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Lamas-Maceiras M, Vizoso-Vázquez Á, Barreiro-Alonso A, Cámara-Quílez M, Cerdán ME. Thanksgiving to Yeast, the HMGB Proteins History from Yeast to Cancer. Microorganisms 2023; 11:microorganisms11040993. [PMID: 37110415 PMCID: PMC10142021 DOI: 10.3390/microorganisms11040993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Yeasts have been a part of human life since ancient times in the fermentation of many natural products used for food. In addition, in the 20th century, they became powerful tools to elucidate the functions of eukaryotic cells as soon as the techniques of molecular biology developed. Our molecular understandings of metabolism, cellular transport, DNA repair, gene expression and regulation, and the cell division cycle have all been obtained through biochemistry and genetic analysis using different yeasts. In this review, we summarize the role that yeasts have had in biological discoveries, the use of yeasts as biological tools, as well as past and on-going research projects on HMGB proteins along the way from yeast to cancer.
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Affiliation(s)
- Mónica Lamas-Maceiras
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Ángel Vizoso-Vázquez
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Aida Barreiro-Alonso
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - María Cámara-Quílez
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - María Esperanza Cerdán
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
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De Santis I, Zanoni M, Pignatta S, Longobardi P, Tesei A, Bevilacqua A. Pro-inflammatory RNA:DNA Hybrids Are p53 Independently Boosted by Hyperbaric Oxygen: a Subcellular Distribution Analysis by Automated Quantitative Imaging. Mol Imaging Biol 2022; 25:504-512. [PMID: 36261778 PMCID: PMC10172224 DOI: 10.1007/s11307-022-01778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022]
Abstract
PURPOSE RNA:DNA hybrids are co-transcriptional products with acknowledged cytoplasmic pro-inflammatory role as activators of the cGAS-STING pathway. We recently proved them also as radiation-induced senescence messages for the abscopal effect mediation, demonstrating the need for a functional p53 for their production and release in A549 and H1299 tumour cells. However, little is known about their role under different stress conditions, especially in cancer cells. METHODS In this work, we open the investigation making use of automated quantitative imaging to characterize the hybrid subcellular distribution in HeLa cells grown under different oxygen pressures or exposed to different ionizing radiation doses. After cell imaging by confocal fluorescent microscopy, we apply automated imaging methods developed on purpose to quantify hybrid foci and nuclear cluster intensity, regional and local density and dimension. RESULTS We show that alteration of culture oxygenation increases hybrid cytoplasmic presence, especially when caused by an hyperoxic environment, with evident hybrid gathering at the cell membrane. Ionizing radiations always fail to increase hybrids, in accordance with the absence of functional p53 in HeLa cells. However, dose-dependent effects are still evident and suggest a threshold dose of 7.5 Gy for remarkable hybrid reduction. CONCLUSION Together with our previous results, these data demonstrate for the first time that different types of stress can increase hybrid production in cancer cells and by at least two different pathways, one p53-dependent triggerable by ionizing radiations and one p53-independent triggerable by oxidative stress. Together, our findings provide a starting point for understanding hybrid role in tumour stress response.
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Affiliation(s)
- Ilaria De Santis
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), University of Bologna, I-40126, Bologna, Italy
| | - Michele Zanoni
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", I-47014, Meldola, Italy
| | - Sara Pignatta
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", I-47014, Meldola, Italy
| | | | - Anna Tesei
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", I-47014, Meldola, Italy.
| | - Alessandro Bevilacqua
- Advanced Research Center on Electronic Systems (ARCES) for Information and Communication Technologies "E. De Castro", University of Bologna, I-40125, Bologna, Italy.
- Department of Computer Science and Engineering (DISI), University of Bologna, I-40136, Bologna, Italy.
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Saayman X, Esashi F. Breaking the paradigm: early insights from mammalian DNA breakomes. FEBS J 2022; 289:2409-2428. [PMID: 33792193 PMCID: PMC9451923 DOI: 10.1111/febs.15849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/04/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022]
Abstract
DNA double-strand breaks (DSBs) can result from both exogenous and endogenous sources and are potentially toxic lesions to the human genome. If improperly repaired, DSBs can threaten genome integrity and contribute to premature ageing, neurodegenerative disorders and carcinogenesis. Through decades of work on genome stability, it has become evident that certain regions of the genome are inherently more prone to breakage than others, known as genome instability hotspots. Recent advancements in sequencing-based technologies now enable the profiling of genome-wide distributions of DSBs, also known as breakomes, to systematically map these instability hotspots. Here, we review the application of these technologies and their implications for our current understanding of the genomic regions most likely to drive genome instability. These breakomes ultimately highlight both new and established breakage hotspots including actively transcribed regions, loop boundaries and early-replicating regions of the genome. Further, these breakomes challenge the paradigm that DNA breakage primarily occurs in hard-to-replicate regions. With these advancements, we begin to gain insights into the biological mechanisms both invoking and protecting against genome instability.
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Affiliation(s)
- Xanita Saayman
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, UK
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Camarillo R, Jimeno S, Huertas P. The Effect of Atypical Nucleic Acids Structures in DNA Double Strand Break Repair: A Tale of R-loops and G-Quadruplexes. Front Genet 2021; 12:742434. [PMID: 34691154 PMCID: PMC8531813 DOI: 10.3389/fgene.2021.742434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/28/2021] [Indexed: 01/08/2023] Open
Abstract
The fine tuning of the DNA double strand break repair pathway choice relies on different regulatory layers that respond to environmental and local cues. Among them, the presence of non-canonical nucleic acids structures seems to create challenges for the repair of nearby DNA double strand breaks. In this review, we focus on the recently published effects of G-quadruplexes and R-loops on DNA end resection and homologous recombination. Finally, we hypothesized a connection between those two atypical DNA structures in inhibiting the DNA end resection step of HR.
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Affiliation(s)
- Rosa Camarillo
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain.,Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Sonia Jimeno
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain.,Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Pablo Huertas
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain.,Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
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Uruci S, Lo CSY, Wheeler D, Taneja N. R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. Hyde. Int J Mol Sci 2021; 22:ijms22168850. [PMID: 34445553 PMCID: PMC8396322 DOI: 10.3390/ijms22168850] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
Since their discovery, R-loops have been associated with both physiological and pathological functions that are conserved across species. R-loops are a source of replication stress and genome instability, as seen in neurodegenerative disorders and cancer. In response, cells have evolved pathways to prevent R-loop accumulation as well as to resolve them. A growing body of evidence correlates R-loop accumulation with changes in the epigenetic landscape. However, the role of chromatin modification and remodeling in R-loops homeostasis remains unclear. This review covers various mechanisms precluding R-loop accumulation and highlights the role of chromatin modifiers and remodelers in facilitating timely R-loop resolution. We also discuss the enigmatic role of RNA:DNA hybrids in facilitating DNA repair, epigenetic landscape and the potential role of replication fork preservation pathways, active fork stability and stalled fork protection pathways, in avoiding replication-transcription conflicts. Finally, we discuss the potential role of several Chro-Mates (chromatin modifiers and remodelers) in the likely differentiation between persistent/detrimental R-loops and transient/benign R-loops that assist in various physiological processes relevant for therapeutic interventions.
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Affiliation(s)
- Sidrit Uruci
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - Calvin Shun Yu Lo
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA;
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
- Correspondence:
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6
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R-loops as Janus-faced modulators of DNA repair. Nat Cell Biol 2021; 23:305-313. [PMID: 33837288 DOI: 10.1038/s41556-021-00663-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 02/01/2023]
Abstract
R-loops are non-B DNA structures with intriguing dual consequences for gene expression and genome stability. In addition to their recognized roles in triggering DNA double-strand breaks (DSBs), R-loops have recently been demonstrated to accumulate in cis to DSBs, especially those induced in transcriptionally active loci. In this Review, we discuss whether R-loops actively participate in DSB repair or are detrimental by-products that must be removed to avoid genome instability.
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7
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Vågbø CB, Slupphaug G. RNA in DNA repair. DNA Repair (Amst) 2020; 95:102927. [DOI: 10.1016/j.dnarep.2020.102927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/22/2022]
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Meers C, Keskin H, Banyai G, Mazina O, Yang T, Gombolay AL, Mukherjee K, Kaparos EI, Newnam G, Mazin A, Storici F. Genetic Characterization of Three Distinct Mechanisms Supporting RNA-Driven DNA Repair and Modification Reveals Major Role of DNA Polymerase ζ. Mol Cell 2020; 79:1037-1050.e5. [PMID: 32882183 DOI: 10.1016/j.molcel.2020.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/30/2020] [Accepted: 08/12/2020] [Indexed: 01/08/2023]
Abstract
DNA double-stranded breaks (DSBs) are dangerous lesions threatening genomic stability. Fidelity of DSB repair is best achieved by recombination with a homologous template sequence. In yeast, transcript RNA was shown to template DSB repair of DNA. However, molecular pathways of RNA-driven repair processes remain obscure. Utilizing assays of RNA-DNA recombination with and without an induced DSB in yeast DNA, we characterize three forms of RNA-mediated genomic modifications: RNA- and cDNA-templated DSB repair (R-TDR and c-TDR) using an RNA transcript or a DNA copy of the RNA transcript for DSB repair, respectively, and a new mechanism of RNA-templated DNA modification (R-TDM) induced by spontaneous or mutagen-induced breaks. While c-TDR requires reverse transcriptase, translesion DNA polymerase ζ (Pol ζ) plays a major role in R-TDR, and it is essential for R-TDM. This study characterizes mechanisms of RNA-DNA recombination, uncovering a role of Pol ζ in transferring genetic information from transcript RNA to DNA.
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Affiliation(s)
- Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Havva Keskin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gabor Banyai
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Olga Mazina
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Efiyenia I Kaparos
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alexander Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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9
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Ueberham U, Arendt T. Genomic Indexing by Somatic Gene Recombination of mRNA/ncRNA - Does It Play a Role in Genomic Mosaicism, Memory Formation, and Alzheimer's Disease? Front Genet 2020; 11:370. [PMID: 32411177 PMCID: PMC7200996 DOI: 10.3389/fgene.2020.00370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/25/2020] [Indexed: 12/26/2022] Open
Abstract
Recent evidence indicates that genomic individuality of neurons, characterized by DNA-content variation, is a common if not universal phenomenon in the human brain that occurs naturally but can also show aberrancies that have been linked to the pathomechanism of Alzheimer’s disease and related neurodegenerative disorders. Etiologically, this genomic mosaic has been suggested to arise from defects of cell cycle regulation that may occur either during brain development or in the mature brain after terminal differentiation of neurons. Here, we aim to draw attention towards another mechanism that can give rise to genomic individuality of neurons, with far-reaching consequences. This mechanism has its origin in the transcriptome rather than in replication defects of the genome, i.e., somatic gene recombination of RNA. We continue to develop the concept that somatic gene recombination of RNA provides a physiological process that, through integration of intronless mRNA/ncRNA into the genome, allows a particular functional state at the level of the individual neuron to be indexed. By insertion of defined RNAs in a somatic recombination process, the presence of specific mRNA transcripts within a definite temporal context can be “frozen” and can serve as an index that can be recalled at any later point in time. This allows information related to a specific neuronal state of differentiation and/or activity relevant to a memory trace to be fixed. We suggest that this process is used throughout the lifetime of each neuron and might have both advantageous and deleterious consequences.
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Affiliation(s)
- Uwe Ueberham
- Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Thomas Arendt
- Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
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Kazadi D, Lim J, Rothschild G, Grinstein V, Laffleur B, Becherel O, Lavin MJ, Basu U. Effects of senataxin and RNA exosome on B-cell chromosomal integrity. Heliyon 2020; 6:e03442. [PMID: 32195383 PMCID: PMC7075999 DOI: 10.1016/j.heliyon.2020.e03442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/07/2020] [Accepted: 02/13/2020] [Indexed: 11/10/2022] Open
Abstract
Loss of function of senataxin (SETX), a bona-fide RNA/DNA helicase, is associated with neuronal degeneration leading to Ataxia and Ocular Apraxia (AOA) in human patients. SETX is proposed to promote transcription termination, DNA replication, DNA repair, and to unwind deleterious RNA:DNA hybrids in the genome. In all the above-mentioned mechanisms, SETX unwinds transcription complex-associated nascent RNA which is then degraded by the RNA exosome complex. Here we have used B cells isolated from a SETX mutant mouse model and compared genomic instability and immunoglobulin heavy chain locus (IgH) class switch recombination (CSR) to evaluate aberrant and programmed genomic rearrangements, respectively. Similar to RNA exosome mutant primary B cells, SETX mutant primary B cells display genomic instability but a modest decrease in efficiency of CSR. Furthermore, knockdown of Setx mRNAs from CH12–F3 B-cell lines leads to a defect in IgA CSR and accumulation of aberrant patterns of mutations in IgH switch sequences. Given that SETX mutant mice do not recapitulate the AOA neurodegenerative phenotype, it is possible that some aspects of SETX biology are rescued by redundant helicases in mice. Overall, our study provides new insights into the role of the SETX/RNA exosome axis in suppressing genomic instability so that programmed DNA breaks are properly orchestrated.
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Affiliation(s)
- David Kazadi
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Veronika Grinstein
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Olivier Becherel
- Centre for Clinical Research, University of Queensland, Brisbane, Qld, Australia
| | - Martin J Lavin
- Centre for Clinical Research, University of Queensland, Brisbane, Qld, Australia
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
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From R-Loops to G-Quadruplexes: Emerging New Threats for the Replication Fork. Int J Mol Sci 2020; 21:ijms21041506. [PMID: 32098397 PMCID: PMC7073102 DOI: 10.3390/ijms21041506] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Replicating the entire genome is one of the most complex tasks for all organisms. Research carried out in the last few years has provided us with a clearer picture on how cells preserve genomic information from the numerous insults that may endanger its stability. Different DNA repair pathways, coping with exogenous or endogenous threat, have been dissected at the molecular level. More recently, there has been an increasing interest towards intrinsic obstacles to genome replication, paving the way to a novel view on genomic stability. Indeed, in some cases, the movement of the replication fork can be hindered by the presence of stable DNA: RNA hybrids (R-loops), the folding of G-rich sequences into G-quadruplex structures (G4s) or repetitive elements present at Common Fragile Sites (CFS). Although differing in their nature and in the way they affect the replication fork, all of these obstacles are a source of replication stress. Replication stress is one of the main hallmarks of cancer and its prevention is becoming increasingly important as a target for future chemotherapeutics. Here we will try to summarize how these three obstacles are generated and how the cells handle replication stress upon their encounter. Finally, we will consider their role in cancer and their exploitation in current chemotherapeutic approaches.
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12
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Hanawalt P, Sweasy J. Mechanistic understanding of cellular responses to genomic stress. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:25-33. [PMID: 31793074 DOI: 10.1002/em.22349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Within the past half century we have learned of multiple pathways for repairing damaged DNA, based upon the intrinsic redundancy of information in its complementary double strands. Mechanistic details of these pathways have provided insights into environmental and endogenous threats to genomic stability. Studies on bacterial responses to ultraviolet light led to the discovery of excision repair, as well as the inducible SOS response to DNA damage. Similar responses in eukaryotes promote upregulation of error-prone translesion DNA polymerases. Recent advances in this burgeoning field include duplex DNA sequencing to provide strikingly accurate profiling of mutational signatures, analyses of gene expression patterns in single cells, CRISPR/Cas9 to generate changes at precise genomic positions, novel roles for RNA in gene expression and DNA repair, phase-separated aqueous environments for specialized cellular transactions, and DNA lesions as epigenetic signals for gene expression. The Environmental Mutagenesis and Genomics Society (EMGS), through the broad range of expertise in its membership, stands at the crossroad of basic understanding of mechanisms for genomic maintenance and the field of genetic toxicology, with the need for regulation of exposures to toxic substances. Our future challenges include devising strategies and technologies to identify individuals who are susceptible to specific genomic stresses, along with basic research on the underlying mechanisms of cellular stress responses that promote disease-causing mutations. As the science moves forward it should also be a responsibility for the EMGS to expand its outreach programs for the enlightenment and benefit of all humans and the biosphere. Environ. Mol. Mutagen. 61:25-33, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Philip Hanawalt
- Department of Biology, Stanford University, Stanford, California
| | - Joann Sweasy
- University of Arizona Cancer Center, Tucson, Arizona
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13
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Saha A, Nanavaty VP, Li B. Telomere and Subtelomere R-loops and Antigenic Variation in Trypanosomes. J Mol Biol 2019; 432:4167-4185. [PMID: 31682833 DOI: 10.1016/j.jmb.2019.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 12/12/2022]
Abstract
Trypanosoma brucei is a kinetoplastid parasite that causes African trypanosomiasis, which is fatal if left untreated. T. brucei regularly switches its major surface antigen, VSG, to evade the host immune responses. VSGs are exclusively expressed from subtelomeric expression sites (ESs) where VSG genes are flanked by upstream 70 bp repeats and downstream telomeric repeats. The telomere downstream of the active VSG is transcribed into a long-noncoding RNA (TERRA), which forms RNA:DNA hybrids (R-loops) with the telomeric DNA. At an elevated level, telomere R-loops cause more telomeric and subtelomeric double-strand breaks (DSBs) and increase VSG switching rate. In addition, stabilized R-loops are observed at the 70 bp repeats and immediately downstream of ES-linked VSGs in RNase H defective cells, which also have an increased amount of subtelomeric DSBs and more frequent VSG switching. Although subtelomere plasticity is expected to be beneficial to antigenic variation, severe defects in subtelomere integrity and stability increase cell lethality. Therefore, regulation of the telomere and 70 bp repeat R-loop levels is important for the balance between antigenic variation and cell fitness in T. brucei. In addition, the high level of the active ES transcription favors accumulation of R-loops at the telomere and 70 bp repeats, providing an intrinsic mechanism for local DSB formation, which is a strong inducer of VSG switching.
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Affiliation(s)
- Arpita Saha
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Science and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
| | - Vishal P Nanavaty
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Science and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
| | - Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Science and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA.
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