliferation. Individual cells displayed substantial intercellular heterogeneity in cell cycle dynamics and CDK activity. Each phenotype improved rapidly despite high cyclin E-associated activity. Transcriptome analysis revealed adapted cells down-regulated a cohort of G1-regulated genes. Withdrawing cyclin E from adapted cells only partially reversed underlicensing indicating that adaptation is at least partly non-genetic. This study provides evidence that mammalian cyclin E/CDK inhibits origin licensing indirectly through premature S phase onset and provides mechanistic insight into the relationship between CDKs and licensing. It serves as an example of oncogene adaptation that may recapitulate molecular changes during tumorigenesis.
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Affiliation(s)
- Juanita C Limas
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amiee N Littlejohn
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amy M House
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katarzyna M Kedziora
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Bioinformatics and Analytics Research Collaborative (BARC), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brandon L Mouery
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyang Ma
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dalia Fleifel
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrea Walens
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maria M Aleman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeanette Gowen Cook
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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16
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Richards L, Das S, Nordman JT. Rif1-Dependent Control of Replication Timing. Genes (Basel) 2022; 13:genes13030550. [PMID: 35328102 PMCID: PMC8955891 DOI: 10.3390/genes13030550] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 02/01/2023] Open
Abstract
Successful duplication of the genome requires the accurate replication of billions of base pairs of DNA within a relatively short time frame. Failure to accurately replicate the genome results in genomic instability and a host of diseases. To faithfully and rapidly replicate the genome, DNA replication must be tightly regulated and coordinated with many other nuclear processes. These regulations, however, must also be flexible as replication kinetics can change through development and differentiation. Exactly how DNA replication is regulated and how this regulation changes through development is an active field of research. One aspect of genome duplication where much remains to be discovered is replication timing (RT), which dictates when each segment of the genome is replicated during S phase. All organisms display some level of RT, yet the precise mechanisms that govern RT remain are not fully understood. The study of Rif1, a protein that actively regulates RT from yeast to humans, provides a key to unlock the underlying molecular mechanisms controlling RT. The paradigm for Rif1 function is to delay helicase activation within certain regions of the genome, causing these regions to replicate late in S phase. Many questions, however, remain about the intricacies of Rif1 function. Here, we review the current models for the activity of Rif1 with the goal of trying to understand how Rif1 functions to establish the RT program.
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17
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Lee SY, Kim JJ, Miller KM. Bromodomain proteins: protectors against endogenous DNA damage and facilitators of genome integrity. Exp Mol Med 2021; 53:1268-1277. [PMID: 34548613 PMCID: PMC8492697 DOI: 10.1038/s12276-021-00673-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022] Open
Abstract
Endogenous DNA damage is a major contributor to mutations, which are drivers of cancer development. Bromodomain (BRD) proteins are well-established participants in chromatin-based DNA damage response (DDR) pathways, which maintain genome integrity from cell-intrinsic and extrinsic DNA-damaging sources. BRD proteins are most well-studied as regulators of transcription, but emerging evidence has revealed their importance in other DNA-templated processes, including DNA repair and replication. How BRD proteins mechanistically protect cells from endogenous DNA damage through their participation in these pathways remains an active area of investigation. Here, we review several recent studies establishing BRD proteins as key influencers of endogenous DNA damage, including DNA–RNA hybrid (R-loops) formation during transcription and participation in replication stress responses. As endogenous DNA damage is known to contribute to several human diseases, including neurodegeneration, immunodeficiencies, cancer, and aging, the ability of BRD proteins to suppress DNA damage and mutations is likely to provide new insights into the involvement of BRD proteins in these diseases. Although many studies have focused on BRD proteins in transcription, evidence indicates that BRD proteins have emergent functions in DNA repair and genome stability and are participants in the etiology and treatment of diseases involving endogenous DNA damage. Bromodomain (BRD) proteins, known to regulate gene expression, switching particular genes on and off, also play key roles in repairing DNA damage, and studying them may help identify treatments for various diseases, including cancer. DNA damage can occur during normal cellular metabolism, for example, during copying DNA and gene expression. DNA damage is implicated in tumor formation as well as in neurodegeneration, immunodeficiency, and aging. Seo Yun Lee and colleagues at The University of Texas at Austin, USA, have reviewed new results showing how BRD proteins function in repairing DNA damage. They report that when DNA is damaged during copying in BRD-deficient cells, tumors can result. They also report that defects in BRD proteins are often present in cancers. Studying how BRD proteins function in both healthy and diseased cells could help to identify new therapies.
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Affiliation(s)
- Seo Yun Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jae Jin Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA. .,Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Korea.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA. .,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
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18
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The structure of ORC-Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6. Nat Commun 2021; 12:3883. [PMID: 34162887 PMCID: PMC8222357 DOI: 10.1038/s41467-021-24199-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 06/07/2021] [Indexed: 01/31/2023] Open
Abstract
The Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell cycle but becomes active only when it binds to the replication initiator Cdc6. It has been unclear at the molecular level how Cdc6 activates ORC, converting it to an active recruiter of the Mcm2-7 hexamer, the core of the replicative helicase. Here we report the cryo-EM structure at 3.3 Å resolution of the yeast ORC–Cdc6 bound to an 85-bp ARS1 origin DNA. The structure reveals that Cdc6 contributes to origin DNA recognition via its winged helix domain (WHD) and its initiator-specific motif. Cdc6 binding rearranges a short α-helix in the Orc1 AAA+ domain and the Orc2 WHD, leading to the activation of the Cdc6 ATPase and the formation of the three sites for the recruitment of Mcm2-7, none of which are present in ORC alone. The results illuminate the molecular mechanism of a critical biochemical step in the licensing of eukaryotic replication origins. Eukaryotic DNA replication is mediated by many proteins which are tightly regulated for an efficient firing of replication at each cell cycle. Here the authors report a cryo-EM structure of the yeast ORC–Cdc6 bound to an 85-bp ARS1 origin DNA revealing additional insights into how Cdc6 contributes to origin DNA recognition.
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19
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Hammond-Martel I, Verreault A, Wurtele H. Chromatin dynamics and DNA replication roadblocks. DNA Repair (Amst) 2021; 104:103140. [PMID: 34087728 DOI: 10.1016/j.dnarep.2021.103140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
A broad spectrum of spontaneous and genotoxin-induced DNA lesions impede replication fork progression. The DNA damage response that acts to promote completion of DNA replication is associated with dynamic changes in chromatin structure that include two distinct processes which operate genome-wide during S-phase. The first, often referred to as histone recycling or parental histone segregation, is characterized by the transfer of parental histones located ahead of replication forks onto nascent DNA. The second, known as de novo chromatin assembly, consists of the deposition of new histone molecules onto nascent DNA. Because these two processes occur at all replication forks, their potential to influence a multitude of DNA repair and DNA damage tolerance mechanisms is considerable. The purpose of this review is to provide a description of parental histone segregation and de novo chromatin assembly, and to illustrate how these processes influence cellular responses to DNA replication roadblocks.
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Affiliation(s)
- Ian Hammond-Martel
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montreal, H1T 2M4, Canada
| | - Alain Verreault
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Succursale Centre-Ville, Montreal, H3C 3J7, Canada; Département de Pathologie et Biologie Cellulaire, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, H3T 1J4, Canada
| | - Hugo Wurtele
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montreal, H1T 2M4, Canada; Département de Médecine, Université de Montréal, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, H3T 1J4, Canada.
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20
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Merchut-Maya JM, Maya-Mendoza A. The Contribution of Lysosomes to DNA Replication. Cells 2021; 10:cells10051068. [PMID: 33946407 PMCID: PMC8147142 DOI: 10.3390/cells10051068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
Lysosomes, acidic, membrane-bound organelles, are not only the core of the cellular recycling machinery, but they also serve as signaling hubs regulating various metabolic pathways. Lysosomes maintain energy homeostasis and provide pivotal substrates for anabolic processes, such as DNA replication. Every time the cell divides, its genome needs to be correctly duplicated; therefore, DNA replication requires rigorous regulation. Challenges that negatively affect DNA synthesis, such as nucleotide imbalance, result in replication stress with severe consequences for genome integrity. The lysosomal complex mTORC1 is directly involved in the synthesis of purines and pyrimidines to support DNA replication. Numerous drugs have been shown to target lysosomal function, opening an attractive avenue for new treatment strategies against various pathologies, including cancer. In this review, we focus on the interplay between lysosomal function and DNA replication through nucleic acid degradation and nucleotide biosynthesis and how these could be exploited for therapeutic purposes.
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Affiliation(s)
- Joanna Maria Merchut-Maya
- DNA Replication and Cancer Group, Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark;
- Genome Integrity, Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Apolinar Maya-Mendoza
- DNA Replication and Cancer Group, Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark;
- Correspondence: ; Tel.: +45-35-25-73-10
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21
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Combined Inactivation of Pocket Proteins and APC/C Cdh1 by Cdk4/6 Controls Recovery from DNA Damage in G1 Phase. Cells 2021; 10:cells10030550. [PMID: 33806417 PMCID: PMC7999910 DOI: 10.3390/cells10030550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/29/2021] [Accepted: 02/24/2021] [Indexed: 11/20/2022] Open
Abstract
Most Cyclin-dependent kinases (Cdks) are redundant for normal cell division. Here we tested whether these redundancies are maintained during cell cycle recovery after a DNA damage-induced arrest in G1. Using non-transformed RPE-1 cells, we find that while Cdk4 and Cdk6 act redundantly during normal S-phase entry, they both become essential for S-phase entry after DNA damage in G1. We show that this is due to a greater overall dependency for Cdk4/6 activity, rather than to independent functions of either kinase. In addition, we show that inactivation of pocket proteins is sufficient to overcome the inhibitory effects of complete Cdk4/6 inhibition in otherwise unperturbed cells, but that this cannot revert the effects of Cdk4/6 inhibition in DNA damaged cultures. Indeed, we could confirm that, in addition to inactivation of pocket proteins, Cdh1-dependent anaphase-promoting complex/cyclosome (APC/CCdh1) activity needs to be inhibited to promote S-phase entry in damaged cultures. Collectively, our data indicate that DNA damage in G1 creates a unique situation where high levels of Cdk4/6 activity are required to inactivate pocket proteins and APC/CCdh1 to promote the transition from G1 to S phase.
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22
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Novák B, Tyson JJ. Computational modeling of chromosome re-replication in mutant strains of fission yeast. Mol Biol Cell 2021; 32:830-841. [PMID: 33534609 PMCID: PMC8108527 DOI: 10.1091/mbc.e20-09-0610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Typically cells replicate their genome only once per division cycle, but under some circumstances, both natural and unnatural, cells synthesize an overabundance of DNA, either in a disorganized manner (“overreplication”) or by a systematic doubling of chromosome number (“endoreplication”). These variations on the theme of DNA replication and division have been studied in strains of fission yeast, Schizosaccharomyces pombe, carrying mutations that interfere with the function of mitotic cyclin-dependent kinase (Cdk1:Cdc13) without impeding the roles of DNA-replication loading factor (Cdc18) and S-phase cyclin-dependent kinase (Cdk1:Cig2). Some of these mutations support endoreplication, and some overreplication. In this paper, we propose a dynamical model of the interactions among the proteins governing DNA replication and cell division in fission yeast. By computational simulations of the mathematical model, we account for the observed phenotypes of these re-replicating mutants, and by theoretical analysis of the dynamical system, we provide insight into the molecular distinctions between overreplicating and endoreplicating cells. In the case of induced overproduction of regulatory proteins, our model predicts that cells first switch from normal mitotic cell cycles to growth-controlled endoreplication, and ultimately to disorganized overreplication, parallel to the slow increase of protein to very high levels.
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Affiliation(s)
- Béla Novák
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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23
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Johnson MC, Can G, Santos MM, Alexander D, Zegerman P. Checkpoint inhibition of origin firing prevents inappropriate replication outside of S-phase. eLife 2021; 10:e63589. [PMID: 33399537 PMCID: PMC7806266 DOI: 10.7554/elife.63589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/04/2021] [Indexed: 01/02/2023] Open
Abstract
Checkpoints maintain the order of cell cycle events during DNA damage or incomplete replication. How the checkpoint response is tailored to different phases of the cell cycle remains poorly understood. The S-phase checkpoint for example results in the slowing of replication, which in budding yeast occurs by Rad53-dependent inhibition of the initiation factors Sld3 and Dbf4. Despite this, we show here that Rad53 phosphorylates both of these substrates throughout the cell cycle at the same sites as in S-phase, suggesting roles for this pathway beyond S-phase. Indeed, we show that Rad53-dependent inhibition of Sld3 and Dbf4 limits re-replication in G2/M, preventing gene amplification. In addition, we show that inhibition of Sld3 and Dbf4 in G1 prevents premature initiation at all origins at the G1/S transition. This study redefines the scope of the 'S-phase checkpoint' with implications for understanding checkpoint function in cancers that lack cell cycle controls.
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Affiliation(s)
- Mark C Johnson
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute and Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Geylani Can
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute and Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Miguel Monteiro Santos
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute and Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Diana Alexander
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute and Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Philip Zegerman
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute and Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
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24
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Zheng W, Xu S. Analysis of Differential Expression Proteins of Paclitaxel-Treated Lung Adenocarcinoma Cell A549 Using Tandem Mass Tag-Based Quantitative Proteomics. Onco Targets Ther 2020; 13:10297-10313. [PMID: 33116610 PMCID: PMC7569177 DOI: 10.2147/ott.s259895] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/15/2020] [Indexed: 11/23/2022] Open
Abstract
Background Paclitaxel is widely used in the treatment of cancer and has a good effect in the treatment of non-small cell lung cancer. The combination of TMT proteomics and bioinformatics is used to systematically analyze the molecular mechanism of paclitaxel in the treatment of lung adenocarcinoma A549 cell, which is helpful to screen new therapeutic targets. Methods MTT assay was used to analyze the inhibitory effect of paclitaxel on the proliferation of A549 cells. The proteins were identified by TMT quantitative proteomics and the differential expression proteins (DEPs) database was constructed. The DEPs were enriched by Gene Ontology (GO) and KEGG pathway annotation. Based on the information in the STRING database, find the interaction between DEPs, and the protein-protein interaction (PPI) networks of DEPs were constructed and analyzed by using the Cytoscape software. According to the PPI network results, select the hub proteins from DEPs for WB verification. Results A total of 5449 proteins were identified in A549 by TMT proteomics. Compared with the control group, 281 DEPs were significantly up-regulated and 218 were significantly down-regulated after paclitaxel treatment. GO functional analysis, we found that the main functions of these DEPs are binding, catalytic activity, molecular function regulator and so on. They are mainly involved in cellular process, metabolic process, biological regulation and so on. KEGG analysis showed that the three most significant signal transduction pathways of DEPs enrichment were DNA replication, steroid biosynthesis, oxidative phosphorylation. In PPI network, there are 294 nodes among which CDK1, MCM2-5 and PCNA are located at the center of proteins interaction. WB analysis confirmed that the expression of CDK1 was significantly down-regulated, consistent with the TMT results. Conclusion Paclitaxel significantly increased the expression of tubulin, binding tubulin to promote A549 cell death. In addition, paclitaxel significantly inhibited the expression of hub proteins, DNA replication and cell cycle pathways, thus killing lung adenocarcinoma cell A549. These findings will enhance the understanding of the mechanism of paclitaxel in the treatment of lung adenocarcinoma cell A549 and provide new valuable targets.
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Affiliation(s)
- Wanchun Zheng
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, People's Republic of China
| | - Shouming Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, People's Republic of China
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25
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Guarino Almeida E, Renaudin X, Venkitaraman AR. A kinase-independent function for AURORA-A in replisome assembly during DNA replication initiation. Nucleic Acids Res 2020; 48:7844-7855. [PMID: 32652013 PMCID: PMC7430631 DOI: 10.1093/nar/gkaa570] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/03/2020] [Accepted: 06/29/2020] [Indexed: 12/25/2022] Open
Abstract
The catalytic activity of human AURORA-A kinase (AURKA) regulates mitotic progression, and its frequent overexpression in major forms of epithelial cancer is associated with aneuploidy and carcinogenesis. Here, we report an unexpected, kinase-independent function for AURKA in DNA replication initiation whose inhibition through a class of allosteric inhibitors opens avenues for cancer therapy. We show that genetic depletion of AURKA, or its inhibition by allosteric but not catalytic inhibitors, blocks the G1-S cell cycle transition. A catalytically inactive AURKA mutant suffices to overcome this block. We identify a multiprotein complex between AURKA and the replisome components MCM7, WDHD1 and POLD1 formed during G1, and demonstrate that allosteric but not catalytic inhibitors prevent the chromatin assembly of functional replisomes. Indeed, allosteric but not catalytic AURKA inhibitors sensitize cancer cells to inhibition of the CDC7 kinase subunit of the replication-initiating factor DDK. Thus, our findings define a mechanism essential for replisome assembly during DNA replication initiation that is vulnerable to inhibition as combination therapy in cancer.
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Affiliation(s)
- Estrella Guarino Almeida
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Xavier Renaudin
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Ashok R Venkitaraman
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
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26
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Gupta M, Concepcion CP, Fahey CG, Keshishian H, Bhutkar A, Brainson CF, Sanchez-Rivera FJ, Pessina P, Kim JY, Simoneau A, Paschini M, Beytagh MC, Stanclift CR, Schenone M, Mani DR, Li C, Oh A, Li F, Hu H, Karatza A, Bronson RT, Shaw AT, Hata AN, Wong KK, Zou L, Carr SA, Jacks T, Kim CF. BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency. Cancer Res 2020; 80:3841-3854. [PMID: 32690724 PMCID: PMC7501156 DOI: 10.1158/0008-5472.can-20-1744] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/15/2020] [Accepted: 07/15/2020] [Indexed: 12/22/2022]
Abstract
Inactivation of SMARCA4/BRG1, the core ATPase subunit of mammalian SWI/SNF complexes, occurs at very high frequencies in non-small cell lung cancers (NSCLC). There are no targeted therapies for this subset of lung cancers, nor is it known how mutations in BRG1 contribute to lung cancer progression. Using a combination of gain- and loss-of-function approaches, we demonstrate that deletion of BRG1 in lung cancer leads to activation of replication stress responses. Single-molecule assessment of replication fork dynamics in BRG1-deficient cells revealed increased origin firing mediated by the prelicensing protein, CDC6. Quantitative mass spectrometry and coimmunoprecipitation assays showed that BRG1-containing SWI/SNF complexes interact with RPA complexes. Finally, BRG1-deficient lung cancers were sensitive to pharmacologic inhibition of ATR. These findings provide novel mechanistic insight into BRG1-mutant lung cancers and suggest that their dependency on ATR can be leveraged therapeutically and potentially expanded to BRG1-mutant cancers in other tissues. SIGNIFICANCE: These findings indicate that inhibition of ATR is a promising therapy for the 10% of non-small cell lung cancer patients harboring mutations in SMARCA4/BRG1. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/18/3841/F1.large.jpg.
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Affiliation(s)
- Manav Gupta
- Stem Cell Program, Division of Hematology/Oncology and Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Biological and Biomedical Sciences PhD Program, Harvard University, Boston, Massachusetts
| | - Carla P Concepcion
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Caroline G Fahey
- Stem Cell Program, Division of Hematology/Oncology and Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | | | - Arjun Bhutkar
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christine F Brainson
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | | | - Patrizia Pessina
- Stem Cell Program, Division of Hematology/Oncology and Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Y Kim
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Antoine Simoneau
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Margherita Paschini
- Stem Cell Program, Division of Hematology/Oncology and Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Mary C Beytagh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Monica Schenone
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Chendi Li
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | - Audris Oh
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | - Fei Li
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Hai Hu
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Angeliki Karatza
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Roderick T Bronson
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Lee Zou
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Cambridge, Massachusetts
| | - Carla F Kim
- Stem Cell Program, Division of Hematology/Oncology and Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts.
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
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27
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Petty EL, Pillus L. Cell cycle roles for GCN5 revealed through genetic suppression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194625. [PMID: 32798737 DOI: 10.1016/j.bbagrm.2020.194625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 11/17/2022]
Abstract
The conserved acetyltransferase Gcn5 is a member of several complexes in eukaryotic cells, playing roles in regulating chromatin organization, gene expression, metabolism, and cell growth and differentiation via acetylation of both nuclear and cytoplasmic proteins. Distinct functions of Gcn5 have been revealed through a combination of biochemical and genetic approaches in many in vitro studies and model organisms. In this review, we focus on the unique insights that have been gleaned from suppressor studies of gcn5 phenotypes in the budding yeast Saccharomyces cerevisiae. Such studies were fundamental in the early understanding of the balance of counteracting chromatin activities in regulating transcription. Most recently, suppressor screens have revealed roles for Gcn5 in early cell cycle (G1 to S) gene expression and regulation of chromosome segregation during mitosis. Much has been learned, but many questions remain which will be informed by focused analysis of additional genetic and physical interactions.
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Affiliation(s)
- Emily L Petty
- University of California, San Diego, Division of Biological Sciences, Section of Molecular Biology, UCSD Moores Cancer Center, United States of America.
| | - Lorraine Pillus
- University of California, San Diego, Division of Biological Sciences, Section of Molecular Biology, UCSD Moores Cancer Center, United States of America.
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28
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Rainey MD, Quinlan A, Cazzaniga C, Mijic S, Martella O, Krietsch J, Göder A, Lopes M, Santocanale C. CDC7 kinase promotes MRE11 fork processing, modulating fork speed and chromosomal breakage. EMBO Rep 2020; 21:e48920. [PMID: 32496651 PMCID: PMC7403700 DOI: 10.15252/embr.201948920] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 11/24/2022] Open
Abstract
The CDC7 kinase is essential for the activation of DNA replication origins and has been implicated in the replication stress response. Using a highly specific chemical inhibitor and a chemical genetic approach, we now show that CDC7 activity is required to coordinate multiple MRE11‐dependent processes occurring at replication forks, independently from its role in origin firing. CDC7 localizes at replication forks and, similarly to MRE11, mediates active slowing of fork progression upon mild topoisomerase inhibition. Both proteins are also retained on stalled forks, where they promote fork processing and restart. Moreover, MRE11 phosphorylation and localization at replication factories are progressively lost upon CDC7 inhibition. Finally, CDC7 activity at reversed forks is required for their pathological MRE11‐dependent degradation in BRCA2‐deficient cells. Thus, upon replication interference CDC7 is a key regulator of fork progression, processing and integrity. These results highlight a dual role for CDC7 in replication, modulating both initiation and elongation steps of DNA synthesis, and identify a key intervention point for anticancer therapies exploiting replication interference.
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Affiliation(s)
- Michael D Rainey
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Aisling Quinlan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Chiara Cazzaniga
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sofija Mijic
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Oliviano Martella
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Anja Göder
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Corrado Santocanale
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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29
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Pasquier E, Wellinger RJ. In vivo chromatin organization on native yeast telomeric regions is independent of a cis-telomere loopback conformation. Epigenetics Chromatin 2020; 13:23. [PMID: 32443982 PMCID: PMC7243337 DOI: 10.1186/s13072-020-00344-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 05/13/2020] [Indexed: 12/18/2022] Open
Abstract
Background DNA packaging into chromatin regulates all DNA-related processes and at chromosomal ends could affect both essential functions of telomeres: protection against DNA damage response and telomere replication. Despite this primordial role of chromatin, little is known about chromatin organization, and in particular about nucleosome positioning on unmodified subtelomere–telomere junctions in Saccharomyces cerevisiae. Results By ChEC experiments and indirect end-labeling, we characterized nucleosome positioning as well as specialized protein–DNA associations on most subtelomere–telomere junctions present in budding yeast. The results show that there is a relatively large nucleosome-free region at chromosome ends. Despite the absence of sequence homologies between the two major classes of subtelomere–telomere junctions (i.e.: Y’-telomeres and X-telomeres), all analyzed subtelomere–telomere junctions show a terminal nucleosome-free region just distally from the known Rap1-covered telomeric repeats. Moreover, previous evidence suggested a telomeric chromatin fold-back structure onto subtelomeric areas that supposedly was implicated in chromosome end protection. The in vivo ChEC method used herein in conjunction with several proteins in a natural context revealed no evidence for such structures in bulk chromatin. Conclusions Our study allows a structural definition of the chromatin found at chromosome ends in budding yeast. This definition, derived with direct in vivo approaches, includes a terminal area that is free of nucleosomes, certain positioned nucleosomes and conserved DNA-bound protein complexes. This organization of subtelomeric and telomeric areas however does not include a telomeric cis-loopback conformation. We propose that the observations on such fold-back structures may report rare and/or transient associations and not stable or constitutive structures.
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Affiliation(s)
- Emeline Pasquier
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Cancer Research Pavilion, Rm 3025, 3201, rue Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Cancer Research Pavilion, Rm 3025, 3201, rue Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada.
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30
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Zhang W, Feng J, Li Q. The replisome guides nucleosome assembly during DNA replication. Cell Biosci 2020; 10:37. [PMID: 32190287 PMCID: PMC7066812 DOI: 10.1186/s13578-020-00398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleosome assembly during DNA replication is tightly coupled to ongoing DNA synthesis. This process, termed DNA replication-coupled (RC) nucleosome assembly, is essential for chromatin replication and has a great impact on both genome stability maintenance and epigenetic inheritance. This review discusses a set of recent findings regarding the role of replisome components contributing to RC nucleosome assembly. Starting with a brief introduction to the factors involved in nucleosome assembly and some aspects of the architecture of the eukaryotic replisome, we discuss studies from yeast to mammalian cells and the interactions of replisome components with histones and histone chaperones. We describe the proposed functions of replisome components during RC nucleosome assembly and discuss their impacts on histone segregation and implications for epigenetic inheritance.
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Affiliation(s)
- Wenshuo Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
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31
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Ovejero S, Bueno A, Sacristán MP. Working on Genomic Stability: From the S-Phase to Mitosis. Genes (Basel) 2020; 11:E225. [PMID: 32093406 PMCID: PMC7074175 DOI: 10.3390/genes11020225] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/15/2022] Open
Abstract
Fidelity in chromosome duplication and segregation is indispensable for maintaining genomic stability and the perpetuation of life. Challenges to genome integrity jeopardize cell survival and are at the root of different types of pathologies, such as cancer. The following three main sources of genomic instability exist: DNA damage, replicative stress, and chromosome segregation defects. In response to these challenges, eukaryotic cells have evolved control mechanisms, also known as checkpoint systems, which sense under-replicated or damaged DNA and activate specialized DNA repair machineries. Cells make use of these checkpoints throughout interphase to shield genome integrity before mitosis. Later on, when the cells enter into mitosis, the spindle assembly checkpoint (SAC) is activated and remains active until the chromosomes are properly attached to the spindle apparatus to ensure an equal segregation among daughter cells. All of these processes are tightly interconnected and under strict regulation in the context of the cell division cycle. The chromosomal instability underlying cancer pathogenesis has recently emerged as a major source for understanding the mitotic processes that helps to safeguard genome integrity. Here, we review the special interconnection between the S-phase and mitosis in the presence of under-replicated DNA regions. Furthermore, we discuss what is known about the DNA damage response activated in mitosis that preserves chromosomal integrity.
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Affiliation(s)
- Sara Ovejero
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Institute of Human Genetics, CNRS, University of Montpellier, 34000 Montpellier, France
- Department of Biological Hematology, CHU Montpellier, 34295 Montpellier, France
| | - Avelino Bueno
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - María P. Sacristán
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
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32
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Yi ZY, Meng TG, Ma XS, Li J, Zhang CH, Ouyang YC, Schatten H, Qiao J, Sun QY, Qian WP. CDC6 regulates both G2/M transition and metaphase-to-anaphase transition during the first meiosis of mouse oocytes. J Cell Physiol 2020; 235:5541-5554. [PMID: 31984513 DOI: 10.1002/jcp.29469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 01/06/2020] [Indexed: 12/30/2022]
Abstract
Cell division cycle protein, CDC6, is essential for the initiation of DNA replication. CDC6 was recently shown to inhibit the microtubule-organizing activity of the centrosome. Here, we show that CDC6 is localized to the spindle from pro-metaphase I (MI) to MII stages of oocytes, and it plays important roles at two critical steps of oocyte meiotic maturation. CDC6 depletion facilitated the G2/M transition (germinal vesicle breakdown [GVBD]) through regulation of Cdh1 and cyclin B1 expression and CDK1 (CDC2) phosphorylation in a GVBD-inhibiting culture system containing milrinone. Furthermore, GVBD was significantly decreased after knockdown of cyclin B1 in CDC6-depleted oocytes, indicating that the effect of CDC6 loss on GVBD stimulation was mediated, at least in part, by raising cyclin B1. Knockdown of CDC6 also caused abnormal localization of γ-tubulin, resulting in defective spindles, misaligned chromosomes, cyclin B1 accumulation, and spindle assembly checkpoint (SAC) activation, leading to significant pro-MI/MI arrest and PB1 extrusion failure. These phenotypes were also confirmed by time-lapse live cell imaging analysis. The results indicate that CDC6 is indispensable for maintaining G2 arrest of meiosis and functions in G2/M checkpoint regulation in mouse oocytes. Moreover, CDC6 is also a key player regulating meiotic spindle assembly and metaphase-to-anaphase transition in meiotic oocytes.
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Affiliation(s)
- Zi-Yun Yi
- The Reproductive Medicine Center, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Tie-Gang Meng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xue-Shan Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jian Li
- The Reproductive Medicine Center, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Chun-Hui Zhang
- The Reproductive Medicine Center, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Ying-Chun Ouyang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri
| | - Jie Qiao
- Reproductive Medical Center, Peking University Third Hospital, Beijing, China
| | - Qing-Yuan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wei-Ping Qian
- The Reproductive Medicine Center, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
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33
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When RAD52 Allows Mitosis to Accept Unscheduled DNA Synthesis. Cancers (Basel) 2019; 12:cancers12010026. [PMID: 31861741 PMCID: PMC7017103 DOI: 10.3390/cancers12010026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022] Open
Abstract
Faithful duplication of the human genome during the S phase of cell cycle and accurate segregation of sister chromatids in mitosis are essential for the maintenance of chromosome stability from one generation of cells to the next. Cells that are copying their DNA in preparation for division can suffer from ‘replication stress’ (RS) due to various external or endogenous impediments that slow or stall replication forks. RS is a major cause of pathologies including cancer, premature ageing and other disorders associated with genomic instability. It particularly affects genomic loci where progression of replication forks is intrinsically slow or problematic, such as common fragile site (CFS), telomeres, and repetitive sequences. Although the eukaryotic cell cycle is conventionally thought of as several separate steps, each of which must be completed before the next one is initiated, it is now accepted that incompletely replicated chromosomal domains generated in S phase upon RS at these genomic loci can result in late DNA synthesis in G2/M. In 2013, during investigations into the mechanism by which the specialized DNA polymerase eta (Pol η) contributes to the replication and stability of CFS, we unveiled that indeed some DNA synthesis was still occurring in early mitosis at these loci. This surprising observation of mitotic DNA synthesis that differs fundamentally from canonical semi-conservative DNA replication in S-phase has been then confirmed, called “MiDAS”and believed to counteract potentially lethal chromosome mis-segregation and non-disjunction. While other contributions in this Special Issue of Cancers focus on the role of RAS52RAD52 during MiDAS, this review emphases on the discovery of MiDAS and its molecular effectors.
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34
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Abstract
The transition between proliferating and quiescent states must be carefully regulated to ensure that cells divide to create the cells an organism needs only at the appropriate time and place. Cyclin-dependent kinases (CDKs) are critical for both transitioning cells from one cell cycle state to the next, and for regulating whether cells are proliferating or quiescent. CDKs are regulated by association with cognate cyclins, activating and inhibitory phosphorylation events, and proteins that bind to them and inhibit their activity. The substrates of these kinases, including the retinoblastoma protein, enforce the changes in cell cycle status. Single cell analysis has clarified that competition among factors that activate and inhibit CDK activity leads to the cell's decision to enter the cell cycle, a decision the cell makes before S phase. Signaling pathways that control the activity of CDKs regulate the transition between quiescence and proliferation in stem cells, including stem cells that generate muscle and neurons. © 2020 American Physiological Society. Compr Physiol 10:317-344, 2020.
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Affiliation(s)
- Hilary A Coller
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA.,Department of Biological Chemistry, David Geffen School of Medicine, and the Molecular Biology Institute, University of California, Los Angeles, California, USA.,Molecular Biology Institute, University of California, Los Angeles, California, USA
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35
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Dutta P, Islam S, Choppara S, Sengupta P, Kumar A, Kumar A, Wani MR, Chatterjee S, Santra MK. The tumor suppressor FBXO31 preserves genomic integrity by regulating DNA replication and segregation through precise control of cyclin A levels. J Biol Chem 2019; 294:14879-14895. [PMID: 31413110 DOI: 10.1074/jbc.ra118.007055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 08/09/2019] [Indexed: 11/06/2022] Open
Abstract
F-box protein 31 (FBXO31) is a reported putative tumor suppressor, and its inactivation due to loss of heterozygosity is associated with cancers of different origins. An emerging body of literature has documented FBXO31's role in preserving genome integrity following DNA damage and in the cell cycle. However, knowledge regarding the role of FBXO31 during normal cell-cycle progression is restricted to its functions during the G2/M phase. Interestingly, FBXO31 levels remain high even during the early G1 phase, a crucial stage for preparing the cells for DNA replication. Therefore, we sought to investigate the functions of FBXO31 during the G1 phase of the cell cycle. Here, using flow cytometric, biochemical, and immunofluorescence techniques, we show that FBXO31 is essential for maintaining optimum expression of the cell-cycle protein cyclin A for efficient cell-cycle progression. Stable FBXO31 knockdown led to atypical accumulation of cyclin A during the G1 phase, driving premature DNA replication and compromised loading of the minichromosome maintenance complex, resulting in replication from fewer origins and DNA double-strand breaks. Because of these inherent defects in replication, FBXO31-knockdown cells were hypersensitive to replication stress-inducing agents and displayed pronounced genomic instability. Upon entering mitosis, the cells defective in DNA replication exhibited a delay in the prometaphase-to-metaphase transition and anaphase defects such as lagging and bridging chromosomes. In conclusion, our findings establish that FBXO31 plays a pivotal role in preserving genomic integrity by maintaining low cyclin A levels during the G1 phase for faithful genome duplication and segregation.
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Affiliation(s)
- Parul Dutta
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra 411007, India.,Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Sehbanul Islam
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra 411007, India.,Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Srinadh Choppara
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra 411007, India.,Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | | | - Anil Kumar
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra 411007, India.,Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Avinash Kumar
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra 411007, India.,Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York 11201
| | - Mohan R Wani
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | | | - Manas Kumar Santra
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra 411007, India
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36
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Origin Firing Regulations to Control Genome Replication Timing. Genes (Basel) 2019; 10:genes10030199. [PMID: 30845782 PMCID: PMC6470937 DOI: 10.3390/genes10030199] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 12/19/2022] Open
Abstract
Complete genome duplication is essential for genetic homeostasis over successive cell generations. Higher eukaryotes possess a complex genome replication program that involves replicating the genome in units of individual chromatin domains with a reproducible order or timing. Two types of replication origin firing regulations ensure complete and well-timed domain-wise genome replication: (1) the timing of origin firing within a domain must be determined and (2) enough origins must fire with appropriate positioning in a short time window to avoid inter-origin gaps too large to be fully copied. Fundamental principles of eukaryotic origin firing are known. We here discuss advances in understanding the regulation of origin firing to control firing time. Work with yeasts suggests that eukaryotes utilise distinct molecular pathways to determine firing time of distinct sets of origins, depending on the specific requirements of the genomic regions to be replicated. Although the exact nature of the timing control processes varies between eukaryotes, conserved aspects exist: (1) the first step of origin firing, pre-initiation complex (pre-IC formation), is the regulated step, (2) many regulation pathways control the firing kinase Dbf4-dependent kinase, (3) Rif1 is a conserved mediator of late origin firing and (4) competition between origins for limiting firing factors contributes to firing timing. Characterization of the molecular timing control pathways will enable us to manipulate them to address the biological role of replication timing, for example, in cell differentiation and genome instability.
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Köhler K, Sanchez-Pulido L, Höfer V, Marko A, Ponting CP, Snijders AP, Feederle R, Schepers A, Boos D. The Cdk8/19-cyclin C transcription regulator functions in genome replication through metazoan Sld7. PLoS Biol 2019; 17:e2006767. [PMID: 30695077 PMCID: PMC6377148 DOI: 10.1371/journal.pbio.2006767] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/15/2019] [Accepted: 01/08/2019] [Indexed: 02/04/2023] Open
Abstract
Accurate genome duplication underlies genetic homeostasis. Metazoan Mdm2 binding protein (MTBP) forms a main regulatory platform for origin firing together with Treslin/TICRR and TopBP1 (Topoisomerase II binding protein 1 (TopBP1)-interacting replication stimulating protein/TopBP1-interacting checkpoint and replication regulator). We report the first comprehensive analysis of MTBP and reveal conserved and metazoa-specific MTBP functions in replication. This suggests that metazoa have evolved specific molecular mechanisms to adapt replication principles conserved with yeast to the specific requirements of the more complex metazoan cells. We uncover one such metazoa-specific process: a new replication factor, cyclin-dependent kinase 8/19-cyclinC (Cdk8/19-cyclin C), binds to a central domain of MTBP. This interaction is required for complete genome duplication in human cells. In the absence of MTBP binding to Cdk8/19-cyclin C, cells enter mitosis with incompletely duplicated chromosomes, and subsequent chromosome segregation occurs inaccurately. Using remote homology searches, we identified MTBP as the metazoan orthologue of yeast synthetic lethal with Dpb11 7 (Sld7). This homology finally demonstrates that the set of yeast core factors sufficient for replication initiation in vitro is conserved in metazoa. MTBP and Sld7 contain two homologous domains that are present in no other protein, one each in the N and C termini. In MTBP the conserved termini flank the metazoa-specific Cdk8/19-cyclin C binding region and are required for normal origin firing in human cells. The N termini of MTBP and Sld7 share an essential origin firing function, the interaction with Treslin/TICRR or its yeast orthologue Sld3, respectively. The C termini may function as homodimerisation domains. Our characterisation of broadly conserved and metazoa-specific initiation processes sets the basis for further mechanistic dissection of replication initiation in vertebrates. It is a first step in understanding the distinctions of origin firing in higher eukaryotes.
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Affiliation(s)
- Kerstin Köhler
- Vertebrate DNA Replication Lab, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Verena Höfer
- Vertebrate DNA Replication Lab, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Anika Marko
- Vertebrate DNA Replication Lab, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Chris P Ponting
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Ambrosius P Snijders
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Regina Feederle
- Monoclonal Antibody Core Facility and Research Group, Helmholtz Zentrum, Munich GmbH; Institute for Diabetes and Obesity, Neuherberg, Germany
| | - Aloys Schepers
- Monoclonal Antibody Core Facility and Research Group, Helmholtz Zentrum, Munich GmbH; Institute for Diabetes and Obesity, Neuherberg, Germany.,Department of Gene Vectors, Helmholtz Zentrum München GmbH, Munich, Germany
| | - Dominik Boos
- Vertebrate DNA Replication Lab, Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
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Down-regulation of Cdk1 activity in G1 coordinates the G1/S gene expression programme with genome replication. Curr Genet 2019; 65:685-690. [DOI: 10.1007/s00294-018-00926-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/20/2018] [Accepted: 12/22/2018] [Indexed: 02/07/2023]
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Wang X, Ishimi Y. Function of the amino-terminal region of human MCM4 in helicase activity. J Biochem 2019; 164:449-460. [PMID: 30184107 DOI: 10.1093/jb/mvy072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/03/2018] [Indexed: 01/08/2023] Open
Abstract
The amino-terminal region of eukaryotic MCM4 is characteristic of the presence of a number of phosphorylation sites for CDK and DDK, suggesting that the region plays regulatory roles in the MCM2-7 helicase function. However, the roles are not fully understood. We analyzed the role of the amino-terminal region of human MCM4 by using MCM4/6/7 helicase as a model for MCM2-7 helicase. First we found that deletion of 35 amino acids at the amino-terminal end resulted in inhibition of DNA helicase activity of the MCM4/6/7 complex. Conversion of arginine at amino acid no. 10 and 11 to alanine had similar effect to the deletion mutant of Δ1-35, suggesting that these arginine play a role in the DNA helicase activity. The data suggest that expression of these mutant MCM4 in HeLa cells perturbed the progression of the S phase. Substitution of six CDK phosphorylation sites (3, 7, 19, 32, 54 and 110) in the amino-terminal region by phospho-mimetic glutamic acids affected the hexamer formation of the MCM4/6/7 complex. MCM4 phosphorylation by CDK may play a role in DNA replication licensing system, and the present results suggest that the phosphorylation interferes MCM function by lowering stability of MCM complex.
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Affiliation(s)
- Xuan Wang
- College of Science, Ibaraki University, Mito, Ibaraki, Japan
| | - Yukio Ishimi
- College of Science, Ibaraki University, Mito, Ibaraki, Japan
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Hayashi A, Giakoumakis NN, Heidebrecht T, Ishii T, Panagopoulos A, Caillat C, Takahara M, Hibbert RG, Suenaga N, Stadnik-Spiewak M, Takahashi T, Shiomi Y, Taraviras S, von Castelmur E, Lygerou Z, Perrakis A, Nishitani H. Direct binding of Cdt2 to PCNA is important for targeting the CRL4 Cdt2 E3 ligase activity to Cdt1. Life Sci Alliance 2018; 1:e201800238. [PMID: 30623174 PMCID: PMC6312923 DOI: 10.26508/lsa.201800238] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 01/18/2023] Open
Abstract
The C-terminal end of Cdt2 contains a PIP box for binding to PCNA to promote CRL4Cdt2 function, creating a new paradigm where the substrate receptor and substrates bind to a common multivalent docking platform for ubiquitination. The CRL4Cdt2 ubiquitin ligase complex is an essential regulator of cell-cycle progression and genome stability, ubiquitinating substrates such as p21, Set8, and Cdt1, via a display of substrate degrons on proliferating cell nuclear antigens (PCNAs). Here, we examine the hierarchy of the ligase and substrate recruitment kinetics onto PCNA at sites of DNA replication. We demonstrate that the C-terminal end of Cdt2 bears a PCNA interaction protein motif (PIP box, Cdt2PIP), which is necessary and sufficient for the binding of Cdt2 to PCNA. Cdt2PIP binds PCNA directly with high affinity, two orders of magnitude tighter than the PIP box of Cdt1. X-ray crystallographic structures of PCNA bound to Cdt2PIP and Cdt1PIP show that the peptides occupy all three binding sites of the trimeric PCNA ring. Mutating Cdt2PIP weakens the interaction with PCNA, rendering CRL4Cdt2 less effective in Cdt1 ubiquitination and leading to defects in Cdt1 degradation. The molecular mechanism we present suggests a new paradigm for bringing substrates to the CRL4-type ligase, where the substrate receptor and substrates bind to a common multivalent docking platform to enable subsequent ubiquitination.
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Affiliation(s)
- Akiyo Hayashi
- Graduate School of Life Science, University of Hyogo, Kamigori, Japan
| | | | - Tatjana Heidebrecht
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Takashi Ishii
- Graduate School of Life Science, University of Hyogo, Kamigori, Japan
| | | | - Christophe Caillat
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michiyo Takahara
- Graduate School of Life Science, University of Hyogo, Kamigori, Japan
| | - Richard G Hibbert
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Naohiro Suenaga
- Graduate School of Life Science, University of Hyogo, Kamigori, Japan
| | - Magda Stadnik-Spiewak
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Yasushi Shiomi
- Graduate School of Life Science, University of Hyogo, Kamigori, Japan
| | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, Patras, Greece
| | | | - Zoi Lygerou
- Department of Biology, School of Medicine, University of Patras, Patras, Greece
| | - Anastassis Perrakis
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hideo Nishitani
- Graduate School of Life Science, University of Hyogo, Kamigori, Japan
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Schoonen PM, Guerrero Llobet S, van Vugt MATM. Replication stress: Driver and therapeutic target in genomically instable cancers. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 115:157-201. [PMID: 30798931 DOI: 10.1016/bs.apcsb.2018.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genomically instable cancers are characterized by progressive loss and gain of chromosomal fragments, and the acquisition of complex genomic rearrangements. Such cancers, including triple-negative breast cancers and high-grade serous ovarian cancers, typically show aggressive behavior and lack actionable driver oncogenes. Increasingly, oncogene-induced replication stress or defective replication fork maintenance is considered an important driver of genomic instability. Paradoxically, while replication stress causes chromosomal instability and thereby promotes cancer development, it intrinsically poses a threat to cellular viability. Apparently, tumor cells harboring high levels of replication stress have evolved ways to cope with replication stress. As a consequence, therapeutic targeting of such compensatory mechanisms is likely to preferentially target cancers with high levels of replication stress and may prove useful in potentiating chemotherapeutic approaches that exert their effects by interfering with DNA replication. Here, we discuss how replication stress drives chromosomal instability, and the cell cycle-regulated mechanisms that cancer cells employ to deal with replication stress. Importantly, we discuss how mechanisms involving DNA structure-specific resolvases, cell cycle checkpoint kinases and mitotic processing of replication intermediates offer possibilities in developing treatments for difficult-to-treat genomically instable cancers.
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Affiliation(s)
- Pepijn M Schoonen
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sergi Guerrero Llobet
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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Candelli T, Gros J, Libri D. Pervasive transcription fine-tunes replication origin activity. eLife 2018; 7:40802. [PMID: 30556807 PMCID: PMC6314782 DOI: 10.7554/elife.40802] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/17/2018] [Indexed: 12/22/2022] Open
Abstract
RNA polymerase (RNAPII) transcription occurs pervasively, raising the important question of its functional impact on other DNA-associated processes, including replication. In budding yeast, replication originates from Autonomously Replicating Sequences (ARSs), generally located in intergenic regions. The influence of transcription on ARSs function has been studied for decades, but these earlier studies have neglected the role of non-annotated transcription. We studied the relationships between pervasive transcription and replication origin activity using high-resolution transcription maps. We show that ARSs alter the pervasive transcription landscape by pausing and terminating neighboring RNAPII transcription, thus limiting the occurrence of pervasive transcription within origins. We propose that quasi-symmetrical binding of the ORC complex to ARS borders and/or pre-RC formation are responsible for pausing and termination. We show that low, physiological levels of pervasive transcription impact the function of replication origins. Overall, our results have important implications for understanding the impact of genomic location on origin function.
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Affiliation(s)
- Tito Candelli
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Julien Gros
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Domenico Libri
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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Kotsantis P, Petermann E, Boulton SJ. Mechanisms of Oncogene-Induced Replication Stress: Jigsaw Falling into Place. Cancer Discov 2018; 8:537-555. [PMID: 29653955 DOI: 10.1158/2159-8290.cd-17-1461] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/26/2018] [Accepted: 03/09/2018] [Indexed: 12/31/2022]
Abstract
Oncogene activation disturbs cellular processes and accommodates a complex landscape of changes in the genome that contribute to genomic instability, which accelerates mutation rates and promotes tumorigenesis. Part of this cellular turmoil involves deregulation of physiologic DNA replication, widely described as replication stress. Oncogene-induced replication stress is an early driver of genomic instability and is attributed to a plethora of factors, most notably aberrant origin firing, replication-transcription collisions, reactive oxygen species, and defective nucleotide metabolism.Significance: Replication stress is a fundamental step and an early driver of tumorigenesis and has been associated with many activated oncogenes. Deciphering the mechanisms that contribute to the replication stress response may provide new avenues for targeted cancer treatment. In this review, we discuss the latest findings on the DNA replication stress response and examine the various mechanisms through which activated oncogenes induce replication stress. Cancer Discov; 8(5); 537-55. ©2018 AACR.
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Affiliation(s)
| | - Eva Petermann
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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Matthews H, Duffy CW, Merrick CJ. Checks and balances? DNA replication and the cell cycle in Plasmodium. Parasit Vectors 2018; 11:216. [PMID: 29587837 PMCID: PMC5872521 DOI: 10.1186/s13071-018-2800-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/19/2018] [Indexed: 01/10/2023] Open
Abstract
It is over 100 years since the life-cycle of the malaria parasite Plasmodium was discovered, yet its intricacies remain incompletely understood - a knowledge gap that may prove crucial for our efforts to control the disease. Phenotypic screens have partially filled the void in the antimalarial drug market, but as compound libraries eventually become exhausted, new medicines will only come from directed drug development based on a better understanding of fundamental parasite biology. This review focusses on the unusual cell cycles of Plasmodium, which may present a rich source of novel drug targets as well as a topic of fundamental biological interest. Plasmodium does not grow by conventional binary fission, but rather by several syncytial modes of replication including schizogony and sporogony. Here, we collate what is known about the various cell cycle events and their regulators throughout the Plasmodium life-cycle, highlighting the differences between Plasmodium, model organisms and other apicomplexan parasites and identifying areas where further study is required. The possibility of DNA replication and the cell cycle as a drug target is also explored. Finally the use of existing tools, emerging technologies, their limitations and future directions to elucidate the peculiarities of the Plasmodium cell cycle are discussed.
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Affiliation(s)
- Holly Matthews
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Staffordshire, ST55BG, Keele, UK
| | - Craig W Duffy
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Staffordshire, ST55BG, Keele, UK
| | - Catherine J Merrick
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Staffordshire, ST55BG, Keele, UK.
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KISHIMOTO T. MPF-based meiotic cell cycle control: Half a century of lessons from starfish oocytes. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2018; 94:180-203. [PMID: 29643273 PMCID: PMC5968197 DOI: 10.2183/pjab.94.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 02/21/2018] [Indexed: 05/23/2023]
Abstract
In metazoans that undergo sexual reproduction, genomic inheritance is ensured by two distinct types of cell cycle, mitosis and meiosis. Mitosis maintains the genomic ploidy in somatic cells reproducing within a generation, whereas meiosis reduces by half the ploidy in germ cells to prepare for successive generations. The meiotic cell cycle is believed to be a derived form of the mitotic cell cycle; however, the molecular mechanisms underlying both of these processes remain elusive. My laboratory has long studied the meiotic cell cycle in starfish oocytes, particularly the control of meiotic M-phase by maturation- or M phase-promoting factor (MPF) and the kinase cyclin B-associated Cdk1 (cyclin B-Cdk1). Using this system, we have unraveled the molecular principles conserved in metazoans that modify M-phase progression from the mitotic type to the meiotic type needed to produce a haploid genome. Furthermore, we have solved a long-standing enigma concerning the molecular identity of MPF, a universal inducer of M-phase both in mitosis and meiosis of eukaryotic cells.
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Affiliation(s)
- Takeo KISHIMOTO
- Professor Emeritus of Tokyo Institute of Technology
- Visiting Professor of Ochanomizu University, Japan
- Correspondence should be addressed: T. Kishimoto, Science and Education Center, Ochanomizu University, Ootsuka 2-1-1, Bunkyo-ku, Tokyo 112-8610, Japan (e-mail: ; )
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Cheung CHY, Hsu CL, Chen KP, Chong ST, Wu CH, Huang HC, Juan HF. MCM2-regulated functional networks in lung cancer by multi-dimensional proteomic approach. Sci Rep 2017; 7:13302. [PMID: 29038488 PMCID: PMC5643318 DOI: 10.1038/s41598-017-13440-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022] Open
Abstract
DNA replication control is vital for maintaining genome stability and the cell cycle, perhaps most notably during cell division. Malignancies often exhibit defective minichromosome maintenance protein 2 (MCM2), a cancer proliferation biomarker that serves as a licensing factor in the initiation of DNA replication. MCM2 is also known to be one of the ATPase active sites that facilitates conformational changes and drives DNA unwinding at the origin of DNA replication. However, the biological networks of MCM2 in lung cancer cells via protein phosphorylation remain unmapped. The RNA-seq datasets from The Cancer Genome Atlas (TCGA) revealed that MCM2 overexpression is correlated with poor survival rate in lung cancer patients. To uncover MCM2-regulated functional networks in lung cancer, we performed multi-dimensional proteomic approach by integrating analysis of the phosphoproteome and proteome, and identified a total of 2361 phosphorylation sites on 753 phosphoproteins, and 4672 proteins. We found that the deregulation of MCM2 is involved in lung cancer cell proliferation, the cell cycle, and migration. Furthermore, HMGA1S99 phosphorylation was found to be differentially expressed under MCM2 perturbation in opposite directions, and plays an important role in regulating lung cancer cell proliferation. This study therefore enhances our capacity to therapeutically target cancer-specific phosphoproteins.
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Affiliation(s)
- Chantal Hoi Yin Cheung
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chia-Lang Hsu
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Kai-Pu Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
| | - Siao-Ting Chong
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chang-Hsun Wu
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, 11221, Taiwan.
| | - Hsueh-Fen Juan
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan. .,Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan. .,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan.
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The Potential Prognostic Value of Connexin 43 Expression in Head and Neck Squamous Cell Carcinomas. Appl Immunohistochem Mol Morphol 2017; 24:476-81. [PMID: 26447893 DOI: 10.1097/pai.0000000000000212] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Gap juctions are transmembrane communication channels known to be involved in the control of cell proliferation by mediating the exchange of ions and small molecules between cells. Gap junctions are composed of connexon hemichannels made up of 6 connexin proteins, which abnormal expression and functions have been linked to tumor progression and poorer prognosis. Here, we studied the prognostic impact of the most prevalent connexin isotype, connexin 43 (Cx43) in head and neck squamous cell carcinomas (HNSCC). Tissue microarrays made from tumor samples of 90 HNSCC patients were immunostained for Cx43 and cell cycle regulation-related biomarkers including p53, Ki67, p16, aurora A, geminin, and p21 proteins. Scoring and histopathologic evaluation were performed in digital slides. A 4-tier scoring distinguishing the percentage of positively stained tumor cells was used including score 1: <5%, score 2: 6% to 20%, score 3: 21% to 60%, and score 4: >60%. For statistics, Kaplan-Meier curves with log-rank tests, Cox-regression, and Pearson χ/Fisher exact tests were used.A significant positive correlation was found between Cx43 expression and disease-specific survival of patients (P=0.004). The rate of p21 protein-positive tumor cells also proved to be a significant positive prognostic marker (P=0.014). Cx43 levels also showed a significant positive correlation with p53 expression (P=0.036). However, there was no statistical association between Cx43 levels and the rest of the markers tested neither with T, N, or M stage.In conclusion, our data suggest that reduced Cx43 expression and low p21 protein levels may have a significant negative impact on HNSCC prognosis.
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Neves H, Kwok HF. In sickness and in health: The many roles of the minichromosome maintenance proteins. Biochim Biophys Acta Rev Cancer 2017; 1868:295-308. [DOI: 10.1016/j.bbcan.2017.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/29/2017] [Accepted: 06/01/2017] [Indexed: 01/09/2023]
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Tatsumi R, Ishimi Y. An MCM4 mutation detected in cancer cells affects MCM4/6/7 complex formation. J Biochem 2017; 161:259-268. [PMID: 27794528 DOI: 10.1093/jb/mvw065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/20/2016] [Indexed: 02/01/2023] Open
Abstract
An MCM4 mutation detected in human cancer cells from endometrium was characterized. The mutation of G486D is located within MCM-box and the glycine at 486 in human MCM4 is conserved in Saccharomyces cerevisiae MCM4 and Sulfolobus solfataricus MCM. This MCM4 mutation affected human MCM4/6/7 complex formation, since the complex containing the mutant MCM4 protein is unstable and the mutant MCM4 protein is tend to be degraded. It is likely that the MCM4 mutation affects the interaction with MCM7 to destabilize the MCM4/6/7 complex. Cells with abnormal nuclear morphology were detected when the mutant MCM4 was expressed in HeLa cells, suggesting that DNA replication was perturbed in the presence of the mutant MCM4. Role of the conserved amino acid in MCM4 function is discussed.
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50
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DNA damage during S-phase mediates the proliferation-quiescence decision in the subsequent G1 via p21 expression. Nat Commun 2017; 8:14728. [PMID: 28317845 PMCID: PMC5364389 DOI: 10.1038/ncomms14728] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/26/2017] [Indexed: 12/18/2022] Open
Abstract
Following DNA damage caused by exogenous sources, such as ionizing radiation, the tumour suppressor p53 mediates cell cycle arrest via expression of the CDK inhibitor, p21. However, the role of p21 in maintaining genomic stability in the absence of exogenous DNA-damaging agents is unclear. Here, using live single-cell measurements of p21 protein in proliferating cultures, we show that naturally occurring DNA damage incurred over S-phase causes p53-dependent accumulation of p21 during mother G2- and daughter G1-phases. High p21 levels mediate G1 arrest via CDK inhibition, yet lower levels have no impact on G1 progression, and the ubiquitin ligases CRL4Cdt2 and SCFSkp2 couple to degrade p21 prior to the G1/S transition. Mathematical modelling reveals that a bistable switch, created by CRL4Cdt2, promotes irreversible S-phase entry by keeping p21 levels low, preventing premature S-phase exit upon DNA damage. Thus, we characterize how p21 regulates the proliferation-quiescence decision to maintain genomic stability. Cell cycle arrest after DNA damage is achieved by the expression of the CDK inhibitor p21. Here the authors show that spontaneous DNA damage incurred in unperturbed cell cycles, leads to cell populations exhibiting a bistable state, with p53 and p21 regulating the proliferation-quiescence decision.
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