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Zhang X, Xu H, Sun R, Xiong G, Shi X. An insight into G-quadruplexes: Identification and potential therapeutic targets in livestock viruses. Eur J Med Chem 2024; 279:116848. [PMID: 39255642 DOI: 10.1016/j.ejmech.2024.116848] [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: 06/26/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/12/2024]
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that involve in the regulation of some key biological processes, such as replication, transcription, and translation. G4s have been extensively described in the genomes of human and related diseases. In recent years, G4s were identified in several livestock viruses, including those of the emerging epidemics, like Nipah virus (NiV). Since their discovery, G4s have been developed as the potential antiviral targets, and the employment of G4 ligands or interacting proteins has helped to expound the viral infectivity and pathogenesis through G4-mediated mechanisms, and highlight the potential as therapeutic approaches. However, the comprehensively studies of G4s in livestock viruses have not been summarized. This review delves into the reported literatures of G4s in livestock viruses, particular focus on the presence, biophysical identification, and possible function of G4s in viral genome, summarizing the G4 ligands, interacted proteins and aptamers on antiviral applications. The strengths and the challenges of G4 targeting in this field are also discussed. Therefore, this review will shed new light on the future development of highly potent and targeting antiviral therapy.
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Affiliation(s)
- Xianpeng Zhang
- Laboratory of Pesticide Toxicology and Pesticide Efficient Utilization, College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi Province, 330045, PR China; Key Laboratory of Crop Physiology Ecology & Genetic Breeding, Jiangxi Agriculture University, Nanchang, Jiangxi Province, 330045, PR China
| | - Hongyu Xu
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang, Jiangxi Province, 330045, PR China
| | - Ranran Sun
- Laboratory of Pesticide Toxicology and Pesticide Efficient Utilization, College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi Province, 330045, PR China
| | - Guihong Xiong
- Key Laboratory of Crop Physiology Ecology & Genetic Breeding, Jiangxi Agriculture University, Nanchang, Jiangxi Province, 330045, PR China
| | - Xugen Shi
- Laboratory of Pesticide Toxicology and Pesticide Efficient Utilization, College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi Province, 330045, PR China; Key Laboratory of Crop Physiology Ecology & Genetic Breeding, Jiangxi Agriculture University, Nanchang, Jiangxi Province, 330045, PR China; Jiangxi Xiajiang Dry Direct-seeded Rice Science and Technology Backyard, Ji'an, Jiangxi Province, 331400, PR China.
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2
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Chen Y, Long J, Wu S, Wei Y, Yan F, Li Q, Yan J, Zhang N, Xu W. Disruption of a DNA G-quadruplex causes a gain-of-function SCL45A1 variant relevant to developmental disorders. Acta Biochim Biophys Sin (Shanghai) 2024; 56:709-716. [PMID: 38655615 PMCID: PMC11177108 DOI: 10.3724/abbs.2024053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/04/2024] [Indexed: 04/26/2024] Open
Abstract
SLC45A1 encodes a glucose transporter protein highly expressed in the brain. Mutations in SLC45A1 may lead to neurological diseases and developmental disorders, but its exact role is poorly understood. DNA G-quadruplexes (DNA G4s) are stable structures formed by four guanine bases and play a role in gene regulation and genomic stability. Changes in DNA G4s may affect brain development and function. The mechanism linking alterations in DNA G-quadruplex structures to SLC45A1 pathogenicity remains unknown. In this study, we identify a functional DNA G-quadruplex and its key binding site on SLC45A1 (NM_001080397.3: exon 2: c.449 G>A: p.R150K). This variant results in the upregulation of mRNA and protein expression, which may lead to intellectual developmental disorder with neuropsychiatric features. Mechanistically, the mutation is found to disrupt DNA G-quadruplex structures on SLC45A1, leading to transcriptional enhancement and a gain-of-function mutation, which further causes increased expression and function of the SLC45A1 protein. The identification of the functional DNA G-quadruplex and its effects on DNA G4s may provide new insights into the genetic basis of SLC45A1 pathogenicity and highlight the importance of DNA G4s of SLC45A1 in regulating gene expression and brain development.
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Affiliation(s)
- Yuxi Chen
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
- West China School of PharmacySichuan UniversityChengdu610041China
| | - Jiang Long
- The Mental Health Centre and the Psychiatric LaboratoryWest China HospitalSichuan UniversityChengdu610041China
| | - Sixian Wu
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Yazhen Wei
- West China School of PharmacySichuan UniversityChengdu610041China
| | - Fei Yan
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Qing Li
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Jierui Yan
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Nannan Zhang
- National Centre for Birth Defect MonitoringKey Laboratory of Birth Defects and Related Diseases of Women and ChildrenMinistry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Wenming Xu
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
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3
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Wei D, Mai Z, Li X, Yu T, Li J. Poly(G) 7 box: a functional element of mammalian 18S rRNA involved in translation. RNA Biol 2024; 21:8-18. [PMID: 39233564 PMCID: PMC11382726 DOI: 10.1080/15476286.2024.2399310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/20/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024] Open
Abstract
In eukaryotes, the ribosomal small subunit (40S) is composed of 18S rRNA and 33 ribosomal proteins. 18S rRNA has a special secondary structure and is an indispensable part of the translation process. Herein, a special sequence located in mammalian 18S rRNA named Poly(G)7box, which is composed of seven guanines, was found. Poly(G)7 can form a special and stable secondary structure by binding to the translation elongation factor subunit eEF1D and the ribosomal protein RPL32. Poly(G)7box was transfected into cells, and the translation efficiency of cells was inhibited. We believe that Poly(G)7box is an important translation-related functional element located on mammalian 18S rRNA, meanwhile the Poly(G)7 located on mRNA 5' and 3' box does not affect mRNA translation.
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Affiliation(s)
- Dahao Wei
- School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zhangyu Mai
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xinan Li
- Laboratory of Oncology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Tianli Yu
- Laboratory of Oncology and Immunology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiangchao Li
- Laboratory of Oncology and Immunology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
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4
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Lorenzatti A, Piga EJ, Gismondi M, Binolfi A, Margarit E, Calcaterra N, Armas P. Genetic variations in G-quadruplex forming sequences affect the transcription of human disease-related genes. Nucleic Acids Res 2023; 51:12124-12139. [PMID: 37930868 PMCID: PMC10711447 DOI: 10.1093/nar/gkad948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023] Open
Abstract
Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4s). G4s folded in proximal promoter regions (PPR) are associated either with positive or negative transcriptional regulation. Given that single nucleotide variants (SNVs) affecting G4 folding (G4-Vars) may alter gene transcription, and that SNVs are associated with the human diseases' onset, we undertook a novel comprehensive study of the G4-Vars genome-wide (G4-variome) to find disease-associated G4-Vars located into PPRs. We developed a bioinformatics strategy to find disease-related SNVs located into PPRs simultaneously overlapping with putative G4-forming sequences (PQSs). We studied five G4-Vars disturbing in vitro the folding and stability of the G4s located into PPRs, which had been formerly associated with sporadic Alzheimer's disease (GRIN2B), a severe familiar coagulopathy (F7), atopic dermatitis (CSF2), myocardial infarction (SIRT1) and deafness (LHFPL5). Results obtained in cultured cells for these five G4-Vars suggest that the changes in the G4s affect the transcription, potentially contributing to the development of the mentioned diseases. Collectively, data reinforce the general idea that G4-Vars may impact on the different susceptibilities to human genetic diseases' onset, and could be novel targets for diagnosis and drug design in precision medicine.
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Affiliation(s)
- Agustín Lorenzatti
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Ernesto J Piga
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Mauro Gismondi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario, Santa Fe, Argentina
| | - Andrés Binolfi
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Ocampo y Esmeralda, Rosario S200EZP, Santa Fe, Argentina
| | - Ezequiel Margarit
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario, Santa Fe, Argentina
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
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5
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Ferret L, Alvarez-Valadez K, Rivière J, Muller A, Bohálová N, Yu L, Guittat L, Brázda V, Kroemer G, Mergny JL, Djavaheri-Mergny M. G-quadruplex ligands as potent regulators of lysosomes. Autophagy 2023; 19:1901-1915. [PMID: 36740766 PMCID: PMC10283436 DOI: 10.1080/15548627.2023.2170071] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 02/07/2023] Open
Abstract
Guanine-quadruplex structures (G4) are unusual nucleic acid conformations formed by guanine-rich DNA and RNA sequences and known to control gene expression mechanisms, from transcription to protein synthesis. So far, a number of molecules that recognize G4 have been developed for potential therapeutic applications in human pathologies, including cancer and infectious diseases. These molecules are called G4 ligands. When the biological effects of G4 ligands are studied, the analysis is often limited to nucleic acid targets. However, recent evidence indicates that G4 ligands may target other cellular components and compartments such as lysosomes and mitochondria. Here, we summarize our current knowledge of the regulation of lysosome by G4 ligands, underlying their potential functional impact on lysosome biology and autophagic flux, as well as on the transcriptional regulation of lysosomal genes. We outline the consequences of these effects on cell fate decisions and we systematically analyzed G4-prone sequences within the promoter of 435 lysosome-related genes. Finally, we propose some hypotheses about the mechanisms involved in the regulation of lysosomes by G4 ligands.
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Affiliation(s)
- Lucille Ferret
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe labellisée par la Ligue contre le Cancer, Institut universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Karla Alvarez-Valadez
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe labellisée par la Ligue contre le Cancer, Institut universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Jennifer Rivière
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Alexandra Muller
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe labellisée par la Ligue contre le Cancer, Institut universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Natalia Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
| | - Luo Yu
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128Palaiseau, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, Orsay, France
| | - Lionel Guittat
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128Palaiseau, France
- UFR SMBH, Université Sorbonne Paris Nord, Bobigny, France
| | - Vaclav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe labellisée par la Ligue contre le Cancer, Institut universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Jean-Louis Mergny
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128Palaiseau, France
| | - Mojgan Djavaheri-Mergny
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe labellisée par la Ligue contre le Cancer, Institut universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
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6
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Abdallah S, Jampy A, Moison D, Wieckowski M, Messiaen S, Martini E, Campalans A, Radicella JP, Rouiller-Fabre V, Livera G, Guerquin MJ. Foetal exposure to the bisphenols BADGE and BPAF impairs meiosis through DNA oxidation in mouse ovaries. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120791. [PMID: 36464114 DOI: 10.1016/j.envpol.2022.120791] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/16/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Many endocrine disruptors have been proven to impair the meiotic process which is required for the production of healthy gametes. Bisphenol A is emblematic of such disruptors, as it impairs meiotic prophase I and causes oocyte aneuploidy following in utero exposure. However, the mechanisms underlying these deleterious effects remain poorly understood. Furthermore, the increasing use of BPA alternatives raises concerns for public health. Here, we investigated the effects of foetal exposure to two BPA alternatives, bisphenol A Diglycidyl Ether (BADGE) and bisphenol AF (BPAF), on oogenesis in mice. These compounds delay meiosis initiation, increase the number of MLH1 foci per cell and induce oocyte aneuploidy. We further demonstrate that these defects are accompanied by changes in gene expression in foetal premeiotic germ cells and aberrant mRNA splicing of meiotic genes. We observed an increase in DNA oxidation after exposure to BPA alternatives. Specific induction of oxidative DNA damage during foetal germ cell differentiation causes similar defects during oogenesis, as observed in 8-oxoguanine DNA Glycosylase (OGG1)-deficient mice or after in utero exposure to potassium bromate (KBrO3), an inducer of oxidative DNA damage. The supplementation of BPA alternatives with N-acetylcysteine (NAC) counteracts the effects of bisphenols on meiosis. Together, our results propose oxidative DNA lesion as an event that negatively impacts female meiosis with major consequences on oocyte quality. This could be a common mechanism of action for numerous environmental pro-oxidant pollutants, and its discovery, could lead to reconsider the adverse effect of bisphenol mixtures that are simultaneously present in our environment.
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Affiliation(s)
- Sonia Abdallah
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Amandine Jampy
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Delphine Moison
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Margaux Wieckowski
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Sébastien Messiaen
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Emmanuelle Martini
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Anna Campalans
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France
| | - Juan Pablo Radicella
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France
| | - Virginie Rouiller-Fabre
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Gabriel Livera
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France
| | - Marie-Justine Guerquin
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, 92260, Fontenay aux Roses, France; Laboratory of the Development of the Gonads, France.
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7
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Lyu J, Shao R, Kwong Yung PY, Elsässer SJ. Genome-wide mapping of G-quadruplex structures with CUT&Tag. Nucleic Acids Res 2021; 50:e13. [PMID: 34792172 PMCID: PMC8860588 DOI: 10.1093/nar/gkab1073] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 10/01/2021] [Accepted: 10/20/2021] [Indexed: 12/22/2022] Open
Abstract
Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA:RNA hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect gene expression, DNA methylation, replication fork progression and genome stability. When and how G4 structures form and are resolved remains unclear. Here we report the use of Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping native G4 in mammalian cell lines at high resolution and low background. Mild native conditions used for the procedure retain more G4 structures and provide a higher signal-to-noise ratio than ChIP-based methods. We determine the G4 landscape of mouse embryonic stem cells (ESC), observing widespread G4 formation at active promoters, active and poised enhancers. We discover that the presence of G4 motifs and G4 structures distinguishes active and primed enhancers in mouse ESCs. Upon differentiation to neural progenitor cells (NPC), enhancer G4s are lost. Further, performing R-loop CUT&Tag, we demonstrate the genome-wide co-occurrence of single-stranded DNA, G4s and R loops at promoters and enhancers. We confirm that G4 structures exist independent of ongoing transcription, suggesting an intricate relationship between transcription and non-canonical DNA structures.
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Affiliation(s)
- Jing Lyu
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23, 17165 Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden
| | - Rui Shao
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23, 17165 Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden
| | - Philip Yuk Kwong Yung
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23, 17165 Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23, 17165 Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden
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8
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Lyu K, Chow EYC, Mou X, Chan TF, Kwok CK. RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res 2021; 49:5426-5450. [PMID: 33772593 PMCID: PMC8191793 DOI: 10.1093/nar/gkab187] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago. Over the years, these four-stranded structural motifs have been demonstrated to have significant regulatory roles in diverse biological processes, but challenges remain in detecting them globally and reliably. Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently. In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and important functions of rG4 being discovered in vivo across the tree of life, and discuss the key biological questions to be addressed in the near future.
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Affiliation(s)
- Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Eugene Yui-Ching Chow
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xi Mou
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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9
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A Supersymmetry and Quantum Cryptosystem with Path Integral Approach in Biology. Symmetry (Basel) 2020. [DOI: 10.3390/sym12081214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The source of cancerous mutations and the relationship to telomeres is explained in an alternative way. We define the smallest subunit in the genetic code as a loop braid group element. The loop braid group is suitable to be defined as a configuration space in the process of converting the information written in the DNA into the structure of a folded protein. This smallest subunit, or a flying ring in our definition, is a representation of 8-spinor field in the supermanifold of the genetic code. The image of spectral analysis from the tensor correlation of mutation genes as our biological system is produced. We apply the loop braid group for biology and authentication in quantum cryptography to understand the cell cocycle and division mechanism of telomerase aging. A quantum biological cryptosystem is used to detect cancer signatures in 36 genotypes of the bone ALX1 cancer gene. The loop braid group with the RSA algorithm is applied for the calculation of public and private keys as cancer signatures in genes. The key role of this approach is the use of the Chern–Simons current and then the fiber bundle representation of the genetic code that allows a quantization procedure.
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10
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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11
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Stefos GC, Theodorou G, Politis I. DNA G-quadruplexes: functional significance in plant and farm animal science. Anim Biotechnol 2019; 32:262-271. [PMID: 31642375 DOI: 10.1080/10495398.2019.1679823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
G-quadruplexes (G4s) are non-canonical structures that can be formed in DNA and RNA sequences which carry four short runs of guanines. They are distributed in the whole genome but are enriched in gene promoter regions, gene UTRs and chromosome telomeres. The whole array of their functional roles is not fully explored yet but there is solid evidence supporting their implication in a number of processes like regulation of transcription, replication and telomere organization, among others. During the last decade, there is an increased research interest for G4s that has resulted in a better understanding of their role in several physiological and pathological conditions. On the other hand, these structures are poorly studied in plant species and animals of agricultural interest. Here, we summarize the current methods that are used for studying G4s, we review the studies concerning plants and farm animals and we discuss the advantages of a more thorough inclusion of G4s research in the agricultural sciences.
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Affiliation(s)
- Georgios C Stefos
- Independent researcher, Agricultural University of Athens, Athens, Greece
| | - Georgios Theodorou
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Athens, Greece
| | - Ioannis Politis
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Athens, Greece
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12
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Todorov G, Cunha C. Hypothesis: Regulation of neuroplasticity may involve I-motif and G-quadruplex DNA formation modulated by epigenetic mechanisms. Med Hypotheses 2019; 127:129-135. [PMID: 31088636 DOI: 10.1016/j.mehy.2019.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 01/12/2023]
Abstract
Recent studies demonstrated the existence in vivo of various functional DNA structures that differ from the double helix. The G-quadruplex (G4) and intercalated motif (I-motif or IM) DNA structures are formed as knots where, correspondingly, guanines or cytosines on the same strand of DNA bind to each other. There are grounds to believe that G4 and IM sequences play a significant role in regulating gene expression considering their tendency to be found in or near regulatory sites (such as promoters, enhancers, and telomeres) as well as the correlation between the prevalence of G4 or IM conformations and specific phases of cell cycle. Notably, G4 and IM capable sequences tend to be found on the opposite strands of the same DNA site with at most one of the two structures formed at any given time. The recent evidence that K+, Mg2+ concentrations directly affect IM formation (and likely G4 formation indirectly) lead us to believe that these structures may play a major role in synaptic plasticity of neurons, and, therefore, in a variety of central nervous system (CNS) functions including memory, learning, habitual behaviors, pain perception and others. Furthermore, epigenetic mechanisms, which have an important role in synaptic plasticity and memory formation, were also shown to influence formation and stability of G4s and IMs. Our hypothesis is that non-canonical DNA and RNA structures could be an integral part of neuroplasticity control via gene expression regulation at the level of transcription, translation and splicing. We propose that the regulatory activity of DNA IM and G4 structures is modulated by DNA methylation/demethylation of the IM and/or G4 sequences, which facilitates the switch between canonical and non-canonical conformation. Other neuronal mechanisms interacting with the formation and regulatory activity of non-canonical DNA and RNA structures, particularly G4, IM and triplexes, may involve microRNAs as well as ion and proton fluxes. We are proposing experiments in acute brain slices and in vivo to test our hypothesis. The proposed studies would provide new insights into fundamental neuronal mechanisms in health and disease and potentially open new avenues for treating mental health disorders.
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Affiliation(s)
- German Todorov
- Emotional Brain Institute, Nathan Kline Institute, Orangeburg, NY, USA
| | - Catarina Cunha
- Emotional Brain Institute, Nathan Kline Institute, Orangeburg, NY, USA.
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13
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Sengupta A, Ganguly A, Chowdhury S. Promise of G-Quadruplex Structure Binding Ligands as Epigenetic Modifiers with Anti-Cancer Effects. Molecules 2019; 24:E582. [PMID: 30736345 PMCID: PMC6384772 DOI: 10.3390/molecules24030582] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 11/16/2022] Open
Abstract
Evidences from more than three decades of work support the function of non-duplex DNA structures called G-quadruplex (G4) in important processes like transcription and replication. In addition, G4 structures have been studied in connection with DNA base modifications and chromatin/nucleosome arrangements. Recent work, interestingly, shows promise of G4 structures, through interaction with G4 structure-interacting proteins, in epigenetics-in both DNA and histone modification. Epigenetic changes are found to be intricately associated with initiation as well as progression of cancer. Multiple oncogenes have been reported to harbor the G4 structure at regulatory regions. In this context, G4 structure-binding ligands attain significance as molecules with potential to modify the epigenetic state of chromatin. Here, using examples from recent studies we discuss the emerging role of G4 structures in epigenetic modifications and, therefore, the promise of G4 structure-binding ligands in epigenetic therapy.
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Affiliation(s)
- Antara Sengupta
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
- Academy of Scientific and Innovative Research, Rafi Marg, New Delhi-110001, India.
| | - Akansha Ganguly
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
- Academy of Scientific and Innovative Research, Rafi Marg, New Delhi-110001, India.
- GNR Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
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