201
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Tsao WC, Eckert KA. Detours to Replication: Functions of Specialized DNA Polymerases during Oncogene-induced Replication Stress. Int J Mol Sci 2018; 19:ijms19103255. [PMID: 30347795 PMCID: PMC6214091 DOI: 10.3390/ijms19103255] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 01/10/2023] Open
Abstract
Incomplete and low-fidelity genome duplication contribute to genomic instability and cancer development. Difficult-to-Replicate Sequences, or DiToRS, are natural impediments in the genome that require specialized DNA polymerases and repair pathways to complete and maintain faithful DNA synthesis. DiToRS include non B-DNA secondary structures formed by repetitive sequences, for example within chromosomal fragile sites and telomeres, which inhibit DNA replication under endogenous stress conditions. Oncogene activation alters DNA replication dynamics and creates oncogenic replication stress, resulting in persistent activation of the DNA damage and replication stress responses, cell cycle arrest, and cell death. The response to oncogenic replication stress is highly complex and must be tightly regulated to prevent mutations and tumorigenesis. In this review, we summarize types of known DiToRS and the experimental evidence supporting replication inhibition, with a focus on the specialized DNA polymerases utilized to cope with these obstacles. In addition, we discuss different causes of oncogenic replication stress and its impact on DiToRS stability. We highlight recent findings regarding the regulation of DNA polymerases during oncogenic replication stress and the implications for cancer development.
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Affiliation(s)
- Wei-Chung Tsao
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
| | - Kristin A Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
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202
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Abstract
The SLX4/FANCP tumor suppressor has emerged as a key player in the maintenance of genome stability, making pivotal contributions to the repair of interstrand cross-links, homologous recombination, and in response to replication stress genome-wide as well as at specific loci such as common fragile sites and telomeres. SLX4 does so in part by acting as a scaffold that controls and coordinates the XPF-ERCC1, MUS81-EME1, and SLX1 structure-specific endonucleases in different DNA repair and recombination mechanisms. It also interacts with other important DNA repair and cell cycle control factors including MSH2, PLK1, TRF2, and TOPBP1 as well as with ubiquitin and SUMO. This review aims at providing an up-to-date and comprehensive view on the key functions that SLX4 fulfills to maintain genome stability as well as to highlight and discuss areas of uncertainty and emerging concepts.
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Affiliation(s)
- Jean-Hugues Guervilly
- a CRCM, CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes , Marseille , France
| | - Pierre Henri Gaillard
- a CRCM, CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes , Marseille , France
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203
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Thornlow BP, Hough J, Roger JM, Gong H, Lowe TM, Corbett-Detig RB. Transfer RNA genes experience exceptionally elevated mutation rates. Proc Natl Acad Sci U S A 2018; 115:8996-9001. [PMID: 30127029 PMCID: PMC6130373 DOI: 10.1073/pnas.1801240115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Transfer RNAs (tRNAs) are a central component for the biological synthesis of proteins, and they are among the most highly conserved and frequently transcribed genes in all living things. Despite their clear significance for fundamental cellular processes, the forces governing tRNA evolution are poorly understood. We present evidence that transcription-associated mutagenesis and strong purifying selection are key determinants of patterns of sequence variation within and surrounding tRNA genes in humans and diverse model organisms. Remarkably, the mutation rate at broadly expressed cytosolic tRNA loci is likely between 7 and 10 times greater than the nuclear genome average. Furthermore, evolutionary analyses provide strong evidence that tRNA genes, but not their flanking sequences, experience strong purifying selection acting against this elevated mutation rate. We also find a strong correlation between tRNA expression levels and the mutation rates in their immediate flanking regions, suggesting a simple method for estimating individual tRNA gene activity. Collectively, this study illuminates the extreme competing forces in tRNA gene evolution and indicates that mutations at tRNA loci contribute disproportionately to mutational load and have unexplored fitness consequences in human populations.
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Affiliation(s)
- Bryan P Thornlow
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
| | - Josh Hough
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
| | - Jacquelyn M Roger
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
| | - Henry Gong
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064;
- Genomics Institute, University of California, Santa Cruz, CA 95064
| | - Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064;
- Genomics Institute, University of California, Santa Cruz, CA 95064
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204
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Carruthers RD, Ahmed SU, Ramachandran S, Strathdee K, Kurian KM, Hedley A, Gomez-Roman N, Kalna G, Neilson M, Gilmour L, Stevenson KH, Hammond EM, Chalmers AJ. Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells. Cancer Res 2018; 78:5060-5071. [PMID: 29976574 PMCID: PMC6128404 DOI: 10.1158/0008-5472.can-18-0569] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/25/2018] [Accepted: 06/28/2018] [Indexed: 11/16/2022]
Abstract
Glioblastoma (GBM) is a lethal primary brain tumor characterized by treatment resistance and inevitable tumor recurrence, both of which are driven by a subpopulation of GBM cancer stem-like cells (GSC) with tumorigenic and self-renewal properties. Despite having broad implications for understanding GSC phenotype, the determinants of upregulated DNA-damage response (DDR) and subsequent radiation resistance in GSC are unknown and represent a significant barrier to developing effective GBM treatments. In this study, we show that constitutive DDR activation and radiation resistance are driven by high levels of DNA replication stress (RS). CD133+ GSC exhibited reduced DNA replication velocity and a higher frequency of stalled replication forks than CD133- non-GSC in vitro; immunofluorescence studies confirmed these observations in a panel of orthotopic xenografts and human GBM specimens. Exposure of non-GSC to low-level exogenous RS generated radiation resistance in vitro, confirming RS as a novel determinant of radiation resistance in tumor cells. GSC exhibited DNA double-strand breaks, which colocalized with "replication factories" and RNA: DNA hybrids. GSC also demonstrated increased expression of long neural genes (>1 Mbp) containing common fragile sites, supporting the hypothesis that replication/transcription collisions are the likely cause of RS in GSC. Targeting RS by combined inhibition of ATR and PARP (CAiPi) provided GSC-specific cytotoxicity and complete abrogation of GSC radiation resistance in vitro These data identify RS as a cancer stem cell-specific target with significant clinical potential.Significance: These findings shed new light on cancer stem cell biology and reveal novel therapeutics with the potential to improve clinical outcomes by overcoming inherent radioresistance in GBM. Cancer Res; 78(17); 5060-71. ©2018 AACR.
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Affiliation(s)
- Ross D Carruthers
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom.
| | - Shafiq U Ahmed
- School of Pharmacy and Pharmaceutical Sciences, Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, United Kingdom
| | - Shaliny Ramachandran
- Cancer Research UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Karen Strathdee
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Kathreena M Kurian
- Department of Neuropathology, Brain Tumour Research Group, Frenchay Hospital, North Bristol NHS Trust Bristol, Bristol, United Kingdom
| | - Ann Hedley
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Natividad Gomez-Roman
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Gabriela Kalna
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Mathew Neilson
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Lesley Gilmour
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Katrina H Stevenson
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Ester M Hammond
- Cancer Research UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Anthony J Chalmers
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
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205
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Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability. Mol Cell 2018; 71:487-497.e3. [PMID: 30078723 DOI: 10.1016/j.molcel.2018.06.037] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/23/2018] [Accepted: 06/22/2018] [Indexed: 01/04/2023]
Abstract
DNA-RNA hybrids associated with R-loops promote DNA damage and genomic instability. The capacity of hybrids at different genomic sites to cause DNA damage was not known, and the mechanisms leading from hybrid to damage were poorly understood. Here, we adopt a new strategy to map and characterize the sites of hybrid-induced damage genome-wide in budding yeast. We show that hybrid removal is essential for life because persistent hybrids cause irreparable DNA damage and cell death. We identify that a subset of hybrids is prone to cause damage, and the chromosomal context of hybrids dramatically impacts their ability to induce damage. Furthermore, persistent hybrids affect the repair pathway, generating large regions of single-stranded DNA (ssDNA) by two distinct mechanisms, likely resection and re-replication. These damaged regions may act as potential precursors to gross chromosomal rearrangements like deletions and duplications that are associated with R-loops and cancers.
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206
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Watanabe T, Marotta M, Suzuki R, Diede SJ, Tapscott SJ, Niida A, Chen X, Mouakkad L, Kondratova A, Giuliano AE, Orsulic S, Tanaka H. Impediment of Replication Forks by Long Non-coding RNA Provokes Chromosomal Rearrangements by Error-Prone Restart. Cell Rep 2018; 21:2223-2235. [PMID: 29166612 DOI: 10.1016/j.celrep.2017.10.103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/05/2017] [Accepted: 10/25/2017] [Indexed: 01/12/2023] Open
Abstract
Naturally stalled replication forks are considered to cause structurally abnormal chromosomes in tumor cells. However, underlying mechanisms remain speculative, as capturing naturally stalled forks has been a challenge. Here, we captured naturally stalled forks in tumor cells and delineated molecular processes underlying the structural evolution of circular mini-chromosomes (double-minute chromosomes; DMs). Replication forks stalled on the DM by the co-directional collision with the transcription machinery for long non-coding RNA. RPA, BRCA2, and DNA polymerase eta (Polη) were recruited to the stalled forks. The recruitment of Polη was critical for replication to continue, as Polη knockdown resulted in DM loss. Rescued stalled forks were error-prone and switched replication templates repeatedly to create complex fusions of multiple short genomic segments. In mice, such complex fusions circularized the genomic region surrounding MYC to create a DM during tumorigenesis. Our results define a molecular path that guides stalled replication forks to complex chromosomal rearrangements.
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Affiliation(s)
- Takaaki Watanabe
- Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Michael Marotta
- Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Ryusuke Suzuki
- Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Scott J Diede
- Division of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Stephen J Tapscott
- Division of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Atsushi Niida
- Division of Health Medical Computational Science, Health Intelligence Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Xiongfong Chen
- Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., National Cancer Institute at Frederick, Frederick, MD 21701, USA
| | - Lila Mouakkad
- Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Anna Kondratova
- Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | | | - Sandra Orsulic
- Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Hisashi Tanaka
- Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA.
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207
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Li M, Xu X, Chang CW, Zheng L, Shen B, Liu Y. SUMO2 conjugation of PCNA facilitates chromatin remodeling to resolve transcription-replication conflicts. Nat Commun 2018; 9:2706. [PMID: 30006506 PMCID: PMC6045570 DOI: 10.1038/s41467-018-05236-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 06/14/2018] [Indexed: 12/27/2022] Open
Abstract
During DNA synthesis, DNA replication and transcription machinery can collide, and the replication fork may temporarily dislodge RNA polymerase II (RNAPII) to resolve the transcription-replication conflict (TRC), a major source of endogenous DNA double-strand breaks (DSBs) and common fragile site (CFS) instability. However, the mechanism of TRC resolution remains unclear. Here, we show that conjugation of SUMO2, but not SUMO1 or SUMO3, to the essential replication factor PCNA is induced on transcribed chromatin by the RNAPII-bound helicase RECQ5. Proteomic analysis reveals that SUMO2-PCNA enriches histone chaperones CAF1 and FACT in the replication complex via interactions with their SUMO-interacting motifs. SUMO2-PCNA enhances CAF1-dependent histone deposition, which correlates with increased histone H3.1 at CFSs and repressive histone marks in the chromatin to reduce chromatin accessibility. Hence, SUMO2-PCNA dislodges RNAPII at CFSs, and overexpressing either SUMO2-PCNA or CAF1 reduces the incidence of DSBs in TRC-prone RECQ5-deficient cells.
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Affiliation(s)
- Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Xiaohua Xu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Chou-Wei Chang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA.
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208
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CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions. Nature 2018; 559:285-289. [PMID: 29973717 PMCID: PMC6071917 DOI: 10.1038/s41586-018-0291-z] [Citation(s) in RCA: 264] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 06/07/2018] [Indexed: 12/18/2022]
Abstract
The observation that BRCA1- and BRCA2-deficient cells are sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors spurred their development into cancer therapies that target homologous recombination (HR) deficiency1. The cytotoxicity of PARP inhibitors depends on PARP trapping, the formation of non-covalent protein-DNA adducts composed of inhibited PARP1 bound to DNA lesions of unclear origins1–4. To address the nature of such lesions and the cellular consequences of PARP trapping, we undertook three CRISPR screens to identify genes and pathways that mediate cellular resistance to olaparib, a clinically approved PARP inhibitor1. Here were present a high-confidence set of 73 genes whose mutation causes increased PARP inhibitor sensitivity. In addition to an expected enrichment for HR-related genes, we discovered that mutation in all three genes encoding RNase H2 sensitized cells to PARP inhibition. We establish that the underlying cause of the PARP inhibitor hypersensitivity of RNase H2-deficient cells is impaired ribonucleotide excision repair (RER)5. Embedded ribonucleotides, abundant in the genome of RER-deficient cells, are substrates for topoisomerase 1 cleavage, resulting in PARP-trapping lesions that impede DNA replication and endanger genome integrity. We conclude that genomic ribonucleotides are a hitherto unappreciated source of PARP-trapping DNA lesions, and that the frequent deletion of RNASEH2B in metastatic prostate cancer and chronic lymphocytic leukemia could provide an opportunity to exploit these findings therapeutically.
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209
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Lang KS, Merrikh H. The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria. Annu Rev Microbiol 2018; 72:71-88. [PMID: 29856930 DOI: 10.1146/annurev-micro-090817-062514] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Within the last decade, it has become clear that DNA replication and transcription are routinely in conflict with each other in growing cells. Much of the seminal work on this topic has been carried out in bacteria, specifically, Escherichia coli and Bacillus subtilis; therefore, studies of conflicts in these species deserve special attention. Collectively, the recent findings on conflicts have fundamentally changed the way we think about DNA replication in vivo. Furthermore, new insights on this topic have revealed that the conflicts between replication and transcription significantly influence many key parameters of cellular function, including genome organization, mutagenesis, and evolution of stress response and virulence genes. In this review, we discuss the consequences of replication-transcription conflicts on the life of bacteria and describe some key strategies cells use to resolve them. We put special emphasis on two critical aspects of these encounters: ( a) the consequences of conflicts on replisome stability and dynamics, and ( b) the resulting increase in spontaneous mutagenesis.
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Affiliation(s)
- Kevin S Lang
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA;
| | - Houra Merrikh
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA; .,Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5061, USA
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210
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Lindström MS, Jurada D, Bursac S, Orsolic I, Bartek J, Volarevic S. Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis. Oncogene 2018; 37:2351-2366. [PMID: 29429989 PMCID: PMC5931986 DOI: 10.1038/s41388-017-0121-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022]
Abstract
The nucleolus is the major site for synthesis of ribosomes, complex molecular machines that are responsible for protein synthesis. A wealth of research over the past 20 years has clearly indicated that both quantitative and qualitative alterations in ribosome biogenesis can drive the malignant phenotype via dysregulation of protein synthesis. However, numerous recent proteomic, genomic, and functional studies have implicated the nucleolus in the regulation of processes that are unrelated to ribosome biogenesis, including DNA-damage response, maintenance of genome stability and its spatial organization, epigenetic regulation, cell-cycle control, stress responses, senescence, global gene expression, as well as assembly or maturation of various ribonucleoprotein particles. In this review, the focus will be on features of rDNA genes, which make them highly vulnerable to DNA damage and intra- and interchromosomal recombination as well as built-in mechanisms that prevent and repair rDNA damage, and how dysregulation of this interplay affects genome-wide DNA stability, gene expression and the balance between euchromatin and heterochromatin. We will also present the most recent insights into how malfunction of these cellular processes may be a central driving force of human malignancies, and propose a promising new therapeutic approach for the treatment of cancer.
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Affiliation(s)
- Mikael S Lindström
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Deana Jurada
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Sladana Bursac
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Ines Orsolic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Jiri Bartek
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- The Danish Cancer Society Research Centre, Copenhagen, Denmark.
| | - Sinisa Volarevic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia.
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia.
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211
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DNA replication stress and its impact on chromosome segregation and tumorigenesis. Semin Cancer Biol 2018; 55:61-69. [PMID: 29692334 DOI: 10.1016/j.semcancer.2018.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 01/11/2023]
Abstract
Genome instability and cell cycle dysregulation are commonly associated with cancer. DNA replication stress driven by oncogene activation during tumorigenesis is now well established as a source of genome instability. Replication stress generates DNA damage not only during S phase, but also in the subsequent mitosis, where it impacts adversely on chromosome segregation. Some regions of the genome seem particularly sensitive to replication stress-induced instability; most notably, chromosome fragile sites. In this article, we review some of the important issues that have emerged in recent years concerning DNA replication stress and fragile site expression, as well as how chromosome instability is minimized by a family of ring-shaped protein complexes known as SMC proteins. Understanding how replication stress impacts on S phase and mitosis in cancer should provide opportunities for the development of novel and tumour-specific treatments.
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212
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Kotsantis P, Petermann E, Boulton SJ. Mechanisms of Oncogene-Induced Replication Stress: Jigsaw Falling into Place. Cancer Discov 2018; 8:537-555. [PMID: 29653955 DOI: 10.1158/2159-8290.cd-17-1461] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/26/2018] [Accepted: 03/09/2018] [Indexed: 12/31/2022]
Abstract
Oncogene activation disturbs cellular processes and accommodates a complex landscape of changes in the genome that contribute to genomic instability, which accelerates mutation rates and promotes tumorigenesis. Part of this cellular turmoil involves deregulation of physiologic DNA replication, widely described as replication stress. Oncogene-induced replication stress is an early driver of genomic instability and is attributed to a plethora of factors, most notably aberrant origin firing, replication-transcription collisions, reactive oxygen species, and defective nucleotide metabolism.Significance: Replication stress is a fundamental step and an early driver of tumorigenesis and has been associated with many activated oncogenes. Deciphering the mechanisms that contribute to the replication stress response may provide new avenues for targeted cancer treatment. In this review, we discuss the latest findings on the DNA replication stress response and examine the various mechanisms through which activated oncogenes induce replication stress. Cancer Discov; 8(5); 537-55. ©2018 AACR.
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Affiliation(s)
| | - Eva Petermann
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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213
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Bartsch K, Damme M, Regen T, Becker L, Garrett L, Hölter SM, Knittler K, Borowski C, Waisman A, Glatzel M, Fuchs H, Gailus-Durner V, Hrabe de Angelis M, Rabe B. RNase H2 Loss in Murine Astrocytes Results in Cellular Defects Reminiscent of Nucleic Acid-Mediated Autoinflammation. Front Immunol 2018; 9:587. [PMID: 29662492 PMCID: PMC5890188 DOI: 10.3389/fimmu.2018.00587] [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: 11/14/2017] [Accepted: 03/08/2018] [Indexed: 11/13/2022] Open
Abstract
Aicardi-Goutières syndrome (AGS) is a rare early onset childhood encephalopathy caused by persistent neuroinflammation of autoimmune origin. AGS is a genetic disorder and >50% of affected individuals bear hypomorphic mutations in ribonuclease H2 (RNase H2). All available RNase H2 mouse models so far fail to mimic the prominent CNS involvement seen in AGS. To establish a mouse model recapitulating the human disease, we deleted RNase H2 specifically in the brain, the most severely affected organ in AGS. Although RNase H2ΔGFAP mice lacked the nuclease in astrocytes and a majority of neurons, no disease signs were apparent in these animals. We additionally confirmed these results in a second, neuron-specific RNase H2 knockout mouse line. However, when astrocytes were isolated from brains of RNase H2ΔGFAP mice and cultured under mitogenic conditions, they showed signs of DNA damage and premature senescence. Enhanced expression of interferon-stimulated genes (ISGs) represents the most reliable AGS biomarker. Importantly, primary RNase H2ΔGFAP astrocytes displayed significantly increased ISG transcript levels, which we failed to detect in in vivo in brains of RNase H2ΔGFAP mice. Isolated astrocytes primed by DNA damage, including RNase H2-deficiency, exhibited a heightened innate immune response when exposed to bacterial or viral antigens. Taken together, we established a valid cellular AGS model that utilizes the very cell type responsible for disease pathology, the astrocyte, and phenocopies major molecular defects observed in AGS patient cells.
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Affiliation(s)
- Kareen Bartsch
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Markus Damme
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Tommy Regen
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lillian Garrett
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Katharina Knittler
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christopher Borowski
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Björn Rabe
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
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214
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Flach J, Milyavsky M. Replication stress in hematopoietic stem cells in mouse and man. Mutat Res 2018; 808:74-82. [PMID: 29079268 DOI: 10.1016/j.mrfmmm.2017.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 08/31/2017] [Accepted: 10/12/2017] [Indexed: 04/14/2023]
Abstract
Life-long blood regeneration relies on a rare population of self-renewing hematopoietic stem cells (HSCs). These cells' nearly unlimited self-renewal potential and lifetime persistence in the body signifies the need for tight control of their genome integrity. Their quiescent state, tightly linked with low metabolic activity, is one of the main strategies employed by HSCs to preserve an intact genome. On the other hand, HSCs need to be able to quickly respond to increased blood demands and rapidly increase their cellular output in order to fight infection-associated inflammation or extensive blood loss. This increase in proliferation rate, however, comes at the price of exposing HSCs to DNA damage inevitably associated with the process of DNA replication. Any interference with normal replication fork progression leads to a specialized molecular response termed replication stress (RS). Importantly, increased levels of RS are a hallmark feature of aged HSCs, where an accumulating body of evidence points to causative relationships between RS and the aging-associated impairment of the blood system's functional capacity. In this review, we present an overview of RS in HSCs focusing on its causes and consequences for the blood system of mice and men.
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Affiliation(s)
- Johanna Flach
- Department of Hematology and Medical Oncology & Institute of Molecular Oncology, University Medical Center Goettingen, Germany; Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Mannheim, Germany.
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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215
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Abstract
Fanconi anaemia (FA) is a genetic disorder that is characterized by bone marrow failure (BMF), developmental abnormalities and predisposition to cancer. Together with other proteins involved in DNA repair processes and cell division, the FA proteins maintain genome homeostasis, and germline mutation of any one of the genes that encode FA proteins causes FA. Monoallelic inactivation of some FA genes, such as FA complementation group D1 (FANCD1; also known as the breast and ovarian cancer susceptibility gene BRCA2), leads to adult-onset cancer predisposition but does not cause FA, and somatic mutations in FA genes occur in cancers in the general population. Carcinogenesis resulting from a dysregulated FA pathway is multifaceted, as FA proteins monitor multiple complementary genome-surveillance checkpoints throughout interphase, where monoubiquitylation of the FANCD2-FANCI heterodimer by the FA core complex promotes recruitment of DNA repair effectors to chromatin lesions to resolve DNA damage and mitosis. In this Review, we discuss how the FA pathway safeguards genome integrity throughout the cell cycle and show how studies of FA have revealed opportunities to develop rational therapeutics for this genetic disease and for malignancies that acquire somatic mutations within the FA pathway.
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Affiliation(s)
- Grzegorz Nalepa
- Department of Pediatrics, Section of Pediatric Hematology-Oncology, Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 W Walnut Street, R4-421, Indianapolis, Indiana 46202, USA
- Riley Hospital for Children at Indiana University Health, 705 Riley Hospital Drive, Room 5900, Indianapolis, Indiana 46202, USA
- Department of Biochemistry, Indiana University School of Medicine
- Department of Medical and Molecular Genetics, Indiana University School of Medicine
| | - D Wade Clapp
- Riley Hospital for Children at Indiana University Health, 705 Riley Hospital Drive, Room 5900, Indianapolis, Indiana 46202, USA
- Department of Biochemistry, Indiana University School of Medicine
- Department of Microbiology and Immunology, Indiana University School of Medicine
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
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216
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Macheret M, Halazonetis TD. Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress. Nature 2018; 555:112-116. [PMID: 29466339 PMCID: PMC5837010 DOI: 10.1038/nature25507] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 01/09/2018] [Indexed: 12/23/2022]
Abstract
Oncogene-induced DNA replication stress contributes critically to the genomic instability that is present in cancer. However, elucidating how oncogenes deregulate DNA replication has been impeded by difficulty in mapping replication initiation sites on the human genome. Here, using a sensitive assay to monitor nascent DNA synthesis in early S phase, we identified thousands of replication initiation sites in cells before and after induction of the oncogenes CCNE1 and MYC. Remarkably, both oncogenes induced firing of a novel set of DNA replication origins that mapped within highly transcribed genes. These ectopic origins were normally suppressed by transcription during G1, but precocious entry into S phase, before all genic regions had been transcribed, allowed firing of origins within genes in cells with activated oncogenes. Forks from oncogene-induced origins were prone to collapse, as a result of conflicts between replication and transcription, and were associated with DNA double-stranded break formation and chromosomal rearrangement breakpoints both in our experimental system and in a large cohort of human cancers. Thus, firing of intragenic origins caused by premature S phase entry represents a mechanism of oncogene-induced DNA replication stress that is relevant for genomic instability in human cancer.
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Affiliation(s)
- Morgane Macheret
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland
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217
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MOF Suppresses Replication Stress and Contributes to Resolution of Stalled Replication Forks. Mol Cell Biol 2018; 38:MCB.00484-17. [PMID: 29298824 DOI: 10.1128/mcb.00484-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/05/2017] [Indexed: 01/13/2023] Open
Abstract
The human MOF (hMOF) protein belongs to the MYST family of histone acetyltransferases and plays a critical role in transcription and the DNA damage response. MOF is essential for cell proliferation; however, its role during replication and replicative stress is unknown. Here we demonstrate that cells depleted of MOF and under replicative stress induced by cisplatin, hydroxyurea, or camptothecin have reduced survival, a higher frequency of S-phase-specific chromosome damage, and increased R-loop formation. MOF depletion decreased replication fork speed and, when combined with replicative stress, also increased stalled replication forks as well as new origin firing. MOF interacted with PCNA, a key coordinator of replication and repair machinery at replication forks, and affected its ubiquitination and recruitment to the DNA damage site. Depletion of MOF, therefore, compromised the DNA damage repair response as evidenced by decreased Mre11, RPA70, Rad51, and PCNA focus formation, reduced DNA end resection, and decreased CHK1 phosphorylation in cells after exposure to hydroxyurea or cisplatin. These results support the argument that MOF plays an important role in suppressing replication stress induced by genotoxic agents at several stages during the DNA damage response.
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218
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Three classes of recurrent DNA break clusters in brain progenitors identified by 3D proximity-based break joining assay. Proc Natl Acad Sci U S A 2018; 115:1919-1924. [PMID: 29432181 DOI: 10.1073/pnas.1719907115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We recently discovered 27 recurrent DNA double-strand break (DSB) clusters (RDCs) in mouse neural stem/progenitor cells (NSPCs). Most RDCs occurred across long, late-replicating RDC genes and were found only after mild inhibition of DNA replication. RDC genes share intriguing characteristics, including encoding surface proteins that organize brain architecture and neuronal junctions, and are genetically implicated in neuropsychiatric disorders and/or cancers. RDC identification relies on high-throughput genome-wide translocation sequencing (HTGTS), which maps recurrent DSBs based on their translocation to "bait" DSBs in specific chromosomal locations. Cellular heterogeneity in 3D genome organization allowed unequivocal identification of RDCs on 14 different chromosomes using HTGTS baits on three mouse chromosomes. Additional candidate RDCs were also implicated, however, suggesting that some RDCs were missed. To more completely identify RDCs, we exploited our finding that joining of two DSBs occurs more frequently if they lie on the same cis chromosome. Thus, we used CRISPR/Cas9 to introduce specific DSBs into each mouse chromosome in NSPCs that were used as bait for HTGTS libraries. This analysis confirmed all 27 previously identified RDCs and identified many new ones. NSPC RDCs fall into three groups based on length, organization, transcription level, and replication timing of genes within them. While mostly less robust, the largest group of newly defined RDCs share many intriguing characteristics with the original 27. Our findings also revealed RDCs in NSPCs in the absence of induced replication stress, and support the idea that the latter treatment augments an already active endogenous process.
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219
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Abstract
The ribosome is a complex molecular machine composed of numerous distinct proteins and nucleic acids and is responsible for protein synthesis in every living cell. Ribosome biogenesis is one of the most multifaceted and energy- demanding processes in biology, involving a large number of assembly and maturation factors, the functions of which are orchestrated by multiple cellular inputs, including mitogenic signals and nutrient availability. Although causal associations between inherited mutations affecting ribosome biogenesis and elevated cancer risk have been established over the past decade, mechanistic data have emerged suggesting a broader role for dysregulated ribosome biogenesis in the development and progression of most spontaneous cancers. In this Opinion article, we highlight the most recent findings that provide new insights into the molecular basis of ribosome biogenesis in cancer and offer our perspective on how these observations present opportunities for the design of new targeted cancer treatments.
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Affiliation(s)
- Joffrey Pelletier
- Laboratory of Cancer Metabolism, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - George Thomas
- Laboratory of Cancer Metabolism, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain; at the Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, USA; and at the Unit of Biochemistry, Department of Physiological Sciences II, Faculty of Medicine, Campus Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), University of Barcelona, 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Siniša Volarević
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Brace Branchetta 20, 51000 Rijeka, Croatia; and at the Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Brace Branchetta 20, 51000 Rijeka, Croatia
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220
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Bennett CL, La Spada AR. Senataxin, A Novel Helicase at the Interface of RNA Transcriptome Regulation and Neurobiology: From Normal Function to Pathological Roles in Motor Neuron Disease and Cerebellar Degeneration. ADVANCES IN NEUROBIOLOGY 2018; 20:265-281. [DOI: 10.1007/978-3-319-89689-2_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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221
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Abstract
A fragile site is a chromosomal locus that is prone to form a gap or constriction visible within a condensed metaphase chromosome, particularly following exposure of cells to DNA replication stress. Based on their frequency, fragile sites are classified as either common (CFSs; present in all individuals) or rare (RFSs; present in only a few individuals). Interest in fragile sites has remained high since their discovery in 1965, because of their association with human disease. CFSs are recognized as drivers of oncogene activation and genome instability in cancer cells, while some RFSs are associated with neurodegenerative diseases. This review summaries our current understanding of the nature and causes of fragile site "expression", including the recently characterized phenomenon of telomere fragility. In particular, we focus on a description of the methodologies and technologies for detection and analysis of chromosome fragile sites.
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222
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Javadekar SM, Yadav R, Raghavan SC. DNA structural basis for fragility at peak III of BCL2 major breakpoint region associated with t(14;18) translocation. Biochim Biophys Acta Gen Subj 2017; 1862:649-659. [PMID: 29246583 DOI: 10.1016/j.bbagen.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/23/2017] [Accepted: 12/07/2017] [Indexed: 12/23/2022]
Abstract
Maintaining genome integrity is crucial for normal cellular functions. DNA double-strand breaks (DSBs), when unrepaired, can potentiate chromosomal translocations. t(14;18) translocation involving BCL2 gene on chromosome 18 and IgH loci at chromosome 14, could lead to follicular lymphoma. Molecular basis for fragility of translocation breakpoint regions is an active area of investigation. Previously, formation of non-B DNA structures like G-quadruplex, triplex, B/A transition were investigated at peak I of BCL2 major breakpoint region (MBR); however, it is less understood at peak III. In vitro gel shift assays show faster mobility for MBR peak III sequences, unlike controls. CD studies of peak III sequences reveal a spectral pattern different from B-DNA. Although complementary C-rich stretches exhibit single-strandedness, corresponding guanine-rich sequences do not show DMS protection, ruling out G-quadruplex and triplex DNA. Extrachromosomal assay indicates that peak III halts transcription, unlike its mutated version. Taken together, multiple lines of evidence suggest formation of potential cruciform DNA structure at MBR peak III, which was also supported by in silico studies. Thus, our study reveals formation of non-B DNA structure which could be a basis for fragility at BCL2 breakpoint regions, eventually leading to chromosomal translocations.
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Affiliation(s)
- Saniya M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Rakhee Yadav
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India.
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223
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Ljungman M, Parks L, Hulbatte R, Bedi K. The role of H3K79 methylation in transcription and the DNA damage response. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 780:48-54. [PMID: 31395348 DOI: 10.1016/j.mrrev.2017.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/19/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022]
Abstract
Chromatin plays a critical role in organizing and protecting DNA. However, chromatin acts as an impediment for transcription and DNA repair. Histone modifications, such as H3K79 methylation, promote transcription and genomic stability by enhancing transcription elongation and by serving as landing sites for proteins involved in the DNA damage response. This review summarizes the current understanding of the role of H3K79 methylation in transcription, how it affects genome stability and opportunities to develop impactful therapeutic interventions for cancer.
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Affiliation(s)
- Mats Ljungman
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States.
| | - Luke Parks
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States; Department of Cell and Molecular Biology, Uppsala University, Box 256, 75105 Uppsala, Sweden
| | - Radhika Hulbatte
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
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224
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Chastain M, Zhou Q, Shiva O, Fadri-Moskwik M, Whitmore L, Jia P, Dai X, Huang C, Ye P, Chai W. Human CST Facilitates Genome-wide RAD51 Recruitment to GC-Rich Repetitive Sequences in Response to Replication Stress. Cell Rep 2017; 16:1300-1314. [PMID: 27487043 DOI: 10.1016/j.celrep.2016.06.077] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 05/23/2016] [Accepted: 06/17/2016] [Indexed: 11/25/2022] Open
Abstract
The telomeric CTC1/STN1/TEN1 (CST) complex has been implicated in promoting replication recovery under replication stress at genomic regions, yet its precise role is unclear. Here, we report that STN1 is enriched at GC-rich repetitive sequences genome-wide in response to hydroxyurea (HU)-induced replication stress. STN1 deficiency exacerbates the fragility of these sequences under replication stress, resulting in chromosome fragmentation. We find that upon fork stalling, CST proteins form distinct nuclear foci that colocalize with RAD51. Furthermore, replication stress induces physical association of CST with RAD51 in an ATR-dependent manner. Strikingly, CST deficiency diminishes HU-induced RAD51 foci formation and reduces RAD51 recruitment to telomeres and non-telomeric GC-rich fragile sequences. Collectively, our findings establish that CST promotes RAD51 recruitment to GC-rich repetitive sequences in response to replication stress to facilitate replication restart, thereby providing insights into the mechanism underlying genome stability maintenance.
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Affiliation(s)
- Megan Chastain
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Qing Zhou
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Olga Shiva
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Maria Fadri-Moskwik
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Leanne Whitmore
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Pingping Jia
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Xueyu Dai
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Chenhui Huang
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Ping Ye
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, 1000 E 23rd Street, Suite 370, Sioux Falls, SD 57105, USA; Department of Pharmacy Practice, South Dakota State University, Brookings, SD 57007, USA
| | - Weihang Chai
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA.
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225
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Zeller P, Gasser SM. The Importance of Satellite Sequence Repression for Genome Stability. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:15-24. [PMID: 29133300 DOI: 10.1101/sqb.2017.82.033662] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Up to two-thirds of eukaryotic genomes consist of repetitive sequences, which include both transposable elements and tandemly arranged simple or satellite repeats. Whereas extensive progress has been made toward understanding the danger of and control over transposon expression, only recently has it been recognized that DNA damage can arise from satellite sequence transcription. Although the structural role of satellite repeats in kinetochore function and end protection has long been appreciated, it has now become clear that it is not only these functions that are compromised by elevated levels of transcription. RNA from simple repeat sequences can compromise replication fork stability and genome integrity, thus compromising germline viability. Here we summarize recent discoveries on how cells control the transcription of repeat sequence and the dangers that arise from their expression. We propose that the link between the DNA damage response and the transcriptional silencing machinery may help a cell or organism recognize foreign DNA insertions into an evolving genome.
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Affiliation(s)
- Peter Zeller
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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226
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Boulianne B, Feldhahn N. Transcribing malignancy: transcription-associated genomic instability in cancer. Oncogene 2017; 37:971-981. [DOI: 10.1038/onc.2017.402] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 12/17/2022]
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227
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Guénolé A, Legube G. A meeting at risk: Unrepaired DSBs go for broke. Nucleus 2017; 8:589-599. [PMID: 29099269 PMCID: PMC5788565 DOI: 10.1080/19491034.2017.1380138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/06/2017] [Accepted: 09/12/2017] [Indexed: 12/17/2022] Open
Abstract
Translocations are dramatic genomic rearrangements due to aberrant rejoining of distant DNA ends that can trigger cancer onset and progression. Translocations frequently occur in genes, yet the mechanisms underlying their formation remain poorly understood. One potential mechanism involves DNA Double Strand Break mobility and juxtaposition (i.e. clustering), an event that has been intensively debated over the past decade. Using Capture Hi-C, we recently found that DSBs do in fact cluster in human nuclei but only when induced in transcriptionally active genes. Notably, we found that clustering of damaged genes is regulated by cell cycle progression and coincides with damage persistency. Here, we discuss the mechanisms that could sustain clustering and speculate on the functional consequences of this seemingly double edge sword mechanism that may well stand at the heart of translocation biogenesis.
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Affiliation(s)
- Aude Guénolé
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
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228
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Vitelli V, Galbiati A, Iannelli F, Pessina F, Sharma S, d'Adda di Fagagna F. Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks. Annu Rev Genomics Hum Genet 2017; 18:87-113. [PMID: 28859573 DOI: 10.1146/annurev-genom-091416-035314] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.
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Affiliation(s)
- Valerio Vitelli
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | | | - Fabio Iannelli
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Fabio Pessina
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Sheetal Sharma
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Fabrizio d'Adda di Fagagna
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy; .,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia 27100, Italy
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229
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Irony-Tur Sinai M, Kerem B. DNA replication stress drives fragile site instability. Mutat Res 2017; 808:56-61. [PMID: 29074228 DOI: 10.1016/j.mrfmmm.2017.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/26/2017] [Accepted: 10/12/2017] [Indexed: 12/21/2022]
Abstract
DNA replication stress is one of the early drivers enabling the ongoing acquisition of genetic changes arising during tumorigenesis. As such, it is a feature of most pre-malignant and malignant cells. In this review article, we focus on the early events initiating DNA replication stress and the preferential sensitivity of common fragile sites (CFSs) to this stress. CFSs are specific genomic regions within the normal chromosomal structure, which appear as gaps and breaks in the metaphase chromosomes of cells grown under mild replication stress conditions. The main characteristics predisposing CFSs to instability include late replication timing, delayed replication completion, failure to activate additional origins, origin paucity along large genomic regions, collision between replication and transcription complexes along large genes, and the presence of AT-dinucleotide rich sequences. The contribution of these features to instability at CFSs during early cancer development is discussed.
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Affiliation(s)
- Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, 91904, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, 91904, Israel.
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230
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Chang EYC, Novoa CA, Aristizabal MJ, Coulombe Y, Segovia R, Chaturvedi R, Shen Y, Keong C, Tam AS, Jones SJM, Masson JY, Kobor MS, Stirling PC. RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability. J Cell Biol 2017; 216:3991-4005. [PMID: 29042409 PMCID: PMC5716281 DOI: 10.1083/jcb.201703168] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/16/2017] [Accepted: 09/18/2017] [Indexed: 01/01/2023] Open
Abstract
Sgs1, the orthologue of human Bloom's syndrome helicase BLM, is a yeast DNA helicase functioning in DNA replication and repair. We show that SGS1 loss increases R-loop accumulation and sensitizes cells to transcription-replication collisions. Yeast lacking SGS1 accumulate R-loops and γ-H2A at sites of Sgs1 binding, replication pausing regions, and long genes. The mutation signature of sgs1Δ reveals copy number changes flanked by repetitive regions with high R-loop-forming potential. Analysis of BLM in Bloom's syndrome fibroblasts or by depletion of BLM from human cancer cells confirms a role for Sgs1/BLM in suppressing R-loop-associated genome instability across species. In support of a potential direct effect, BLM is found physically proximal to DNA:RNA hybrids in human cells, and can efficiently unwind R-loops in vitro. Together, our data describe a conserved role for Sgs1/BLM in R-loop suppression and support an increasingly broad view of DNA repair and replication fork stabilizing proteins as modulators of R-loop-mediated genome instability.
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Affiliation(s)
| | - Carolina A Novoa
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | | | - Yan Coulombe
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Romulo Segovia
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Richa Chaturvedi
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Yaoqing Shen
- Michael Smith Genome Sciences Centre, Vancouver, Canada
| | - Christelle Keong
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada .,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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231
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Abstract
Semiconservative DNA replication has provided an elegant solution to the fundamental problem of how life is able to proliferate in a way that allows cells, organisms, and populations to survive and replicate many times over. Somewhat lost, however, in our admiration for this mechanism is an appreciation for the asymmetries that occur in the process of DNA replication. As we discuss in this review, these asymmetries arise as a consequence of the structure of the DNA molecule and the enzymatic mechanism of DNA synthesis. Increasing evidence suggests that asymmetries in DNA replication are able to play a central role in the processes of adaptation and evolution by shaping the mutagenic landscape of cells. Additionally, in eukaryotes, recent work has demonstrated that the inherent asymmetries in DNA replication may play an important role in the process of chromatin replication. As chromatin plays an essential role in defining cell identity, asymmetries generated during the process of DNA replication may play critical roles in cell fate decisions related to patterning and development.
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Affiliation(s)
- Jonathan Snedeker
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218; , ,
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218; , ,
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218; , ,
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232
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Sebastian R, Oberdoerffer P. Transcription-associated events affecting genomic integrity. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160288. [PMID: 28847825 PMCID: PMC5577466 DOI: 10.1098/rstb.2016.0288] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 12/25/2022] Open
Abstract
Accurate maintenance of genomic as well as epigenomic integrity is critical for proper cell and organ function. Continuous exposure to DNA damage is, thus, often associated with malignant transformation and degenerative diseases. A significant, chronic threat to genome integrity lies in the process of transcription, which can result in the formation of potentially harmful RNA : DNA hybrid structures (R-loops) and has been linked to DNA damage accumulation as well as dynamic chromatin reorganization. In sharp contrast, recent evidence suggests that active transcription, the resulting transcripts as well as R-loop formation can play multi-faceted roles in maintaining and restoring genome integrity. Here, we will discuss the emerging contributions of transcription as both a source of DNA damage and a mediator of DNA repair. We propose that both aspects have significant implications for genome maintenance, and will speculate on possible long-term consequences for the epigenetic integrity of transcribing cells.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Robin Sebastian
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, Room B907, Bethesda, MD 20892, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, Room B907, Bethesda, MD 20892, USA
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233
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D'Alessandro G, d'Adda di Fagagna F. Transcription and DNA Damage: Holding Hands or Crossing Swords? J Mol Biol 2017; 429:3215-3229. [DOI: 10.1016/j.jmb.2016.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 01/12/2023]
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234
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Di Marco S, Hasanova Z, Kanagaraj R, Chappidi N, Altmannova V, Menon S, Sedlackova H, Langhoff J, Surendranath K, Hühn D, Bhowmick R, Marini V, Ferrari S, Hickson ID, Krejci L, Janscak P. RECQ5 Helicase Cooperates with MUS81 Endonuclease in Processing Stalled Replication Forks at Common Fragile Sites during Mitosis. Mol Cell 2017; 66:658-671.e8. [PMID: 28575661 DOI: 10.1016/j.molcel.2017.05.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/14/2017] [Accepted: 05/04/2017] [Indexed: 11/18/2022]
Abstract
The MUS81-EME1 endonuclease cleaves late replication intermediates at common fragile sites (CFSs) during early mitosis to trigger DNA-repair synthesis that ensures faithful chromosome segregation. Here, we show that these DNA transactions are promoted by RECQ5 DNA helicase in a manner dependent on its Ser727 phosphorylation by CDK1. Upon replication stress, RECQ5 associates with CFSs in early mitosis through its physical interaction with MUS81 and promotes MUS81-dependent mitotic DNA synthesis. RECQ5 depletion or mutational inactivation of its ATP-binding site, RAD51-interacting domain, or phosphorylation site causes excessive binding of RAD51 to CFS loci and impairs CFS expression. This leads to defective chromosome segregation and accumulation of CFS-associated DNA damage in G1 cells. Biochemically, RECQ5 alleviates the inhibitory effect of RAD51 on 3'-flap DNA cleavage by MUS81-EME1 through its RAD51 filament disruption activity. These data suggest that RECQ5 removes RAD51 filaments stabilizing stalled replication forks at CFSs and hence facilitates CFS cleavage by MUS81-EME1.
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Affiliation(s)
- Stefano Di Marco
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Zdenka Hasanova
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic
| | - Radhakrishnan Kanagaraj
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Nagaraja Chappidi
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Veronika Altmannova
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, Brno 656 91, Czech Republic
| | - Shruti Menon
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Hana Sedlackova
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic
| | - Jana Langhoff
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kalpana Surendranath
- Department of Biomedical Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK
| | - Daniela Hühn
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rahul Bhowmick
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Insitute Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Victoria Marini
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic
| | - Stefano Ferrari
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Insitute Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Lumir Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, Brno 656 91, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic.
| | - Pavel Janscak
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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235
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Madireddy A, Kosiyatrakul ST, Boisvert RA, Herrera-Moyano E, García-Rubio ML, Gerhardt J, Vuono EA, Owen N, Yan Z, Olson S, Aguilera A, Howlett NG, Schildkraut CL. FANCD2 Facilitates Replication through Common Fragile Sites. Mol Cell 2017; 64:388-404. [PMID: 27768874 DOI: 10.1016/j.molcel.2016.09.017] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 08/08/2016] [Accepted: 09/14/2016] [Indexed: 12/27/2022]
Abstract
Common fragile sites (CFSs) are genomic regions that are unstable under conditions of replicative stress. Although the characteristics of CFSs that render them vulnerable to stress are associated mainly with replication, the cellular pathways that protect CFSs during replication remain unclear. Here, we identify and describe a role for FANCD2 as a trans-acting facilitator of CFS replication, in the absence of exogenous replicative stress. In the absence of FANCD2, replication forks stall within the AT-rich fragility core of CFS, leading to dormant origin activation. Furthermore, FANCD2 deficiency is associated with DNA:RNA hybrid formation at CFS-FRA16D, and inhibition of DNA:RNA hybrid formation suppresses replication perturbation. In addition, we also found that FANCD2 reduces the number of potential sites of replication initiation. Our data demonstrate that FANCD2 protein is required to ensure efficient CFS replication and provide mechanistic insight into how FANCD2 regulates CFS stability.
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Affiliation(s)
- Advaitha Madireddy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | | | - Rebecca A Boisvert
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Emilia Herrera-Moyano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, 41092 Seville, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, 41092 Seville, Spain
| | - Jeannine Gerhardt
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Elizabeth A Vuono
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Nichole Owen
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Zi Yan
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan Olson
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, 41092 Seville, Spain
| | - Niall G Howlett
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Carl L Schildkraut
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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236
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Ait Saada A, Teixeira-Silva A, Iraqui I, Costes A, Hardy J, Paoletti G, Fréon K, Lambert SAE. Unprotected Replication Forks Are Converted into Mitotic Sister Chromatid Bridges. Mol Cell 2017; 66:398-410.e4. [PMID: 28475874 DOI: 10.1016/j.molcel.2017.04.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/08/2017] [Accepted: 04/03/2017] [Indexed: 01/23/2023]
Abstract
Replication stress and mitotic abnormalities are key features of cancer cells. Temporarily paused forks are stabilized by the intra-S phase checkpoint and protected by the association of Rad51, which prevents Mre11-dependent resection. However, if a fork becomes dysfunctional and cannot resume, this terminally arrested fork is rescued by a converging fork to avoid unreplicated parental DNA during mitosis. Alternatively, dysfunctional forks are restarted by homologous recombination. Using fission yeast, we report that Rad52 and the DNA binding activity of Rad51, but not its strand-exchange activity, act to protect terminally arrested forks from unrestrained Exo1-nucleolytic activity. In the absence of recombination proteins, large ssDNA gaps, up to 3 kb long, occur behind terminally arrested forks, preventing efficient fork merging and leading to mitotic sister chromatid bridging. Thus, Rad52 and Rad51 prevent temporarily and terminally arrested forks from degrading and, despite the availability of converging forks, converting to anaphase bridges causing aneuploidy and cell death.
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Affiliation(s)
- Anissia Ait Saada
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Ana Teixeira-Silva
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Ismail Iraqui
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Audrey Costes
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Julien Hardy
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Giulia Paoletti
- Institut Curie, PSL Research University, CNRS, UMR144, F-75248 Paris, France
| | - Karine Fréon
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Sarah A E Lambert
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France.
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237
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Nguyen HD, Yadav T, Giri S, Saez B, Graubert TA, Zou L. Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1. Mol Cell 2017; 65:832-847.e4. [PMID: 28257700 DOI: 10.1016/j.molcel.2017.01.029] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/05/2016] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
Abstract
R loop, a transcription intermediate containing RNA:DNA hybrids and displaced single-stranded DNA (ssDNA), has emerged as a major source of genomic instability. RNaseH1, which cleaves the RNA in RNA:DNA hybrids, plays an important role in R loop suppression. Here we show that replication protein A (RPA), an ssDNA-binding protein, interacts with RNaseH1 and colocalizes with both RNaseH1 and R loops in cells. In vitro, purified RPA directly enhances the association of RNaseH1 with RNA:DNA hybrids and stimulates the activity of RNaseH1 on R loops. An RPA binding-defective RNaseH1 mutant is not efficiently stimulated by RPA in vitro, fails to accumulate at R loops in cells, and loses the ability to suppress R loops and associated genomic instability. Thus, in addition to sensing DNA damage and replication stress, RPA is a sensor of R loops and a regulator of RNaseH1, extending the versatile role of RPA in suppression of genomic instability.
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Affiliation(s)
- Hai Dang Nguyen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Tribhuwan Yadav
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sumanprava Giri
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Borja Saez
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Timothy A Graubert
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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238
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Bhowmick R, Minocherhomji S, Hickson ID. RAD52 Facilitates Mitotic DNA Synthesis Following Replication Stress. Mol Cell 2017; 64:1117-1126. [PMID: 27984745 DOI: 10.1016/j.molcel.2016.10.037] [Citation(s) in RCA: 266] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/06/2016] [Accepted: 10/28/2016] [Indexed: 11/16/2022]
Abstract
Homologous recombination (HR) is necessary to counteract DNA replication stress. Common fragile site (CFS) loci are particularly sensitive to replication stress and undergo pathological rearrangements in tumors. At these loci, replication stress frequently activates DNA repair synthesis in mitosis. This mitotic DNA synthesis, termed MiDAS, requires the MUS81-EME1 endonuclease and a non-catalytic subunit of the Pol-delta complex, POLD3. Here, we examine the contribution of HR factors in promoting MiDAS in human cells. We report that RAD51 and BRCA2 are dispensable for MiDAS but are required to counteract replication stress at CFS loci during S-phase. In contrast, MiDAS is RAD52 dependent, and RAD52 is required for the timely recruitment of MUS81 and POLD3 to CFSs in early mitosis. Our results provide further mechanistic insight into MiDAS and define a specific function for human RAD52. Furthermore, selective inhibition of MiDAS may comprise a potential therapeutic strategy to sensitize cancer cells undergoing replicative stress.
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Affiliation(s)
- Rahul Bhowmick
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Sheroy Minocherhomji
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark.
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239
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Hamperl S, Bocek MJ, Saldivar JC, Swigut T, Cimprich KA. Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses. Cell 2017; 170:774-786.e19. [PMID: 28802045 DOI: 10.1016/j.cell.2017.07.043] [Citation(s) in RCA: 388] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 05/09/2017] [Accepted: 07/25/2017] [Indexed: 12/19/2022]
Abstract
Conflicts between transcription and replication are a potent source of DNA damage. Co-transcriptional R-loops could aggravate such conflicts by creating an additional barrier to replication fork progression. Here, we use a defined episomal system to investigate how conflict orientation and R-loop formation influence genome stability in human cells. R-loops, but not normal transcription complexes, induce DNA breaks and orientation-specific DNA damage responses during conflicts with replication forks. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the co-directional (CD) orientation but promoting their formation in the head-on (HO) orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings connect DNA replication to R-loop homeostasis and suggest a mechanistic basis for genome instability resulting from deregulated DNA replication, observed in cancer and other disease states.
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Affiliation(s)
- Stephan Hamperl
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bocek
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua C Saldivar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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240
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Abstract
Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not frequently involved in translocations or other cancer-associated recurrent gross chromosome rearrangements. However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers.
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics; the Department of Pathology; and the Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics; and the Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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241
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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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242
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Aguilera A, Gómez-González B. DNA-RNA hybrids: the risks of DNA breakage during transcription. Nat Struct Mol Biol 2017; 24:439-443. [PMID: 28471430 DOI: 10.1038/nsmb.3395] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/05/2017] [Indexed: 12/28/2022]
Abstract
Although R loops can occur at different genomic locations, the factors that determine their formation and frequency remain unclear. Emerging evidence indicates that DNA breaks stimulate DNA-RNA hybrid formation. Here, we discuss the possibility that formation of hybrids may be an inevitable risk of DNA breaks that occur within actively transcribed regions. While such hybrids must be removed to permit repair, their potential role as repair intermediates remains to be established.
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Affiliation(s)
- Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
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243
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Bhatia V, Herrera-Moyano E, Aguilera A, Gómez-González B. The Role of Replication-Associated Repair Factors on R-Loops. Genes (Basel) 2017; 8:E171. [PMID: 28653981 PMCID: PMC5541304 DOI: 10.3390/genes8070171] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/19/2017] [Accepted: 06/20/2017] [Indexed: 12/12/2022] Open
Abstract
The nascent RNA can reinvade the DNA double helix to form a structure termed the R-loop, where a single-stranded DNA (ssDNA) is accompanied by a DNA-RNA hybrid. Unresolved R-loops can impede transcription and replication processes and lead to genomic instability by a mechanism still not fully understood. In this sense, a connection between R-loops and certain chromatin markers has been reported that might play a key role in R-loop homeostasis and genome instability. To counteract the potential harmful effect of R-loops, different conserved messenger ribonucleoprotein (mRNP) biogenesis and nuclear export factors prevent R-loop formation, while ubiquitously-expressed specific ribonucleases and DNA-RNA helicases resolve DNA-RNA hybrids. However, the molecular events associated with R-loop sensing and processing are not yet known. Given that R-loops hinder replication progression, it is plausible that some DNA replication-associated factors contribute to dissolve R-loops or prevent R-loop mediated genome instability. In support of this, R-loops accumulate in cells depleted of the BRCA1, BRCA2 or the Fanconi anemia (FA) DNA repair factors, indicating that they play an active role in R-loop dissolution. In light of these results, we review our current view of the role of replication-associated DNA repair pathways in preventing the harmful consequences of R-loops.
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Affiliation(s)
- Vaibhav Bhatia
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
| | - Emilia Herrera-Moyano
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
| | - Andrés Aguilera
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
| | - Belén Gómez-González
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
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244
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Burke RT, Marcus JM, Orth JD. Inhibition of exportin-1 function results in rapid cell cycle-associated DNA damage in cancer cells. Oncotarget 2017; 8:39460-39475. [PMID: 28467801 PMCID: PMC5503625 DOI: 10.18632/oncotarget.17063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 03/08/2017] [Indexed: 01/05/2023] Open
Abstract
Selective inhibitors of nuclear export (SINE) are small molecules in development as anti-cancer agents. The first-in-class SINE, selinexor, is in clinical trials for blood and solid cancers. Selinexor forms a covalent bond with exportin-1 at cysteine-528, and blocks its ability to export cargos. Previous work has shown strong cell cycle effects and drug-induced cell death across many different cancer-derived cell lines. Here, we report strong cell cycle-associated DNA double-stranded break formation upon the treatment of cancer cells with SINE. In multiple cell models, selinexor treatment results in the formation of clustered DNA damage foci in 30-40% of cells within 8 hours that is dependent upon cysteine-528. DNA damage strongly correlates with G1/S-phase and decreased DNA replication. Live cell microscopy reveals an association between DNA damage and cell fate. Cells that form damage in G1-phase more often die or arrest, while those damaged in S/G2-phase frequently progress to cell division. Up to half of all treated cells form damage foci, and most cells that die after being damaged, were damaged in G1-phase. By comparison, non-transformed cell lines show strong cell cycle effects but little DNA damage and less death than cancer cells. Significant drug combination effects occur when selinexor is paired with different classes of agents that either cause DNA damage or that diminish DNA damage repair. These data present a novel effect of exportin-1 inhibition and provide a strong rationale for multiple combination treatments of selinexor with agents that are currently in use for the treatment of different solid cancers.
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Affiliation(s)
- Russell T. Burke
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Joshua M. Marcus
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- Current/Present address: Cell, Molecular and Developmental Biology, Graduate Biomedical Sciences, University of Alabama Birmingham, Birmingham, AL, USA
| | - James D. Orth
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
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DNA polymerases eta and kappa exchange with the polymerase delta holoenzyme to complete common fragile site synthesis. DNA Repair (Amst) 2017; 57:1-11. [PMID: 28605669 DOI: 10.1016/j.dnarep.2017.05.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/25/2017] [Accepted: 05/29/2017] [Indexed: 12/21/2022]
Abstract
Common fragile sites (CFSs) are inherently unstable genomic loci that are recurrently altered in human tumor cells. Despite their instability, CFS are ubiquitous throughout the human genome and associated with large tumor suppressor genes or oncogenes. CFSs are enriched with repetitive DNA sequences, one feature postulated to explain why these loci are inherently difficult to replicate, and sensitive to replication stress. We have shown that specialized DNA polymerases (Pols) η and κ replicate CFS-derived sequences more efficiently than the replicative Pol δ. However, we lacked an understanding of how these enzymes cooperate to ensure efficient CFS replication. Here, we designed a model of lagging strand replication with RFC loaded PCNA that allows for maximal activity of the four-subunit human Pol δ holoenzyme, Pol η, and Pol κ in polymerase mixing assays. We discovered that Pol η and κ are both able to exchange with Pol δ stalled at repetitive CFS sequences, enhancing Normalized Replication Efficiency. We used this model to test the impact of PCNA mono-ubiquitination on polymerase exchange, and found no change in polymerase cooperativity in CFS replication compared with unmodified PCNA. Finally, we modeled replication stress in vitro using aphidicolin and found that Pol δ holoenzyme synthesis was significantly inhibited in a dose-dependent manner, preventing any replication past the CFS. Importantly, Pol η and κ were still proficient in rescuing this stalled Pol δ synthesis, which may explain, in part, the CFS instability phenotype of aphidicolin-treated Pol η and Pol κ-deficient cells. In total, our data support a model wherein Pol δ stalling at CFSs allows for free exchange with a specialized polymerase that is not driven by PCNA.
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246
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Blumenfeld B, Ben-Zimra M, Simon I. Perturbations in the Replication Program Contribute to Genomic Instability in Cancer. Int J Mol Sci 2017; 18:E1138. [PMID: 28587102 PMCID: PMC5485962 DOI: 10.3390/ijms18061138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/08/2017] [Accepted: 05/21/2017] [Indexed: 12/14/2022] Open
Abstract
Cancer and genomic instability are highly impacted by the deoxyribonucleic acid (DNA) replication program. Inaccuracies in DNA replication lead to the increased acquisition of mutations and structural variations. These inaccuracies mainly stem from loss of DNA fidelity due to replication stress or due to aberrations in the temporal organization of the replication process. Here we review the mechanisms and impact of these major sources of error to the replication program.
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Affiliation(s)
- Britny Blumenfeld
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| | - Micha Ben-Zimra
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
- Pharmacology and Experimental Therapeutics Unit, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
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247
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Abstract
In this review, Prioleau and MacAlpine summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages.
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Affiliation(s)
- Marie-Noëlle Prioleau
- Institut Jacques Monod, UMR7592, Centre National de la Recherche Scientifique, Universite Paris Diderot, Equipe Labellisee Association pour la Recherche sur le Cancer, Paris 75013, France
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710. USA
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248
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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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249
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Conflict Resolution in the Genome: How Transcription and Replication Make It Work. Cell 2017; 167:1455-1467. [PMID: 27912056 DOI: 10.1016/j.cell.2016.09.053] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/20/2016] [Accepted: 09/27/2016] [Indexed: 01/12/2023]
Abstract
The complex machineries involved in replication and transcription translocate along the same DNA template, often in opposing directions and at different rates. These processes routinely interfere with each other in prokaryotes, and mounting evidence now suggests that RNA polymerase complexes also encounter replication forks in higher eukaryotes. Indeed, cells rely on numerous mechanisms to avoid, tolerate, and resolve such transcription-replication conflicts, and the absence of these mechanisms can lead to catastrophic effects on genome stability and cell viability. In this article, we review the cellular responses to transcription-replication conflicts and highlight how these inevitable encounters shape the genome and impact diverse cellular processes.
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250
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Leal SM, Gulley ML. Current and Emerging Molecular Tests for Human Papillomavirus-Related Neoplasia in the Genomic Era. J Mol Diagn 2017; 19:366-377. [PMID: 28325688 PMCID: PMC5417044 DOI: 10.1016/j.jmoldx.2017.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/30/2017] [Indexed: 12/14/2022] Open
Abstract
Laboratory tests have a key role in preventing human papillomavirus (HPV)-driven carcinomas and in guiding therapeutic interventions. An understanding of the virology, immunology, and carcinogenesis of HPV is essential for choosing appropriate diagnostic test modalities and developing new and even more effective cancer prevention strategies. HPV infects basal epithelial cells on multiple surfaces and induces carcinoma primarily in the cervix and the oropharynx. HPV types are stratified as high risk or low risk based on their carcinogenic potential. During oncogenesis, HPV interferes with cell cycle regulation and incites DNA damage responses that thwart apoptosis and enable mutations to accumulate. Such mutations are an adverse effect of innate and adaptive antiviral immune responses that up-regulate DNA-editing enzymes, with natural selection of cells having a chromosomally integrated viral genome lacking expression of viral proteins targeted by the immune system. Infected cancers share a similar mutation signature, reflecting the effect of apolipoprotein B mRNA-editing catalytic polypeptide enzyme DNA-editing enzymes. It is feasible that genomic tests for characteristic mutations or methylation signatures, along with tests for dysregulated HPV gene expression, add value in predicting behavior of premalignant lesions. Furthermore, these tumor markers in cell-free DNA of plasma or body fluids may one day assist in early detection or monitoring cancer burden during treatment.
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Affiliation(s)
- Sixto M Leal
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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