1
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Saha R, Vázquez-Salazar A, Nandy A, Chen IA. Fitness Landscapes and Evolution of Catalytic RNA. Annu Rev Biophys 2024; 53:109-125. [PMID: 39013026 DOI: 10.1146/annurev-biophys-030822-025038] [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] [Indexed: 07/18/2024]
Abstract
The relationship between genotype and phenotype, or the fitness landscape, is the foundation of genetic engineering and evolution. However, mapping fitness landscapes poses a major technical challenge due to the amount of quantifiable data that is required. Catalytic RNA is a special topic in the study of fitness landscapes due to its relatively small sequence space combined with its importance in synthetic biology. The combination of in vitro selection and high-throughput sequencing has recently provided empirical maps of both complete and local RNA fitness landscapes, but the astronomical size of sequence space limits purely experimental investigations. Next steps are likely to involve data-driven interpolation and extrapolation over sequence space using various machine learning techniques. We discuss recent progress in understanding RNA fitness landscapes, particularly with respect to protocells and machine representations of RNA. The confluence of technical advances may significantly impact synthetic biology in the near future.
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Affiliation(s)
- Ranajay Saha
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, USA; ,
| | - Alberto Vázquez-Salazar
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, USA; ,
| | - Aditya Nandy
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, USA; ,
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA
- The James Franck Institute, The University of Chicago, Chicago, Illinois, USA
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, USA; ,
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
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2
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Kaur J, Sharma A, Mundlia P, Sood V, Pandey A, Singh G, Barnwal RP. RNA-Small-Molecule Interaction: Challenging the "Undruggable" Tag. J Med Chem 2024. [PMID: 38498010 DOI: 10.1021/acs.jmedchem.3c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Poonam Mundlia
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
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3
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Brownmiller T, Caplen NJ. The HNRNPF/H RNA binding proteins and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1788. [PMID: 37042074 PMCID: PMC10523889 DOI: 10.1002/wrna.1788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 04/13/2023]
Abstract
The members of the HNRNPF/H family of heterogeneous nuclear RNA proteins-HNRNPF, HNRNPH1, HNRNPH2, HNRNPH3, and GRSF1, are critical regulators of RNA maturation. Documented functions of these proteins include regulating splicing, particularly alternative splicing, 5' capping and 3' polyadenylation of RNAs, and RNA export. The assignment of these proteins to the HNRNPF/H protein family members relates to differences in the amino acid composition of their RNA recognition motifs, which differ from those of other RNA binding proteins (RBPs). HNRNPF/H proteins typically bind RNA sequences enriched with guanine (G) residues, including sequences that, in the presence of a cation, have the potential to form higher-order G-quadruplex structures. The need to further investigate members of the HNRNPF/H family of RBPs has intensified with the recent descriptions of their involvement in several disease states, including the pediatric tumor Ewing sarcoma and the hematological malignancy mantle cell lymphoma; newly described groups of developmental syndromes; and neuronal-related disorders, including addictive behavior. Here, to foster the study of the HNRNPF/H family of RBPs, we discuss features of the genes encoding these proteins, their structures and functions, and emerging contributions to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Tayvia Brownmiller
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland, USA
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4
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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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5
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Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
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Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
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6
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Rehati A, Abuduaini B, Liang Z, Chen D, He F. Identification of heat shock protein family A member 5 (HSPA5) targets involved in nonalcoholic fatty liver disease. Genes Immun 2023:10.1038/s41435-023-00205-y. [PMID: 37156995 DOI: 10.1038/s41435-023-00205-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/27/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
Heat shock protein family A (Hsp70) member 5 (HSPA5) is an endoplasmic reticulum chaperone, which regulates cell metabolism, particularly lipid metabolism. While HSPA5's role in regulating cell function is well described, HSPA5 binding to RNA and its biological function in nonalcoholic fatty liver disease (NAFLD) is still lacking. In the present study, the ability of HSPA5 to modulate alternative splicing (AS) of cellular genes was assessed using Real-Time PCR on 89 NAFLD-associated genes. RNA immunoprecipitation coupled to RNA sequencing (RIP-Seq) assays were also performed to identify cellular mRNAs bound by HSPA5. We obtained the HSPA5-bound RNA profile in HeLa cells and peak calling analysis revealed that HSPA5 binds to coding genes and lncRNAs. Moreover, RIP-Seq assays demonstrated that HSPA5 immunoprecipitates specific cellular mRNAs such as EGFR, NEAT1, LRP1 and TGFß1, which are important in the pathology of NAFLD. Finally, HSPA5 binding sites may be associated with splicing sites. We used the HOMER algorithm to search for motifs enriched in coding sequence (CDs) peaks, which identified over-representation of the AGAG motif in both sets of immunoprecipitated peaks. HSPA5 regulated genes at the 5'UTR alternative splicing and introns and in an AG-rich sequence-dependent manner. We propose that the HSPA5-AGAG interaction might play an important role in regulating alternative splicing of NAFLD-related genes. This report is the first to demonstrate that HSPA5 regulated pre-RNA alternative splicing, stability, or translation and affected target protein(s) via binding to lncRNA and mRNA linked to NAFLD.
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Affiliation(s)
- Aliya Rehati
- Department of Gastroenterology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, China
| | - Buzukela Abuduaini
- Department of Intensive Care Unit, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Urumqi, 830054, Xinjiang, China.
| | - Zhao Liang
- Department of General Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, 430075, Hubei, China
| | - Fangping He
- Department of Gastroenterology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, China.
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7
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Tassinari V, La Rosa P, Guida E, Colopi A, Caratelli S, De Paolis F, Gallo A, Cenciarelli C, Sconocchia G, Dolci S, Cesarini V. Contribution of A-to-I RNA editing, M6A RNA Methylation, and Alternative Splicing to physiological brain aging and neurodegenerative diseases. Mech Ageing Dev 2023; 212:111807. [PMID: 37023929 DOI: 10.1016/j.mad.2023.111807] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Aging is a physiological and progressive phenomenon in all organisms' life cycle, characterized by the accumulation of degenerative processes triggered by several alterations within molecular pathways. These changes compromise cell fate, resulting in the loss of functions in tissues throughout the body, including the brain. Physiological brain aging has been linked to structural and functional alterations, as well as to an increased risk of neurodegenerative diseases. Post-transcriptional RNA modifications modulate mRNA coding properties, stability, translatability, expanding the coding capacity of the genome, and are involved in all cellular processes. Among mRNA post-transcriptional modifications, the A-to-I RNA editing, m6A RNA Methylation and Alternative Splicing play a critical role in all the phases of a neuronal cell life cycle and alterations in their mechanisms of action significantly contribute to aging and neurodegeneration. Here we review our current understanding of the contribution of A-to-I RNA editing, m6A RNA Methylation, and Alternative Splicing to physiological brain aging process and neurodegenerative diseases.
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Affiliation(s)
- Valentina Tassinari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Rome, Italy; European Center for Brain Research, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Eugenia Guida
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Ambra Colopi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Sara Caratelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Francesca De Paolis
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Angela Gallo
- RNA Editing Lab., Oncohaematology Department, Cellular and Gene Therapy Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Cenciarelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Giuseppe Sconocchia
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Susanna Dolci
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Valeriana Cesarini
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy.
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8
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Katsuda Y, Sato SI, Inoue M, Tsugawa H, Kamura T, Kida T, Matsumoto R, Asamitsu S, Shioda N, Shiroto S, Oosawatsu Y, Yatsuzuka K, Kitamura Y, Hagihara M, Ihara T, Uesugi M. Small molecule-based detection of non-canonical RNA G-quadruplex structures that modulate protein translation. Nucleic Acids Res 2022; 50:8143-8153. [PMID: 35801908 PMCID: PMC9371906 DOI: 10.1093/nar/gkac580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/24/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Tandem repeats of guanine-rich sequences in RNA often form thermodynamically stable four-stranded RNA structures. Such RNA G-quadruplexes have long been considered to be linked to essential biological processes, yet their physiological significance in cells remains unclear. Here, we report a approach that permits the detection of RNA G-quadruplex structures that modulate protein translation in mammalian cells. The approach combines antibody arrays and RGB-1, a small molecule that selectively stabilizes RNA G-quadruplex structures. Analysis of the protein and mRNA products of 84 cancer-related human genes identified Nectin-4 and CapG as G-quadruplex-controlled genes whose mRNAs harbor non-canonical G-quadruplex structures on their 5′UTR region. Further investigations revealed that the RNA G-quadruplex of CapG exhibits a structural polymorphism, suggesting a possible mechanism that ensures the translation repression in a KCl concentration range of 25–100 mM. The approach described in the present study sets the stage for further discoveries of RNA G-quadruplexes.
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Affiliation(s)
- Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Maimi Inoue
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Hisashi Tsugawa
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Takuto Kamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Tomoki Kida
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Rio Matsumoto
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Sefan Asamitsu
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan.,Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe, Chuo-ku, Kumamoto 862-0973, Japan
| | - Shuhei Shiroto
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Yoshiki Oosawatsu
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Kenji Yatsuzuka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Masaki Hagihara
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.,School of Pharmacy, Fudan University, Shanghai 201203, China
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9
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Georgakopoulos-Soares I, Parada GE, Hemberg M. Secondary structures in RNA synthesis, splicing and translation. Comput Struct Biotechnol J 2022; 20:2871-2884. [PMID: 35765654 PMCID: PMC9198270 DOI: 10.1016/j.csbj.2022.05.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022] Open
Abstract
Even though the functional role of mRNA molecules is primarily decided by the nucleotide sequence, several properties are determined by secondary structure conformations. Examples of secondary structures include long range interactions, hairpins, R-loops and G-quadruplexes and they are formed through interactions of non-adjacent nucleotides. Here, we discuss advances in our understanding of how secondary structures can impact RNA synthesis, splicing, translation and mRNA half-life. During RNA synthesis, secondary structures determine RNA polymerase II (RNAPII) speed, thereby influencing splicing. Splicing is also determined by RNA binding proteins and their binding rates are modulated by secondary structures. For the initiation of translation, secondary structures can control the choice of translation start site. Here, we highlight the mechanisms by which secondary structures modulate these processes, discuss advances in technologies to detect and study them systematically, and consider the roles of RNA secondary structures in disease.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Guillermo E. Parada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5A 1A8, Canada
| | - Martin Hemberg
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
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10
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Xu J, Huang H, Zhou X. G-Quadruplexes in Neurobiology and Virology: Functional Roles and Potential Therapeutic Approaches. JACS AU 2021; 1:2146-2161. [PMID: 34977886 PMCID: PMC8715485 DOI: 10.1021/jacsau.1c00451] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 05/11/2023]
Abstract
A G-quadruplex (G4) is a four-stranded nucleic acid secondary structure maintained by Hoogsteen hydrogen bonds established between four guanines. Experimental studies and bioinformatics predictions support the hypothesis that these structures are involved in different cellular functions associated with both DNA and RNA processes. An increasing number of diseases have been shown to be associated with abnormal G4 regulation. Here, we describe the existence of G4 and then discuss G4-related pathogenic mechanisms in neurodegenerative diseases and the viral life cycle. Furthermore, we focus on the role of G4s in the design of antiviral therapy and neuropharmacology, including G4 ligands, G4-based aptamers, G4-related proteins, and CRISPR-based sequence editing, along with a discussion of limitations and insights into the prospects of this unusual nucleic acid secondary structure in therapeutics. Finally, we highlight progress and challenges in this field and the potential G4-related research fields.
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Affiliation(s)
- Jinglei Xu
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
| | - Haiyan Huang
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Xiang Zhou
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
- Email to X.Z.:
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11
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Marilovtseva EV, Studitsky VM. Guanine Quadruplexes in Cell Nucleus Metabolism. Mol Biol 2021. [DOI: 10.1134/s0026893321040075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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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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13
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Wang E, Thombre R, Shah Y, Latanich R, Wang J. G-Quadruplexes as pathogenic drivers in neurodegenerative disorders. Nucleic Acids Res 2021; 49:4816-4830. [PMID: 33784396 PMCID: PMC8136783 DOI: 10.1093/nar/gkab164] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/20/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
G-quadruplexes (G4s), higher-order DNA and RNA secondary structures featuring guanine-rich nucleic acid sequences with various conformations, are widely distributed in the human genome. These structural motifs are known to participate in basic cellular processes, including transcription, splicing, and translation, and their functions related to health and disease are becoming increasingly recognized. In this review, we summarize the landscape of G4s involved in major neurodegenerative disorders, describing the genes that contain G4-forming sequences and proteins that have high affinity for G4-containing elements. The functions of G4s are diverse, with potentially protective or deleterious effects in the pathogenic cascades of various neurological diseases. While the studies of the functions of G4s in vivo, including those involved in pathophysiology, are still in their early stages, we will nevertheless discuss the evidence pointing to their biological relevance. A better understanding of this unique structural element in the biological context is important for unveiling its potential roles in the pathogenesis of diseases such as neurodegeneration and for designing new diagnostic and therapeutic strategies.
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Affiliation(s)
- Ernest Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ravi Thombre
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yajas Shah
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Rachel Latanich
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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14
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Guiblet WM, DeGiorgio M, Cheng X, Chiaromonte F, Eckert KA, Huang YF, Makova KD. Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. Genome Res 2021; 31:1136-1149. [PMID: 34187812 PMCID: PMC8256861 DOI: 10.1101/gr.269589.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
Approximately 1% of the human genome has the ability to fold into G-quadruplexes (G4s)-noncanonical strand-specific DNA structures forming at G-rich motifs. G4s regulate several key cellular processes (e.g., transcription) and have been hypothesized to participate in others (e.g., firing of replication origins). Moreover, G4s differ in their thermostability, and this may affect their function. Yet, G4s may also hinder replication, transcription, and translation and may increase genome instability and mutation rates. Therefore, depending on their genomic location, thermostability, and functionality, G4 loci might evolve under different selective pressures, which has never been investigated. Here we conducted the first genome-wide analysis of G4 distribution, thermostability, and selection. We found an overrepresentation, high thermostability, and purifying selection for G4s within genic components in which they are expected to be functional-promoters, CpG islands, and 5' and 3' UTRs. A similar pattern was observed for G4s within replication origins, enhancers, eQTLs, and TAD boundary regions, strongly suggesting their functionality. In contrast, G4s on the nontranscribed strand of exons were underrepresented, were unstable, and evolved neutrally. In general, G4s on the nontranscribed strand of genic components had lower density and were less stable than those on the transcribed strand, suggesting that the former are avoided at the RNA level. Across the genome, purifying selection was stronger at stable G4s. Our results suggest that purifying selection preserves the sequences of functional G4s, whereas nonfunctional G4s are too costly to be tolerated in the genome. Thus, G4s are emerging as fundamental, functional genomic elements.
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Affiliation(s)
- Wilfried M Guiblet
- Bioinformatics and Genomics Graduate Program, Penn State University, University Park, Pennsylvania 16802, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, USA
| | - Xiaoheng Cheng
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Sant'Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Kristin A Eckert
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Department of Pathology, Penn State University, College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Yi-Fei Huang
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
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15
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AKSOY G, LÜLEYAP Ü, EVYAPAN G, PAZARCI P, ALPTEKİN D, PAZARBAŞI A, YILMAZ MB. Sh-Sy5y hücre hattında sodyum bütiratın bazı alternatif kırpılma genleri ve BACE1 izoformları üzeindeki etkisi. CUKUROVA MEDICAL JOURNAL 2021. [DOI: 10.17826/cumj.870361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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16
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Harpster C, Boyle E, Musier-Forsyth K, Kankia B. HIV-1 genomic RNA U3 region forms a stable quadruplex-hairpin structure. Biophys Chem 2021; 272:106567. [PMID: 33713997 PMCID: PMC8051326 DOI: 10.1016/j.bpc.2021.106567] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/22/2021] [Accepted: 02/28/2021] [Indexed: 01/14/2023]
Abstract
The U3 promoter region of the HIV-1 long terminal repeat (LTR) has previously been shown to fold into a series of dynamic G-quadruplex structures. Among the G-quadruplexes identified in the LTR sequence, LTR-III was shown to be the most stable in vitro. NMR studies of this 28-nucleotide (nt) DNA revealed a unique quadruplex-hairpin structure. Whether the hairpin forms in RNA element is unknown and the role of the hairpin in the structure and stability of quadruplexes has not been characterized. Here, we used optical and thermodynamic studies to address these questions. The wild-type LTR-III RNA formed a monomolecular quadruplex with a parallel topology using only propeller loops, including the hairpin loop element. By comparison to the WT and variant RNAs, LTR-III DNA structures were more heterogeneous and less stable. Increased stability of the RNA suggests that the RNA quadruplex-hairpin structure may be a more attractive therapeutic target than the analogous DNA element.
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Affiliation(s)
- Chelsea Harpster
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Elaina Boyle
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Besik Kankia
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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17
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Cave JW, Willis DE. G-quadruplex regulation of neural gene expression. FEBS J 2021; 289:3284-3303. [PMID: 33905176 DOI: 10.1111/febs.15900] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/24/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022]
Abstract
G-quadruplexes are four-stranded helical nucleic acid structures characterized by stacked tetrads of guanosine bases. These structures are widespread throughout mammalian genomic DNA and RNA transcriptomes, and prevalent across all tissues. The role of G-quadruplexes in cancer is well-established, but there has been a growing exploration of these structures in the development and homeostasis of normal tissue. In this review, we focus on the roles of G-quadruplexes in directing gene expression in the nervous system, including the regulation of gene transcription, mRNA processing, and trafficking, as well as protein translation. The role of G-quadruplexes and their molecular interactions in the pathology of neurological diseases is also examined. Outside of cancer, there has been only limited exploration of G-quadruplexes as potential intervention targets to treat disease or injury. We discuss studies that have used small-molecule ligands to manipulate G-quadruplex stability in order to treat disease or direct neural stem/progenitor cell proliferation and differentiation into therapeutically relevant cell types. Understanding the many roles that G-quadruplexes have in the nervous system not only provides critical insight into fundamental molecular mechanisms that control neurological function, but also provides opportunities to identify novel therapeutic targets to treat injury and disease.
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Affiliation(s)
- John W Cave
- InVitro Cell Research LLC, Englewood, NJ, USA
| | - Dianna E Willis
- Burke Neurological Institute, White Plains, NY, USA.,Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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18
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Lidberg KA, Annalora AJ, Jozic M, Elson DJ, Wang L, Bammler TK, Ramm S, Monteiro MB, Himmelfarb J, Marcus CB, Iversen PL, Kelly EJ. Antisense oligonucleotide development for the selective modulation of CYP3A5 in renal disease. Sci Rep 2021; 11:4722. [PMID: 33633318 PMCID: PMC7907328 DOI: 10.1038/s41598-021-84194-w] [Citation(s) in RCA: 3] [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: 08/21/2020] [Accepted: 02/10/2021] [Indexed: 11/09/2022] Open
Abstract
CYP3A5 is the primary CYP3A subfamily enzyme expressed in the human kidney and its aberrant expression may contribute to a broad spectrum of renal disorders. Pharmacogenetic studies have reported inconsistent linkages between CYP3A5 expression and hypertension, however, most investigators have considered CYP3A5*1 as active and CYP3A5*3 as an inactive allele. Observations of gender specific differences in CYP3A5*3/*3 protein expression suggest additional complexity in gene regulation that may underpin an environmentally responsive role for CYP3A5 in renal function. Reconciliation of the molecular mechanism driving conditional restoration of functional CYP3A5*3 expression from alternatively spliced transcripts, and validation of a morpholino-based approach for selectively suppressing renal CYP3A5 expression, is the focus of this work. Morpholinos targeting a cryptic splice acceptor created by the CYP3A5*3 mutation in intron 3 rescued functional CYP3A5 expression in vitro, and salt-sensitive cellular mechanisms regulating splicing and conditional expression of CYP3A5*3 transcripts are reported. The potential for a G-quadruplex (G4) in intron 3 to mediate restored splicing to exon 4 in CYP3A5*3 transcripts was also investigated. Finally, a proximal tubule microphysiological system (PT-MPS) was used to evaluate the safety profile of morpholinos in proximal tubule epithelial cells, highlighting their potential as a therapeutic platform for the treatment of renal disease.
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Affiliation(s)
- Kevin A Lidberg
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Andrew J Annalora
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA.
| | - Marija Jozic
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Daniel J Elson
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Susanne Ramm
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Maria Beatriz Monteiro
- Depto Clinica Medica, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, São Paulo, Brazil
| | | | - Craig B Marcus
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Patrick L Iversen
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Edward J Kelly
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA.
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19
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021. [PMID: 33565261 DOI: 10.1002/wrna.1643.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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20
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1643. [PMID: 33565261 DOI: 10.1002/wrna.1643] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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21
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Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
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22
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Varshney D, Spiegel J, Zyner K, Tannahill D, Balasubramanian S. The regulation and functions of DNA and RNA G-quadruplexes. Nat Rev Mol Cell Biol 2020; 21:459-474. [PMID: 32313204 PMCID: PMC7115845 DOI: 10.1038/s41580-020-0236-x] [Citation(s) in RCA: 619] [Impact Index Per Article: 154.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
DNA and RNA can adopt various secondary structures. Four-stranded G-quadruplex (G4) structures form through self-recognition of guanines into stacked tetrads, and considerable biophysical and structural evidence exists for G4 formation in vitro. Computational studies and sequencing methods have revealed the prevalence of G4 sequence motifs at gene regulatory regions in various genomes, including in humans. Experiments using chemical, molecular and cell biology methods have demonstrated that G4s exist in chromatin DNA and in RNA, and have linked G4 formation with key biological processes ranging from transcription and translation to genome instability and cancer. In this Review, we first discuss the identification of G4s and evidence for their formation in cells using chemical biology, imaging and genomic technologies. We then discuss possible functions of DNA G4s and their interacting proteins, particularly in transcription, telomere biology and genome instability. Roles of RNA G4s in RNA biology, especially in translation, are also discussed. Furthermore, we consider the emerging relationships of G4s with chromatin and with RNA modifications. Finally, we discuss the connection between G4 formation and synthetic lethality in cancer cells, and recent progress towards considering G4s as therapeutic targets in human diseases.
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Affiliation(s)
- Dhaval Varshney
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jochen Spiegel
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Katherine Zyner
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - David Tannahill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK.
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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23
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Abstract
Several decades elapsed between the first descriptions of G-quadruplex nucleic acid structures (G4s) assembled in vitro and the emergence of experimental findings indicating that such structures can form and function in living systems. A large body of evidence now supports roles for G4s in many aspects of nucleic acid biology, spanning processes from transcription and chromatin structure, mRNA processing, protein translation, DNA replication and genome stability, and telomere and mitochondrial function. Nonetheless, it must be acknowledged that some of this evidence is tentative, which is not surprising given the technical challenges associated with demonstrating G4s in biology. Here I provide an overview of evidence for G4 biology, focusing particularly on the many potential pitfalls that can be encountered in its investigation, and briefly discuss some of broader biological processes that may be impacted by G4s including cancer.
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Affiliation(s)
- F. Brad Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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24
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Matsumoto S, Tateishi-Karimata H, Takahashi S, Ohyama T, Sugimoto N. Effect of Molecular Crowding on the Stability of RNA G-Quadruplexes with Various Numbers of Quartets and Lengths of Loops. Biochemistry 2020; 59:2640-2649. [PMID: 32578417 DOI: 10.1021/acs.biochem.0c00346] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
G-Quadruplexes are noncanonical structures formed by guanine-rich regions of not only DNA but also RNA. RNA G-quadruplexes are widely present in the transcriptome as mRNAs and noncoding RNAs and take part in various essential functions in cells. Furthermore, stable RNA G-quadruplexes control the extent of biological functions, such as mRNA translation and antigen presentation. To understand and regulate the functions controlled by RNA G-quadruplexes in cellular environments, which are molecularly crowded, we would be required to investigate the stability of G-quadruplexes in molecular crowding. Here, we systematically investigated the thermodynamic stability of RNA G-quadruplexes with different numbers of G-quartets and lengths of loops. The molecular crowding conditions of polyethylene glycol with an average molecular weight of 200 (PEG200) were found to stabilize RNA G-quadruplexes with three and four G-quartets, while G-quadruplexes with two G-quartets did not exhibit any stabilization upon addition of PEG200. On the other hand, no difference in stabilization by PEG200 was observed among the G-quadruplexes with different loop lengths. Thermodynamic analysis of the RNA G-quadruplexes revealed more appropriate motifs for identifying G-quadruplex-forming sequences. The informatics analysis with new motifs demonstrated that the distributions of G-quadruplexes in human noncoding RNAs differed depending on the number of G-quartets. Therefore, RNA G-quadruplexes with different numbers of G-quartets may play different roles in response to environmental changes in cells.
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Affiliation(s)
- Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
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25
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Li C, Zhao B, Fan YN, Jia X, Liu Y. Expression of BACE1 in the Rat Carotid Body. Front Physiol 2020; 11:505. [PMID: 32508682 PMCID: PMC7251150 DOI: 10.3389/fphys.2020.00505] [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: 02/17/2020] [Accepted: 04/24/2020] [Indexed: 11/13/2022] Open
Abstract
This study explored the expression of BACE1 (β-amyloid precursor protein cleaving enzyme 1) in the rat carotid body and the effect of CIH (cyclic intermittent hypoxia) on the expression of BACE1. We found that BACE1 was expressed in the rat carotid body and located in the nerve endings and type II cells but not in type I cells. CIH reduced BACE1 level in the carotid body, and reoxygenation or ROS scavenger alleviated this reduction. Furthermore, we found that CIH augmented the mRNA level of PGC-1α but attenuated the mRNA level of BACE1 in the carotid body. Taken together, our results suggest that CIH promotes the production of ROS that upregulates the level of PGC-1α, which may in turn inhibits the transcription of BACE1, and that a reduction in the BACE1 level may be related to CIH-induced reversible and ROS-dependent carotid body plasticity. Our study provides a new candidate molecule for further study of the mechanism of carotid body plasticity.
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Affiliation(s)
- Chaohong Li
- Henan Key Laboratory of Neural Regeneration and Repairment, Henan Neurology Institute, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Baosheng Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Ya-Nan Fan
- Henan Key Laboratory of Neural Regeneration and Repairment, Henan Neurology Institute, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xianglei Jia
- Henan Key Laboratory of Neural Regeneration and Repairment, Henan Neurology Institute, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Yuzhen Liu
- Henan Key Laboratory of Neural Regeneration and Repairment, Henan Neurology Institute, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
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26
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Wall ML, Bera A, Wong FK, Lewis SM. Cellular stress orchestrates the localization of hnRNP H to stress granules. Exp Cell Res 2020; 394:112111. [PMID: 32473225 DOI: 10.1016/j.yexcr.2020.112111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/01/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein (hnRNP) H is a member of hnRNP H/F protein subfamily of hnRNPs that regulate the maturation and post-transcriptional processing of pre-mRNA. As a component of an mRNA export complex, hnRNP H shuttles mature mRNA from the nucleus to the cytoplasm. Although hnRNP H is primarily a nuclear protein, it can accumulate in the cytoplasm in certain tissues and cell types; however, the physiological relevance of hnRNP H cytoplasmic accumulation is unknown. Here we show that under cellular stress hnRNP H accumulates in the cytoplasm and is required for efficient recovery from cellular stress. Moreover, we find that cytoplasmic hnRNP H localizes to stress granules and that the RRM3 domain of hnRNP H is necessary for this localization. Together, our results demonstrate that hnRNP H accumulates in the cytoplasm under cellular stress and is recruited to stress granules.
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Affiliation(s)
- Michael L Wall
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Amit Bera
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Florence K Wong
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Stephen M Lewis
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada; Department of Chemistry & Biochemistry, Université de Moncton, Moncton, New Brunswick, Canada; Senior Scientist, Beatrice Hunter Cancer Research Institute, Canada.
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27
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Kamura T, Katsuda Y, Kitamura Y, Ihara T. G-quadruplexes in mRNA: A key structure for biological function. Biochem Biophys Res Commun 2020; 526:261-266. [PMID: 32209257 DOI: 10.1016/j.bbrc.2020.02.168] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/16/2020] [Accepted: 02/29/2020] [Indexed: 10/24/2022]
Abstract
The last several years have seen exciting advances in the understanding of the structure and function of higher-order structures of RNA. Expression levels of some specific genes were shown to be directly regulated by environmentally-responsive formation of certain secondary structures such as stem-loops and pseudoknots. Even among these noncanonical structures, RNA G-quadruplexes, which form on the regions of guanine-rich sequences in mRNA, are highly stable structures that are involved in a variety of biological processes. However, many questions regarding the biological significance of RNA G-quadruplexes remain unsettled, mainly because it is difficult to locate the structures in mRNA. This review focuses on emerging methods that locate RNA G-quadruplexes in mRNA by computational and biochemical techniques. In addition, recent reports on the biological functions of RNA G-quadruplexes are also covered to highlight their various roles in cells, such as in regulating mRNA processing and translation.
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Affiliation(s)
- Takuto Kamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan.
| | - Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
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28
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Neckles C, Boer RE, Aboreden N, Cross AM, Walker RL, Kim BH, Kim S, Schneekloth JS, Caplen NJ. HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction. RNA (NEW YORK, N.Y.) 2019; 25:1731-1750. [PMID: 31511320 PMCID: PMC6859848 DOI: 10.1261/rna.072454.119] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/08/2019] [Indexed: 05/05/2023]
Abstract
The primary oncogenic event in ∼85% of Ewing sarcomas is a chromosomal translocation that generates a fusion oncogene encoding an aberrant transcription factor. The exact genomic breakpoints within the translocated genes, EWSR1 and FLI1, vary; however, in EWSR1, breakpoints typically occur within introns 7 or 8. We previously found that in Ewing sarcoma cells harboring EWSR1 intron 8 breakpoints, the RNA-binding protein HNRNPH1 facilitates a splicing event that excludes EWSR1 exon 8 from the EWS-FLI1 pre-mRNA to generate an in-frame mRNA. Here, we show that the processing of distinct EWS-FLI1 pre-mRNAs by HNRNPH1, but not other homologous family members, resembles alternative splicing of transcript variants of EWSR1 We demonstrate that HNRNPH1 recruitment is driven by guanine-rich sequences within EWSR1 exon 8 that have the potential to fold into RNA G-quadruplex structures. Critically, we demonstrate that an RNA mimetic of one of these G-quadruplexes modulates HNRNPH1 binding and induces a decrease in the growth of an EWSR1 exon 8 fusion-positive Ewing sarcoma cell line. Finally, we show that EWSR1 exon 8 fusion-positive cell lines are more sensitive to treatment with the pan-quadruplex binding molecule, pyridostatin (PDS), than EWSR1 exon 8 fusion-negative lines. Also, the treatment of EWSR1 exon 8 fusion-positive cells with PDS decreases EWS-FLI1 transcriptional activity, reversing the transcriptional deregulation driven by EWS-FLI1. Our findings illustrate that modulation of the alternative splicing of EWS-FLI1 pre-mRNA is a novel strategy for future therapeutics against the EWSR1 exon 8 containing fusion oncogenes present in a third of Ewing sarcoma.
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Affiliation(s)
- Carla Neckles
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Robert E Boer
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Nicholas Aboreden
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Allison M Cross
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Robert L Walker
- Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Bong-Hyun Kim
- CCR Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702, USA
| | - Suntae Kim
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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29
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Kharel P, Balaratnam S, Beals N, Basu S. The role of RNA G-quadruplexes in human diseases and therapeutic strategies. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1568. [PMID: 31514263 DOI: 10.1002/wrna.1568] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 08/09/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022]
Abstract
G-quadruplexes (GQs) are four-stranded secondary structures formed by G-rich nucleic acid sequence(s). DNA GQs are present abundantly in the genome and affect a wide range of processes associated with DNA. Recent studies show that RNA GQs are present in different transcripts, including coding and noncoding areas of mRNA, telomeric RNA as well as in other premature and mature noncoding RNAs. When present at specific locations within the RNAs, GQs play important roles in key biological functions, including the regulation of gene expression and telomere homeostasis. RNA GQs regulate pre-mRNA processing, such as splicing and polyadenylation. Evidently, among other processes, RNA GQs also control mRNA translation, miRNA and piRNA biogenesis, and RNA localization. The regulatory mechanisms controlled by RNA GQs mainly involve binding to RNA binding protein that modulate GQ conformation or serve as an entity in recruiting additional protein regulators to act as a block element to the processing machinery. Here we provide an overview of the ever-increasing number of discoveries revealing the role of RNA GQs in biology and their relevance in human diseases and therapeutics. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Prakash Kharel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Division of Rheumatology, Immunology, and Allergy, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sumirtha Balaratnam
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland
| | - Nathan Beals
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio
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30
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Lightfoot HL, Hagen T, Tatum NJ, Hall J. The diverse structural landscape of quadruplexes. FEBS Lett 2019; 593:2083-2102. [PMID: 31325371 DOI: 10.1002/1873-3468.13547] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022]
Abstract
G-quadruplexes are secondary structures formed in G-rich sequences in DNA and RNA. Considerable research over the past three decades has led to in-depth insight into these unusual structures in DNA. Since the more recent exploration into RNA G-quadruplexes, such structures have demonstrated their in cellulo existence, function and roles in pathology. In comparison to Watson-Crick-based secondary structures, most G-quadruplexes display highly redundant structural characteristics. However, numerous reports of G-quadruplex motifs/structures with unique features (e.g. bulges, long loops, vacancy) have recently surfaced, expanding the repertoire of G-quadruplex scaffolds. This review addresses G-quadruplex formation and structure, including recent reports of non-canonical G-quadruplex structures. Improved methods of detection will likely further expand this collection of novel structures and ultimately change the face of quadruplex-RNA targeting as a therapeutic strategy.
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Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Timo Hagen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Natalie J Tatum
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
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31
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Weldon C, Dacanay JG, Gokhale V, Boddupally PVL, Behm-Ansmant I, Burley GA, Branlant C, Hurley LH, Dominguez C, Eperon IC. Specific G-quadruplex ligands modulate the alternative splicing of Bcl-X. Nucleic Acids Res 2019; 46:886-896. [PMID: 29156002 PMCID: PMC5778605 DOI: 10.1093/nar/gkx1122] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022] Open
Abstract
Sequences with the potential to form RNA G-quadruplexes (G4s) are common in mammalian introns, especially in the proximity of the 5′ splice site (5′SS). However, the difficulty of demonstrating that G4s form in pre-mRNA in functional conditions has meant that little is known about their effects or mechanisms of action. We have shown previously that two G4s form in Bcl-X pre-mRNA, one close to each of the two alternative 5′SS. If these G4s affect splicing but are in competition with other RNA structures or RNA binding proteins, then ligands that stabilize them would increase the proportion of Bcl-X pre-mRNA molecules in which either or both G4s had formed, shifting Bcl-X splicing. We show here that a restricted set of G4 ligands do affect splicing, that their activity and specificity are strongly dependent on their structures and that they act independently at the two splice sites. One of the ligands, the ellipticine GQC-05, antagonizes the major 5′SS that expresses the anti-apoptotic isoform of Bcl-X and activates the alternative 5′SS that expresses a pro-apoptotic isoform. We propose mechanisms that would account for these see-saw effects and suggest that these effects contribute to the ability of GQC-05 to induce apoptosis.
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Affiliation(s)
- Carika Weldon
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Justine G Dacanay
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Vijay Gokhale
- College of Pharmacy and College of Pharmacy and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Peda Venkat L Boddupally
- Fluoroorganic Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana 500 007, India
| | - Isabelle Behm-Ansmant
- IMoPA (Ingénierie Moléculaire et Physiopathologie Articulaire), UMR 7365 CNRS-UL, Biopôle de l'Université de Lorraine, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-lès-Nancy, France
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, UK
| | - Christiane Branlant
- IMoPA (Ingénierie Moléculaire et Physiopathologie Articulaire), UMR 7365 CNRS-UL, Biopôle de l'Université de Lorraine, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-lès-Nancy, France
| | - Laurence H Hurley
- College of Pharmacy and College of Pharmacy and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA.,Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - Cyril Dominguez
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Ian C Eperon
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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32
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Mirihana Arachchilage G, Hetti Arachchilage M, Venkataraman A, Piontkivska H, Basu S. Stable G-quadruplex enabling sequences are selected against by the context-dependent codon bias. Gene 2019; 696:149-161. [PMID: 30753890 DOI: 10.1016/j.gene.2019.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/14/2019] [Accepted: 02/05/2019] [Indexed: 12/22/2022]
Abstract
The distributions of secondary structural elements appear to differ between coding regions (CDS) of mRNAs compared to the untranslated regions (UTRs), presumably as a mechanism to fine-tune gene expression, including efficiency of translation. However, a systematic and comprehensive analysis of secondary structure avoidance because of potential bias in codon usage is difficult as some of the common secondary structures, such as, hairpins can be formed by numerous sequence combinations. Using G-quadruplex (GQ) as the model secondary structure we studied the impact of codon bias on GQs within the CDS. Because GQs can be predicted using specific consensus sequence motifs, they provide an excellent platform for investigation of the selectivity of such putative structures at the codon level. Using a bioinformatics approach, we calculated the frequencies of putative GQs within the CDS of a variety of species. Our results suggest that the most stable GQs appear to be significantly underrepresented within the CDS, through the use of specific synonymous codon combinations. Furthermore, we identified many peptide sequence motifs in which silent mutations can potentially alter translation via stable GQ formation. This work not only provides a comprehensive analysis on how stable secondary structures appear to be avoided within the CDS of mRNA, but also broadens the current understanding of synonymous codon usage as they relate to the structure-function relationship of RNA.
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Affiliation(s)
| | | | - Aparna Venkataraman
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States of America
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States of America
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States of America.
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33
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Verma SP, Das P. Novel splicing in IGFN1 intron 15 and role of stable G-quadruplex in the regulation of splicing in renal cell carcinoma. PLoS One 2018; 13:e0205660. [PMID: 30335789 PMCID: PMC6193652 DOI: 10.1371/journal.pone.0205660] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 09/28/2018] [Indexed: 12/25/2022] Open
Abstract
The IGFN1 (Immunoglobulin-Like And Fibronectin Type III Domain Containing 1) gene has a role in skeletal muscle function and is also involved in metastatic breast cancer, and the isoforms with three N-terminal globular domains are sufficient for its function in skeletal muscle. Two novel splicing isoforms of IGFN1 have been identified in renal cell carcinoma (RCC), one with 5’exon extension and an isoform with a novel exon. The role of G-quadruplex, a non-B DNA, was explored for the splicing alteration of IGFN1 in RCC. G-quadruplexes are the secondary structures acquired by stacking of G-quartets by Hoogsteen hydrogen bonding in DNA and RNA. IGFN1 has intronic potential G-quadruplex forming sequence (PQS) folding into G-quadruplex and is studied for its involvement in aberrant splicing. A PQS in the intron 15 of IGFN1 gene was observed in our in silico analysis by QGRS mapper and non BdB web servers. We observed PQS folds into stable G-quadruplex structure in gel shift assay and circular dichroism (CD) spectroscopy in the presence of G-quadruplex stabilizing agents Pyridostatin (PDS) and KCl, respectively. G-quadruplex formation site with single base resolution was mapped by Sanger sequencing of the plasmid constructs harbouring the cloned PQS and its mutant. This stable G-quadruplex inhibits reverse transcriptase and taq polymerase in reverse transcriptase & PCR stop assays. PDS changes the different splicing isoforms of IGFN1 in UOK146 cell line, displaying involvement of intronic G-quadruplex in IGFN1 splicing. These results lead us to propose that a stable G-quadruplex structure is formed in IGFN1 intron and a reason behind IGFN1 aberrant splicing which could be targeted for therapeutic intervention.
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Affiliation(s)
- Shiv Prakash Verma
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, INDIA
| | - Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, INDIA
- * E-mail: ,
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34
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Braun S, Enculescu M, Setty ST, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S, König J, Zarnack K. Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nat Commun 2018; 9:3315. [PMID: 30120239 PMCID: PMC6098099 DOI: 10.1038/s41467-018-05748-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 07/19/2018] [Indexed: 01/22/2023] Open
Abstract
Mutations causing aberrant splicing are frequently implicated in human diseases including cancer. Here, we establish a high-throughput screen of randomly mutated minigenes to decode the cis-regulatory landscape that determines alternative splicing of exon 11 in the proto-oncogene MST1R (RON). Mathematical modelling of splicing kinetics enables us to identify more than 1000 mutations affecting RON exon 11 skipping, which corresponds to the pathological isoform RON∆165. Importantly, the effects correlate with RON alternative splicing in cancer patients bearing the same mutations. Moreover, we highlight heterogeneous nuclear ribonucleoprotein H (HNRNPH) as a key regulator of RON splicing in healthy tissues and cancer. Using iCLIP and synergy analysis, we pinpoint the functionally most relevant HNRNPH binding sites and demonstrate how cooperative HNRNPH binding facilitates a splicing switch of RON exon 11. Our results thereby offer insights into splicing regulation and the impact of mutations on alternative splicing in cancer.
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Affiliation(s)
- Simon Braun
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mihaela Enculescu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Samarth T Setty
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | | | - Bernardo P de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.,Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus Gambelas, 8005-139, Faro, Portugal
| | | | - Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Markus Seiler
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | | | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.
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35
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Zahin M, Dean WL, Ghim SJ, Joh J, Gray RD, Khanal S, Bossart GD, Mignucci-Giannoni AA, Rouchka EC, Jenson AB, Trent JO, Chaires JB, Chariker JH. Identification of G-quadruplex forming sequences in three manatee papillomaviruses. PLoS One 2018; 13:e0195625. [PMID: 29630682 PMCID: PMC5891072 DOI: 10.1371/journal.pone.0195625] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/25/2018] [Indexed: 11/30/2022] Open
Abstract
The Florida manatee (Trichechus manatus latirotris) is a threatened aquatic mammal in United States coastal waters. Over the past decade, the appearance of papillomavirus-induced lesions and viral papillomatosis in manatees has been a concern for those involved in the management and rehabilitation of this species. To date, three manatee papillomaviruses (TmPVs) have been identified in Florida manatees, one forming cutaneous lesions (TmPV1) and two forming genital lesions (TmPV3 and TmPV4). We identified DNA sequences with the potential to form G-quadruplex structures (G4) across the three genomes. G4 were located on both DNA strands and across coding and non-coding regions on all TmPVs, offering multiple targets for viral control. Although G4 have been identified in several viral genomes, including human PVs, most research has focused on canonical structures comprised of three G-tetrads. In contrast, the vast majority of sequences we identified would allow the formation of non-canonical structures with only two G-tetrads. Our biophysical analysis confirmed the formation of G4 with parallel topology in three such sequences from the E2 region. Two of the structures appear comprised of multiple stacked two G-tetrad structures, perhaps serving to increase structural stability. Computational analysis demonstrated enrichment of G4 sequences on all TmPVs on the reverse strand in the E2/E4 region and on both strands in the L2 region. Several G4 sequences occurred at similar regional locations on all PVs, most notably on the reverse strand in the E2 region. In other cases, G4 were identified at similar regional locations only on PVs forming genital lesions. On all TmPVs, G4 sequences were located in the non-coding region near putative E2 binding sites. Together, these findings suggest that G4 are possible regulatory elements in TmPVs.
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Affiliation(s)
- Maryam Zahin
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - William L. Dean
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Shin-je Ghim
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Joongho Joh
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Robert D. Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Sujita Khanal
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
| | - Gregory D. Bossart
- Georgia Aquarium, Atlanta, Georgia, United States of America
- Division of Comparative Pathology, Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | | | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Duthie Center for Engineering, Louisville, Kentucky, United States of America
- KBRIN Bioinformatics Core, University of Louisville, Louisville, Kentucky, United States of America
| | - Alfred B. Jenson
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - John O. Trent
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
| | - Julia H. Chariker
- KBRIN Bioinformatics Core, University of Louisville, Louisville, Kentucky, United States of America
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, Kentucky, United States of America
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36
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G-quadruplex structure at intron 2 of TFE3 and its role in Xp11.2 translocation and splicing. Biochim Biophys Acta Gen Subj 2017; 1862:630-636. [PMID: 29138008 DOI: 10.1016/j.bbagen.2017.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 10/16/2017] [Accepted: 11/10/2017] [Indexed: 12/19/2022]
Abstract
Transcription Factor E3 (TFE3) translocation is found in a group of different type of cancers and most of the translocations are located in the 5' region of TFE3 which may be considered as Breakpoint Region (BR). In our In silico study by QGRS mapper and non BdB web servers we found a Potential G-quadruplex forming Sequence (PQS) in the intron 2 of TFE3 gene. In vitro G-quadruplex formation was shown by native PAGE in presence of Pyridostatin(PDS), which with inter molecular secondary structure caused reduced mobility to migrate slower. G-quadruplex formation was mapped at single base resolution by Sanger sequencing and Circular Dichroism showed the formation of parallel G-quadruplex. FRET analysis revealed increased and decreased formation of G-quadruplex in presence of PDS and antisense oligonucleotide respectively. PCR stop assay, transcriptional and translational inhibition by PQS showed stable G-quadruplex formation affecting the biological processes. TFE3 minigene splicing study showed the involvement of this G-quadruplex in TFE3 splicing too. Therefore, G-quadruplex is evident to be the reason behind TFE3 induced oncogenesis executed by translocation and also involved in the mRNA splicing.
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37
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Deschênes M, Chabot B. The emerging role of alternative splicing in senescence and aging. Aging Cell 2017; 16:918-933. [PMID: 28703423 PMCID: PMC5595669 DOI: 10.1111/acel.12646] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2017] [Indexed: 12/22/2022] Open
Abstract
Deregulation of precursor mRNA splicing is associated with many illnesses and has been linked to age-related chronic diseases. Here we review recent progress documenting how defects in the machinery that performs intron removal and controls splice site selection contribute to cellular senescence and organismal aging. We discuss the functional association linking p53, IGF-1, SIRT1, and ING-1 splice variants with senescence and aging, and review a selection of splicing defects occurring in accelerated aging (progeria), vascular aging, and Alzheimer's disease. Overall, it is becoming increasingly clear that changes in the activity of splicing factors and in the production of key splice variants can impact cellular senescence and the aging phenotype.
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Affiliation(s)
- Mathieu Deschênes
- Department of Microbiology and Infectious DiseasesFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQuebecJ1E 4K8Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious DiseasesFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQuebecJ1E 4K8Canada
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38
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Chakravarthy M, Chen S, Dodd PR, Veedu RN. Nucleic Acid-Based Theranostics for Tackling Alzheimer's Disease. Theranostics 2017; 7:3933-3947. [PMID: 29109789 PMCID: PMC5667416 DOI: 10.7150/thno.21529] [Citation(s) in RCA: 23] [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: 06/20/2017] [Accepted: 07/28/2017] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid-based technologies have received significant interest in recent years as novel theranostic strategies for various diseases. The approval by the United States Food and Drug Administration (FDA) of Nusinersen, an antisense oligonucleotide drug, for the treatment of spinal muscular dystrophy highlights the potential of nucleic acids to treat neurological diseases, including Alzheimer's disease (AD). AD is a devastating neurodegenerative disease characterized by progressive impairment of cognitive function and behavior. It is the most common form of dementia; it affects more than 20% of people over 65 years of age and leads to death 7-15 years after diagnosis. Intervention with novel agents addressing the underlying molecular causes is critical. Here we provide a comprehensive review on recent developments in nucleic acid-based theranostic strategies to diagnose and treat AD.
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Affiliation(s)
- Madhuri Chakravarthy
- Centre for Comparative Genomics, Murdoch University, Murdoch, Perth, Australia 6150
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Nedlands, Perth, Australia 6005
| | - Suxiang Chen
- Centre for Comparative Genomics, Murdoch University, Murdoch, Perth, Australia 6150
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Nedlands, Perth, Australia 6005
| | - Peter R. Dodd
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Australia 4072
| | - Rakesh N. Veedu
- Centre for Comparative Genomics, Murdoch University, Murdoch, Perth, Australia 6150
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Nedlands, Perth, Australia 6005
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Australia 4072
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Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses. Sci Rep 2017; 7:2018. [PMID: 28515481 PMCID: PMC5435695 DOI: 10.1038/s41598-017-02291-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/03/2017] [Indexed: 12/25/2022] Open
Abstract
G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5′-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NFκB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5′-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place.
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Lago S, Tosoni E, Nadai M, Palumbo M, Richter SN. The cellular protein nucleolin preferentially binds long-looped G-quadruplex nucleic acids. Biochim Biophys Acta Gen Subj 2017; 1861:1371-1381. [PMID: 27913192 PMCID: PMC5466061 DOI: 10.1016/j.bbagen.2016.11.036] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND G-quadruplexes (G4s) are four-stranded nucleic acid structures that form in G-rich sequences. Nucleolin (NCL) is a cellular protein reported for its functions upon G4 recognition, such as induction of neurodegenerative diseases, tumor and virus mechanisms activation. We here aimed at defining NCL/G4 binding determinants. METHODS Electrophoresis mobility shift assay was used to detect NCL/G4 binding; circular dichroism to assess G4 folding, topology and stability; dimethylsulfate footprinting to detect G bases involved in G4 folding. RESULTS The purified full-length human NCL was initially tested on telomeric G4 target sequences to allow for modulation of loop, conformation, length, G-tract number, stability. G4s in promoter regions with more complex sequences were next employed. We found that NCL binding to G4s heavily relies on G4 loop length, independently of the conformation and oligonucleotide/loop sequence. Low stability G4s are preferred. When alternative G4 conformations are possible, those with longer loops are preferred upon binding to NCL, even if G-tracts need to be spared from G4 folding. CONCLUSIONS Our data provide insight into how G4s and the associated proteins may control the ON/OFF molecular switch to several pathological processes, including neurodegeneration, tumor and virus activation. Understanding these regulatory determinants is the first step towards the development of targeted therapies. GENERAL SIGNIFICANCE The indication that NCL binding preferentially stimulates and induces folding of G4s containing long loops suggests NCL ability to modify the overall structure and steric hindrance of the involved nucleic acid regions. This protein-induced modification of the G4 structure may represent a cellular mechanosensor mechanism to molecular signaling and disease pathogenesis. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Sara Lago
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Elena Tosoni
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical Sciences, University of Padua, via Marzolo 5, 35131 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
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Pandey S, Agarwala P, Maiti S. Targeting RNA G-Quadruplexes for Potential Therapeutic Applications. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Rouleau S, Jodoin R, Garant JM, Perreault JP. RNA G-Quadruplexes as Key Motifs of the Transcriptome. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 170:1-20. [PMID: 28382477 DOI: 10.1007/10_2017_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
G-Quadruplexes are non-canonical secondary structures that can be adopted under physiological conditions by guanine-rich DNA and RNA molecules. They have been reported to occur, and to perform multiple biological functions, in the genomes and transcriptomes of many species, including humans. This chapter focuses specifically on RNA G-quadruplexes and reviews the most recent discoveries in the field, as well as addresses the upcoming challenges researchers studying these structures face.
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Affiliation(s)
- Samuel Rouleau
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8
| | - Rachel Jodoin
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8
| | - Jean-Michel Garant
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8.
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Weldon C, Eperon IC, Dominguez C. Do we know whether potential G-quadruplexes actually form in long functional RNA molecules? Biochem Soc Trans 2016; 44:1761-1768. [PMID: 27913687 PMCID: PMC5135001 DOI: 10.1042/bst20160109] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/30/2016] [Accepted: 07/04/2016] [Indexed: 01/25/2023]
Abstract
The roles of deoxyribonucleic acid (DNA) G-quadruplex structures in gene expression and telomere maintenance have been well characterized. Recent results suggest that such structures could also play pivotal roles in ribonucleic acid (RNA) biology, such as splicing or translation regulation. However, it has been difficult to show that RNA G-quadruplexes (G4s) exist in specific long RNA sequences, such as precursor messenger RNA, in a functional or cellular context. Most current methods for identifying G4s involve the use of short, purified RNA sequences in vitro, in the absence of competition with secondary structures or protein binding. Therefore, novel methods need to be developed to allow the characterization of G4s in long functional RNAs and in a cellular context. This need has in part been met by our recent development of a method based on a comparison of RNA and 7-deaza-RNA that provides a test for identifying RNA G4s in such conditions.
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Affiliation(s)
- Carika Weldon
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cellular Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, U.K
| | - Ian C Eperon
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cellular Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, U.K
| | - Cyril Dominguez
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cellular Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, U.K
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Zuffo M, Doria F, Botti S, Bergamaschi G, Freccero M. G-quadruplex fluorescence sensing by core-extended naphthalene diimides. Biochim Biophys Acta Gen Subj 2016; 1861:1303-1311. [PMID: 27902935 DOI: 10.1016/j.bbagen.2016.11.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Fluorescent sensing of G-quadruplex nucleic acids (G4s) is an effective strategy to elucidate their role in vitro and in vivo. Small molecule ligands have often been exploited, producing an emission light up upon binding. Naphthalene diimides (NDIs), although potent G4 binders exhibiting red-NIR fluorophores, have only been marginally exploited, as they are usually quenched upon binding. Contrary, aggregating core-extended naphthalene diimides (cex-NDIs) proved to be effective probes. METHODS We prepared a library of eighteen cex-NDIs by organic synthesis, characterising their aggregation-dependent absorption and emission properties. Absorption and emission titrations, fluorescent intercalator displacement assay (FID) and circular dichroism (CD) analysis were performed to elucidate their behavior as G4 fluorescent sensors, selectivity and binding mode. RESULTS cex-NDIs aggregate under aqueous solvents and as a result, their fluorescence is mostly quenched under physiological conditions. Upon G4 binding, they disaggregate into binding monomers, producing a fluorescent light-up with anti-parallel and hybrid G4s. Contrary, with parallel G4s a light-off was recorded. For the formers a groove-like interaction was inferred by ICD signals, while for the latter an end-stacking interaction mode was hypothesized by G4-FID data. CONCLUSIONS cex-NDIs G4 sensing mechanism works via a induced disaggregation. The emission response depends on the G4 topology, which dictates the prevailing -groove or end-stacking- binding mode. GENERAL SIGNIFICANCE This study highlights the potential of cex-NDIs as G4 fluorescent probes. Besides being readily synthesized and conveniently emitting above 600nm, they light-up upon binding to anti-parallel and hybrid G4, complementing a number of other probes' selectivity for the parallel topology. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Michela Zuffo
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
| | - Filippo Doria
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
| | - Silvia Botti
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
| | - Greta Bergamaschi
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
| | - Mauro Freccero
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
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Biswas B, Kandpal M, Jauhari UK, Vivekanandan P. Genome-wide analysis of G-quadruplexes in herpesvirus genomes. BMC Genomics 2016; 17:949. [PMID: 27871228 PMCID: PMC5117502 DOI: 10.1186/s12864-016-3282-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/09/2016] [Indexed: 11/10/2022] Open
Abstract
Background G-quadruplexes are increasingly recognized as regulatory elements in human, animal, bacterial and plant genomes. The presence and function of G-quadruplexes are not well studied among herpesviruses; in particular, there are no systematic genome-wide analysis of these important secondary structures in herpesvirus genomes. Results We performed genome-wide analysis of putative quadruplex sequences (PQS) in human herpesviruses. We found unusually high PQS densities among human herpesviruses. PQS are enriched in the repeat regions and regulatory regions of human herpesviruses. Interestingly, PQS densities are higher in regulatory regions of immediate early genes compared to early and late genes in most herpesviruses. In addition, the majority of genes functionally conserved across human herpesviruses contain one or more PQS within the regulatory regions. We also describe the existence of unique intramolecular PQS repeats or repetitive G-quadruplex motifs in herpesviruses. Functional studies confirm a role for G-quadruplexes in regulating the gene expression of human herpesviruses. Conclusion The pervasiveness of PQS, their enrichment and conservation at specific genomic locations suggest that these structural entities may represent a novel class of functional elements in herpesviruses. Our findings provide the necessary framework for studies on the biological role of G-quadruplexes in herpesviruses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3282-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Banhi Biswas
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Manish Kandpal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Utkarsh Kumar Jauhari
- Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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Qin JL, Qin QP, Wei ZZ, Yu YC, Meng T, Wu CX, Liang YL, Liang H, Chen ZF. Stabilization of c-myc G-Quadruplex DNA, inhibition of telomerase activity, disruption of mitochondrial functions and tumor cell apoptosis by platinum(II) complex with 9-amino-oxoisoaporphine. Eur J Med Chem 2016; 124:417-427. [DOI: 10.1016/j.ejmech.2016.08.054] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 07/29/2016] [Accepted: 08/23/2016] [Indexed: 10/21/2022]
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Chariker JH, Miller DM, Rouchka EC. Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends. PLoS One 2016; 11:e0165101. [PMID: 27776185 PMCID: PMC5077116 DOI: 10.1371/journal.pone.0165101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/06/2016] [Indexed: 12/17/2022] Open
Abstract
G-quadruplex structures (G4) are found throughout the human genome and are known to play a regulatory role in a variety of molecular processes. Structurally, they have many configurations and can form from one or more DNA strands. At the gene level, they regulate gene expression and protein synthesis. In this paper, chromosomal-level patterns of distribution are analyzed on the human genome to identify high-level distribution patterns potentially related to global functional processes. Here we show unique high density banding patterns on individual chromosomes that are highly correlated, appearing in a mirror pattern, across forward and reverse DNA strands. The highest density of G4 sequences occurs within four megabases of one end of most chromosomes and contains G4 motifs that bind with zinc finger proteins. These findings suggest that G4 may play a role in global chromosomal processes such as those found in meiosis.
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Affiliation(s)
- Julia H. Chariker
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY, United States of America
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, KY, United States of America
| | - Donald M. Miller
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, United States of America
- Department of Medicine, University of Louisville, Louisville, KY, United States of America
| | - Eric C. Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, KY, United States of America
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville KY, United States of America
- * E-mail:
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Conlon EG, Lu L, Sharma A, Yamazaki T, Tang T, Shneider NA, Manley JL. The C9ORF72 GGGGCC expansion forms RNA G-quadruplex inclusions and sequesters hnRNP H to disrupt splicing in ALS brains. eLife 2016; 5. [PMID: 27623008 PMCID: PMC5050020 DOI: 10.7554/elife.17820] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/08/2016] [Indexed: 12/12/2022] Open
Abstract
An expanded GGGGCC hexanucleotide in C9ORF72 (C9) is the most frequent known cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). It has been proposed that expanded transcripts adopt G-quadruplex (G-Q) structures and associate with proteins, but whether this occurs and contributes to disease is unknown. Here we show first that the protein that predominantly associates with GGGGCC repeat RNA in vitro is the splicing factor hnRNP H, and that this interaction is linked to G-Q formation. We then show that G-Q RNA foci are more abundant in C9 ALS patient fibroblasts and astrocytes compared to those without the expansion, and more frequently colocalize with hnRNP H. Importantly, we demonstrate dysregulated splicing of multiple known hnRNP H-target transcripts in C9 patient brains, which correlates with elevated insoluble hnRNP H/G-Q aggregates. Together, our data implicate C9 expansion-mediated sequestration of hnRNP H as a significant contributor to neurodegeneration in C9 ALS/FTD. DOI:http://dx.doi.org/10.7554/eLife.17820.001
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Affiliation(s)
- Erin G Conlon
- Department of Biological Sciences, Columbia University, New York, United States
| | - Lei Lu
- Department of Neurology, Columbia University Medical Center, New York, United States
| | - Aarti Sharma
- Department of Neurology, Columbia University Medical Center, New York, United States
| | - Takashi Yamazaki
- Department of Biological Sciences, Columbia University, New York, United States
| | - Timothy Tang
- Department of Biological Sciences, Columbia University, New York, United States
| | - Neil A Shneider
- Department of Neurology, Columbia University Medical Center, New York, United States
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, United States
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Szameit K, Berg K, Kruspe S, Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U. Structure and target interaction of a G-quadruplex RNA-aptamer. RNA Biol 2016; 13:973-987. [PMID: 27471797 DOI: 10.1080/15476286.2016.1212151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
G-quadruplexes have recently moved into focus of research in nucleic acids, thereby evolving in scientific significance from exceptional secondary structure motifs to complex modulators of gene regulation. Aptamers (nucleic acid based ligands with recognition properties for a specific target) that form Gquadruplexes may have particular potential for therapeutic applications as they combine the characteristics of specific targeting and Gquadruplex mediated stability and regulation. We have investigated the structure and target interaction properties of one such aptamer: AIR-3 and its truncated form AIR-3A. These RNA aptamers are specific for human interleukin-6 receptor (hIL-6R), a key player in inflammatory diseases and cancer, and have recently been exploited for in vitro drug delivery studies. With the aim to resolve the RNA structure, global shape, RNA:protein interaction site and binding stoichiometry, we now investigated AIR-3 and AIR-3A by different methods including RNA structure probing, Small Angle X-ray scattering and microscale thermophoresis. Our findings suggest a broader spectrum of folding species than assumed so far and remarkable tolerance toward different modifications. Mass spectrometry based binding site analysis, supported by molecular modeling and docking studies propose a general Gquadruplex affinity for the target molecule hIL-6R.
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Affiliation(s)
- Kristina Szameit
- a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany
| | - Katharina Berg
- a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany
| | - Sven Kruspe
- a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany
| | - Erica Valentini
- b European Molecular Biology Laboratory, Hamburg Unit , Hamburg , Germany
| | - Eileen Magbanua
- a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany
| | - Marcel Kwiatkowski
- c University Medical Center Hamburg-Eppendorf , Department of Clinical Chemistry , Hamburg , Germany
| | | | - Boris Krichel
- e Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany
| | - Kira Schamoni
- e Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany
| | - Charlotte Uetrecht
- e Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany.,f European XFEL GmbH , Hamburg , Germany
| | - Dmitri I Svergun
- b European Molecular Biology Laboratory, Hamburg Unit , Hamburg , Germany
| | - Hartmut Schlüter
- c University Medical Center Hamburg-Eppendorf , Department of Clinical Chemistry , Hamburg , Germany
| | - Martin Zacharias
- d Physics Department , Technical University Munich , Garching , Germany
| | - Ulrich Hahn
- a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany
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De Nicola B, Lech CJ, Heddi B, Regmi S, Frasson I, Perrone R, Richter SN, Phan AT. Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome. Nucleic Acids Res 2016; 44:6442-51. [PMID: 27298260 PMCID: PMC5291261 DOI: 10.1093/nar/gkw432] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 02/07/2023] Open
Abstract
The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics.
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Affiliation(s)
- Beatrice De Nicola
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore Department of Molecular Medicine, University of Padua, Italy
| | - Christopher J Lech
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Sagar Regmi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Italy
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Italy
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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