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Chudy P, Kochan J, Wawro M, Nguyen P, Gorczyca M, Varanko A, Retka A, Ghadei SS, Napieralska E, Grochot-Przęczek A, Szade K, Berendes LS, Park J, Sokołowski G, Yu Q, Józkowicz A, Nowak WN, Krzeptowski W. Heme oxygenase-1 protects cells from replication stress. Redox Biol 2024; 75:103247. [PMID: 39047636 DOI: 10.1016/j.redox.2024.103247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Heme oxygenase-1 (HO-1, HMOX1) degrades heme protecting cells from heme-induced oxidative damage. Beyond its well-established cellular functions, heme has emerged as a stabilizer of G-quadruplexes. These secondary DNA structures interfere with DNA replication. We recently revealed that nuclear HO-1 colocalizes with DNA G-quadruplexes and promotes their removal. Here, we investigate whether HO-1 safeguards cells against replication stress. Experiments were conducted in control and HMOX1-deficient HEK293T cell lines. Immunostaining unveiled that DNA G-quadruplexes accumulated in the absence of HO-1, the effect that was further enhanced in response to δ-aminolevulinic acid (ALA), a substrate in heme synthesis. This was associated with replication stress, as evidenced by an elevated proportion of stalled forks analyzed by fiber assay. We observed the same effects in hematopoietic stem cells isolated from Hmox1 knockout mice and in a lymphoblastoid cell line from an HMOX1-deficient patient. Interestingly, in the absence of HO-1, the speed of fork progression was higher, and the response to DNA conformational hindrance less stringent, indicating dysfunction of the PARP1-p53-p21 axis. PARP1 activity was not decreased in the absence of HO-1. Instead, we observed that HO-1 deficiency impairs the nuclear import and accumulation of p53, an effect dependent on the removal of excess heme. We also demonstrated that administering ALA is a more specific method for increasing intracellular free heme compared to treatment with hemin, which in turn induces strong lipid peroxidation. Our results indicate that protection against replication stress is a universal feature of HO-1, presumably contributing to its widely recognized cytoprotective activity.
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Affiliation(s)
- Patryk Chudy
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mateusz Wawro
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Phu Nguyen
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Monika Gorczyca
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aliaksandra Varanko
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aleksandra Retka
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Swati Sweta Ghadei
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Emilija Napieralska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Anna Grochot-Przęczek
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Szade
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Lea-Sophie Berendes
- Department of General Pediatrics, University Hospital Münster, Münster, Germany
| | - Julien Park
- Department of General Pediatrics, University Hospital Münster, Münster, Germany
| | - Grzegorz Sokołowski
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Qiuliyang Yu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, China
| | - Alicja Józkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Witold N Nowak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; August Chełkowski Institute of Physics, Faculty of Science and Technology, University of Silesia, Chorzów, Poland.
| | - Wojciech Krzeptowski
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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Han ZQ, Wen LN. Application of G-quadruplex targets in gastrointestinal cancers: Advancements, challenges and prospects. World J Gastrointest Oncol 2023; 15:1149-1173. [PMID: 37546556 PMCID: PMC10401460 DOI: 10.4251/wjgo.v15.i7.1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 07/12/2023] Open
Abstract
Genomic instability and inflammation are considered to be two enabling characteristics that support cancer development and progression. G-quadruplex structure is a key element that contributes to genomic instability and inflammation. G-quadruplexes were once regarded as simply an obstacle that can block the transcription of oncogenes. A ligand targeting G-quadruplexes was found to have anticancer activity, making G-quadruplexes potential anticancer targets. However, further investigation has revealed that G-quadruplexes are widely distributed throughout the human genome and have many functions, such as regulating DNA replication, DNA repair, transcription, translation, epigenetics, and inflammatory response. G-quadruplexes play double regulatory roles in transcription and translation. In this review, we focus on G-quadruplexes as novel targets for the treatment of gastrointestinal cancers. We summarize the application basis of G-quadruplexes in gastrointestinal cancers, including their distribution sites, structural characteristics, and physiological functions. We describe the current status of applications for the treatment of esophageal cancer, pancreatic cancer, hepatocellular carcinoma, gastric cancer, colorectal cancer, and gastrointestinal stromal tumors, as well as the associated challenges. Finally, we review the prospective clinical applications of G-quadruplex targets, providing references for targeted treatment strategies in gastrointestinal cancers.
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Affiliation(s)
- Zong-Qiang Han
- Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing 102211, China
| | - Li-Na Wen
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
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Sui Y, Liu F, Zheng S, Liu X, Sun P, Yao C, Zhang Y, Gao H, Gao X, Liu J. G-quadruplexes folding mediates downregulation of PBX1 expression in melanoma. Signal Transduct Target Ther 2023; 8:12. [PMID: 36604432 PMCID: PMC9816092 DOI: 10.1038/s41392-022-01222-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/19/2022] [Accepted: 10/09/2022] [Indexed: 01/07/2023] Open
Affiliation(s)
- Yutong Sui
- grid.64924.3d0000 0004 1760 5735Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Feilin Liu
- grid.452829.00000000417660726The Second Hospital of Jilin University, Changchun, China
| | - Song Zheng
- grid.412636.40000 0004 1757 9485Department of Dermatology, The First Hospital of China Medical University, Key Laboratory of Immunodermatology, Ministry of Education/Public Health, Shenyang, China
| | - Xiaomei Liu
- grid.64924.3d0000 0004 1760 5735Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Pingli Sun
- grid.452829.00000000417660726The Second Hospital of Jilin University, Changchun, China
| | - Chunli Yao
- grid.452829.00000000417660726The Second Hospital of Jilin University, Changchun, China
| | - Yingyao Zhang
- grid.64924.3d0000 0004 1760 5735Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Hongwen Gao
- The Second Hospital of Jilin University, Changchun, China.
| | - Xinghua Gao
- Department of Dermatology, The First Hospital of China Medical University, Key Laboratory of Immunodermatology, Ministry of Education/Public Health, Shenyang, China.
| | - Jinyu Liu
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China.
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Sterrenberg JN, Folkerts ML, Rangel V, Lee SE, Pannunzio NR. Diversity upon diversity: linking DNA double-strand break repair to blood cancer health disparities. Trends Cancer 2022; 8:328-343. [PMID: 35094960 PMCID: PMC9248772 DOI: 10.1016/j.trecan.2022.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/20/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022]
Abstract
Chromosomal translocations arising from aberrant repair of multiple DNA double-strand breaks (DSBs) are a defining characteristic of many cancers. DSBs are an essential part of physiological processes in antibody-producing B cells. The B cell environment is poised to generate genome instability leading to translocations relevant to the pathology of blood cancers. These are a diverse set of cancers, but limited data from under-represented groups have pointed to health disparities associated with each. We focus on the DSBs that occur in developing B cells and propose the most likely mechanism behind the formation of translocations. We also highlight specific cancers in which these rearrangements occur and address the growing concern of health disparities associated with them.
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Kosiol N, Juranek S, Brossart P, Heine A, Paeschke K. G-quadruplexes: a promising target for cancer therapy. Mol Cancer 2021; 20:40. [PMID: 33632214 PMCID: PMC7905668 DOI: 10.1186/s12943-021-01328-4] [Citation(s) in RCA: 215] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
DNA and RNA can fold into a variety of alternative conformations. In recent years, a particular nucleic acid structure was discussed to play a role in malignant transformation and cancer development. This structure is called a G-quadruplex (G4). G4 structure formation can drive genome instability by creating mutations, deletions and stimulating recombination events. The importance of G4 structures in the characterization of malignant cells was currently demonstrated in breast cancer samples. In this analysis a correlation between G4 structure formation and an increased intratumor heterogeneity was identified. This suggests that G4 structures might allow breast cancer stratification and supports the identification of new personalized treatment options. Because of the stability of G4 structures and their presence within most human oncogenic promoters and at telomeres, G4 structures are currently tested as a therapeutic target to downregulate transcription or to block telomere elongation in cancer cells. To date, different chemical molecules (G4 ligands) have been developed that aim to target G4 structures. In this review we discuss and compare G4 function and relevance for therapeutic approaches and their impact on cancer development for three cancer entities, which differ significantly in their amount and type of mutations: pancreatic cancer, leukemia and malignant melanoma. G4 structures might present a promising new strategy to individually target tumor cells and could support personalized treatment approaches in the future.
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Affiliation(s)
- Nils Kosiol
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Stefan Juranek
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Peter Brossart
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Annkristin Heine
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany.
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Singh S, Berroyer A, Kim M, Kim N. Yeast Nucleolin Nsr1 Impedes Replication and Elevates Genome Instability at an Actively Transcribed Guanine-Rich G4 DNA-Forming Sequence. Genetics 2020; 216:1023-1037. [PMID: 33106247 PMCID: PMC7768239 DOI: 10.1534/genetics.120.303736] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/21/2020] [Indexed: 12/01/2022] Open
Abstract
A significant increase in genome instability is associated with the conformational shift of a guanine-run-containing DNA strand into the four-stranded G-quadruplex (G4) DNA. The mechanism underlying the recombination and genome rearrangements following the formation of G4 DNA in vivo has been difficult to elucidate but has become better clarified by the identification and functional characterization of several key G4 DNA-binding proteins. Mammalian nucleolin (NCL) is a highly specific G4 DNA-binding protein with a well-defined role in the transcriptional regulation of genes with associated G4 DNA-forming sequence motifs at their promoters. The consequence of the in vivo interaction between G4 DNA and nucleolin in respect to the genome instability has not been previously investigated. We show here that the yeast nucleolin Nsr1 is enriched at a G4 DNA-forming sequence in vivo and is a major factor in inducing the genome instability associated with the cotranscriptionally formed G4 DNA in the yeast genome. We also show that Nsr1 results in impeding replication past such a G4 DNA-forming sequence. The G4-associated genome instability and the G4 DNA-binding in vivo require the arginine-glycine-glycine (RGG) repeats located at the C-terminus of the Nsr1 protein. Nsr1 with the deletion of RGG domain supports normal cell growth and is sufficient for its pre-rRNA processing function. However, the truncation of the RGG domain of Nsr1 significantly weakens its interaction with G4 DNA in vivo and restores unhindered replication, overall resulting in a sharp reduction in the genome instability associated with a guanine-rich G4 DNA-forming sequence. Our data suggest that the interaction between Nsr1 with the intact RGG repeats and G4 DNA impairs genome stability by precluding the access of G4-resolving proteins and impeding replication.
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Affiliation(s)
- Shivani Singh
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Alexandra Berroyer
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Minseon Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
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7
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Williams JD, Houserova D, Johnson BR, Dyniewski B, Berroyer A, French H, Barchie AA, Bilbrey DD, Demeis JD, Ghee KR, Hughes AG, Kreitz NW, McInnis CH, Pudner SC, Reeves MN, Stahly AN, Turcu A, Watters BC, Daly GT, Langley RJ, Gillespie MN, Prakash A, Larson ED, Kasukurthi MV, Huang J, Jinks-Robertson S, Borchert GM. Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. Nucleic Acids Res 2020; 48:5907-5925. [PMID: 32383760 PMCID: PMC7293029 DOI: 10.1093/nar/gkaa357] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 12/27/2022] Open
Abstract
Mammalian antibody switch regions (∼1500 bp) are composed of a series of closely neighboring G4-capable sequences. Whereas numerous structural and genome-wide analyses of roles for minimal G4s in transcriptional regulation have been reported, Long G4-capable regions (LG4s)-like those at antibody switch regions-remain virtually unexplored. Using a novel computational approach we have identified 301 LG4s in the human genome and find LG4s prone to mutation and significantly associated with chromosomal rearrangements in malignancy. Strikingly, 217 LG4s overlap annotated enhancers, and we find the promoters regulated by these enhancers markedly enriched in G4-capable sequences suggesting G4s facilitate promoter-enhancer interactions. Finally, and much to our surprise, we also find single-stranded loops of minimal G4s within individual LG4 loci are frequently highly complementary to one another with 178 LG4 loci averaging >35 internal loop:loop complements of >8 bp. As such, we hypothesized (then experimentally confirmed) that G4 loops within individual LG4 loci directly basepair with one another (similar to characterized stem-loop kissing interactions) forming a hitherto undescribed, higher-order, G4-based secondary structure we term a 'G4 Kiss or G4K'. In conclusion, LG4s adopt novel, higher-order, composite G4 structures directly contributing to the inherent instability, regulatory capacity, and maintenance of these conspicuous genomic regions.
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Affiliation(s)
- Jonathan D Williams
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Bradley R Johnson
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Brad Dyniewski
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Alexandra Berroyer
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Hannah French
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Addison A Barchie
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Dakota D Bilbrey
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Jeffrey D Demeis
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Kanesha R Ghee
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alexandra G Hughes
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Naden W Kreitz
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Cameron H McInnis
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Susanna C Pudner
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Monica N Reeves
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Ashlyn N Stahly
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Ana Turcu
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Brianna C Watters
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Grant T Daly
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Raymond J Langley
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Mark N Gillespie
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mitchell Cancer Institute, Mobile, AL 36688, USA
| | - Erik D Larson
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
- Department of Biomedical Sciences, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, MI 49007, USA
| | | | - Jingshan Huang
- School of Computing, University of South Alabama, Mobile, AL 36688, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Glen M Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
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8
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Berroyer A, Alvarado G, Larson ED. Response of Sulfolobus solfataricus Dpo4 polymerase in vitro to a DNA G-quadruplex. Mutagenesis 2020; 34:289-297. [PMID: 31169295 DOI: 10.1093/mutage/gez010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/06/2019] [Indexed: 12/12/2022] Open
Abstract
Repetitive DNA sequences support the formation of structures that can interrupt replication and repair, leading to breaks and mutagenesis. One particularly stable structure is G-quadruplex (G4) DNA, which is four-stranded and formed from tandemly repetitive guanine bases. When folded within a template, G4 interferes with DNA synthesis. Similar to non-duplex structures, DNA base lesions can also halt an advancing replication fork, but the Y-family polymerases solve this problem by bypassing the damage. In order to better understand how guanine-rich DNA is replicated, we have investigated the activity of the model Y-family polymerase, Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), on guanine-rich templates in vitro. We find that Dpo4 progression on templates containing either a single GC-rich hairpin or a G4 DNA structure is greatly reduced and synthesis stalls at the structure. Human polymerase eta (hPol eta) showed the same pattern of stalling at G4; however, and in contrast to Klenow, hPol eta and Dpo4 partially synthesise into the guanine repeat. Substitution of the nucleotide selectivity residue in Dpo4 with alanine permitted ribonucleotide incorporation on unstructured templates, but this further reduced the ability of Dpo4 to synthesise across from the guanine repeats. The advancement of Dpo4 on G4 templates was highest when the reaction was supplied with only deoxycytidine triphosphate, suggesting that high-fidelity synthesis is favoured over misincorporation. Our results are consistent with a model where the Y-family polymerases pause upon encountering G4 structures but have an ability to negotiate some synthesis through tetrad-associated guanines. This suggests that the Y-family polymerases reduce mutagenesis by catalysing the accurate replication of repetitive DNA sequences, but most likely in concert with additional replication and structure resolution activities.
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Affiliation(s)
- Alexandra Berroyer
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Gloria Alvarado
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Erik D Larson
- School of Biological Sciences, Illinois State University, Normal, IL, USA
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9
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Kim N. The Interplay between G-quadruplex and Transcription. Curr Med Chem 2019; 26:2898-2917. [PMID: 29284393 PMCID: PMC6026074 DOI: 10.2174/0929867325666171229132619] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/22/2017] [Accepted: 12/21/2017] [Indexed: 12/25/2022]
Abstract
G4 DNA is a non-canonical DNA structure consisting of a stacked array of Gquartets held together by base pairing between guanine bases. The formation of G4 DNA requires a cluster of guanine-runs within a strand of DNA. Even though the chemistry of this remarkable DNA structure has been under investigation for decades, evidence supporting the biological relevance of G4 DNA has only begun to emerge and point to very important and conserved biological functions. This review will specifically focus on the interplay between transcription and G4 DNA and discuss two alternative but interconnected perspectives. The first part of the review will describe the evidence substantiating the intriguing idea that a shift in DNA structural conformation could be another layer of non-genetic or epigenetic regulator of gene expression and thereby an important determinant of cell fate. The second part will describe the recent genetic studies showing that those genomic loci containing G4 DNA-forming guanine-rich sequences are potential hotspots of genome instability and that the level and orientation of transcription is critical in the materialization of genome instability associated with these sequences.
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Affiliation(s)
- Nayun Kim
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston; The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
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10
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Saranathan N, Biswas B, Patra A, Vivekanandan P. G-quadruplexes may determine the landscape of recombination in HSV-1. BMC Genomics 2019; 20:382. [PMID: 31096907 PMCID: PMC6524338 DOI: 10.1186/s12864-019-5731-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Background Several lines of evidence suggest that recombination plays a central role in replication and evolution of herpes simplex virus-1 (HSV-1). G-quadruplex (G4)-motifs have been linked to recombination events in human and microbial genomes, but their role in recombination has not been studied in DNA viruses. Results The availability of near full-length sequences from 40 HSV-1 recombinant strains with exact position of the recombination breakpoints provided us with a unique opportunity to investigate the role of G4-motifs in recombination among herpes viruses. We mapped the G4-motifs in the parental and all the 40 recombinant strains. Interestingly, the genome-wide distribution of breakpoints closely mirrors the G4 densities in the HSV-1 genome; regions of the genome with higher G4 densities had higher number of recombination breakpoints. Biophysical characterization of oligonucleotides from a subset of predicted G4-motifs confirmed the formation of G-quadruplex structures. Our analysis also reveals that G4-motifs are enriched in regions flanking the recombination breakpoints. Interestingly, about 11% of breakpoints lie within a G4-motif, making these DNA secondary structures hotspots for recombination in the HSV-1 genome. Breakpoints within G4-motifs predominantly lie within G4-clusters rather than individual G4-motifs. Of note, we identified the terminal guanosine of G4-clusters at the boundaries of the UL (unique long) region on either side of the OriL (origin of replication within UL) represented the commonest breakpoint among the HSV-1 recombinants. Conclusion Our findings suggest a correlation between the HSV-1 recombination landscape and the distribution of G4-motifs and G4-clusters, with possible implications for the evolution of DNA viruses. Electronic supplementary material The online version of this article (10.1186/s12864-019-5731-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Banhi Biswas
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Anupam Patra
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
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11
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Pannunzio NR, Lieber MR. Concept of DNA Lesion Longevity and Chromosomal Translocations. Trends Biochem Sci 2018; 43:490-498. [PMID: 29735400 DOI: 10.1016/j.tibs.2018.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/07/2018] [Accepted: 04/08/2018] [Indexed: 01/11/2023]
Abstract
A subset of chromosomal translocations related to B cell malignancy in human patients arises due to DNA breaks occurring within defined 20-600 base pair (bp) zones. Several factors influence the breakage rate at these sites including transcription, DNA sequence, and topological tension. These factors favor non-B DNA structures that permit formation of transient single-stranded DNA (ssDNA), making the DNA more vulnerable to agents such as the enzyme activation-induced cytidine deaminase (AID) and reactive oxygen species (ROS). Certain DNA lesions created during the ssDNA state persist after the DNA resumes its normal duplex structure. We propose that factors favoring both formation of transient ssDNA and persistent DNA lesions are key in determining the DNA breakage mechanism.
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Affiliation(s)
- Nicholas R Pannunzio
- University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Michael R Lieber
- University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA; Department of Molecular Microbiology and Immunology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA; Department of Biochemistry and Molecular Biology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA; Section of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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12
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Abstract
Topoisomerases manage the torsional stress associated with the separation of DNA strands during transcription and DNA replication. Eukaryotic Topoisomerase I (Top1) is a Type IB enzyme that nicks and rejoins only one strand of duplex DNA, and it is especially important during transcription. By resolving transcription-associated torsional stress, Top1 reduces the accumulation of genome-destabilizing R-loops and non-B DNA structures. The DNA nicking activity of Top1, however, can also initiate genome instability in the form of illegitimate recombination, homologous recombination and mutagenesis. In this review, we focus on the diverse, and often opposing, roles of Top1 in regulating eukaryotic genome stability.
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13
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Gadaleta MC, Noguchi E. Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome. Genes (Basel) 2017; 8:genes8030098. [PMID: 28272375 PMCID: PMC5368702 DOI: 10.3390/genes8030098] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/03/2017] [Indexed: 02/07/2023] Open
Abstract
All living organisms need to duplicate their genetic information while protecting it from unwanted mutations, which can lead to genetic disorders and cancer development. Inaccuracies during DNA replication are the major cause of genomic instability, as replication forks are prone to stalling and collapse, resulting in DNA damage. The presence of exogenous DNA damaging agents as well as endogenous difficult-to-replicate DNA regions containing DNA–protein complexes, repetitive DNA, secondary DNA structures, or transcribing RNA polymerases, increases the risk of genomic instability and thus threatens cell survival. Therefore, understanding the cellular mechanisms required to preserve the genetic information during S phase is of paramount importance. In this review, we will discuss our current understanding of how cells cope with these natural impediments in order to prevent DNA damage and genomic instability during DNA replication.
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Affiliation(s)
- Mariana C Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
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14
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Holton NW, Larson ED. G-quadruplex DNA structures can interfere with uracil glycosylase activity in vitro. Mutagenesis 2015; 31:385-92. [PMID: 26671821 DOI: 10.1093/mutage/gev083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Genome sequences that contain tandem repeats of guanine can form stable four-stranded structures known as G-quadruplex, or G4 DNA. While the molecular mechanisms are not fully defined, such guanine-rich loci are prone to mutagenesis and recombination. Various repair pathways function to reduce the potential for genome instability by correcting base damage and replication errors; however, it is not yet fully defined how well these processes function at G4 DNA. One frequent form of base damage occurs from cytidine deamination, resulting in deoxyuracil and UG mismatches. In duplex and single-stranded DNA, uracil bases are recognised and excised by uracil glycosylases. Here, we tested the efficiency of uracil glycosylase activity in vitro on uracil bases located directly adjacent to guanine repeats and G4 DNA. We show that uracil excision by bacterial UDG and human hUNG2 is reduced at uracils positioned directly 5' or 3' of a guanine tetrad. Control reactions using oligonucleotides disrupted for G4 formation or reaction conditions that do not favour G4 formation resulted in full uracil excision activity. Based on these in vitro results, we suggest that folding of guanine-rich DNA into G4 DNA results in a DNA conformation that is resistant to uracil glycosylase-initiated repair and this has the potential to increase the risk of instability at guanine repeats in the genome.
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Affiliation(s)
- Nate W Holton
- School of Biological Sciences, Illinois State University, Campus Box 4120, Normal, IL 61790-4120, USA
| | - Erik D Larson
- School of Biological Sciences, Illinois State University, Campus Box 4120, Normal, IL 61790-4120, USA
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15
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Kamat MA, Bacolla A, Cooper DN, Chuzhanova N. A Role for Non-B DNA Forming Sequences in Mediating Microlesions Causing Human Inherited Disease. Hum Mutat 2015; 37:65-73. [PMID: 26466920 DOI: 10.1002/humu.22917] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/22/2015] [Indexed: 12/25/2022]
Abstract
Missense/nonsense mutations and microdeletions/microinsertions (<21 bp) represent ∼ 76% of all mutations causing human inherited disease, and their occurrence has been associated with sequence motifs (direct, inverted, and mirror repeats; G-quartets) capable of adopting non-B DNA structures. We found that a significant proportion (∼ 21%) of both microdeletions and microinsertions occur within direct repeats, and are explicable by slipped misalignment. A novel mutational mechanism, DNA triplex formation followed by DNA repair, may explain ∼ 5% of microdeletions and microinsertions at mirror repeats. Further, G-quartets, direct, and inverted repeats also appear to play a prominent role in mediating missense mutations, whereas only direct and inverted repeats mediate nonsense mutations. We suggest a mutational mechanism involving slipped strand mispairing, slipped structure formation, and DNA repair, to explain ∼ 15% of missense and ∼ 12% of nonsense mutations yielding perfect direct repeats from imperfect repeats, or the extension of existing direct repeats. Similar proportions of missense and nonsense mutations were explicable by hairpin/loop formation and DNA repair, yielding perfect inverted repeats from imperfect repeats. We also propose a model for single base-pair substitution based on one-electron oxidation reactions at G-quadruplex DNA. Overall, the proposed mechanisms provide support for a role for non-B DNA structures in human gene mutagenesis.
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Affiliation(s)
- Mihir Anant Kamat
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, UK
| | - Albino Bacolla
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Nadia Chuzhanova
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, UK
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16
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Yadav P, Owiti N, Kim N. The role of topoisomerase I in suppressing genome instability associated with a highly transcribed guanine-rich sequence is not restricted to preventing RNA:DNA hybrid accumulation. Nucleic Acids Res 2015; 44:718-29. [PMID: 26527723 PMCID: PMC4737143 DOI: 10.1093/nar/gkv1152] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/19/2015] [Indexed: 11/21/2022] Open
Abstract
Highly transcribed guanine-run containing sequences, in Saccharomyces cerevisiae, become unstable when topoisomerase I (Top1) is disrupted. Topological changes, such as the formation of extended RNA:DNA hybrids or R-loops or non-canonical DNA structures including G-quadruplexes has been proposed as the major underlying cause of the transcription-linked genome instability. Here, we report that R-loop accumulation at a guanine-rich sequence, which is capable of assembling into the four-stranded G4 DNA structure, is dependent on the level and the orientation of transcription. In the absence of Top1 or RNase Hs, R-loops accumulated to substantially higher extent when guanine-runs were located on the non-transcribed strand. This coincides with the orientation where higher genome instability was observed. However, we further report that there are significant differences between the disruption of RNase Hs and Top1 in regards to the orientation-specific elevation in genome instability at the guanine-rich sequence. Additionally, genome instability in Top1-deficient yeasts is not completely suppressed by removal of negative supercoils and further aggravated by expression of mutant Top1. Together, our data provide a strong support for a function of Top1 in suppressing genome instability at the guanine-run containing sequence that goes beyond preventing the transcription-associated RNA:DNA hybrid formation.
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Affiliation(s)
- Puja Yadav
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Norah Owiti
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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