51
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Sharma VR, Thomas SD, Miller DM, Rezzoug F. Nucleolin Overexpression Confers Increased Sensitivity to the Anti-Nucleolin Aptamer, AS1411. Cancer Invest 2018; 36:475-491. [PMID: 30396283 PMCID: PMC6396827 DOI: 10.1080/07357907.2018.1527930] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 09/20/2018] [Indexed: 02/04/2023]
Abstract
AS1411 is an antiproliferative DNA aptamer, which binds the ubiquitous protein, nucleolin. In this study, we show that constitutive overexpression of nucleolin confers increased sensitivity to the growth inhibitory effects of AS1411. HeLa cells overexpressing nucleolin have an increased growth rate and invasiveness relative to control cells. Nucleolin overexpressing cells demonstrate increased growth inhibition in response to the AS1411 treatment, which correlates with increased apoptosis and cell cycle arrest, when compared to non-transfected cells. AS1411 induces nucleolin expression at the RNA and protein level in HeLa cells, suggesting a feedback loop with important implications for the clinical use of AS1411.
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Affiliation(s)
- Vivek R. Sharma
- University of Louisville, Division of Medical Oncology/Hematology, Department of Medicine, James Graham Brown Cancer Center, Louisville, Kentucky, USA
| | - Shelia D. Thomas
- University of Louisville, Division of Medical Oncology/Hematology, Department of Medicine, James Graham Brown Cancer Center, Louisville, Kentucky, USA
| | - Donald M. Miller
- University of Louisville, Division of Medical Oncology/Hematology, Department of Medicine, James Graham Brown Cancer Center, Louisville, Kentucky, USA
| | - Francine Rezzoug
- University of Louisville, Division of Medical Oncology/Hematology, Department of Medicine, James Graham Brown Cancer Center, Louisville, Kentucky, USA
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52
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Al-Zeer MA, Kurreck J. Deciphering the Enigmatic Biological Functions of RNA Guanine-Quadruplex Motifs in Human Cells. Biochemistry 2018; 58:305-311. [PMID: 30350579 DOI: 10.1021/acs.biochem.8b00904] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanine-rich sequences in nucleic acids can form noncanonical structures known as guanine quadruplexes (G-quadruplexes), which constitute a not yet fully elucidated layer of regulatory function for central cellular processes. RNA G-quadruplexes have been shown to be involved in the modulation of translation, the regulation of (alternative) splicing, and the subcellular transport of mRNAs, among other processes. However, in living cells, an equilibrium between the formation of G-quadruplex structures and their unwinding by RNA helicases is likely. The extent to which G-rich sequences adopt G-quadruplex structures in living eukaryotic cells is currently a matter of debate. Multiple lines of evidence confirm the intracellular formation of G-quadruplex structures, such as their detection by immunochemical approaches, fluorogenic probes, and in vivo nuclear magnetic resonance. However, intracellular chemical probing suggests most if not all are in an unfolded state. It is therefore tempting to speculate that some G-quadruplex structures are only temporarily formed when they are required to contribute to the fine-tuning of the processes mentioned above. Future research should focus on the analysis of G-quadruplex formation under physiological conditions, which will allow the re-evaluation of the biological function of G-quadruplex motifs in regulatory processes in their natural environment and at physiological expression levels. This will help in the elucidation of their significance in the regulation of central processes in molecular biology and the exploitation of their potential as therapeutic targets.
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Affiliation(s)
- Munir A Al-Zeer
- Institute of Biotechnology, Department of Applied Biochemistry , Technische Universität Berlin , 13355 Berlin , Germany
| | - Jens Kurreck
- Institute of Biotechnology, Department of Applied Biochemistry , Technische Universität Berlin , 13355 Berlin , Germany
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53
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Gunaratnam M, Collie GW, Reszka AP, Todd AK, Parkinson GN, Neidle S. A naphthalene diimide G-quadruplex ligand inhibits cell growth and down-regulates BCL-2 expression in an imatinib-resistant gastrointestinal cancer cell line. Bioorg Med Chem 2018; 26:2958-2964. [DOI: 10.1016/j.bmc.2018.04.050] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 12/24/2022]
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54
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Kawauchi K, Sugimoto W, Yasui T, Murata K, Itoh K, Takagi K, Tsuruoka T, Akamatsu K, Tateishi-Karimata H, Sugimoto N, Miyoshi D. An anionic phthalocyanine decreases NRAS expression by breaking down its RNA G-quadruplex. Nat Commun 2018; 9:2271. [PMID: 29891945 PMCID: PMC5995912 DOI: 10.1038/s41467-018-04771-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/18/2018] [Indexed: 02/06/2023] Open
Abstract
Aberrant activation of RAS signalling pathways contributes to aggressive phenotypes of cancer cells. The RAS-targeted therapies for cancer, therefore, have been recognised to be effective; however, current developments on targeting RAS have not advanced due to structural features of the RAS protein. Here, we show that expression of NRAS, a major isoform of RAS, can be controlled by photo-irradiation with an anionic phthalocyanine, ZnAPC, targeting NRAS mRNA. In vitro experiments reveal that ZnAPC binds to a G-quadruplex-forming oligonucleotide derived from the 5'-untranslated region of NRAS mRNA even in the presence of excess double-stranded RNA, which is abundant in cells, resulting in selective cleavage of the target RNA's G-quadruplex upon photo-irradiation. In line with these results, upon photo-irradiation, ZnAPC decreases NRAS mRNA and NRAS expression and thus viability of cancer cells. These results indicate that ZnAPC may be a prominent photosensitiser for a molecularly targeted photodynamic therapy for cancer.
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Affiliation(s)
- Keiko Kawauchi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan.
| | - Wataru Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Takatoshi Yasui
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Kohei Murata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Katsuhiko Itoh
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Kazuki Takagi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Takaaki Tsuruoka
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Kensuke Akamatsu
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan.
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55
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Ethyl-substitutive Thioflavin T as a highly-specific fluorescence probe for detecting G-quadruplex structure. Sci Rep 2018; 8:2666. [PMID: 29422637 PMCID: PMC5805748 DOI: 10.1038/s41598-018-20960-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 01/26/2018] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex has attracted considerable attention due to their prevalent distribution in functional genomic regions and transcripts, which can importantly influence biological processes such as regulation of telomere maintenance, gene transcription and gene translation. Artificial receptor study has been developed for accurate identification of G-quadruplex from DNA species, since it is important for the G-quadruplex related basic research, clinical diagnosis, and therapy. Herein, fluorescent dye ThT-E, a derivative of the known fluorescence probe Thioflavin T (ThT), was designed and synthesized to effectively differentiate various G-quadruplex structures from other nucleic acid forms. Compared with methyl groups in ThT, three ethyl groups were introduced to ThT-E, which leads to strengthened affinity, selectivity and little inducing effect on the G-quadruplex formation. More importantly, ThT-E could be served as a visual tool to directly differentiate G-quadruplex solution even with naked eyes under illumination of ultraviolet light. Thus, this probe reported herein may hold great promise for high-throughput assay to screen G-quadruplex, which may widely apply to G-quadruplex-based potential diagnosis and therapy.
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56
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Serikawa T, Spanos C, von Hacht A, Budisa N, Rappsilber J, Kurreck J. Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5' UTR of tumor-associated mRNAs. Biochimie 2017; 144:169-184. [PMID: 29129743 DOI: 10.1016/j.biochi.2017.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Abstract
G-quadruplex structures in the 5' UTR of mRNAs are widely considered to suppress translation without affecting transcription. The current study describes the comprehensive analysis of proteins binding to four different G-quadruplex motifs located in mRNAs of the cancer-related genes Bcl-2, NRAS, MMP16, and ARPC2. Following metabolic labeling (Stable Isotope Labeling with Amino acids in Cell culture, SILAC) of proteins in the human cell line HEK293, G-quadruplex binding proteins were enriched by pull-down assays and identified by LC-orbitrap mass spectrometry. We found different patterns of interactions for the G-quadruplex motifs under investigation. While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively. The use of a control composed of samples from all G-quadruplex-forming sequences and their mutated controls ensured that the identified proteins are specific for RNA G-quadruplex structures and are not general RNA-binding proteins. Independent validation experiments based on pull-down assays and Western blotting confirmed the MS data. Among the interaction partners were many proteins known to bind to RNA, including multiple heterogenous nuclear ribonucleoproteins (hnRNPs). Several of the candidate proteins are likely to reflect stalling of the ribosome by RNA G-quadruplex structures. Interestingly, additional proteins were identified that have not previously been described to interact with RNA. Gene ontology analysis of the candidate proteins revealed that many interaction partners are known to be tumor related. The majority of the identified RNA G-quadruplex interacting proteins are thought to be involved in post-transcriptional processes, particularly in splicing. These findings indicate that protein-G-quadruplex interactions are not only important for the fine-tuning of translation but are also relevant to the regulation of mRNA maturation and may play an important role in tumor biology. Proteomic data are available via ProteomeXchange with identifier PXD005761.
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Affiliation(s)
- Tatsuo Serikawa
- Department of Applied Biochemistry, Institute of Biotechnology, TIB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Annekathrin von Hacht
- Department of Applied Biochemistry, Institute of Biotechnology, TIB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Nediljko Budisa
- Department of Biocatalysis, Institute of Chemistry, L 1, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623, Berlin, Germany
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK; Department of Bioanalytics, Institute of Biotechnology, TIB 4/4-3, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Jens Kurreck
- Department of Applied Biochemistry, Institute of Biotechnology, TIB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany.
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57
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Zheng KW, He YD, Liu HH, Li XM, Hao YH, Tan Z. Superhelicity Constrains a Localized and R-Loop-Dependent Formation of G-Quadruplexes at the Upstream Region of Transcription. ACS Chem Biol 2017; 12:2609-2618. [PMID: 28846373 DOI: 10.1021/acschembio.7b00435] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transcription induces formation of intramolecular G-quadruplex structures at the upstream region of a DNA duplex by an upward transmission of negative supercoiling through the DNA. Currently the regulation of such G-quadruplex formation remains unclear. Using plasmid as a model, we demonstrate that while it is the dynamic negative supercoiling generated by a moving RNA polymerase that triggers a formation of a G-quadruplex, the constitutional superhelicity determines the potential and range of the formation of a G-quadruplex by constraining the propagation of the negative supercoiling. G-quadruplex formation is maximal in negatively supercoiled and nearly abolished in relaxed plasmids while being moderate in nicked and linear ones. The formation of a G-quadruplex strongly correlates with the presence of an R-loop. Preventing R-loop formation virtually abolished G-quadruplex formation even in the negatively supercoiled plasmid. Enzymatic action and protein binding that manipulate supercoiling or its propagation all impact the formation of G-quadruplexes. Because chromosomes and plasmids in cells in their natural form are maintained in a supercoiled state, our findings reveal a physical basis that justifies the formation and regulation of G-quadruplexes in vivo. The structural features involved in G-quadruplex formation may all serve as potential targets in clinical and therapeutic applications.
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Affiliation(s)
- Ke-wei Zheng
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yi-de He
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Hong-he Liu
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xin-min Li
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yu-hua Hao
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Zheng Tan
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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58
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Serikawa T, Eberle J, Kurreck J. Effects of genomic disruption of a guanine quadruplex in the 5′ UTR of the Bcl-2 mRNA in melanoma cells. FEBS Lett 2017; 591:3649-3659. [DOI: 10.1002/1873-3468.12855] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/13/2017] [Accepted: 09/13/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Tatsuo Serikawa
- Department of Applied Biochemistry; Institute of Biotechnology; Berlin University of Technology; Germany
| | - Jürgen Eberle
- Department of Dermatology; Venerology und Allergology; Skin Cancer Center Charité, Charité - Universitätsmedizin Berlin; Berlin, Germany
| | - Jens Kurreck
- Department of Applied Biochemistry; Institute of Biotechnology; Berlin University of Technology; Germany
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59
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Agarwala P, Pal G, Pandey S, Maiti S. Mutagenesis Reveals an Unusual Combination of Guanines in RNA G-Quadruplex Formation. ACS OMEGA 2017; 2:4790-4799. [PMID: 31457759 PMCID: PMC6641730 DOI: 10.1021/acsomega.7b00377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/01/2017] [Indexed: 06/10/2023]
Abstract
The classic G-quadruplex motif consists of a continuous array of 3-4 guanine residues with an intermittent loop size of 1-7 nucleotides (G3-4N1-7G3-4N1-7G3-4N1-7G3-4). An RNA G-quadruplex is able to attain only one parallel G-quadruplex topology owing to steric constraints. Investigating the possibilities of the formation of RNA G-quadruplexes with a stretch of sequences deviating from this classic motif will add to the overall conformations of RNA G-quadruplexes, bestowing diversity to this structure. Here, we report unusual combinations of guanine residues involved in RNA G-quadruplex formation in the 5' untranslated region (UTR) of the von Willebrand factor (VWF) mRNA using the mutagenesis approach. Different permutations and combinations of guanine residues form G-quadruplexes. Upon investigation, G-quadruplexes in 5' UTR of VWF mRNA are shown to exhibit an inhibitory function.
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Affiliation(s)
- Prachi Agarwala
- Chemical
and Systems Biology, CSIR-Institute of Genomics
and Integrative Biology, Mall Road, Delhi 110007, India
- Academy
of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Gargi Pal
- Academy
of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Satyaprakash Pandey
- Chemical
and Systems Biology, CSIR-Institute of Genomics
and Integrative Biology, Mall Road, Delhi 110007, India
- Academy
of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Souvik Maiti
- Chemical
and Systems Biology, CSIR-Institute of Genomics
and Integrative Biology, Mall Road, Delhi 110007, India
- Academy
of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
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60
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McAninch DS, Heinaman AM, Lang CN, Moss KR, Bassell GJ, Rita Mihailescu M, Evans TL. Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5'-UTR. MOLECULAR BIOSYSTEMS 2017; 13:1448-1457. [PMID: 28612854 PMCID: PMC5544254 DOI: 10.1039/c7mb00070g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
G quadruplex structures have been predicted by bioinformatics to form in the 5'- and 3'-untranslated regions (UTRs) of several thousand mature mRNAs and are believed to play a role in translation regulation. Elucidation of these roles has primarily been focused on the 3'-UTR, with limited focus on characterizing the G quadruplex structures and functions in the 5'-UTR. Investigation of the affinity and specificity of RNA binding proteins for 5'-UTR G quadruplexes and the resulting regulatory effects have also been limited. Among the mRNAs predicted to form a G quadruplex structure within the 5'-UTR is the survival motor neuron domain containing 1 (SMNDC1) mRNA, encoding a protein that is critical to the spliceosome. Additionally, this mRNA has been identified as a potential target of the fragile X mental retardation protein (FMRP), whose loss of expression leads to fragile X syndrome. FMRP is an RNA binding protein involved in translation regulation that has been shown to bind mRNA targets that form G quadruplex structures. In this study we have used biophysical methods to investigate G quadruplex formation in the 5'-UTR of SMNDC1 mRNA and analyzed its interactions with FMRP. Our results show that SMNDC1 mRNA 5'-UTR forms an intramolecular, parallel G quadruplex structure comprised of three G quartet planes, which is bound specifically by FMRP both in vitro and in mouse brain lysates. These findings suggest a model by which FMRP might regulate the translation of a subset of its mRNA targets by recognizing the G quadruplex structure present in their 5'-UTR, and affecting their accessibility by the protein synthesis machinery.
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Affiliation(s)
- Damian S McAninch
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA.
| | - Ashley M Heinaman
- Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, Pennsylvania 15904, USA
| | - Cara N Lang
- Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, Pennsylvania 15904, USA
| | - Kathryn R Moss
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Mihaela Rita Mihailescu
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA.
| | - Timothy L Evans
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA. and Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, Pennsylvania 15904, USA
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61
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Fay MM, Lyons SM, Ivanov P. RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms. J Mol Biol 2017; 429:2127-2147. [PMID: 28554731 PMCID: PMC5603239 DOI: 10.1016/j.jmb.2017.05.017] [Citation(s) in RCA: 264] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/12/2017] [Accepted: 05/16/2017] [Indexed: 11/26/2022]
Abstract
G-quadruplexes (G4s) are extremely stable DNA or RNA secondary structures formed by sequences rich in guanine. These structures are implicated in many essential cellular processes, and the number of biological functions attributed to them continues to grow. While DNA G4s are well understood on structural and, to some extent, functional levels, RNA G4s and their functions have received less attention. The presence of bona fide RNA G4s in cells has long been a matter of debate. The development of G4-specific antibodies and ligands hinted on their presence in vivo, but recent advances in RNA sequencing coupled with chemical footprinting suggested the opposite. In this review, we will critically discuss the biology of RNA G4s focusing on the molecular mechanisms underlying their proposed functions.
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Affiliation(s)
- Marta M Fay
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn M Lyons
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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62
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G-Quadruplex surveillance in BCL-2 gene: a promising therapeutic intervention in cancer treatment. Drug Discov Today 2017; 22:1165-1186. [PMID: 28506718 DOI: 10.1016/j.drudis.2017.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/20/2017] [Accepted: 05/05/2017] [Indexed: 02/07/2023]
Abstract
Recently, therapeutic implications of BCL-2 quadruplex invigorated the field of clinical oncology. This Keynote review discusses how a BCL-2 quadruplex-selective approach circumvents the limitations of existing therapeutics; and which improvisations might ameliorate the recent trends of quadruplex-based treatment.
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63
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Zeraati M, Moye AL, Wong JWH, Perera D, Cowley MJ, Christ DU, Bryan TM, Dinger ME. Cancer-associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression. Sci Rep 2017; 7:708. [PMID: 28386116 PMCID: PMC5429658 DOI: 10.1038/s41598-017-00739-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/09/2017] [Indexed: 11/10/2022] Open
Abstract
Cancer is a multifactorial disease driven by a combination of genetic and environmental factors. Many cancer driver mutations have been characterised in protein-coding regions of the genome. However, mutations in noncoding regions associated with cancer have been less investigated. G-quadruplex (G4) nucleic acids are four-stranded secondary structures formed in guanine-rich sequences and prevalent in the regulatory regions. In this study, we used published whole cancer genome sequence data to find mutations in cancer patients that overlap potential RNA G4-forming sequences in 5′ UTRs. Using RNAfold, we assessed the effect of these mutations on the thermodynamic stability of predicted RNA G4s in the context of full-length 5′ UTRs. Of the 217 identified mutations, we found that 33 are predicted to destabilise and 21 predicted to stabilise potential RNA G4s. We experimentally validated the effect of destabilising mutations in the 5′ UTRs of BCL2 and CXCL14 and one stabilising mutation in the 5′ UTR of TAOK2. These mutations resulted in an increase or a decrease in translation of these mRNAs, respectively. These findings suggest that mutations that modulate the G4 stability in the noncoding regions could act as cancer driver mutations, which present an opportunity for early cancer diagnosis using individual sequencing information.
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Affiliation(s)
- Mahdi Zeraati
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Aaron L Moye
- Children's Medical Research Institute, University of Sydney, Sydney, NSW, 2145, Australia
| | - Jason W H Wong
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Dilmi Perera
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Mark J Cowley
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Daniel U Christ
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Tracy M Bryan
- Children's Medical Research Institute, University of Sydney, Sydney, NSW, 2145, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia. .,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.
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64
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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65
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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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66
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G-Quadruplex in the NRF2 mRNA 5' Untranslated Region Regulates De Novo NRF2 Protein Translation under Oxidative Stress. Mol Cell Biol 2016; 37:MCB.00122-16. [PMID: 27736771 DOI: 10.1128/mcb.00122-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 09/27/2016] [Indexed: 12/26/2022] Open
Abstract
Inhibition of protein synthesis serves as a general measure of cellular consequences of chemical stress. A few proteins are translated selectively and influence cell fate. How these proteins can bypass the general control of translation remains unknown. We found that low to mild doses of oxidants induce de novo translation of the NRF2 protein. Here we demonstrate the presence of a G-quadruplex structure in the 5' untranslated region (UTR) of NRF2 mRNA, as measured by circular dichroism, nuclear magnetic resonance, and dimethylsulfate footprinting analyses. Such a structure is important for 5'-UTR activity, since its removal by sequence mutation eliminated H2O2-induced activation of the NRF2 5' UTR. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics revealed elongation factor 1 alpha (EF1a) as a protein binding to the G-quadruplex sequence. Cells responded to H2O2 treatment by increasing the EF1a protein association with NRF2 mRNA, as measured by RNA-protein interaction assays. The EF1a interaction with small and large subunits of ribosomes did not appear to change due to H2O2 treatment, nor did posttranslational modifications, as measured by two-dimensional (2-D) Western blot analysis. Since NRF2 encodes a transcription factor essential for protection against tissue injury, our data have revealed a novel mechanism of cellular defense involving de novo NRF2 protein translation governed by the EF1a interaction with the G-quadruplex in the NRF2 5' UTR during oxidative stress.
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67
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Role of Eukaryotic Initiation Factors during Cellular Stress and Cancer Progression. J Nucleic Acids 2016; 2016:8235121. [PMID: 28083147 PMCID: PMC5204094 DOI: 10.1155/2016/8235121] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 11/14/2016] [Indexed: 12/12/2022] Open
Abstract
Protein synthesis can be segmented into distinct phases comprising mRNA translation initiation, elongation, and termination. Translation initiation is a highly regulated and rate-limiting step of protein synthesis that requires more than 12 eukaryotic initiation factors (eIFs). Extensive evidence shows that the transcriptome and corresponding proteome do not invariably correlate with each other in a variety of contexts. In particular, translation of mRNAs specific to angiogenesis, tumor development, and apoptosis is altered during physiological and pathophysiological stress conditions. In cancer cells, the expression and functions of eIFs are hampered, resulting in the inhibition of global translation and enhancement of translation of subsets of mRNAs by alternative mechanisms. A precise understanding of mechanisms involving eukaryotic initiation factors leading to differential protein expression can help us to design better strategies to diagnose and treat cancer. The high spatial and temporal resolution of translation control can have an immediate effect on the microenvironment of the cell in comparison with changes in transcription. The dysregulation of mRNA translation mechanisms is increasingly being exploited as a target to treat cancer. In this review, we will focus on this context by describing both canonical and noncanonical roles of eIFs, which alter mRNA translation.
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Prokofjeva M, Tsvetkov V, Basmanov D, Varizhuk A, Lagarkova M, Smirnov I, Prusakov K, Klinov D, Prassolov V, Pozmogova G, Mikhailov SN. Anti-HIV Activities of Intramolecular G4 and Non-G4 Oligonucleotides. Nucleic Acid Ther 2016; 27:56-66. [PMID: 27763826 DOI: 10.1089/nat.2016.0624] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
New natural and chemically modified DNA aptamers that inhibit HIV-1 activity at submicromolar concentrations (presumably via preventing viral entry into target cells) are reported. The new DNA aptamers were developed based on known intramolecular G-quadruplexes (G4s) that were functionally unrelated to HIV inhibition [the thrombin-binding aptamer and the fragment of the human oncogene promoter (Bcl2)]. The majority of previously described DNA inhibitors of HIV infection adopt intermolecular structures, and thus their folding variability represents an obvious disadvantage. Intramolecular architectures refold correctly after denaturation and are generally easier to handle. However, whether the G4 topology or other factors account for the anti-HIV activity of our aptamers is unknown. The impact of chemical modification (thiophosphoryl internucleotide linkages) on aptamer activity is discussed. The exact secondary structures of the active compounds and further elucidation of their mechanisms of action hopefully will be the subjects of future studies.
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Affiliation(s)
- Maria Prokofjeva
- 1 Engelhardt Institute of Molecular Biology RAS , Moscow, Russia
| | - Vladimir Tsvetkov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia .,3 Topchiev Institute of Petrochemical Synthesis Russian Academy of Sciences , Moscow, Russia
| | - Dmitry Basmanov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Anna Varizhuk
- 1 Engelhardt Institute of Molecular Biology RAS , Moscow, Russia .,2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Maria Lagarkova
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Igor Smirnov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Kirill Prusakov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Dmitry Klinov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia .,4 Moscow Institute of Physics and Technology (State University) , Moscow Region, Russia
| | | | - Galina Pozmogova
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
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69
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Song J, Perreault JP, Topisirovic I, Richard S. RNA G-quadruplexes and their potential regulatory roles in translation. ACTA ACUST UNITED AC 2016; 4:e1244031. [PMID: 28090421 PMCID: PMC5173311 DOI: 10.1080/21690731.2016.1244031] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022]
Abstract
DNA guanine (G)-rich 4-stranded helical nucleic acid structures called G-quadruplexes (G4), have been extensively studied during the last decades. However, emerging evidence reveals that 5′- and 3′-untranslated regions (5′- and 3′-UTRs) as well as open reading frames (ORFs) contain putative RNA G-quadruplexes. These stable secondary structures play key roles in telomere homeostasis and RNA metabolism including pre-mRNA splicing, polyadenylation, mRNA targeting and translation. Interestingly, multiple RNA binding proteins such as nucleolin, FMRP, DHX36, and Aven were identified to bind RNA G-quadruplexes. Moreover, accumulating reports suggest that RNA G-quadruplexes regulate translation in cap-dependent and -independent manner. Herein, we discuss potential roles of RNA G-quadruplexes and associated trans-acting factors in the regulation of mRNA translation.
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Affiliation(s)
- Jingwen Song
- Terry Fox Molecular Oncology Group and Segal Cancer Center, McGill University, Montréal, Québec, Canada; Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada; Department of Medicine, McGill University, Montréal, Québec, Canada
| | | | - Ivan Topisirovic
- Terry Fox Molecular Oncology Group and Segal Cancer Center, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada; Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Stéphane Richard
- Terry Fox Molecular Oncology Group and Segal Cancer Center, McGill University, Montréal, Québec, Canada; Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada; Department of Medicine, McGill University, Montréal, Québec, Canada
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Translational dysregulation in cancer: eIF4A isoforms and sequence determinants of eIF4A dependence. Biochem Soc Trans 2016; 43:1227-33. [PMID: 26614665 DOI: 10.1042/bst20150163] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The malignant phenotype is largely the consequence of dysregulated gene expression. Transformed cells depend upon not just a global increase in protein synthesis but an altered translational landscape in which pro-oncogenic mRNAs are translationally up-regulated. Such mRNAs have been shown to possess longer and more structured 5'-UTRs requiring high levels of eukaryotic initiation factor 4A (eIF4A) helicase activity for efficient translation. As such there is a developing focus on targeting eIF4A as a cancer therapy. In order for such treatments to be successful, we must develop a detailed understanding of the mechanisms which make specific mRNAs more dependent on eIF4A activity than others. It is also crucial to fully characterize the potentially distinct roles of eIF4A1 and eIF4A2, which until recently were thought to be functionally interchangeable. This review will highlight the recent advances made in this field that address these issues.
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71
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Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal Cations in G-Quadruplex Folding and Stability. Front Chem 2016; 4:38. [PMID: 27668212 PMCID: PMC5016522 DOI: 10.3389/fchem.2016.00038] [Citation(s) in RCA: 361] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
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Xu S, Li Q, Xiang J, Yang Q, Sun H, Guan A, Wang L, Liu Y, Yu L, Shi Y, Chen H, Tang Y. Thioflavin T as an efficient fluorescence sensor for selective recognition of RNA G-quadruplexes. Sci Rep 2016; 6:24793. [PMID: 27098781 PMCID: PMC4838840 DOI: 10.1038/srep24793] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/05/2016] [Indexed: 12/29/2022] Open
Abstract
RNA G-quadruplexes (G4s) play important roles in translational regulation, mRNA processing events and gene expression. Therefore, a fluorescent probe that is capable of efficiently recognizing RNA G-quadruplex structures among other RNA forms is highly desirable. In this study, a water-soluble fluorogenic dye (i.e., Thioflavin T (ThT)) was employed to recognize RNA G-quadruplex structures using UV-Vis absorption spectra, fluorescence spectra and emission lifetime experiments. By stacking on the G-tetrad, the ThT probe exhibited highly specific recognition of RNA G-quadruplex structures with striking fluorescence enhancement compared with other RNA forms. The specific binding demonstrates that ThT is an efficient fluorescence sensor that can distinguish G4 and non-G4 RNA structures.
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Affiliation(s)
- Shujuan Xu
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qian Li
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Junfeng Xiang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Qianfan Yang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongxia Sun
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Aijiao Guan
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lixia Wang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yan Liu
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lijia Yu
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yunhua Shi
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongbo Chen
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
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Abstract
G-quadruplexes are non-canonical secondary structures found in guanine rich regions of DNA and RNA. Reports have indicated the wide occurrence of RNA G-quadruplexes across the transcriptome in various regions of mRNAs and non-coding RNAs. RNA G-quadruplexes have been implicated in playing an important role in translational regulation, mRNA processing events and maintenance of chromosomal end integrity. In this review, we summarize the structural and functional aspects of RNA G-quadruplexes with emphasis on recent progress to understand the protein/trans factors binding these motifs. With the revelation of the importance of these secondary structures as regulatory modules in biology, we have also evaluated the various advancements towards targeting these structures and the challenges associated with them. Apart from this, numerous potential applications of this secondary motif have also been discussed.
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Affiliation(s)
- Prachi Agarwala
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
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Abstract
Quadruplex-forming sequences are widely prevalent in human and other genomes, including bacterial ones. These sequences are over-represented in eukaryotic telomeres, promoters, and 5' untranslated regions. They can form quadruplex structures, which may be transient in many situations in normal cells since they can be effectively resolved by helicase action. Mutated helicases in cancer cells are unable to unwind quadruplexes, which are impediments to transcription, translation, or replication, depending on their location within a particular gene. Small molecules that can stabilize quadruplex structures augment these effects and produce cell and proliferation growth inhibition. This article surveys the chemical biology of quadruplexes. It critically examines the major classes of quadruplex-binding small molecules that have been developed to date and the various approaches to discovering selective agents. The challenges of requiring (and achieving) small-molecule targeted selectivity for a particular quadruplex are discussed in relation to the potential of these small molecules as clinically useful therapeutic agents.
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Affiliation(s)
- Stephen Neidle
- UCL School of Pharmacy, University College London , 29-39 Brunswick Square, London WC1N 1AX, U.K
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Booy EP, McRae EKS, Howard R, Deo SR, Ariyo EO, Dzananovic E, Meier M, Stetefeld J, McKenna SA. RNA Helicase Associated with AU-rich Element (RHAU/DHX36) Interacts with the 3'-Tail of the Long Non-coding RNA BC200 (BCYRN1). J Biol Chem 2016; 291:5355-72. [PMID: 26740632 DOI: 10.1074/jbc.m115.711499] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 12/14/2022] Open
Abstract
RNA helicase associated with AU-rich element (RHAU) is an ATP-dependent RNA helicase that demonstrates high affinity for quadruplex structures in DNA and RNA. To elucidate the significance of these quadruplex-RHAU interactions, we have performed RNA co-immunoprecipitation screens to identify novel RNAs bound to RHAU and characterize their function. In the course of this study, we have identified the non-coding RNA BC200 (BCYRN1) as specifically enriched upon RHAU immunoprecipitation. Although BC200 does not adopt a quadruplex structure and does not bind the quadruplex-interacting motif of RHAU, it has direct affinity for RHAU in vitro. Specifically designed BC200 truncations and RNase footprinting assays demonstrate that RHAU binds to an adenosine-rich region near the 3'-end of the RNA. RHAU truncations support binding that is dependent upon a region within the C terminus and is specific to RHAU isoform 1. Tests performed to assess whether BC200 interferes with RHAU helicase activity have demonstrated the ability of BC200 to act as an acceptor of unwound quadruplexes via a cytosine-rich region near the 3'-end of the RNA. Furthermore, an interaction between BC200 and the quadruplex-containing telomerase RNA was confirmed by pull-down assays of the endogenous RNAs. This leads to the possibility that RHAU may direct BC200 to bind and exert regulatory functions at quadruplex-containing RNA or DNA sequences.
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Affiliation(s)
| | | | | | | | | | | | | | - Jörg Stetefeld
- From the Departments of Chemistry and Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A McKenna
- From the Departments of Chemistry and Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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76
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Grijalvo S, Alagia A, Gargallo R, Eritja R. Cellular uptake studies of antisense oligonucleotides using G-quadruplex-nanostructures. The effect of cationic residue on the biophysical and biological properties. RSC Adv 2016. [DOI: 10.1039/c6ra15336d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Cellular uptake studies of G-quadruplex constructs having the Tetrahymena telomeric repeat sequence d(TGGGGT) modified with amino and guanidinium residues at the 3′-termini and an antisense oligonucleotide at 5′-termini were studied.
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Affiliation(s)
- Santiago Grijalvo
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- E-08034 Barcelona
- Spain
- Networking Centre on Bioengineering
- Biomaterials and Nanomedicine (CIBER-BBN)
| | - Adele Alagia
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- E-08034 Barcelona
- Spain
| | - Raimundo Gargallo
- University of Barcelona
- Department of Chemical Engineering and Analytical Chemistry
- E-08028 Barcelona
- Spain
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- E-08034 Barcelona
- Spain
- Networking Centre on Bioengineering
- Biomaterials and Nanomedicine (CIBER-BBN)
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Crenshaw E, Leung BP, Kwok CK, Sharoni M, Olson K, Sebastian NP, Ansaloni S, Schweitzer-Stenner R, Akins MR, Bevilacqua PC, Saunders AJ. Amyloid Precursor Protein Translation Is Regulated by a 3'UTR Guanine Quadruplex. PLoS One 2015; 10:e0143160. [PMID: 26618502 PMCID: PMC4664259 DOI: 10.1371/journal.pone.0143160] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 11/02/2015] [Indexed: 12/13/2022] Open
Abstract
A central event in Alzheimer’s disease is the accumulation of amyloid β (Aβ) peptides generated by the proteolytic cleavage of the amyloid precursor protein (APP). APP overexpression leads to increased Aβ generation and Alzheimer’s disease in humans and altered neuronal migration and increased long term depression in mice. Conversely, reduction of APP expression results in decreased Aβ levels in mice as well as impaired learning and memory and decreased numbers of dendritic spines. Together these findings indicate that therapeutic interventions that aim to restore APP and Aβ levels must do so within an ideal range. To better understand the effects of modulating APP levels, we explored the mechanisms regulating APP expression focusing on post-transcriptional regulation. Such regulation can be mediated by RNA regulatory elements such as guanine quadruplexes (G-quadruplexes), non-canonical structured RNA motifs that affect RNA stability and translation. Via a bioinformatics approach, we identified a candidate G-quadruplex within the APP mRNA in its 3’UTR (untranslated region) at residues 3008–3027 (NM_201414.2). This sequence exhibited characteristics of a parallel G-quadruplex structure as revealed by circular dichroism spectrophotometry. Further, as with other G-quadruplexes, the formation of this structure was dependent on the presence of potassium ions. This G-quadruplex has no apparent role in regulating transcription or mRNA stability as wild type and mutant constructs exhibited equivalent mRNA levels as determined by real time PCR. Instead, we demonstrate that this G-quadruplex negatively regulates APP protein expression using dual luciferase reporter and Western blot analysis. Taken together, our studies reveal post-transcriptional regulation by a 3’UTR G-quadruplex as a novel mechanism regulating APP expression.
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Affiliation(s)
- Ezekiel Crenshaw
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Brian P. Leung
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
- Department of Chemistry, Drexel University, Philadelphia, PA, United States of America
| | - Chun Kit Kwok
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States of America
- Department of Biochemistry & Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States of America
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michal Sharoni
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Kalee Olson
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States of America
| | - Neeraj P. Sebastian
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Sara Ansaloni
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | | | - Michael R. Akins
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - Philip C. Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States of America
- Department of Biochemistry & Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States of America
| | - Aleister J. Saunders
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States of America
- * E-mail:
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78
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Xu S, Li Q, Xiang J, Yang Q, Sun H, Guan A, Wang L, Liu Y, Yu L, Shi Y, Chen H, Tang Y. Directly lighting up RNA G-quadruplexes from test tubes to living human cells. Nucleic Acids Res 2015; 43:9575-86. [PMID: 26476445 PMCID: PMC4787783 DOI: 10.1093/nar/gkv1040] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/30/2015] [Indexed: 11/20/2022] Open
Abstract
RNA G-quadruplexes (G4s) are one of the key components of the transcriptome that act as efficient post-transcriptional regulatory elements in living cells. To conduct further studies of the unique biological functions of RNA G4s, techniques need to be developed that can efficiently recognize RNA G4 structures under various conditions, in fixed cells and living cells, as well as in vitro. This paper presents the development of such a method, a new technique using a cyanine dye called CyT, which can detect both canonical and non-canonical RNA G4 structures from test tubes to living human cells. The ability of CyT to distinguish between G4 and nonG4 RNA offers a promising tool for future RNA G4-based biomarker discovery and potential diagnostic applications.
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Affiliation(s)
- Shujuan Xu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qian Li
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Junfeng Xiang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Qianfan Yang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongxia Sun
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Aijiao Guan
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lixia Wang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yan Liu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lijia Yu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yunhua Shi
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongbo Chen
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
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79
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Ohnmacht SA, Marchetti C, Gunaratnam M, Besser RJ, Haider SM, Di Vita G, Lowe HL, Mellinas-Gomez M, Diocou S, Robson M, Šponer J, Islam B, Barbara Pedley R, Hartley JA, Neidle S. A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer. Sci Rep 2015; 5:11385. [PMID: 26077929 PMCID: PMC4468576 DOI: 10.1038/srep11385] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/22/2015] [Indexed: 01/05/2023] Open
Abstract
We report here that a tetra-substituted naphthalene-diimide derivative (MM41) has significant in vivo anti-tumour activity against the MIA PaCa-2 pancreatic cancer xenograft model. IV administration with a twice-weekly 15 mg/kg dose produces ca 80% tumour growth decrease in a group of tumour-bearing animals. Two animals survived tumour-free after 279 days. High levels of MM41 are rapidly transported into cell nuclei and were found to accumulate in the tumour. MM41 is a quadruplex-interactive compound which binds strongly to the quadruplexes encoded in the promoter sequences of the BCL-2 and k-RAS genes, both of which are dis-regulated in many human pancreatic cancers. Levels of BCL-2 were reduced by ca 40% in tumours from MM41-treated animals relative to controls, consistent with BCL-2 being a target for MM41. Molecular modelling suggests that MM41 binds to a BCL-2 quadruplex in a manner resembling that previously observed in co-crystal structures with human telomeric quadruplexes. This supports the concept that MM41 (and by implication other quadruplex-targeting small molecules) can bind to quadruplex-forming promoter regions in a number of genes and down-regulate their transcription. We suggest that quadruplexes within those master genes that are up-regulated drivers for particular cancers, may be selective targets for compounds such as MM41.
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Affiliation(s)
| | - Chiara Marchetti
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Mekala Gunaratnam
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Rachael J Besser
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Shozeb M Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Gloria Di Vita
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Helen L Lowe
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | | | - Seckou Diocou
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Mathew Robson
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Jiri Šponer
- Central European Institute of Technology (CEITEC), Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65, Brno, Czech Republic
| | - Barira Islam
- Central European Institute of Technology (CEITEC), Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - R Barbara Pedley
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - John A Hartley
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
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80
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Kwok CK, Balasubramanian S. Targeted Detection of G-Quadruplexes in Cellular RNAs. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500891] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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81
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Kwok CK, Balasubramanian S. Targeted Detection of G-Quadruplexes in Cellular RNAs. Angew Chem Int Ed Engl 2015; 54:6751-4. [PMID: 25907625 PMCID: PMC4510783 DOI: 10.1002/anie.201500891] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/25/2015] [Indexed: 02/03/2023]
Abstract
The G-quadruplex (G4) is a non-canonical nucleic acid structure which regulates important cellular processes. RNA G4s have recently been shown to exist in human cells and be biologically significant. Described herein is a new approach to detect and map RNA G4s in cellular transcripts. This method exploits the specific control of RNA G4-cation and RNA G4-ligand interactions during reverse transcription, by using a selective reverse transcriptase to monitor RNA G4-mediated reverse transcriptase stalling (RTS) events. Importantly, a ligation-amplification strategy is coupled with RTS, and enables detection and mapping of G4s in important, low-abundance cellular RNAs. Strong evidence is provided for G4 formation in full-length cellular human telomerase RNA, offering important insights into its cellular function.
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Affiliation(s)
- Chun Kit Kwok
- The University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Shankar Balasubramanian
- The University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW (UK).
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82
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Dai J, Liu ZQ, Wang XQ, Lin J, Yao PF, Huang SL, Ou TM, Tan JH, Li D, Gu LQ, Huang ZS. Discovery of Small Molecules for Up-Regulating the Translation of Antiamyloidogenic Secretase, a Disintegrin and Metalloproteinase 10 (ADAM10), by Binding to the G-Quadruplex-Forming Sequence in the 5' Untranslated Region (UTR) of Its mRNA. J Med Chem 2015; 58:3875-91. [PMID: 25822852 DOI: 10.1021/acs.jmedchem.5b00139] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Up-regulation of a disintegrin and metalloproteinase 10 (ADAM10) to prevent the formation of β-amyloid (Aβ) peptides might be a promising strategy to treat Alzheimer's disease (AD). RNA G-quadruplex motif within the 5'-UTR of the ADAM10 mRNA is an inhibitory element for ADAM10 translation. Thus, mitigation of the suppressive effect of this motif using an RNA G-quadruplex-forming G-rich sequence (QGRS) binder might be a new approach for AD therapy. Herein, a series of new methylquinolinium derivatives were synthesized and screened by surface plasmon resonance (SPR) and the dual-luciferase reporter assay. Among them, compound 24 showed selective affinity for the QGRS of ADAM10 and could strongly up-regulate the translation of it. Moreover, treatment with 24 led to a significant increase of the secretion of sAPPα, consequently decreasing the Aβ40 in cellular. These results illustrate that the interaction between the RNA QGRS and a small molecule may be a new molecular strategy to modulate the translation of ADAM10.
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Affiliation(s)
- Jie Dai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Zhen-Quan Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Xiao-Qin Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Jing Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Pei-Fen Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Shi-Liang Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Lian-Quan Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
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83
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Kwok CK, Ding Y, Shahid S, Assmann SM, Bevilacqua PC. A stable RNA G-quadruplex within the 5'-UTR of Arabidopsis thaliana ATR mRNA inhibits translation. Biochem J 2015; 467:91-102. [PMID: 25793418 DOI: 10.1042/bj20141063] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Guanine quadruplex structures (GQSs) play important roles in the regulation of gene expression and cellular processes. Recent studies provide strong evidence for the formation and function of DNA and RNA GQSs in human cells. However, whether GQSs form and are functional in plants remains essentially unexplored. On the basis of circular dichroism (CD)-detected titration, UV-detected melting, in-line probing (ILP) and reporter gene assay studies, we report the first example of a plant RNA GQS that inhibits translation. This GQS is located within the 5'-UTR of the ATAXIA TELANGIECTASIA-MUTATED AND RAD3-RELATED (ATR) mRNA of Arabidopsis thaliana (mouse-ear cress). We show that this GQS is highly stable and is thermodynamically favoured over a competing hairpin structure in the 5'-UTR at physiological K⁺ and Mg²⁺ concentrations. Results from ILP reveal the secondary structure of the RNA and support formation of the GQS in vitro in the context of the complete 5'-UTR. Transient reporter gene assays performed in living plants reveal that the GQS inhibits translation but not transcription, implicating this GQS as a translational repressor in vivo. Our results provide the first complete demonstration of the formation and function of a regulatory RNA GQS in plants and open new avenues to explore potential functional roles of GQS in the plant kingdom.
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Affiliation(s)
- Chun Kit Kwok
- *Department of Chemistry, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Yiliang Ding
- *Department of Chemistry, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Saima Shahid
- †Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Sarah M Assmann
- †Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Philip C Bevilacqua
- *Department of Chemistry, Pennsylvania State University, University Park, PA 16802, U.S.A
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84
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Bhattacharyya D, Diamond P, Basu S. An Independently folding RNA G-quadruplex domain directly recruits the 40S ribosomal subunit. Biochemistry 2015; 54:1879-85. [PMID: 25730526 DOI: 10.1021/acs.biochem.5b00091] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we report that a 17-nucleotide independently folding RNA G-quadruplex (GQ) domain within the 294-nucleotide human VEGF IRES A interacts with the 40S ribosomal subunit. Footprinting and structure mapping analyses indicate that the RNA GQ forms independently and interacts directly with the 40S ribosomal subunit in the absence of other protein factors. Moreover, a filter binding assay in conjunction with enzymatic footprinting clearly established that the GQ-forming domain singularly dictates the binding affinity and also the function of internal ribosomal entry site (IRES) A. The deletion of the GQ domain abrogates the binding of the 40S ribosomal subunit to the IRES, which impairs cap-independent translation initiation. The findings provide a unique and defined role for a noncanonical RNA structure in cap-independent translation initiation by cellular IRESs. The GQ structure when present in an IRES acts as an essential element in contrast to their generally accepted inhibitory role in translation. The results of this study explain the hitherto unknown mechanistic necessity of the GQ structure in IRES function.
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Affiliation(s)
| | - Paige Diamond
- ‡Department of Biochemistry, Cell and Molecular Biology, Drake University, Des Moines, Iowa 50311, United States
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85
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Biochemical characterization of G4 quadruplex telomerase RNA unwinding by the RNA helicase RHAU. Methods Mol Biol 2015; 1259:125-35. [PMID: 25579584 DOI: 10.1007/978-1-4939-2214-7_9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
G4 quadruplexes are stable secondary structures prevalent in DNA and RNA that exhibit diverse regulatory functions. Herein, we describe an in vitro technique using the purified RNA helicase RHAU to unwind a G4 quadruplex identified near the 5' end of the human telomerase RNA (hTR). A synthetic RNA corresponding to the quadruplex forming region of hTR (hTR10-43), as well as a predicted complementary strand (25P1), are combined in a reaction containing the purified helicase and ATP. Reaction products and appropriate controls are resolved by native gel electrophoresis. Gels can be stained using a combination of total RNA and quadruplex-specific dyes to observe the expected quadruplex to duplex conversion. This straightforward method can be extended to study structural changes in other inter- or intramolecular quadruplex containing DNA/RNA molecules with the RHAU helicase or other RNA/DNA remodeling enzymes.
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86
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Agarwala P, Pandey S, Maiti S. Role of G-quadruplex located at 5ʹ end of mRNAs. Biochim Biophys Acta Gen Subj 2014; 1840:3503-10. [DOI: 10.1016/j.bbagen.2014.08.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 08/27/2014] [Accepted: 08/28/2014] [Indexed: 02/06/2023]
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87
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Jayaraj GG, Pandey S, Scaria V, Maiti S. Potential G-quadruplexes in the human long non-coding transcriptome. RNA Biol 2014; 9:81-6. [DOI: 10.4161/rna.9.1.18047] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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88
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Wolfe AL, Singh K, Zhong Y, Drewe P, Rajasekhar VK, Sanghvi VR, Mavrakis KJ, Jiang M, Roderick JE, Van der Meulen J, Schatz JH, Rodrigo CM, Zhao C, Rondou P, de Stanchina E, Teruya-Feldstein J, Kelliher MA, Speleman F, Porco JA, Pelletier J, Rätsch G, Wendel HG. RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature 2014; 513:65-70. [PMID: 25079319 PMCID: PMC4492470 DOI: 10.1038/nature13485] [Citation(s) in RCA: 444] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/01/2014] [Indexed: 02/07/2023]
Abstract
The translational control of oncoprotein expression is implicated in many cancers. Here we report an eIF4A RNA helicase-dependent mechanism of translational control that contributes to oncogenesis and underlies the anticancer effects of silvestrol and related compounds. For example, eIF4A promotes T-cell acute lymphoblastic leukaemia development in vivo and is required for leukaemia maintenance. Accordingly, inhibition of eIF4A with silvestrol has powerful therapeutic effects against murine and human leukaemic cells in vitro and in vivo. We use transcriptome-scale ribosome footprinting to identify the hallmarks of eIF4A-dependent transcripts. These include 5' untranslated region (UTR) sequences such as the 12-nucleotide guanine quartet (CGG)4 motif that can form RNA G-quadruplex structures. Notably, among the most eIF4A-dependent and silvestrol-sensitive transcripts are a number of oncogenes, superenhancer-associated transcription factors, and epigenetic regulators. Hence, the 5' UTRs of select cancer genes harbour a targetable requirement for the eIF4A RNA helicase.
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Affiliation(s)
- Andrew L. Wolfe
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Kamini Singh
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Yi Zhong
- Computational Biology Department, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Philipp Drewe
- Computational Biology Department, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Vinagolu K. Rajasekhar
- Stem Cell Center and Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Viraj R. Sanghvi
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | | | - Man Jiang
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Justine E. Roderick
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Joni Van der Meulen
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Jonathan H. Schatz
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Christina M. Rodrigo
- Department of Chemistry, Center for Chemical Methodology and Library Development, Boston University, Boston, MA 02215, USA
| | - Chunying Zhao
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Pieter Rondou
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Julie Teruya-Feldstein
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Michelle A. Kelliher
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Frank Speleman
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - John A. Porco
- Department of Chemistry, Center for Chemical Methodology and Library Development, Boston University, Boston, MA 02215, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, H3G 1Y6
- Department of Oncology, McGill University, Montreal, Quebec, Canada, H3G 1Y6
- The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada, H3G 1Y6
| | - Gunnar Rätsch
- Computational Biology Department, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Hans-Guido Wendel
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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89
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Bhattacharyya D, Nguyen K, Basu S. Rationally induced RNA:DNA G-quadruplex structures elicit an anticancer effect by inhibiting endogenous eIF-4E expression. Biochemistry 2014; 53:5461-70. [PMID: 25072107 DOI: 10.1021/bi5008904] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNA G-quadruplex (GQ) structures act as regulators of a diverse array of cellular processes including translation, pre-mRNA processing, and mRNA targeting. We report here a strategy of harnessing the natural ability of RNA GQs to inhibit translation by rationally inducing a GQ on a targeted mRNA to knockdown endogenous gene expression. We chose to target eIF-4E because of its key role in translation initiation and overexpression in multiple cancers and with the expectation that downregulation of eIF-4E would result in antiproliferation of cancer cells. Targeted hybrid (RNA:DNA) GQ structures were induced at the 5'-untranslated region (UTR) and the protein coding region of the eIF-4E mRNA by rationally designed and partially modified extraneous DNA sequences and their effect on eIF-4E expression was determined. The formation of a stable induced G-quadruplex was established by biophysical and biochemical methods. Thermodynamic parameters calculated from CD melting indicate formation of a stable induced GQ at a physiologically relevant salt concentration. We established the specificity and efficacy of the induced GQ formation by monitoring the targeted repression of a reporter gene. Most importantly we have demonstrated that inducing GQ in the 5'-UTR and the protein coding region of eIF-4E mRNA in human cancer cells results in 30% and 60% inhibition of the endogenous protein expression, respectively. Treating with the GQ inducing oligonucleotide sequences resulted in a decrease in the viability of human cancer cells in a dose-dependent manner. The above concept opens up a new strategy for targeted modulation of endogenous gene expression.
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Affiliation(s)
- Debmalya Bhattacharyya
- Department of Chemistry & Biochemistry, Kent State University , Kent, Ohio 44242, United States
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90
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von Hacht A, Seifert O, Menger M, Schütze T, Arora A, Konthur Z, Neubauer P, Wagner A, Weise C, Kurreck J. Identification and characterization of RNA guanine-quadruplex binding proteins. Nucleic Acids Res 2014; 42:6630-44. [PMID: 24771345 PMCID: PMC4041461 DOI: 10.1093/nar/gku290] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Guanine quadruplex (G-quadruplex) motifs in the 5′ untranslated region (5′-UTR) of mRNAs were recently shown to influence the efficiency of translation. In the present study, we investigate the interaction between cellular proteins and the G-quadruplexes located in two mRNAs (MMP16 and ARPC2). Formation of the G-quadruplexes was confirmed by biophysical characterization and the inhibitory activity on translation was shown by luciferase reporter assays. In experiments with whole cell extracts from different eukaryotic cell lines, G-quadruplex-binding proteins were isolated by pull-down assays and subsequently identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The binding partners of the RNA G-quadruplexes we discovered included several heterogenous nuclear ribonucleoproteins, ribosomal proteins, and splicing factors, as well as other proteins that have previously not been described to interact with nucleic acids. While most of the proteins were specific for either of the investigated G-quadruplexes, some of them bound to both motifs. Selected candidate proteins were subsequently produced by recombinant expression and dissociation constants for the interaction between the proteins and RNA G-quadruplexes in the low nanomolar range were determined by surface plasmon resonance spectroscopy. The present study may thus help to increase our understanding of the mechanisms by which G-quadruplexes regulate translation.
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Affiliation(s)
- Annekathrin von Hacht
- Institute of Biotechnology, Department of Applied Biochemistry, TUB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Oliver Seifert
- Institute for Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | | | - Tatjana Schütze
- Institute of Biotechnology, Department of Applied Biochemistry, TUB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Amit Arora
- Institute for Molecular Biosciences, University of Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Zoltán Konthur
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter Neubauer
- Institute of Biotechnology, Department of Bioprocess Engineering, ACK-24, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Anke Wagner
- Institute of Biotechnology, Department of Applied Biochemistry, TUB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jens Kurreck
- Institute of Biotechnology, Department of Applied Biochemistry, TUB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
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91
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Booy EP, Howard R, Marushchak O, Ariyo EO, Meier M, Novakowski SK, Deo SR, Dzananovic E, Stetefeld J, McKenna SA. The RNA helicase RHAU (DHX36) suppresses expression of the transcription factor PITX1. Nucleic Acids Res 2013; 42:3346-61. [PMID: 24369427 PMCID: PMC3950718 DOI: 10.1093/nar/gkt1340] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
RNA Helicase associated with AU-rich element (RHAU) (DHX36) is a DEAH (Aspartic acid, Glumatic Acid, Alanine, Histidine)-box RNA helicase that can bind and unwind G4-quadruplexes in DNA and RNA. To detect novel RNA targets of RHAU, we performed an RNA co-immunoprecipitation screen and identified the PITX1 messenger RNA (mRNA) as specifically and highly enriched. PITX1 is a homeobox transcription factor with roles in both development and cancer. Primary sequence analysis identified three probable quadruplexes within the 3′-untranslated region of the PITX1 mRNA. Each of these sequences, when isolated, forms stable quadruplex structures that interact with RHAU. We provide evidence that these quadruplexes exist in the endogenous mRNA; however, we discovered that RHAU is tethered to the mRNA via an alternative non–quadruplex-forming region. RHAU knockdown by small interfering RNA results in significant increases in PITX1 protein levels with only marginal changes in mRNA, suggesting a role for RHAU in translational regulation. Involvement of components of the microRNA machinery is supported by similar and non-additive increases in PITX1 protein expression on Dicer and combined RHAU/Dicer knockdown. We also demonstrate a requirement of argonaute-2, a key RNA-induced silencing complex component, to mediate RHAU-dependent changes in PITX1 protein levels. These results demonstrate a novel role for RHAU in microRNA-mediated translational regulation at a quadruplex-containing 3′-untranslated region.
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Affiliation(s)
- Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada, University of Manitoba, Winnipeg, Manitoba, Canada, Department of Biochemistry and Molecular Biology, University of British Columbia, V6T 1Z4 Vancouver, British Columbia, Canada and Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada, R3T 2N2
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92
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Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells. Nat Chem 2013; 6:75-80. [PMID: 24345950 DOI: 10.1038/nchem.1805] [Citation(s) in RCA: 430] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 10/17/2013] [Indexed: 12/23/2022]
Abstract
Following extensive evidence for the formation of four-stranded DNA G-quadruplex structures in vitro, DNA G-quadruplexes have been observed within human cells. Although chemically distinct, RNA can also fold in vitro into G-quadruplex structures that are highly stable because of the 2'-hydroxyl group. However, RNA G-quadruplexes have not yet been reported in cells. Here, we demonstrate the visualization of RNA G-quadruplex structures within the cytoplasm of human cells using a G-quadruplex structure-specific antibody. We also demonstrate that small molecules that bind to G-quadruplexes in vitro can trap endogenous RNA G-quadruplexes when applied to cells. Furthermore, a small molecule that exhibits a preference for RNA G-quadruplexes rather than DNA G-quadruplexes in biophysical experiments also shows the same selectivity within a cellular context. Our findings provide substantive evidence for RNA G-quadruplex formation in the human transcriptome, and corroborate the selectivity and application of stabilizing ligands that target G-quadruplexes within a cellular context.
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93
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Lorenz R, Bernhart SH, Qin J, Höner zu Siederdissen C, Tanzer A, Amman F, Hofacker IL, Stadler PF. 2D meets 4G: G-quadruplexes in RNA secondary structure prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:832-844. [PMID: 24334379 DOI: 10.1109/tcbb.2013.7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes using a simple but plausible energy model. With preliminary energy parameters, we find that the overwhelming majority of putative quadruplex-forming sequences in the human genome are likely to fold into canonical secondary structures instead. Stable G-quadruplexes are strongly enriched, however, in the 5'UTR of protein coding mRNAs.
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Affiliation(s)
| | | | - Jing Qin
- Max Planck Institute for Mathematics in the Sciences, Leipzig and University of Leipzig, Leipzig
| | | | - Andrea Tanzer
- University of Vienna, Vienna and Center for Genomic Regulation (CRG), Barcelona
| | | | - Ivo L Hofacker
- University of Vienna, Vienna and University of Copenhagen
| | - Peter F Stadler
- University of Leipzig, Leipzig, Max Planck Institute for Mathematics in the Sciences, Leipzig, Fraunhofer Institute for CellTherapy and Immunology and University of Copenhagen
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94
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Pandey S, Agarwala P, Maiti S. Effect of loops and G-quartets on the stability of RNA G-quadruplexes. J Phys Chem B 2013; 117:6896-905. [PMID: 23683360 DOI: 10.1021/jp401739m] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The loop length, loop composition, salt concentration, and number of G-quartets are major determinants of G-quadruplex stability. We examined the effect of each of these factors on the thermal stability and folding topology of a library of RNA quadruplexes. The thermal stability of G2 and G3 RNA quadruplexes was investigated upon varying the loop length (from 1-1-1 to 15-15-15) and salt concentration (from 1 to 100 mM KCl), while the effect of loop composition was explored using 18 naturally occurring potential RNA quadruplexes predicted in untranslated regions (UTRs). We found loop length and quadruplex stability to be inversely related for G2 RNA quadruplexes and G3 RNA quadruplexes with shorter loops. However, melting temperature saturates for G3 RNA quadruplexes with longer loops. RNA G-quadruplexes with longer loops (G3 15-15-15) displayed Tm values significantly higher than the physiological temperature. This study thus highlights the need to modify the consensus motif presently used by quadruplex prediction tools. An increase in the loop size from 7 bases to 15 bases in the consensus motif will add to its predictive value for the discovery of potential RNA quadruplexes across transcriptomes.
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Affiliation(s)
- Satyaprakash Pandey
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110007, India
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95
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Ruthenium (II) polypyridyl complexes stabilize the bcl-2 promoter quadruplex and induce apoptosis of Hela tumor cells. Biometals 2013; 26:387-402. [DOI: 10.1007/s10534-013-9622-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 03/21/2013] [Indexed: 10/27/2022]
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96
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Agarwala P, Pandey S, Mapa K, Maiti S. The G-quadruplex augments translation in the 5' untranslated region of transforming growth factor β2. Biochemistry 2013; 52:1528-38. [PMID: 23387555 DOI: 10.1021/bi301365g] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transforming growth factor β2 (TGFβ2) is a versatile cytokine with a prominent role in cell migration, invasion, cellular development, and immunomodulation. TGFβ2 promotes the malignancy of tumors by inducing epithelial-mesenchymal transition, angiogenesis, and immunosuppression. As it is well-documented that nucleic acid secondary structure can regulate gene expression, we assessed whether any secondary motif regulates its expression at the post-transcriptional level. Bioinformatics analysis predicts an existence of a 23-nucleotide putative G-quadruplex sequence (PG4) in the 5' untranslated region (UTR) of TGFβ2 mRNA. The ability of this stretch of sequence to form a highly stable, intramolecular parallel quadruplex was demonstrated using ultraviolet and circular dichroism spectroscopy. Footprinting studies further validated its existence in the presence of a neighboring nucleotide sequence. Following structural characterization, we evaluated the biological relevance of this secondary motif using a dual luciferase assay. Although PG4 inhibits the expression of the reporter gene, its presence in the context of the entire 5' UTR sequence interestingly enhances gene expression. Mutation or removal of the G-quadruplex sequence from the 5' UTR of the gene diminished the level of expression of this gene at the translational level. Thus, here we highlight an activating role of the G-quadruplex in modulating gene expression of TGFβ2 at the translational level and its potential to be used as a target for the development of therapeutics against cancer.
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Affiliation(s)
- Prachi Agarwala
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110007, India
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97
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Nikan M, Di Antonio M, Abecassis K, McLuckie K, Balasubramanian S. An acetylene-bridged 6,8-purine dimer as a fluorescent switch-on probe for parallel G-quadruplexes. Angew Chem Int Ed Engl 2013; 52:1428-31. [PMID: 23238938 PMCID: PMC3652027 DOI: 10.1002/anie.201207075] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/15/2012] [Indexed: 11/14/2022]
Affiliation(s)
- Mehran Nikan
- Department of Chemistry, The University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
- Cambridge Research Institute, Cancer Research UK, Li Ka Shing CenterCambridge, CB2 0RE (UK)
| | - Marco Di Antonio
- Department of Chemistry, The University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Keren Abecassis
- Department of Chemistry, The University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Keith McLuckie
- Cambridge Research Institute, Cancer Research UK, Li Ka Shing CenterCambridge, CB2 0RE (UK)
| | - Shankar Balasubramanian
- Department of Chemistry, The University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
- Cambridge Research Institute, Cancer Research UK, Li Ka Shing CenterCambridge, CB2 0RE (UK)
- School of Clinical Medicine, The University of Cambridge, Addenbrooke's HospitalHills Road, Cambridge, CB2 0SP (UK)
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98
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Nikan M, Di Antonio M, Abecassis K, McLuckie K, Balasubramanian S. An Acetylene-Bridged 6,8-Purine Dimer as a Fluorescent Switch-On Probe for Parallel G-Quadruplexes. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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99
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Weng HY, Huang HL, Zhao PP, Zhou H, Qu LH. Translational repression of cyclin D3 by a stable G-quadruplex in its 5' UTR: implications for cell cycle regulation. RNA Biol 2012; 9:1099-109. [PMID: 22858673 DOI: 10.4161/rna.21210] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
cyclin D3 (CCND3) is one of the three D-type cyclins that regulate the G1/S phase transition of the cell cycle. Expression of CCND3 is observed in nearly all proliferating cells; however, the presence of high levels of CCND3 has been linked to a poor prognosis for several types of cancer. Therefore, further mechanistic studies on the regulation of CCND3 expression are urgently needed to provide therapeutic implications. In this study, we report that a conserved RNA G-quadruplex-forming sequence (hereafter CRQ), located in the 5' UTR of mammalian CCND3 mRNA, is able to fold into an extremely stable, intramolecular, parallel G-quadruplex in vitro. The CRQ G-quadruplex dramatically reduces the activity of a reporter gene in human cell lines, but it has little impact on its mRNA level, indicating a translational repression. Moreover, the CRQ sequence in its natural context inhibits translation of CCND3. Disruption of the G-quadruplex structure by G/U-mutation or deletion results in an elevated expression of CCND3 and an increased phosphorylation of Rb, a downstream target of CCND3, which promotes progression of cells through the G1 phase. Our results add to the growing understanding of the regulation of CCND3 expression and provide a potential therapeutic target for cancer treatment.
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Affiliation(s)
- Heng-You Weng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
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100
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Tekedereli I, Alpay SN, Tavares CDJ, Cobanoglu ZE, Kaoud TS, Sahin I, Sood AK, Lopez-Berestein G, Dalby KN, Ozpolat B. Targeted silencing of elongation factor 2 kinase suppresses growth and sensitizes tumors to doxorubicin in an orthotopic model of breast cancer. PLoS One 2012; 7:e41171. [PMID: 22911754 PMCID: PMC3401164 DOI: 10.1371/journal.pone.0041171] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 06/18/2012] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic elongation factor 2 kinase (eEF-2K), through its phosphorylation of elongation factor 2 (eEF2), provides a mechanism by which cells can control the rate of the elongation phase of protein synthesis. The activity of eEF-2K is increased in rapidly proliferating malignant cells, is inhibited during mitosis, and may contribute to the promotion of autophagy in response to anti-cancer therapies. The purpose of this study was to examine the therapeutic potential of targeting eEF-2K in breast cancer tumors. Through the systemic administration of liposomal eEF-2K siRNA (twice a week, i.v. 150 µg/kg), the expression of eEF-2K was down-regulated in vivo in an orthotopic xenograft mouse model of a highly aggressive triple negative MDA-MB-231 tumor. This targeting resulted in a substantial decrease in eEF2 phosphorylation in the tumors, and led to the inhibition of tumor growth, the induction of apoptosis and the sensitization of tumors to the chemotherapy agent doxorubicin. eEF-2K down-modulation in vitro resulted in a decrease in the expression of c-Myc and cyclin D1 with a concomitant increase in the expression of p27Kip1. A decrease in the basal activity of c-Src (phospho-Tyr-416), focal adhesion kinase (phospho-Tyr-397), and Akt (phospho-Ser-473) was also detected following eEF-2K down-regulation in MDA-MB-231 cells, as determined by Western blotting. Where tested, similar results were seen in ER-positive MCF-7 cells. These effects were also accompanied by a decrease in the observed invasive phenotype of the MDA-MB-231 cells. These data support the notion that the disruption of eEF-2K expression in breast cancer cells results in the down-regulation of signaling pathways affecting growth, survival and resistance and has potential as a therapeutic approach for the treatment of breast cancer.
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Affiliation(s)
- Ibrahim Tekedereli
- Department of Experimental Therapeutics, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - S. Neslihan Alpay
- Department of Experimental Therapeutics, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Clint D. J. Tavares
- Graduate Program in Cell and Molecular Biology, The University of Texas, Austin, Texas, United States of America
| | - Zehra E. Cobanoglu
- Department of Experimental Therapeutics, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Tamer S. Kaoud
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, Texas, United States of America
| | - Ibrahim Sahin
- Department of Experimental Therapeutics, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Anil K. Sood
- Department of Gynecologic Oncology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- Department of Cancer Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- Center for RNAi and Non-Coding RNA, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- Department of Cancer Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- Center for RNAi and Non-Coding RNA, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Kevin N. Dalby
- Graduate Program in Cell and Molecular Biology, The University of Texas, Austin, Texas, United States of America
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, Texas, United States of America
- * E-mail: (BO); (KND)
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- Center for RNAi and Non-Coding RNA, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (BO); (KND)
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