251
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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: 230] [Impact Index Per Article: 38.3] [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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252
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Qian J, Chen Y, Hu Y, Deng Y, Liu Y, Li G, Zou W, Zhao J. Arabidopsis replication factor C4 is critical for DNA replication during the mitotic cell cycle. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:288-303. [PMID: 29406597 DOI: 10.1111/tpj.13855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/16/2018] [Accepted: 01/23/2018] [Indexed: 06/07/2023]
Abstract
Replication factor C (RFC) is a conserved eukaryotic complex consisting of RFC1/2/3/4/5. It plays important roles in DNA replication and the cell cycle in yeast and fruit fly. However, it is not very clear how RFC subunits function in higher plants, except for the Arabidopsis (At) subunits AtRFC1 and AtRFC3. In this study, we investigated the functions of AtRFC4 and found that loss of function of AtRFC4 led to an early sporophyte lethality that initiated as early as the elongated zygote stage, all defective embryos arrested at the two- to four-cell embryo proper stage, and the endosperm possessed six to eight free nuclei. Complementation of rfc4-1/+ with AtRFC4 expression driven through the embryo-specific DD45pro and ABI3pro or the endosperm-specific FIS2pro could not completely restore the defective embryo or endosperm, whereas a combination of these three promoters in rfc4-1/+ enabled the aborted ovules to develop into viable seeds. This suggests that AtRFC4 functions simultaneously in endosperm and embryo and that the proliferation of endosperm is critical for embryo maturation. Assays of DNA content in rfc4-1/+ verified that DNA replication was disrupted in endosperm and embryo, resulting in blocked mitosis. Moreover, we observed a decreased proportion of late S-phase and M-phase cells in the rfc4-1/-FIS2;DD45;ABI3pro::AtRFC4 seedlings, suggesting that incomplete DNA replication triggered cell cycle arrest in cells of the root apical meristem. Therefore, we conclude that AtRFC4 is a crucial gene for DNA replication.
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Affiliation(s)
- Jie Qian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yueyue Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ying Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yingtian Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yang Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Gang Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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253
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Razin SV, Gavrilov AA. Structural–Functional Domains of the Eukaryotic Genome. BIOCHEMISTRY (MOSCOW) 2018; 83:302-312. [DOI: 10.1134/s0006297918040028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/27/2017] [Indexed: 08/30/2023]
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254
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Foss EJ, Lao U, Bedalov A. G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome. J Vis Exp 2018. [PMID: 29630039 DOI: 10.3791/56286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Numerous techniques have been developed to follow the progress of DNA replication through the S phase of the cell cycle. Most of these techniques have been directed toward elucidation of the location and timing of initiation of genome duplication rather than its completion. However, it is critical that we understand regions of the genome that are last to complete replication, because these regions suffer elevated levels of chromosomal breakage and mutation, and they have been associated with both disease and aging. Here we describe how we have extended a technique that has been used to monitor replication initiation to instead identify those regions of the genome last to complete replication. This approach is based on a combination of flow cytometry and high throughput sequencing. Although this report focuses on the application of this technique to yeast, the approach can be used with any cells that can be sorted in a flow cytometer according to DNA content.
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Affiliation(s)
- Eric J Foss
- Division of Clinical Research, Fred Hutchinson Cancer Research Center
| | - Uyen Lao
- Division of Clinical Research, Fred Hutchinson Cancer Research Center
| | - Antonio Bedalov
- Division of Clinical Research, Fred Hutchinson Cancer Research Center; Departments of Medicine and Biochemistry, University of Washington;
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255
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Stewart JA, Wang Y, Ackerson SM, Schuck PL. Emerging roles of CST in maintaining genome stability and human disease. Front Biosci (Landmark Ed) 2018; 23:1564-1586. [PMID: 29293451 DOI: 10.2741/4661] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The human CTC1-STN1-TEN1 (CST) complex is a single-stranded DNA binding protein that shares homology with RPA and interacts with DNA polymerase alpha/primase. CST complexes are conserved from yeasts to humans and function in telomere maintenance. A common role of CST across species is in the regulation of telomere extension by telomerase and C-strand fill-in synthesis. However, recent studies also indicate that CST promotes telomere duplex replication as well the rescue of stalled DNA replication at non-telomeric sites. Furthermore, CST dysfunction and mutation is associated with several genetic diseases and cancers. In this review, we will summarize what is known about CST with a particular focus on the emerging roles of CST in DNA replication and human disease.
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Affiliation(s)
- Jason A Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA,
| | - Yilin Wang
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Stephanie M Ackerson
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Percy Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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256
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Bouffard S, Dambroise E, Brombin A, Lempereur S, Hatin I, Simion M, Corre R, Bourrat F, Joly JS, Jamen F. Fibrillarin is essential for S-phase progression and neuronal differentiation in zebrafish dorsal midbrain and retina. Dev Biol 2018; 437:1-16. [PMID: 29477341 DOI: 10.1016/j.ydbio.2018.02.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/11/2018] [Accepted: 02/13/2018] [Indexed: 10/18/2022]
Abstract
Fibrillarin (Fbl) is a highly conserved protein that plays an essential role in ribosome biogenesis and more particularly in the methylation of ribosomal RNAs and rDNA histones. In cellular models, FBL was shown to play an important role in tumorigenesis and stem cell differentiation. We used the zebrafish as an in vivo model to study Fbl function during embryonic development. We show here that the optic tectum and the eye are severely affected by Fbl depletion whereas ventral regions of the brain are less impacted. The morphogenesis defects are associated with impaired neural differentiation and massive apoptosis. Polysome gradient experiments show that fbl mutant larvae display defects in ribosome biogenesis and activity. Strikingly, flow cytometry analyses revealed different S-phase profiles between wild-type and mutant cells, suggesting a defect in S-phase progression.
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Affiliation(s)
- Stéphanie Bouffard
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Emilie Dambroise
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Alessandro Brombin
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Sylvain Lempereur
- Tefor Core Facility, TEFOR Infrastructure, NeuroPSI, CNRS, Gif-sur-Yvette, France; Université Paris-Est, LIGM, ESIEE, Noisy-le-Grand, France
| | - Isabelle Hatin
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Matthieu Simion
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Raphaël Corre
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Franck Bourrat
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Jean-Stéphane Joly
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France; Tefor Core Facility, TEFOR Infrastructure, NeuroPSI, CNRS, Gif-sur-Yvette, France
| | - Françoise Jamen
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France.
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257
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Bhattacharya D, Hiregange D, Rao BJ. ATR kinase regulates its attenuation via PPM1D phosphatase recruitment to chromatin during recovery from DNA replication stress signalling. J Biosci 2018. [DOI: 10.1007/s12038-018-9736-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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258
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Zhao PA, Rivera-Mulia JC, Gilbert DM. Replication Domains: Genome Compartmentalization into Functional Replication Units. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:229-257. [DOI: 10.1007/978-981-10-6955-0_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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259
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Fang D, Lengronne A, Shi D, Forey R, Skrzypczak M, Ginalski K, Yan C, Wang X, Cao Q, Pasero P, Lou H. Dbf4 recruitment by forkhead transcription factors defines an upstream rate-limiting step in determining origin firing timing. Genes Dev 2018; 31:2405-2415. [PMID: 29330352 PMCID: PMC5795786 DOI: 10.1101/gad.306571.117] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/30/2017] [Indexed: 12/26/2022]
Abstract
Fang et al. show that Dbf4 is enriched at early origins through its interaction with forkhead transcription factors Fkh1 and Fkh2. Dbf4 interacts directly with Sld3 and promotes the recruitment of downstream limiting factors. Initiation of eukaryotic chromosome replication follows a spatiotemporal program. The current model suggests that replication origins compete for a limited pool of initiation factors. However, it remains to be answered how these limiting factors are preferentially recruited to early origins. Here, we report that Dbf4 is enriched at early origins through its interaction with forkhead transcription factors Fkh1 and Fkh2. This interaction is mediated by the Dbf4 C terminus and was successfully reconstituted in vitro. An interaction-defective mutant, dbf4ΔC, phenocopies fkh alleles in terms of origin firing. Remarkably, genome-wide replication profiles reveal that the direct fusion of the DNA-binding domain (DBD) of Fkh1 to Dbf4 restores the Fkh-dependent origin firing but interferes specifically with the pericentromeric origin activation. Furthermore, Dbf4 interacts directly with Sld3 and promotes the recruitment of downstream limiting factors. These data suggest that Fkh1 targets Dbf4 to a subset of noncentromeric origins to promote early replication in a manner that is reminiscent of the recruitment of Dbf4 to pericentromeric origins by Ctf19.
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Affiliation(s)
- Dingqiang Fang
- State Key Laboratory of Agro-Biotechnology, Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Armelle Lengronne
- Institute of Human Genetics, Centre National de la Recherche Scientifique, University of Montpellier, Equipe Labellisée Ligue Contre le Cancer, F-34396 Montpellier Cedex 5, France
| | - Di Shi
- State Key Laboratory of Agro-Biotechnology, Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Romain Forey
- Institute of Human Genetics, Centre National de la Recherche Scientifique, University of Montpellier, Equipe Labellisée Ligue Contre le Cancer, F-34396 Montpellier Cedex 5, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
| | - Changhui Yan
- Department of Computer Science, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Xiaoke Wang
- State Key Laboratory of Agro-Biotechnology, Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology, Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Philippe Pasero
- Institute of Human Genetics, Centre National de la Recherche Scientifique, University of Montpellier, Equipe Labellisée Ligue Contre le Cancer, F-34396 Montpellier Cedex 5, France
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology, Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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260
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Marques CA, McCulloch R. Conservation and Variation in Strategies for DNA Replication of Kinetoplastid Nuclear Genomes. Curr Genomics 2018; 19:98-109. [PMID: 29491738 PMCID: PMC5814967 DOI: 10.2174/1389202918666170815144627] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/19/2017] [Accepted: 04/11/2017] [Indexed: 12/21/2022] Open
Abstract
Introduction: Understanding how the nuclear genome of kinetoplastid parasites is replicated received experimental stimulus from sequencing of the Leishmania major, Trypanosoma brucei and Trypanosoma cruzi genomes around 10 years ago. Gene annotations suggested key players in DNA replication initiation could not be found in these organisms, despite considerable conservation amongst characterised eukaryotes. Initial studies that indicated trypanosomatids might possess an archaeal-like Origin Recognition Complex (ORC), composed of only a single factor termed ORC1/CDC6, have been supplanted by the more recent identification of an ORC in T. brucei. However, the constituent subunits of T. brucei ORC are highly diverged relative to other eukaryotic ORCs and the activity of the complex appears subject to novel, positive regulation. The availability of whole genome sequences has also allowed the deployment of genome-wide strategies to map DNA replication dynamics, to date in T. brucei and Leishmania. ORC1/CDC6 binding and function in T. brucei displays pronounced overlap with the unconventional organisation of gene expression in the genome. Moreover, mapping of sites of replication initiation suggests pronounced differences in replication dynamics in Leishmania relative to T. brucei. Conclusion: Here we discuss what implications these emerging data may have for parasite and eukaryotic biology of DNA replication.
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Affiliation(s)
- Catarina A Marques
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, Dow Street, University of Dundee, Dundee, DD1 5EH, UK
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, University of Glasgow, Glasgow, G12 8TA, UK
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261
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Fischer M, Dang CV, DeCaprio JA. Control of Cell Division. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00017-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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262
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Diseases Associated with Mutation of Replication and Repair Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1076:215-234. [PMID: 29951822 DOI: 10.1007/978-981-13-0529-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alterations in proteins that function in DNA replication and repair have been implicated in the development of human diseases including cancer, premature ageing, skeletal disorders, mental retardation, microcephaly, and neurodegeneration. Drosophila has orthologues of most human replication and repair proteins and high conservation of the relevant cellular pathways, thus providing a versatile system in which to study how these pathways are corrupted leading to the diseased state. In this chapter I will briefly review the diseases associated with defects in replication and repair proteins and discuss how past and future studies on the Drosophila orthologues of such proteins can contribute to the dissection of the mechanisms involved in disease development.
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263
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Aze A, Fragkos M, Bocquet S, Cau J, Méchali M. RNAs coordinate nuclear envelope assembly and DNA replication through ELYS recruitment to chromatin. Nat Commun 2017; 8:2130. [PMID: 29242643 PMCID: PMC5730577 DOI: 10.1038/s41467-017-02180-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 11/13/2017] [Indexed: 12/17/2022] Open
Abstract
Upon fertilisation, the sperm pronucleus acquires the competence to replicate the genome through a cascade of events that link chromatin remodelling to nuclear envelope formation. The factors involved have been partially identified and are poorly characterised. Here, using Xenopus laevis egg extracts we show that RNAs are required for proper nuclear envelope assembly following sperm DNA decondensation. Although chromatin remodelling and pre-replication complex formation occur normally, RNA-depleted extracts show a defect in pre-RC activation. The nuclear processes affected by RNA-depletion included ELYS recruitment, which accounts for the deficiency in nuclear pore complex assembly. This results in failure in chromatin relaxation as well as in the import and proper nuclear concentration of the S-phase kinases necessary for DNA replication activation. Our results highlight a translation-independent RNA function necessary for the parental genome progression towards the early embryonic cell cycle programme. The factors that link chromatin remodelling to nuclear envelope formation in the sperm pronucleus are not fully characterised. Here, the authors show that in RNA-depleted Xenopus laevis egg extracts, ELYS recruitment and nuclear pore complex formation are impaired, resulting in defective nuclear processes.
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Affiliation(s)
- Antoine Aze
- Institute of Human Genetics, UMR 9002, CNRS and the University of Montpellier, Replication and Genome Dynamics, 141 rue de la Cardonille, 34396, Montpellier, France.
| | - Michalis Fragkos
- Institute of Human Genetics, UMR 9002, CNRS and the University of Montpellier, Replication and Genome Dynamics, 141 rue de la Cardonille, 34396, Montpellier, France.,Institut Gustave Roussy, Genetic Stability and Oncogenesis Department, 39 rue Camille Desmoulins, 94805, Villejuif, France
| | - Stéphane Bocquet
- Institute of Human Genetics, UMR 9002, CNRS and the University of Montpellier, Replication and Genome Dynamics, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Julien Cau
- Institute of Human Genetics, UMR 9002, CNRS and the University of Montpellier, Montpellier RIO Imaging, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Marcel Méchali
- Institute of Human Genetics, UMR 9002, CNRS and the University of Montpellier, Replication and Genome Dynamics, 141 rue de la Cardonille, 34396, Montpellier, France.
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264
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Arbi M, Pefani DE, Taraviras S, Lygerou Z. Controlling centriole numbers: Geminin family members as master regulators of centriole amplification and multiciliogenesis. Chromosoma 2017; 127:151-174. [PMID: 29243212 DOI: 10.1007/s00412-017-0652-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 01/18/2023]
Abstract
To ensure that the genetic material is accurately passed down to daughter cells during mitosis, dividing cells must duplicate their chromosomes and centrosomes once and only once per cell cycle. The same key steps-licensing, duplication, and segregation-control both the chromosome and the centrosome cycle, which must occur in concert to safeguard genome integrity. Aberrations in genome content or centrosome numbers lead to genomic instability and are linked to tumorigenesis. Such aberrations, however, can also be part of the normal life cycle of specific cell types. Multiciliated cells best exemplify the deviation from a normal centrosome cycle. They are post-mitotic cells which massively amplify their centrioles, bypassing the rule for once-per-cell-cycle centriole duplication. Hundreds of centrioles dock to the apical cell surface and generate motile cilia, whose concerted movement ensures fluid flow across epithelia. The early steps that control the generation of multiciliated cells have lately started to be elucidated. Geminin and the vertebrate-specific GemC1 and McIdas are distantly related coiled-coil proteins, initially identified as cell cycle regulators associated with the chromosome cycle. Geminin is required to ensure once-per-cell-cycle genome replication, while McIdas and GemC1 bind to Geminin and are implicated in DNA replication control. Recent findings highlight Geminin family members as early regulators of multiciliogenesis. GemC1 and McIdas specify the multiciliate cell fate by forming complexes with the E2F4/5 transcription factors to switch on a gene expression program leading to centriole amplification and cilia formation. Positive and negative interactions among Geminin family members may link cell cycle control to centriole amplification and multiciliogenesis, acting close to the point of transition from proliferation to differentiation. We review key steps of centrosome duplication and amplification, present the role of Geminin family members in the centrosome and chromosome cycle, and discuss links with disease.
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Affiliation(s)
- Marina Arbi
- Laboratory of Biology, School of Medicine, University of Patras, 26504 Rio, Patras, Greece
| | - Dafni-Eleftheria Pefani
- Laboratory of Biology, School of Medicine, University of Patras, 26504 Rio, Patras, Greece.,CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Stavros Taraviras
- Laboratory of Physiology, School of Medicine, University of Patras, 26504 Rio, Patras, Greece
| | - Zoi Lygerou
- Laboratory of Biology, School of Medicine, University of Patras, 26504 Rio, Patras, Greece.
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265
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DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner. Cell Rep 2017; 17:2927-2942. [PMID: 27974207 DOI: 10.1016/j.celrep.2016.11.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/07/2016] [Accepted: 11/11/2016] [Indexed: 11/22/2022] Open
Abstract
Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division.
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266
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Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS. Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI). Science 2017; 356:189-194. [PMID: 28408603 DOI: 10.1126/science.aak9787] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 02/03/2017] [Accepted: 03/17/2017] [Indexed: 12/12/2022]
Abstract
Single-cell genomics is important for biology and medicine. However, current whole-genome amplification (WGA) methods are limited by low accuracy of copy-number variation (CNV) detection and low amplification fidelity. Here we report an improved single-cell WGA method, Linear Amplification via Transposon Insertion (LIANTI), which outperforms existing methods, enabling micro-CNV detection with kilobase resolution. This allowed direct observation of stochastic firing of DNA replication origins, which differs from cell to cell. We also show that the predominant cytosine-to-thymine mutations observed in single-cell genomics often arise from the artifact of cytosine deamination upon cell lysis. However, identifying single-nucleotide variations (SNVs) can be accomplished by sequencing kindred cells. We determined the spectrum of SNVs in a single human cell after ultraviolet radiation, revealing their nonrandom genome-wide distribution.
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Affiliation(s)
- Chongyi Chen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dong Xing
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Longzhi Tan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Heng Li
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Guangyu Zhou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lei Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. .,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
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267
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Sanchez JC, Kwan EX, Pohl TJ, Amemiya HM, Raghuraman MK, Brewer BJ. Defective replication initiation results in locus specific chromosome breakage and a ribosomal RNA deficiency in yeast. PLoS Genet 2017; 13:e1007041. [PMID: 29036220 PMCID: PMC5658192 DOI: 10.1371/journal.pgen.1007041] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 10/26/2017] [Accepted: 09/21/2017] [Indexed: 01/23/2023] Open
Abstract
A form of dwarfism known as Meier-Gorlin syndrome (MGS) is caused by recessive mutations in one of six different genes (ORC1, ORC4, ORC6, CDC6, CDT1, and MCM5). These genes encode components of the pre-replication complex, which assembles at origins of replication prior to S phase. Also, variants in two additional replication initiation genes have joined the list of causative mutations for MGS (Geminin and CDC45). The identity of the causative MGS genetic variants strongly suggests that some aspect of replication is amiss in MGS patients; however, little evidence has been obtained regarding what aspect of chromosome replication is faulty. Since the site of one of the missense mutations in the human ORC4 alleles is conserved between humans and yeast, we sought to determine in what way this single amino acid change affects the process of chromosome replication, by introducing the comparable mutation into yeast (orc4Y232C). We find that yeast cells with the orc4Y232C allele have a prolonged S-phase, due to compromised replication initiation at the ribosomal DNA (rDNA) locus located on chromosome XII. The inability to initiate replication at the rDNA locus results in chromosome breakage and a severely reduced rDNA copy number in the survivors, presumably helping to ensure complete replication of chromosome XII. Although reducing rDNA copy number may help ensure complete chromosome replication, orc4Y232C cells struggle to meet the high demand for ribosomal RNA synthesis. This finding provides additional evidence linking two essential cellular pathways-DNA replication and ribosome biogenesis.
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Affiliation(s)
- Joseph C. Sanchez
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Elizabeth X. Kwan
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Thomas J. Pohl
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Haley M. Amemiya
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Bonita J. Brewer
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
- * E-mail:
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268
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Stormo BM, Fox DT. Polyteny: still a giant player in chromosome research. Chromosome Res 2017; 25:201-214. [PMID: 28779272 PMCID: PMC5768140 DOI: 10.1007/s10577-017-9562-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/17/2022]
Abstract
In this era of high-resolution mapping of chromosome territories, topological interactions, and chromatin states, it is increasingly appreciated that the positioning of chromosomes and their interactions within the nucleus is critical for cellular function. Due to their large size and distinctive structure, polytene chromosomes have contributed a wealth of knowledge regarding chromosome regulation. In this review, we discuss the diversity of polytene chromosomes in nature and in disease, examine the recurring structural features of polytene chromosomes in terms of what they reveal about chromosome biology, and discuss recent advances regarding how polytene chromosomes are assembled and disassembled. After over 130 years of study, these giant chromosomes are still powerful tools to understand chromosome biology.
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Affiliation(s)
- Benjamin M Stormo
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Donald T Fox
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA.
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269
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Zilio N, Eifler-Olivi K, Ulrich HD. Functions of SUMO in the Maintenance of Genome Stability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:51-87. [PMID: 28197906 DOI: 10.1007/978-3-319-50044-7_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Like in most other areas of cellular metabolism, the functions of the ubiquitin-like modifier SUMO in the maintenance of genome stability are manifold and varied. Perturbations of global sumoylation causes a wide spectrum of phenotypes associated with defects in DNA maintenance, such as hypersensitivity to DNA-damaging agents, gross chromosomal rearrangements and loss of entire chromosomes. Consistent with these observations, many key factors involved in various DNA repair pathways have been identified as SUMO substrates. However, establishing a functional connection between a given SUMO target, the cognate SUMO ligase and a relevant phenotype has remained a challenge, mainly because of the difficulties involved in identifying important modification sites and downstream effectors that specifically recognize the target in its sumoylated state. This review will give an overview over the major pathways of DNA repair and genome maintenance influenced by the SUMO system and discuss selected examples of SUMO's actions in these pathways where the biological consequences of the modification have been elucidated.
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Affiliation(s)
- Nicola Zilio
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany
| | | | - Helle D Ulrich
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.
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270
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Kumagai A, Dunphy WG. MTBP, the partner of Treslin, contains a novel DNA-binding domain that is essential for proper initiation of DNA replication. Mol Biol Cell 2017; 28:2998-3012. [PMID: 28877985 PMCID: PMC5662258 DOI: 10.1091/mbc.e17-07-0448] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 01/24/2023] Open
Abstract
MTBP, the partner of Treslin, contains a novel DNA-binding domain that associates with double-stranded DNA and G-quadruplex DNA. Mutants of MTBP that lack a functional version of this domain cannot support normal initiation of DNA replication. Treslin, which is essential for incorporation of Cdc45 into the replicative helicase, possesses a partner called MTBP (Mdm2-binding protein). We have analyzed Xenopus and human MTBP to assess its role in DNA replication. Depletion of MTBP from Xenopus egg extracts, which also removes Treslin, abolishes DNA replication. These extracts be can rescued with recombinant Treslin-MTBP but not Treslin or MTBP alone. Thus, Treslin-MTBP is collectively necessary for replication. We have identified a C-terminal region of MTBP (the CTM domain) that binds efficiently to both double-stranded DNA and G-quadruplex (G4) DNA. This domain also exhibits homology with budding yeast Sld7. Mutants of MTBP without a functional CTM domain are defective for DNA replication in Xenopus egg extracts. These mutants display an impaired localization to chromatin and the inability to support loading of Cdc45. Human cells harboring such a mutant also display severe S-phase defects. Thus, the CTM domain of MTBP plays a critical role in localizing Treslin-MTBP to the replication apparatus for initiation.
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Affiliation(s)
- Akiko Kumagai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - William G Dunphy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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271
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Razin SV, Ulianov SV. Gene functioning and storage within a folded genome. Cell Mol Biol Lett 2017; 22:18. [PMID: 28861108 PMCID: PMC5575855 DOI: 10.1186/s11658-017-0050-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/24/2017] [Indexed: 01/28/2023] Open
Abstract
In mammals, genomic DNA that is roughly 2 m long is folded to fit the size of the cell nucleus that has a diameter of about 10 μm. The folding of genomic DNA is mediated via assembly of DNA-protein complex, chromatin. In addition to the reduction of genomic DNA linear dimensions, the assembly of chromatin allows to discriminate and to mark active (transcribed) and repressed (non-transcribed) genes. Consequently, epigenetic regulation of gene expression occurs at the level of DNA packaging in chromatin. Taking into account the increasing attention of scientific community toward epigenetic systems of gene regulation, it is very important to understand how DNA folding in chromatin is related to gene activity. For many years the hierarchical model of DNA folding was the most popular. It was assumed that nucleosome fiber (10-nm fiber) is folded into 30-nm fiber and further on into chromatin loops attached to a nuclear/chromosome scaffold. Recent studies have demonstrated that there is much less regularity in chromatin folding within the cell nucleus. The very existence of 30-nm chromatin fibers in living cells was questioned. On the other hand, it was found that chromosomes are partitioned into self-interacting spatial domains that restrict the area of enhancers action. Thus, TADs can be considered as structural-functional domains of the chromosomes. Here we discuss the modern view of DNA packaging within the cell nucleus in relation to the regulation of gene expression. Special attention is paid to the possible mechanisms of the chromatin fiber self-assembly into TADs. We discuss the model postulating that partitioning of the chromosome into TADs is determined by the distribution of active and inactive chromatin segments along the chromosome. This article was specially invited by the editors and represents work by leading researchers.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, 119334 Moscow, Russia.,Lomonosov Moscow State University, Biological Faculty, Leninskie Gory 1, building 12, 119192 Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, 119334 Moscow, Russia.,Lomonosov Moscow State University, Biological Faculty, Leninskie Gory 1, building 12, 119192 Moscow, Russia
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272
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Lee I, Kim GS, Bae JS, Kim J, Rhee K, Hwang DS. The DNA replication protein Cdc6 inhibits the microtubule-organizing activity of the centrosome. J Biol Chem 2017; 292:16267-16276. [PMID: 28827311 DOI: 10.1074/jbc.m116.763680] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 08/14/2017] [Indexed: 11/06/2022] Open
Abstract
The centrosome serves as a major microtubule-organizing center (MTOC). The Cdc6 protein is a component of the pre-replicative complex and a licensing factor for the initiation of chromosome replication and localizes to centrosomes during the S and G2 phases of the cfell cycle of human cells. This cell cycle-dependent localization of Cdc6 to the centrosome motivated us to investigate whether Cdc6 negatively regulates MTOC activity and to determine the integral proteins that comprise the pericentriolar material (PCM). Time-lapse live-cell imaging of microtubule regrowth revealed that Cdc6 depletion increased microtubule nucleation at the centrosomes and that expression of Cdc6 in Cdc6-depleted cells reversed this effect. This increase and decrease in microtubule nucleation correlated with the centrosomal intensities of PCM proteins such as γ-tubulin, pericentrin, CDK5 regulatory subunit-associated protein 2 (CDK5RAP2), and centrosomal protein 192 (Cep192). The regulation of microtubule nucleation and the recruitment of PCM proteins to the centrosome required Cdc6 ATPase activity, as well as a centrosomal localization of Cdc6. These results suggest a novel function for Cdc6 in coordinating centrosome assembly and function.
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Affiliation(s)
- Inyoung Lee
- From the Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Gwang Su Kim
- From the Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jun Sung Bae
- From the Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jaeyoun Kim
- From the Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Kunsoo Rhee
- From the Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Deog Su Hwang
- From the Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
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273
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Saldivar JC, Cortez D, Cimprich KA. The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nat Rev Mol Cell Biol 2017; 18:622-636. [PMID: 28811666 DOI: 10.1038/nrm.2017.67] [Citation(s) in RCA: 518] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
One way to preserve a rare book is to lock it away from all potential sources of damage. Of course, an inaccessible book is also of little use, and the paper and ink will continue to degrade with age in any case. Like a book, the information stored in our DNA needs to be read, but it is also subject to continuous assault and therefore needs to be protected. In this Review, we examine how the replication stress response that is controlled by the kinase ataxia telangiectasia and Rad3-related (ATR) senses and resolves threats to DNA integrity so that the DNA remains available to read in all of our cells. We discuss the multiple data that have revealed an elegant yet increasingly complex mechanism of ATR activation. This involves a core set of components that recruit ATR to stressed replication forks, stimulate kinase activity and amplify ATR signalling. We focus on the activities of ATR in the control of cell cycle checkpoints, origin firing and replication fork stability, and on how proper regulation of these processes is crucial to ensure faithful duplication of a challenging genome.
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Affiliation(s)
- Joshua C Saldivar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, California 94305-5441, USA
| | - David Cortez
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, California 94305-5441, USA
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274
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Abstract
Complete duplication of large metazoan chromosomes requires thousands of potential initiation sites, only a small fraction of which are selected in each cell cycle. Assembly of the replication machinery is highly conserved and tightly regulated during the cell cycle, but the sites of initiation are highly flexible, and their temporal order of firing is regulated at the level of large-scale multi-replicon domains. Importantly, the number of replication forks must be quickly adjusted in response to replication stress to prevent genome instability. Here we argue that large genomes are divided into domains for exactly this reason. Once established, domain structure abrogates the need for precise initiation sites and creates a scaffold for the evolution of other chromosome functions.
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Affiliation(s)
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL 32306-4295, USA.
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275
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Wang Y, Khan A, Marks AB, Smith OK, Giri S, Lin YC, Creager R, MacAlpine DM, Prasanth KV, Aladjem MI, Prasanth SG. Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization. Nucleic Acids Res 2017; 45:2490-2502. [PMID: 27924004 PMCID: PMC5389698 DOI: 10.1093/nar/gkw1211] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/23/2016] [Indexed: 12/19/2022] Open
Abstract
DNA replication requires the recruitment of a pre-replication complex facilitated by Origin Recognition Complex (ORC) onto the chromatin during G1 phase of the cell cycle. The ORC-associated protein (ORCA/LRWD1) stabilizes ORC on chromatin. Here, we evaluated the genome-wide distribution of ORCA using ChIP-seq during specific time points of G1. ORCA binding sites on the G1 chromatin are dynamic and temporally regulated. ORCA association to specific genomic sites decreases as the cells progressed towards S-phase. The majority of the ORCA-bound sites represent replication origins that also associate with the repressive chromatin marks H3K9me3 and methylated-CpGs, consistent with ORCA-bound origins initiating DNA replication late in S-phase. Further, ORCA directly associates with the repressive marks and interacts with the enzymes that catalyze these marks. Regions that associate with both ORCA and H3K9me3, exhibit diminished H3K9 methylation in ORCA-depleted cells, suggesting a role for ORCA in recruiting the H3K9me3 mark at certain genomic loci. Similarly, DNA methylation is altered at ORCA-occupied sites in cells lacking ORCA. Furthermore, repressive chromatin marks influence ORCA's binding on chromatin. We propose that ORCA coordinates with the histone and DNA methylation machinery to establish a repressive chromatin environment at a subset of origins, which primes them for late replication.
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Affiliation(s)
- Yating Wang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Abid Khan
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Anna B Marks
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Owen K Smith
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Sumanprava Giri
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Yo-Chuen Lin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Rachel Creager
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
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276
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Charrasse S, Gharbi-Ayachi A, Burgess A, Vera J, Hached K, Raynaud P, Schwob E, Lorca T, Castro A. Ensa controls S-phase length by modulating Treslin levels. Nat Commun 2017; 8:206. [PMID: 28785014 PMCID: PMC5547116 DOI: 10.1038/s41467-017-00339-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 06/22/2017] [Indexed: 12/26/2022] Open
Abstract
The Greatwall/Ensa/PP2A-B55 pathway is essential for controlling mitotic substrate phosphorylation and mitotic entry. Here, we investigate the effect of the knockdown of the Gwl substrate, Ensa, in human cells. Unexpectedly, Ensa knockdown promotes a dramatic extension of S phase associated with a lowered density of replication forks. Notably, Ensa depletion results in a decrease of Treslin levels, a pivotal protein for the firing of replication origins. Accordingly, the extended S phase in Ensa-depleted cells is completely rescued by the overexpression of Treslin. Our data herein reveal a new mechanism by which normal cells regulate S-phase duration by controlling the ubiquitin-proteasome degradation of Treslin in a Gwl/Ensa-dependent pathway. The Greatwall/Ensa/PP2A-B55 pathway controls mitotic substrate phosphorylation and mitotic entry. Here the authors show that cells regulate S phase duration by controlling the ubiquitin-proteasome degradation of Treslin in a Gwl/Ensa-dependent pathway.
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Affiliation(s)
- Sophie Charrasse
- Université de Montpellier, Centre de Recherche de Biologie Cellulaire de Montpellier, Equipe Labellisée 'Ligue Contre le Cancer', CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France
| | - Aicha Gharbi-Ayachi
- Université de Montpellier, Centre de Recherche de Biologie Cellulaire de Montpellier, Equipe Labellisée 'Ligue Contre le Cancer', CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France
| | - Andrew Burgess
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia
| | - Jorge Vera
- Université de Montpellier, Centre de Recherche de Biologie Cellulaire de Montpellier, Equipe Labellisée 'Ligue Contre le Cancer', CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France
| | - Khaled Hached
- Université de Montpellier, Centre de Recherche de Biologie Cellulaire de Montpellier, Equipe Labellisée 'Ligue Contre le Cancer', CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France
| | - Peggy Raynaud
- Université de Montpellier, Centre de Recherche de Biologie Cellulaire de Montpellier, Equipe Labellisée 'Ligue Contre le Cancer', CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France
| | - Etienne Schwob
- Institute of Molecular Genetics, CNRS UMR 5535, University of Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Thierry Lorca
- Université de Montpellier, Centre de Recherche de Biologie Cellulaire de Montpellier, Equipe Labellisée 'Ligue Contre le Cancer', CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France.
| | - Anna Castro
- Université de Montpellier, Centre de Recherche de Biologie Cellulaire de Montpellier, Equipe Labellisée 'Ligue Contre le Cancer', CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France.
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277
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Brustel J, Kirstein N, Izard F, Grimaud C, Prorok P, Cayrou C, Schotta G, Abdelsamie AF, Déjardin J, Méchali M, Baldacci G, Sardet C, Cadoret JC, Schepers A, Julien E. Histone H4K20 tri-methylation at late-firing origins ensures timely heterochromatin replication. EMBO J 2017; 36:2726-2741. [PMID: 28778956 DOI: 10.15252/embj.201796541] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 06/19/2017] [Accepted: 07/07/2017] [Indexed: 01/09/2023] Open
Abstract
Among other targets, the protein lysine methyltransferase PR-Set7 induces histone H4 lysine 20 monomethylation (H4K20me1), which is the substrate for further methylation by the Suv4-20h methyltransferase. Although these enzymes have been implicated in control of replication origins, the specific contribution of H4K20 methylation to DNA replication remains unclear. Here, we show that H4K20 mutation in mammalian cells, unlike in Drosophila, partially impairs S-phase progression and protects from DNA re-replication induced by stabilization of PR-Set7. Using Epstein-Barr virus-derived episomes, we further demonstrate that conversion of H4K20me1 to higher H4K20me2/3 states by Suv4-20h is not sufficient to define an efficient origin per se, but rather serves as an enhancer for MCM2-7 helicase loading and replication activation at defined origins. Consistent with this, we find that Suv4-20h-mediated H4K20 tri-methylation (H4K20me3) is required to sustain the licensing and activity of a subset of ORCA/LRWD1-associated origins, which ensure proper replication timing of late-replicating heterochromatin domains. Altogether, these results reveal Suv4-20h-mediated H4K20 tri-methylation as a critical determinant in the selection of active replication initiation sites in heterochromatin regions of mammalian genomes.
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Affiliation(s)
- Julien Brustel
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier, France.,University of Montpellier, Montpellier, France
| | - Nina Kirstein
- Research Unit Gene Vectors, Helmholtz Zentrum München, Munich, Germany
| | - Fanny Izard
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier, France.,University of Montpellier, Montpellier, France
| | - Charlotte Grimaud
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier, France.,University of Montpellier, Montpellier, France
| | - Paulina Prorok
- Institute of Human Genetics (IGH), CNRS, Montpellier, France
| | | | | | | | - Jérôme Déjardin
- Institute of Human Genetics (IGH), CNRS, Montpellier, France
| | - Marcel Méchali
- Institute of Human Genetics (IGH), CNRS, Montpellier, France
| | - Giuseppe Baldacci
- Institut Jacques Monod, UMR7592, CNRS and University Paris-Diderot, Paris, France
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier, France.,University of Montpellier, Montpellier, France
| | - Jean-Charles Cadoret
- Institut Jacques Monod, UMR7592, CNRS and University Paris-Diderot, Paris, France
| | - Aloys Schepers
- Research Unit Gene Vectors, Helmholtz Zentrum München, Munich, Germany
| | - Eric Julien
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier, France .,University of Montpellier, Montpellier, France
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278
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Shima N, Pederson KD. Dormant origins as a built-in safeguard in eukaryotic DNA replication against genome instability and disease development. DNA Repair (Amst) 2017; 56:166-173. [PMID: 28641940 PMCID: PMC5547906 DOI: 10.1016/j.dnarep.2017.06.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DNA replication is a prerequisite for cell proliferation, yet it can be increasingly challenging for a eukaryotic cell to faithfully duplicate its genome as its size and complexity expands. Dormant origins now emerge as a key component for cells to successfully accomplish such a demanding but essential task. In this perspective, we will first provide an overview of the fundamental processes eukaryotic cells have developed to regulate origin licensing and firing. With a special focus on mammalian systems, we will then highlight the role of dormant origins in preventing replication-associated genome instability and their functional interplay with proteins involved in the DNA damage repair response for tumor suppression. Lastly, deficiencies in the origin licensing machinery will be discussed in relation to their influence on stem cell maintenance and human diseases.
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Affiliation(s)
- Naoko Shima
- The University of Minnesota, Twin Cities, Department of Genetics, Cell Biology and Development, Masonic Cancer Center, 6-160 Jackson Hall, 321 Church St SE., Minneapolis, MN 55455, United States.
| | - Kayla D Pederson
- The University of Minnesota, Twin Cities, Department of Genetics, Cell Biology and Development, Masonic Cancer Center, 6-160 Jackson Hall, 321 Church St SE., Minneapolis, MN 55455, United States
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279
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Loss of Brap Results in Premature G1/S Phase Transition and Impeded Neural Progenitor Differentiation. Cell Rep 2017; 20:1148-1160. [DOI: 10.1016/j.celrep.2017.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 12/14/2016] [Accepted: 07/10/2017] [Indexed: 12/31/2022] Open
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280
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Ying W, Qimin W, Jinghua L, Jinhong H, Lili W, Chen C, Jianhua Z, Lei T, Xufei L, Yuan Z, Yixiang L, Zongxuan H, Ning L, Lei C, Wenjun L, Zhenggang C. [Effects of geranylgeranyltransferaseⅠsilencing on the proliferation of tongue squamous cancer cells]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2017; 35:373-378. [PMID: 28853502 DOI: 10.7518/hxkq.2017.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Objective This study aims to investigate the effect of geranylgeranyltransferaseⅠ (GGTase-Ⅰ) on the proliferation and growth of tongue squamous cancer cells. Methods Three small interfering RNAs (siRNAs) were designed on the basis of the GGTase-Ⅰ sequence in GeneBank. These siRNAs were then transfected into tongue squamous cancer cells Cal-27. The mRNA and protein expression of GGTase-Ⅰ and RhoA were examined by real-time quantitative polymerase chain reaction and Western blotting, respectively. The expression of Cyclin D1 and p21 were examined by Western blotting. The proliferation and growth ability were analyzed by cell counting kit-8 assay and flow cytometry. Results The mRNA and protein expression of GGTase-Ⅰ in Cal-27 was reduced significantly after the GGTase-Ⅰ siRNAs were transfected (P<0.05). No significant difference in RhoA mRNA and protein expression was detected (P>0.05). Cyclin D1 expression decreased, whereas p21 expression increased significantly. The cell cycle was altered, and the growth-proliferative activity was inhibited (P<0.05). Conclusion GGTase-Ⅰ siRNA can inhibit the expression of GGTase-Ⅰ and the proliferative activity of tongue squamous cancer cells. GGTase-Ⅰ may be a potential target for gene therapy in tongue squamous cell cancer.
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Affiliation(s)
- Wang Ying
- College of Stomatology, Weifang Medical University, Weifang 261021, China
| | - Wang Qimin
- Dept. of Oral and Maxillofacial Surgery, Qingdao Municipal Hospital, Qingdao 266071, China
| | - Li Jinghua
- Central Lab, Qingdao Municipal Hospital, Qingdao 266071, China
| | - Han Jinhong
- Dept. of Oral and Maxillofacial Surgery, Qingdao Municipal Hospital, Qingdao 266071, China;Dept. of Oral and Maxillofacial Surgery, Yantai Stomatological Hospital, Yantai 264008, China
| | - Wang Lili
- Central Lab, Qingdao Municipal Hospital, Qingdao 266071, China
| | - Chao Chen
- Dept. of Surgery, Qingdao Clinical Hospital Affiliated to Nanjing Medical University, Qingdao 266071, China
| | - Zhou Jianhua
- Dept. of Oral and Maxillofacial Surgery, Qingdao Municipal Hospital, Qingdao 266071, China
| | - Tong Lei
- Dept. of Oral and Maxillofacial Surgery, Qingdao Municipal Hospital, Qingdao 266071, China
| | - Lu Xufei
- Dept. of Oral and Maxillofacial Surgery, Qingdao Municipal Hospital, Qingdao 266071, China;Dept. of Stomatology, Pudong Hospital of Jimo City, Qingdao 266234, China
| | - Zhou Yuan
- College of Stomatology, Weifang Medical University, Weifang 261021, China
| | - Liao Yixiang
- Dept. of Oral and Maxillofacial Surgery, Qingdao Municipal Hospital, Qingdao 266071, China
| | - He Zongxuan
- Dept. of Oral and Maxillofacial Surgery, Qingdao Municipal Hospital, Qingdao 266071, China
| | - Li Ning
- Postgraduate School, Dalian Medical University, Dalian 116044, China
| | - Cao Lei
- Postgraduate School, Dalian Medical University, Dalian 116044, China
| | - Liu Wenjun
- Dept. of Otorhinolaryngology, Qingdao Municipal Hospital, Qingdao 266071, China
| | - Chen Zhenggang
- Dept. of Oral and Maxillofacial Surgery, Qingdao Municipal Hospital, Qingdao 266071, China;Dept. of Oral and Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
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281
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Utani K, Fu H, Jang SM, Marks AB, Smith OK, Zhang Y, Redon CE, Shimizu N, Aladjem MI. Phosphorylated SIRT1 associates with replication origins to prevent excess replication initiation and preserve genomic stability. Nucleic Acids Res 2017; 45:7807-7824. [PMID: 28549174 PMCID: PMC5570034 DOI: 10.1093/nar/gkx468] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/09/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022] Open
Abstract
Chromatin structure affects DNA replication patterns, but the role of specific chromatin modifiers in regulating the replication process is yet unclear. We report that phosphorylation of the human SIRT1 deacetylase on Threonine 530 (T530-pSIRT1) modulates DNA synthesis. T530-pSIRT1 associates with replication origins and inhibits replication from a group of 'dormant' potential replication origins, which initiate replication only when cells are subject to replication stress. Although both active and dormant origins bind T530-pSIRT1, active origins are distinguished from dormant origins by their unique association with an open chromatin mark, histone H3 methylated on lysine 4. SIRT1 phosphorylation also facilitates replication fork elongation. SIRT1 T530 phosphorylation is essential to prevent DNA breakage upon replication stress and cells harboring SIRT1 that cannot be phosphorylated exhibit a high prevalence of extrachromosomal elements, hallmarks of perturbed replication. These observations suggest that SIRT1 phosphorylation modulates the distribution of replication initiation events to insure genomic stability.
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Affiliation(s)
- Koichi Utani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sang-Min Jang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna B. Marks
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Owen K. Smith
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ya Zhang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christophe E. Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8521, Japan
| | - Mirit I. Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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282
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The impact of replication stress on replication dynamics and DNA damage in vertebrate cells. Nat Rev Genet 2017; 18:535-550. [DOI: 10.1038/nrg.2017.46] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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283
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Chromatin Dynamics in Genome Stability: Roles in Suppressing Endogenous DNA Damage and Facilitating DNA Repair. Int J Mol Sci 2017; 18:ijms18071486. [PMID: 28698521 PMCID: PMC5535976 DOI: 10.3390/ijms18071486] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 02/06/2023] Open
Abstract
Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage.
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284
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Gilberto S, Peter M. Dynamic ubiquitin signaling in cell cycle regulation. J Cell Biol 2017; 216:2259-2271. [PMID: 28684425 PMCID: PMC5551716 DOI: 10.1083/jcb.201703170] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/11/2017] [Accepted: 05/25/2017] [Indexed: 12/16/2022] Open
Abstract
Gilberto and Peter discuss the role of ubiquitylation in the regulation of DNA replication and mitosis. The cell division cycle is driven by a collection of enzymes that coordinate DNA duplication and separation, ensuring that genomic information is faithfully and perpetually maintained. The activity of the effector proteins that perform and coordinate these biological processes oscillates by regulated expression and/or posttranslational modifications. Ubiquitylation is a cardinal cellular modification and is long known for driving cell cycle transitions. In this review, we emphasize emerging concepts of how ubiquitylation brings the necessary dynamicity and plasticity that underlie the processes of DNA replication and mitosis. New studies, often focusing on the regulation of chromosomal proteins like DNA polymerases or kinetochore kinases, are demonstrating that ubiquitylation is a versatile modification that can be used to fine-tune these cell cycle events, frequently through processes that do not involve proteasomal degradation. Understanding how the increasing variety of identified ubiquitin signals are transduced will allow us to develop a deeper mechanistic perception of how the multiple factors come together to faithfully propagate genomic information. Here, we discuss these and additional conceptual challenges that are currently under study toward understanding how ubiquitin governs cell cycle regulation.
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Affiliation(s)
- Samuel Gilberto
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland.,Molecular Life Science PhD Program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
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285
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Abstract
Genomic instability plays a key role in driving cancer development. It is already found in precancerous lesions and allows the acquisition of additional cancerous features. A major source of genomic instability in early stages of tumorigenesis is DNA replication stress. Normally, origin licensing and activation, as well as replication fork progression, are tightly regulated to allow faithful duplication of the genome. Aberrant origin usage and/or perturbed replication fork progression leads to DNA damage and genomic instability. Oncogene activation is an endogenous source of replication stress, disrupting replication regulation and inducing DNA damage. Oncogene-induced replication stress and its role in cancer development have been studied comprehensively, however its molecular basis is still unclear. Here, we review the current understanding of replication regulation, its potential disruption and how oncogenes perturb the replication and induce DNA damage leading to genomic instability in cancer.
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Affiliation(s)
| | - Batsheva Kerem
- Correspondence: ; Tel.: +972-2-658-5678; Fax: +972-2-658-4810
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286
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Single-molecule analysis reveals that DNA replication dynamics vary across the course of schizogony in the malaria parasite Plasmodium falciparum. Sci Rep 2017. [PMID: 28638076 PMCID: PMC5479783 DOI: 10.1038/s41598-017-04407-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The mechanics of DNA replication and cell cycling are well-characterized in model organisms, but less is known about these basic aspects of cell biology in early-diverging Apicomplexan parasites, which do not divide by canonical binary fission but undergo unconventional cycles. Schizogony in the malaria parasite, Plasmodium, generates ~16–24 new nuclei via independent, asynchronous rounds of genome replication prior to cytokinesis and little is known about the control of DNA replication that facilitates this. We have characterised replication dynamics in P. falciparum throughout schizogony, using DNA fibre labelling and combing to visualise replication forks at a single-molecule level. We show that origins are very closely spaced in Plasmodium compared to most model systems, and that replication dynamics vary across the course of schizogony, from faster synthesis rates and more widely-spaced origins through to slower synthesis rates and closer-spaced origins. This is the opposite of the pattern usually seen across S-phase in human cells, when a single genome is replicated. Replication forks also appear to stall at an unusually high rate throughout schizogony. Our work explores Plasmodium DNA replication in unprecedented detail and opens up tremendous scope for analysing cell cycle dynamics and developing interventions targetting this unique aspect of malaria biology.
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287
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Abstract
Cellular senescence is a cell fate characterized by an irreversible cell cycle arrest, but the molecular mechanism underlying this senescence hallmark remains poorly understood. Through an unbiased search for novel senescence regulators in airway basal cells, we discovered that the epigenetic regulator ubiquitin-like with PHD and ring finger domain-containing protein 1 (UHRF1) is critical for regulating cell cycle progression. Upon injury, basal cells in the mouse airway rapidly induce the expression of UHRF1 in order to stimulate stem cell proliferation and tissue repair. Targeted depletion of Uhrf1 specifically in airway basal cells causes a profound defect in cell cycle progression. Consistently, cultured primary human basal cells lacking UHRF1 do not exhibit cell death or differentiation phenotypes but undergo a spontaneous program of senescence. Mechanistically, UHRF1 loss induces G1 cell cycle arrest by abrogating DNA replication factory formation as evidenced by loss of proliferating cell nuclear antigen (PCNA) puncta and an inability to enter the first cell cycle. This proliferation defect is partially mediated by the p15 pathway. Overall, our study provides the first evidence of an indispensable role of UHRF1 in somatic stem cells proliferation during the process of airway regeneration.
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288
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Bhowmick R, Hickson ID. The "enemies within": regions of the genome that are inherently difficult to replicate. F1000Res 2017; 6:666. [PMID: 28620461 PMCID: PMC5461909 DOI: 10.12688/f1000research.11024.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/11/2017] [Indexed: 12/23/2022] Open
Abstract
An unusual feature of many eukaryotic genomes is the presence of regions that appear intrinsically difficult to copy during the process of DNA replication. Curiously, the location of these difficult-to-replicate regions is often conserved between species, implying a valuable role in some aspect of genome organization or maintenance. The most prominent class of these regions in mammalian cells is defined as chromosome fragile sites, which acquired their name because of a propensity to form visible gaps/breaks on otherwise-condensed chromosomes in mitosis. This fragility is particularly apparent following perturbation of DNA replication-a phenomenon often referred to as "replication stress". Here, we review recent data on the molecular basis for chromosome fragility and the role of fragile sites in the etiology of cancer. In particular, we highlight how studies on fragile sites have provided unexpected insights into how the DNA repair machinery assists in the completion of DNA replication.
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Affiliation(s)
- Rahul Bhowmick
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
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289
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DNA Replication Origins and Fork Progression at Mammalian Telomeres. Genes (Basel) 2017; 8:genes8040112. [PMID: 28350373 PMCID: PMC5406859 DOI: 10.3390/genes8040112] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 12/20/2022] Open
Abstract
Telomeres are essential chromosomal regions that prevent critical shortening of linear chromosomes and genomic instability in eukaryotic cells. The bulk of telomeric DNA is replicated by semi-conservative DNA replication in the same way as the rest of the genome. However, recent findings revealed that replication of telomeric repeats is a potential cause of chromosomal instability, because DNA replication through telomeres is challenged by the repetitive telomeric sequences and specific structures that hamper the replication fork. In this review, we summarize current understanding of the mechanisms by which telomeres are faithfully and safely replicated in mammalian cells. Various telomere-associated proteins ensure efficient telomere replication at different steps, such as licensing of replication origins, passage of replication forks, proper fork restart after replication stress, and dissolution of post-replicative structures. In particular, shelterin proteins have central roles in the control of telomere replication. Through physical interactions, accessory proteins are recruited to maintain telomere integrity during DNA replication. Dormant replication origins and/or homology-directed repair may rescue inappropriate fork stalling or collapse that can cause defects in telomere structure and functions.
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290
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Form and function of topologically associating genomic domains in budding yeast. Proc Natl Acad Sci U S A 2017; 114:E3061-E3070. [PMID: 28348222 DOI: 10.1073/pnas.1612256114] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The genome of metazoan cells is organized into topologically associating domains (TADs) that have similar histone modifications, transcription level, and DNA replication timing. Although similar structures appear to be conserved in fission yeast, computational modeling and analysis of high-throughput chromosome conformation capture (Hi-C) data have been used to argue that the small, highly constrained budding yeast chromosomes could not have these structures. In contrast, herein we analyze Hi-C data for budding yeast and identify 200-kb scale TADs, whose boundaries are enriched for transcriptional activity. Furthermore, these boundaries separate regions of similarly timed replication origins connecting the long-known effect of genomic context on replication timing to genome architecture. To investigate the molecular basis of TAD formation, we performed Hi-C experiments on cells depleted for the Forkhead transcription factors, Fkh1 and Fkh2, previously associated with replication timing. Forkhead factors do not regulate TAD formation, but do promote longer-range genomic interactions and control interactions between origins near the centromere. Thus, our work defines spatial organization within the budding yeast nucleus, demonstrates the conserved role of genome architecture in regulating DNA replication, and identifies a molecular mechanism specifically regulating interactions between pericentric origins.
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291
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Azmi IF, Watanabe S, Maloney MF, Kang S, Belsky JA, MacAlpine DM, Peterson CL, Bell SP. Nucleosomes influence multiple steps during replication initiation. eLife 2017; 6. [PMID: 28322723 PMCID: PMC5400510 DOI: 10.7554/elife.22512] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/20/2017] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic replication origin licensing, activation and timing are influenced by chromatin but a mechanistic understanding is lacking. Using reconstituted nucleosomal DNA replication assays, we assessed the impact of nucleosomes on replication initiation. To generate distinct nucleosomal landscapes, different chromatin-remodeling enzymes (CREs) were used to remodel nucleosomes on origin-DNA templates. Nucleosomal organization influenced two steps of replication initiation: origin licensing and helicase activation. Origin licensing assays showed that local nucleosome positioning enhanced origin specificity and modulated helicase loading by influencing ORC DNA binding. Interestingly, SWI/SNF- and RSC-remodeled nucleosomes were permissive for origin licensing but showed reduced helicase activation. Specific CREs rescued replication of these templates if added prior to helicase activation, indicating a permissive chromatin state must be established during origin licensing to allow efficient origin activation. Our studies show nucleosomes directly modulate origin licensing and activation through distinct mechanisms and provide insights into the regulation of replication initiation by chromatin.
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Affiliation(s)
- Ishara F Azmi
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Shinya Watanabe
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Michael F Maloney
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Sukhyun Kang
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.,Center for Genomic Integrity, Institute for Basic Science, Ulsan, South Korea
| | - Jason A Belsky
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, United States.,Program in Computational Biology and Bioinformatics, Duke University, Durham, United States
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, United States
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Stephen P Bell
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
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292
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Roles of CDK and DDK in Genome Duplication and Maintenance: Meiotic Singularities. Genes (Basel) 2017; 8:genes8030105. [PMID: 28335524 PMCID: PMC5368709 DOI: 10.3390/genes8030105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 12/16/2022] Open
Abstract
Cells reproduce using two types of divisions: mitosis, which generates two daughter cells each with the same genomic content as the mother cell, and meiosis, which reduces the number of chromosomes of the parent cell by half and gives rise to four gametes. The mechanisms that promote the proper progression of the mitotic and meiotic cycles are highly conserved and controlled. They require the activities of two types of serine-threonine kinases, the cyclin-dependent kinases (CDKs) and the Dbf4-dependent kinase (DDK). CDK and DDK are essential for genome duplication and maintenance in both mitotic and meiotic divisions. In this review, we aim to highlight how these kinases cooperate to orchestrate diverse processes during cellular reproduction, focusing on meiosis-specific adaptions of their regulation and functions in DNA metabolism.
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293
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Li J, Liu J, Liang Z, He F, Yang L, Li P, Jiang Y, Wang B, Zhou C, Wang Y, Ren Y, Yang J, Zhang J, Luo Z, Vaziri C, Liu P. Simvastatin and Atorvastatin inhibit DNA replication licensing factor MCM7 and effectively suppress RB-deficient tumors growth. Cell Death Dis 2017; 8:e2673. [PMID: 28300827 PMCID: PMC5386551 DOI: 10.1038/cddis.2017.46] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
Loss or dysfunction of tumor suppressor retinoblastoma (RB) is a common feature in various tumors, and contributes to cancer cell stemness and drug resistance to cancer therapy. However, the strategy to suppress or eliminate Rb-deficient tumor cells remains unclear. In the present study, we accidentally found that reduction of DNA replication licensing factor MCM7 induced more apoptosis in RB-deficient tumor cells than in control tumor cells. Moreover, after a drug screening and further studies, we demonstrated that statin drug Simvastatin and Atorvastatin were able to inhibit MCM7 and RB expressions. Further study showed that Simvastatin and Atorvastatin induced more chromosome breaks and gaps of Rb-deficient tumor cells than control tumor cells. In vivo results showed that Simvastatin and Atorvastatin significantly suppressed Rb-deficient tumor growth than control in xenograft mouse models. The present work demonstrates that ‘old' lipid-lowering drugs statins are novel weapons against RB-deficient tumors due to their effects on suppressing MCM7 protein levels.
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Affiliation(s)
- Juan Li
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Jie Liu
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Zheyong Liang
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Fang He
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Lu Yang
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Pingping Li
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Yina Jiang
- Department of Pathology, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Bo Wang
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Can Zhou
- Department of Breast Surgery, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Yaochun Wang
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Yu Ren
- Department of Breast Surgery, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Jin Yang
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Jianmin Zhang
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo 14263, NY 14263, USA
| | - Zhijun Luo
- Department of Biochemistry, Boston University School of Medicine, Boston 02118, MA, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Peijun Liu
- Center for Translational Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, Shaanxi, China
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294
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Hosogane M, Bosu L, Fukumoto E, Yamada H, Sato S, Nakayama K. Geminin is an indispensable inhibitor of Cdt1 in mouse embryonic stem cells. Genes Cells 2017; 22:360-375. [DOI: 10.1111/gtc.12482] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/26/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Masaki Hosogane
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine; Tohoku University; 2-1 Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Lena Bosu
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine; Tohoku University; 2-1 Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Emiko Fukumoto
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine; Tohoku University; 2-1 Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Hidetoshi Yamada
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine; Tohoku University; 2-1 Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Soichiro Sato
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine; Tohoku University; 2-1 Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Keiko Nakayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine; Tohoku University; 2-1 Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
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295
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Xie J, Wooten M, Tran V, Chen X. Breaking Symmetry - Asymmetric Histone Inheritance in Stem Cells. Trends Cell Biol 2017; 27:527-540. [PMID: 28268050 DOI: 10.1016/j.tcb.2017.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 01/27/2017] [Accepted: 02/01/2017] [Indexed: 01/17/2023]
Abstract
Asymmetric cell division (ACD) gives rise to two daughter cells with distinct fates. ACD is widely used during development and by many types of adult stem cells during tissue homeostasis and regeneration. ACD can be regulated by extrinsic cues, such as signaling molecules, as well as by intrinsic factors, such as organelles and cortex proteins. The recent discovery of asymmetric histone inheritance during stem cell ACD has revealed another intrinsic mechanism by which ACD produces two distinct daughters. In this review we discuss these findings in the context of cell-cycle regulation, as well as other studies of ACD, to begin understanding the underlying mechanisms and biological relevance of this phenomenon.
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Affiliation(s)
- Jing Xie
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vuong Tran
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Current address: Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North Seattle, Seattle, WA 98109, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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296
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Fukushima K, Wang M, Naito Y, Uchihashi T, Kato Y, Mukai S, Yabuta N, Nojima H. GAK is phosphorylated by c-Src and translocated from the centrosome to chromatin at the end of telophase. Cell Cycle 2017; 16:415-427. [PMID: 28135906 DOI: 10.1080/15384101.2016.1241916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Cyclin G-associated kinase (GAK) harbors a consensus phosphorylation motif (Y412) for c-Src; however, its physiological significance remains elusive. Here, we show that GAK is phosphorylated by c-Src not only at Y412 but also at Y1149. An anti-GAK-pY412 antibody recognized the shifted band of GAK during M phase. Immunofluorescence (IF) showed that GAK-pY412/pY1149 signals were present in the nucleus during interphase, translocated to chromosomes at prophase and prometaphase, moved to centrosomes at metaphase, and finally translocated to chromosomes at the end of telophase, when nuclear membrane formation was almost complete. These subcellular movements of GAK resemble those of DNA licensing factors. Indeed, mass spectrometry identified mini-chromosome maintenance (MCM) 3, an essential component of the DNA licensing system, as one of the association partners of GAK; immunoprecipitation-mediated Western blotting confirmed their association in vivo. These results suggest that the c-Src_GAK_MCM axis plays an important role in cell cycle progression through control of the DNA replication licensing system.
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Affiliation(s)
- Kohshiro Fukushima
- a Department of Molecular Genetics , Research Institute for Microbial Diseases, Osaka University , Yamadaoka, Suita, Osaka , Japan
| | - Mian Wang
- a Department of Molecular Genetics , Research Institute for Microbial Diseases, Osaka University , Yamadaoka, Suita, Osaka , Japan
| | - Yoko Naito
- a Department of Molecular Genetics , Research Institute for Microbial Diseases, Osaka University , Yamadaoka, Suita, Osaka , Japan
| | - Toshihiro Uchihashi
- b First Department of Oral and Maxillofacial Surgery , Graduate School of Dentistry, Osaka University , Yamadaoka, Suita, Osaka , Japan
| | - Yorika Kato
- a Department of Molecular Genetics , Research Institute for Microbial Diseases, Osaka University , Yamadaoka, Suita, Osaka , Japan
| | - Satomi Mukai
- a Department of Molecular Genetics , Research Institute for Microbial Diseases, Osaka University , Yamadaoka, Suita, Osaka , Japan
| | - Norikazu Yabuta
- a Department of Molecular Genetics , Research Institute for Microbial Diseases, Osaka University , Yamadaoka, Suita, Osaka , Japan
| | - Hiroshi Nojima
- a Department of Molecular Genetics , Research Institute for Microbial Diseases, Osaka University , Yamadaoka, Suita, Osaka , Japan
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297
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Herlihy AE, de Bruin RAM. The Role of the Transcriptional Response to DNA Replication Stress. Genes (Basel) 2017; 8:E92. [PMID: 28257104 PMCID: PMC5368696 DOI: 10.3390/genes8030092] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 01/14/2023] Open
Abstract
During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage.
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Affiliation(s)
- Anna E Herlihy
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
| | - Robertus A M de Bruin
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
- The UCL Cancer Institute, University College London, London WC1E 6BT, UK.
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298
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Mlcochova P, Sutherland KA, Watters SA, Bertoli C, de Bruin RA, Rehwinkel J, Neil SJ, Lenzi GM, Kim B, Khwaja A, Gage MC, Georgiou C, Chittka A, Yona S, Noursadeghi M, Towers GJ, Gupta RK. A G1-like state allows HIV-1 to bypass SAMHD1 restriction in macrophages. EMBO J 2017; 36:604-616. [PMID: 28122869 PMCID: PMC5331754 DOI: 10.15252/embj.201696025] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 01/09/2023] Open
Abstract
An unresolved question is how HIV-1 achieves efficient replication in terminally differentiated macrophages despite the restriction factor SAMHD1. We reveal inducible changes in expression of cell cycle-associated proteins including MCM2 and cyclins A, E, D1/D3 in macrophages, without evidence for DNA synthesis or mitosis. These changes are induced by activation of the Raf/MEK/ERK kinase cascade, culminating in upregulation of CDK1 with subsequent SAMHD1 T592 phosphorylation and deactivation of its antiviral activity. HIV infection is limited to these G1-like phase macrophages at the single-cell level. Depletion of SAMHD1 in macrophages decouples the association between infection and expression of cell cycle-associated proteins, with terminally differentiated macrophages becoming highly susceptible to HIV-1. We observe both embryo-derived and monocyte-derived tissue-resident macrophages in a G1-like phase at frequencies approaching 20%, suggesting how macrophages sustain HIV-1 replication in vivo Finally, we reveal a SAMHD1-dependent antiretroviral activity of histone deacetylase inhibitors acting via p53 activation. These data provide a basis for host-directed therapeutic approaches aimed at limiting HIV-1 burden in macrophages that may contribute to curative interventions.
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Affiliation(s)
- Petra Mlcochova
- Division of Infection and Immunity, University College London, London, UK
| | | | - Sarah A Watters
- Division of Infection and Immunity, University College London, London, UK
| | - Cosetta Bertoli
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Rob Am de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stuart J Neil
- Division of Immunology, Infection and Inflammatory Disease, King's College, London, UK
| | - Gina M Lenzi
- Department of Pediatrics, Center for Drug Discovery, Emory School of Medicine, Atlanta, GA, USA
| | - Baek Kim
- Department of Pediatrics, Center for Drug Discovery, Emory School of Medicine, Atlanta, GA, USA
| | - Asim Khwaja
- Research Department of Haematology, UCL, London, UK
| | - Matthew C Gage
- Division of Medicine, University College London, London, UK
| | | | | | - Simon Yona
- Division of Medicine, University College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - Ravindra K Gupta
- Division of Infection and Immunity, University College London, London, UK
- Africa Health Research Institute, KwaZulu Natal, South Africa
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299
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Miotto B. Comment l’approche génomique aide à comprendre le processus d’initiation de la réplication. Med Sci (Paris) 2017; 33:143-150. [DOI: 10.1051/medsci/20173302009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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300
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Abstract
Cellular DNA replication factories depend on ring-shaped hexameric helicases to aid DNA synthesis by processively unzipping the parental DNA helix. Replicative helicases are loaded onto DNA by dedicated initiator, loader, and accessory proteins during the initiation of DNA replication in a tightly regulated, multistep process. We discuss here the molecular choreography of DNA replication initiation across the three domains of life, highlighting similarities and differences in the strategies used to deposit replicative helicases onto DNA and to melt the DNA helix in preparation for replisome assembly. Although initiators and loaders are phylogenetically related, the mechanisms they use for accomplishing similar tasks have diverged considerably and in an unpredictable manner.
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Affiliation(s)
- Franziska Bleichert
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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