1
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Choudhury SD, Kumar P, Choudhury D. Bioactive nutraceuticals as G4 stabilizers: potential cancer prevention and therapy-a critical review. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:3585-3616. [PMID: 38019298 DOI: 10.1007/s00210-023-02857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023]
Abstract
G-quadruplexes (G4) are non-canonical, four-stranded, nucleic acid secondary structures formed in the guanine-rich sequences, where guanine nucleotides associate with each other via Hoogsteen hydrogen bonding. These structures are widely found near the functional regions of the mammalian genome, such as telomeres, oncogenic promoters, and replication origins, and play crucial regulatory roles in replication and transcription. Destabilization of G4 by various carcinogenic agents allows oncogene overexpression and extension of telomeric ends resulting in dysregulation of cellular growth-promoting oncogenesis. Therefore, targeting and stabilizing these G4 structures with potential ligands could aid cancer prevention and therapy. The field of G-quadruplex targeting is relatively nascent, although many articles have demonstrated the effect of G4 stabilization on oncogenic expressions; however, no previous study has provided a comprehensive analysis about the potency of a wide variety of nutraceuticals and some of their derivatives in targeting G4 and the lattice of oncogenic cell signaling cascade affected by them. In this review, we have discussed bioactive G4-stabilizing nutraceuticals, their sources, mode of action, and their influence on cellular signaling, and we believe our insight would bring new light to the current status of the field and motivate researchers to explore this relatively poorly studied arena.
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Affiliation(s)
- Satabdi Datta Choudhury
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology (IIT), Mandi, Himachal Pradesh, 175005, India
| | - Diptiman Choudhury
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
- Centre for Excellence in Emerging Materials, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
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2
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Lee CY, Joshi M, Wang A, Myong S. 5'UTR G-quadruplex structure enhances translation in size dependent manner. Nat Commun 2024; 15:3963. [PMID: 38729943 PMCID: PMC11087576 DOI: 10.1038/s41467-024-48247-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Translation initiation in bacteria is frequently regulated by various structures in the 5' untranslated region (5'UTR). Previously, we demonstrated that G-quadruplex (G4) formation in non-template DNA enhances transcription. In this study, we aim to explore how G4 formation in mRNA (RG4) at 5'UTR impacts translation using a T7-based in vitro translation system and in E. coli. We show that RG4 strongly promotes translation efficiency in a size-dependent manner. Additionally, inserting a hairpin upstream of the RG4 further enhances translation efficiency, reaching up to a 12-fold increase. We find that the RG4-dependent effect is not due to increased ribosome affinity, ribosome binding site accessibility, or mRNA stability. We propose a physical barrier model in which bulky structures in 5'UTR biases ribosome movement toward the downstream start codon, thereby increasing the translation output. This study provides biophysical insights into the regulatory role of 5'UTR structures in in vitro and bacterial translation, highlighting their potential applications in tuning gene expression.
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Affiliation(s)
- Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Meera Joshi
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ashley Wang
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, IL, 61801, USA.
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3
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Tang D, Chen Y, Chen H, Jia T, Chen Q, Yu Y. Multiple enzymatic activities of a Sir2-HerA system cooperate for anti-phage defense. Mol Cell 2023; 83:4600-4613.e6. [PMID: 38096825 DOI: 10.1016/j.molcel.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/14/2023] [Accepted: 11/13/2023] [Indexed: 12/24/2023]
Abstract
In response to the persistent exposure to phage infection, bacteria have evolved diverse antiviral defense mechanisms. In this study, we report a bacterial two-component defense system consisting of a Sir2 NADase and a HerA helicase. Cryo-electron microscopy reveals that Sir2 and HerA assemble into a ∼1 MDa supramolecular octadecamer. Unexpectedly, this complex exhibits various enzymatic activities, including ATPase, NADase, helicase, and nuclease, which work together in a sophisticated manner to fulfill the antiphage function. Therefore, we name this defense system "Nezha" after a divine warrior in Chinese mythology who employs multiple weapons to defeat enemies. Our findings demonstrate that Nezha could sense phage infections, self-activate to arrest cell growth, eliminate phage genomes, and subsequently deactivate to allow for cell recovery. Collectively, Nezha represents a paradigm of sophisticated and multifaceted strategies bacteria use to defend against viral infections.
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Affiliation(s)
- Dongmei Tang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yijun Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tingting Jia
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiang Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Yamei Yu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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4
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Guzman BB, Son A, Litberg TJ, Huang Z, Dominguez D, Horowitz S. Emerging roles for G-quadruplexes in proteostasis. FEBS J 2023; 290:4614-4625. [PMID: 36017725 PMCID: PMC10071977 DOI: 10.1111/febs.16608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/22/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022]
Abstract
How nucleic acids interact with proteins, and how they affect protein folding, aggregation, and misfolding is a still-evolving area of research. Considerable effort is now focusing on a particular structure of RNA and DNA, G-quadruplexes, and their role in protein homeostasis and disease. In this state-of-the-art review, we track recent reports on how G-quadruplexes influence protein aggregation, proteolysis, phase separation, and protein misfolding diseases, and pose currently unanswered questions in the advance of this scientific field.
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Affiliation(s)
- Bryan B Guzman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Theodore J Litberg
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Zijue Huang
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
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5
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Myong S, Lee CY, Joshi M, Wang A. 5'UTR G-quadruplex structure enhances translation in size dependent manner. RESEARCH SQUARE 2023:rs.3.rs-3352233. [PMID: 37790436 PMCID: PMC10543253 DOI: 10.21203/rs.3.rs-3352233/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Translation initiation in bacteria is frequently regulated by various structures in the 5' untranslated region (5'UTR). Previously, we demonstrated that G-quadruplex (G4) formation in non-template DNA enhances transcription. In this study, we aimed to explore how G4 formation in mRNA (RG4) at 5'UTR impacts translation using a T7-based in vitro translation system and in E. coli. We showed that RG4 strongly promotes translation efficiency in a size-dependent manner. Additionally, inserting a hairpin upstream of the RG4 further enhances translation efficiency, reaching up to a 12-fold increase. We found that the RG4-dependent effect is not due to increased ribosome affinity, ribosome binding site accessibility, or mRNA stability. We proposed a physical barrier model in which bulky structures in 5'UTR prevent ribosome dislodging and thereby increase the translation output. This study provides biophysical insights into the regulatory role of 5'UTR structures in bacterial translation, highlighting their potential applications in tuning gene expression.
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Affiliation(s)
- Sua Myong
- Boston Children's Hospital/Harvard Medical School
| | | | - Meera Joshi
- Boston Children's Hospital/Harvard Medical School
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6
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Danino YM, Molitor L, Rosenbaum-Cohen T, Kaiser S, Cohen Y, Porat Z, Marmor-Kollet H, Katina C, Savidor A, Rotkopf R, Ben-Isaac E, Golani O, Levin Y, Monchaud D, Hickson I, Hornstein E. BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures. Nucleic Acids Res 2023; 51:9369-9384. [PMID: 37503837 PMCID: PMC10516661 DOI: 10.1093/nar/gkad613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
Bloom's syndrome (BLM) protein is a known nuclear helicase that is able to unwind DNA secondary structures such as G-quadruplexes (G4s). However, its role in the regulation of cytoplasmic processes that involve RNA G-quadruplexes (rG4s) has not been previously studied. Here, we demonstrate that BLM is recruited to stress granules (SGs), which are cytoplasmic biomolecular condensates composed of RNAs and RNA-binding proteins. BLM is enriched in SGs upon different stress conditions and in an rG4-dependent manner. Also, we show that BLM unwinds rG4s and acts as a negative regulator of SG formation. Altogether, our data expand the cellular activity of BLM and shed light on the function that helicases play in the dynamics of biomolecular condensates.
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Affiliation(s)
- Yehuda M Danino
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lena Molitor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Rosenbaum-Cohen
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Brain science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sebastian Kaiser
- Center for Chromosome Stability, Dept. of Cellular and Molecular Medicine, Panum Institute, Copenhagen Univ, 2200 København N., Denmark
| | - Yahel Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hagai Marmor-Kollet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- 1E therapeutics, Rehovot, Israel
| | - Corine Katina
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Rotkopf
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal Ben-Isaac
- MICC Cell Observatory Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ofra Golani
- MICC Cell Observatory Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, uB Dijon, France
| | - Ian D Hickson
- Center for Chromosome Stability, Dept. of Cellular and Molecular Medicine, Panum Institute, Copenhagen Univ, 2200 København N., Denmark
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
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7
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Sapir T, Reiner O. HNRNPU's multi-tasking is essential for proper cortical development. Bioessays 2023; 45:e2300039. [PMID: 37439444 DOI: 10.1002/bies.202300039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 05/27/2023] [Accepted: 06/12/2023] [Indexed: 07/14/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein U (HNRNPU) is a nuclear protein that plays a crucial role in various biological functions, such as RNA splicing and chromatin organization. HNRNPU/scaffold attachment factor A (SAF-A) activities are essential for regulating gene expression, DNA replication, genome integrity, and mitotic fidelity. These functions are critical to ensure the robustness of developmental processes, particularly those involved in shaping the human brain. As a result, HNRNPU is associated with various neurodevelopmental disorders (HNRNPU-related neurodevelopmental disorder, HNRNPU-NDD) characterized by developmental delay and intellectual disability. Our research demonstrates that the loss of HNRNPU function results in the death of both neural progenitor cells and post-mitotic neurons, with a higher sensitivity observed in the former. We reported that HNRNPU truncation leads to the dysregulation of gene expression and alternative splicing of genes that converge on several signaling pathways, some of which are likely to be involved in the pathology of HNRNPU-related NDD.
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Affiliation(s)
- Tamar Sapir
- Weizmann Institute of Science, Molecular Genetics and Molecular Neuroscience, Rehovot, Central, Israel
| | - Orly Reiner
- Weizmann Institute of Science, Molecular Genetics and Molecular Neuroscience, Rehovot, Central, Israel
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8
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Singh D, Desai N, Shah V, Datta B. In Silico Identification of Potential Quadruplex Forming Sequences in LncRNAs of Cervical Cancer. Int J Mol Sci 2023; 24:12658. [PMID: 37628839 PMCID: PMC10454738 DOI: 10.3390/ijms241612658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as auxiliary regulators of gene expression influencing tumor microenvironment, metastasis and radio-resistance in cancer. The presence of lncRNA in extracellular fluids makes them promising diagnostic markers. LncRNAs deploy higher-order structures to facilitate a complex range of functions. Among such structures, G-quadruplexes (G4s) can be detected or targeted by small molecular probes to drive theranostic applications. The in vitro identification of G4 formation in lncRNAs can be a tedious and expensive proposition. Bioinformatics-driven strategies can provide comprehensive and economic alternatives in conjunction with suitable experimental validation. We propose a pipeline to identify G4-forming sequences, protein partners and biological functions associated with dysregulated lncRNAs in cervical cancer. We identified 17 lncRNA clusters which possess transcripts that can fold into a G4 structure. We confirmed in vitro G4 formation in the four biologically active isoforms of SNHG20, MEG3, CRNDE and LINP1 by Circular Dichroism spectroscopy and Thioflavin-T-assisted fluorescence spectroscopy and reverse-transcriptase stop assay. Gene expression data demonstrated that these four lncRNAs can be potential prognostic biomarkers of cervical cancer. Two approaches were employed for identifying G4 specific protein partners for these lncRNAs and FMR2 was a potential interacting partner for all four clusters. We report a detailed investigation of G4 formation in lncRNAs that are dysregulated in cervical cancer. LncRNAs MEG3, CRNDE, LINP1 and SNHG20 are shown to influence cervical cancer progression and we report G4 specific protein partners for these lncRNAs. The protein partners and G4s predicted in lncRNAs can be exploited for theranostic objectives.
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Affiliation(s)
- Deepshikha Singh
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Nakshi Desai
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Viraj Shah
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Bhaskar Datta
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India
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9
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Ratajczak K, Stobiecka M. DNA Aptamer Beacon Probe (ABP) for Monitoring of Adenosine Triphosphate Level in SW480 Cancer Cells Treated with Glycolysis Inhibitor 2-Deoxyglucose. Int J Mol Sci 2023; 24:ijms24119295. [PMID: 37298245 DOI: 10.3390/ijms24119295] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Early cancer screening enables timely detection of carcinogenesis, and aids in prompt clinical intervention. Herein, we report on the development of a simple, sensitive, and rapid fluorometric assay based on the aptamer probe (aptamer beacon probe, ABP) for monitoring the energy-demand biomarker adenosine triphosphate (ATP), an essential energy source that is released into the tumor microenvironment. Its level plays a significant role in risk assessment of malignancies. The operation of the ABP for ATP was examined using solutions of ATP and other nucleotides (UTP, GTP, CTP), followed by monitoring of ATP production in SW480 cancer cells. Then, the effect of a glycolysis inhibitor, 2-deoxyglucose (2-DG), on SW480 cells was investigated. The stability of predominant ABP conformations in the temperature range of 23-91 °C and the effects of temperature on ABP interactions with ATP, UTP, GTP, and CTP were evaluated based on quenching efficiencies (QE) and Stern-Volmer constants (KSV). The optimized temperature for best selectivity of ABP toward ATP was 40 °C (KSV = 1093 M-1, QE = 42%). We have found that the inhibition of glycolysis in SW480 cancer cells by 2-deoxyglucose resulted in lowering of ATP production by 31.7%. Therefore, monitoring and modulation of ATP concentration may aid in future cancer treatment.
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Affiliation(s)
- Katarzyna Ratajczak
- Department of Physics and Biophysics, Warsaw University of Life Sciences, 159 Nowoursynowska Street, 02776 Warsaw, Poland
| | - Magdalena Stobiecka
- Department of Physics and Biophysics, Warsaw University of Life Sciences, 159 Nowoursynowska Street, 02776 Warsaw, Poland
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10
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Drino A, König L, Capitanchik C, Sanadgol N, Janisiw E, Rappol T, Vilardo E, Schaefer MR. Identification of RNA helicases with unwinding activity on angiogenin-processed tRNAs. Nucleic Acids Res 2023; 51:1326-1352. [PMID: 36718960 PMCID: PMC9943664 DOI: 10.1093/nar/gkad033] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 02/01/2023] Open
Abstract
Stress-induced tRNA fragmentation upon environmental insult is a conserved cellular process catalysed by endonucleolytic activities targeting mature tRNAs. The resulting tRNA-derived small RNAs (tsRNAs) have been implicated in various biological processes that impact cell-to-cell signalling, cell survival as well as gene expression regulation during embryonic development. However, how endonuclease-targeted tRNAs give rise to individual and potentially biologically active tsRNAs remains poorly understood. Here, we report on the in vivo identification of proteins associated with stress-induced tsRNAs-containing protein complexes, which, together with a 'tracer tRNA' assay, were used to uncover enzymatic activities that can bind and process specific endonuclease-targeted tRNAs in vitro. Among those, we identified conserved ATP-dependent RNA helicases which can robustly separate tRNAs with endonuclease-mediated 'nicks' in their anticodon loops. These findings shed light on the existence of cellular pathways dedicated to producing individual tsRNAs after stress-induced tRNA hydrolysis, which adds to our understanding as to how tRNA fragmentation and the resulting tsRNAs might exert physiological impact.
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Affiliation(s)
- Aleksej Drino
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | - Lisa König
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | | | - Nasim Sanadgol
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | - Eva Janisiw
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | - Tom Rappol
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | - Elisa Vilardo
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
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11
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Ma Y, Yang Y, Xin J, He L, Hu Z, Gao T, Pan F, Guo Z. RNA G-Quadruplex within the 5'-UTR of FEN1 Regulates mRNA Stability under Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12020276. [PMID: 36829835 PMCID: PMC9952066 DOI: 10.3390/antiox12020276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Reactive oxygen species (ROS) are a group of highly oxidative molecules that induce DNA damage, affecting DNA damage response (DDR) and gene expression. It is now recognized that DNA base excision repair (BER) is one of the important pathways responsible for sensing oxidative stress to eliminate DNA damage, in which FEN1 plays an important role in this process. However, the regulation of FEN1 under oxidative stress is still unclear. Here, we identified a novel RNA G-quadruplex (rG4) sequence in the 5'untranslated region (5'UTR) of FEN1 mRNA. Under oxidative stress, the G bases in the G4-forming sequence can be oxidized by ROS, resulting in structural disruption of the G-quadruplex. ROS or TMPyP4, a G4-structural ligand, disrupted the formation of G4 structure and affected the expression of FEN1. Furthermore, pull-down experiments identified a novel FEN1 rG4-binding protein, heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), and cellular studies have shown that hnRNPA1 plays an important role in regulating FEN1 expression. This work demonstrates that rG4 acts as a ROS sensor in the 5'UTR of FEN1 mRNA. Taken together, these results suggest a novel role for rG4 in translational control under oxidative stress.
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Affiliation(s)
- Ying Ma
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yang Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jingyu Xin
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Tao Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (F.P.); (Z.G.)
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (F.P.); (Z.G.)
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12
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Lyu K, Chen SB, Chow EYC, Zhao H, Yuan JH, Cai M, Shi J, Chan TF, Tan JH, Kwok CK. An RNA G-Quadruplex Structure within the ADAR 5'UTR Interacts with DHX36 Helicase to Regulate Translation. Angew Chem Int Ed Engl 2022; 61:e202203553. [PMID: 36300875 DOI: 10.1002/anie.202203553] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Indexed: 11/25/2022]
Abstract
RNA G-quadruplex (rG4) structures in the 5' untranslated region (5'UTR) play crucial roles in fundamental cellular processes. ADAR is an important enzyme that binds to double-strand RNA and accounts for the conversion of Adenosine to Inosine in RNA editing. However, so far there is no report on the formation and regulatory role of rG4 on ADAR expression. Here, we identify and characterize a thermostable rG4 structure within the 5'UTR of the ADAR1 mRNA and demonstrate its formation and inhibitory role on translation in reporter gene and native gene constructs. We reveal rG4-specific helicase DHX36 interacts with this rG4 in vitro and in cells under knockdown and knockout conditions by GTFH (G-quadruplex-triggered fluorogenic hybridization) probes and modulates translation in an rG4-dependent manner. Our results further substantiate the rG4 structure-DHX36 protein interaction in cells and highlight rG4 to be a key player in controlling ADAR1 translation.
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Affiliation(s)
- Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, 510006, China
| | - Eugene Yui-Ching Chow
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Haizhou Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | - Jia-Hao Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, 510006, China
| | - Meng Cai
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, Tung Biomedical Sciences Center, City University of Hong Kong, Hong Kong SAR, China
| | - Jiahai Shi
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, Tung Biomedical Sciences Center, City University of Hong Kong, Hong Kong SAR, China.,Department of Biochemistry, Synthetic Biology Translational Research Programmes, Yong Loo Lin School of Medicine, National University of, Singapore, Singapore
| | - Ting-Fung Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, 510006, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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13
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Song QX, Lai CW, Liu NN, Hou XM, Xi XG. DEAD-box RNA helicase Dbp2 binds to G-quadruplex nucleic acids and regulates different conformation of G-quadruplex DNA. Biochem Biophys Res Commun 2022; 634:182-188. [DOI: 10.1016/j.bbrc.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/01/2022] [Indexed: 11/25/2022]
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14
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Belachew B, Gao J, Byrd AK, Raney KD. Hepatitis C virus non-structural protein NS3 unfolds viral G-quadruplex RNA structures. J Biol Chem 2022; 298:102486. [PMID: 36108740 PMCID: PMC9582721 DOI: 10.1016/j.jbc.2022.102486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/17/2022] [Accepted: 09/03/2022] [Indexed: 11/29/2022] Open
Abstract
Hepatitis C virus (HCV) is a major cause of liver-related diseases and hepatocellular carcinoma. The helicase domain of one of the nonstructural proteins of HCV, NS3 (nonstructural protein 3), is essential for viral replication; however, its specific biological role is still under investigation. Here, we set out to determine the interaction between a purified recombinant full length NS3 and synthetic guanine-rich substrates that represent the conserved G-quadruplex (G4)-forming sequences in the HCV-positive and HCV-negative strands. We performed fluorescence anisotropy binding, G4 reporter duplex unwinding, and G4RNA trapping assays to determine the binding and G4 unfolding activity of NS3. Our data suggest that NS3 can unfold the conserved G4 structures present within the genome and the negative strand of HCV. Additionally, we found the activity of NS3 on a G4RNA was reduced significantly in the presence of a G4 ligand. The ability of NS3 to unfold HCV G4RNA could imply a novel biological role of the viral helicase in replication.
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Affiliation(s)
- Binyam Belachew
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205.
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15
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Yang C, Yao J, Yi H, Huang X, Zhao W, Yang Z. To unwind the biological knots: The DNA/RNA G-quadruplex resolvase RHAU (DHX36) in development and disease. Animal Model Exp Med 2022; 5:542-549. [PMID: 35789129 PMCID: PMC9773310 DOI: 10.1002/ame2.12251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/21/2022] [Indexed: 12/30/2022] Open
Abstract
The G-quadruplex (G4) sequences are short fragments of 4-interval triple guanine (G) with frequent and ubiquitous distribution in the genome and RNA transcripts. The G4 sequences are usually folded into secondary "knot" structure via Hoogsteen hydrogen bond to exert negative regulation on a variety of biological processes, including DNA replication and transcription, mRNA translation, and telomere maintenance. Recent structural biological and mouse genetics studies have demonstrated that RHAU (DHX36) can bind and unwind the G4 "knots" to modulate embryonic development and postnatal organ function. Deficiency of RHAU gives rise to embryonic lethality, impaired organogenesis, and organ dysfunction. These studies uncovered the pivotal G4 resolvase function of RHAU to release the G4 barrier, which plays fundamental roles in development and physiological homeostasis. This review discusses the latest advancements and findings in deciphering RHAU functions using animal models.
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Affiliation(s)
- Chensi Yang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Jie Yao
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Huijuan Yi
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Xinyi Huang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Wukui Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
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16
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Wang L, Xu YP, Bai D, Shan SW, Xie J, Li Y, Wu WQ. Insights into the structural dynamics and helicase-catalyzed unfolding of plant RNA G-quadruplexes. J Biol Chem 2022; 298:102165. [PMID: 35738400 PMCID: PMC9293640 DOI: 10.1016/j.jbc.2022.102165] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/21/2022] Open
Abstract
RNA G-quadruplexes (rG4s) are noncanonical RNA secondary structures formed by guanine (G)-rich sequences. These complexes play important regulatory roles in both animals and plants through their structural dynamics and are closely related to human diseases and plant growth, development, and adaption. Thus, studying the structural dynamics of rG4s is fundamentally important; however, their folding pathways and their unfolding by specialized helicases are not well understood. In addition, no plant rG4-specialized helicases have been identified. Here, using single-molecule FRET, we experimentally elucidated for the first time the folding pathway and intermediates, including a G-hairpin and G-triplex. In addition, using proteomics screening and microscale thermophoresis, we identified and validated five rG4-specialized helicases in Arabidopsis thaliana. Furthermore, DExH1, the ortholog of the famous human rG4 helicase RHAU/DHX36, stood out for its robust rG4 unwinding ability. Taken together, these results shed light on the structural dynamics of plant rG4s.
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Affiliation(s)
- Liu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Ya-Peng Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Di Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Song-Wang Shan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Jie Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Yan Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Wen-Qiang Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475001, China.
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17
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Georgakopoulos-Soares I, Parada GE, Wong HY, Medhi R, Furlan G, Munita R, Miska EA, Kwok CK, Hemberg M. Alternative splicing modulation by G-quadruplexes. Nat Commun 2022; 13:2404. [PMID: 35504902 PMCID: PMC9065059 DOI: 10.1038/s41467-022-30071-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 03/30/2022] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is central to metazoan gene regulation, but the regulatory mechanisms are incompletely understood. Here, we show that G-quadruplex (G4) motifs are enriched ~3-fold near splice junctions. The importance of G4s in RNA is emphasised by a higher enrichment for the non-template strand. RNA-seq data from mouse and human neurons reveals an enrichment of G4s at exons that were skipped following depolarisation induced by potassium chloride. We validate the formation of stable RNA G4s for three candidate splice sites by circular dichroism spectroscopy, UV-melting and fluorescence measurements. Moreover, we find that sQTLs are enriched at G4s, and a minigene experiment provides further support for their role in promoting exon inclusion. Analysis of >1,800 high-throughput experiments reveals multiple RNA binding proteins associated with G4s. Finally, exploration of G4 motifs across eleven species shows strong enrichment at splice sites in mammals and birds, suggesting an evolutionary conserved splice regulatory mechanism. Here the authors shows that G-quadruplexes, non-canonical DNA/RNA structures, can have a direct impact on alternative splicing and that binding of splicing regulators is affected by their presence.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Guillermo E Parada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5A 1A8, Canada
| | - Hei Yuen Wong
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Ragini Medhi
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Giulia Furlan
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Eric A Miska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK. .,Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK. .,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA.
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18
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Meier-Stephenson V. G4-quadruplex-binding proteins: review and insights into selectivity. Biophys Rev 2022; 14:635-654. [PMID: 35791380 PMCID: PMC9250568 DOI: 10.1007/s12551-022-00952-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.
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Affiliation(s)
- Vanessa Meier-Stephenson
- Department of Medicine, Division of Infectious Diseases, University of Alberta, Edmonton, AB Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
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19
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Paul T, Myong S. Protocol for generation and regeneration of PEG-passivated slides for single-molecule measurements. STAR Protoc 2022; 3:101152. [PMID: 35146451 PMCID: PMC8819390 DOI: 10.1016/j.xpro.2022.101152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-molecule fluorescence detection by total internal reflection microscope requires surface passivation by polyethylene glycol (PEG) coating, which is labor intensive and is only good for one or two experiments. Here, we present an efficient and reliable protocol for generating and regenerating the PEG surface for multiple rounds of experiments (∼5–10 times) in the same channel. This protocol is very simple, robust, rapid, and versatile; i.e., multiple strategies can be implemented to regenerate different layers of surface. The regeneration strategy saves time, improves the cost effectiveness, and enhances the efficiency of single-molecule experiments. For complete details on the use and execution of this profile, please refer to Paul et al. (2021a). Regeneration of PEG-passivated slide is simple, quick, and cost effective Multiple experiments can be performed in a single channel Different strategies are implemented for different level of regeneration Regeneration leads to highly reproducible results
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.,Physics Frontier Center, Center for the Physics of Living Cells, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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20
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Gao B, Zheng YT, Su AM, Sun B, Xi XG, Hou XM. Remodeling the conformational dynamics of I-motif DNA by helicases in ATP-independent mode at acidic environment. iScience 2022; 25:103575. [PMID: 34988409 PMCID: PMC8704484 DOI: 10.1016/j.isci.2021.103575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/09/2021] [Accepted: 12/03/2021] [Indexed: 01/18/2023] Open
Abstract
I-motifs are noncanonical four-stranded DNA structures formed by C-rich sequences at acidic environment with critical biofunctions. The particular pH sensitivity has inspired the development of i-motifs as pH sensors and DNA motors in nanotechnology. However, the folding and regulation mechanisms of i-motifs remain elusive. Here, using single-molecule FRET, we first show that i-motifs are more dynamic than G4s. Impressively, i-motifs display a high diversity of six folding species with slow interconversion. Further results indicate that i-motifs can be linearized by Replication protein A. More importantly, we identified a number of helicases with high specificity to i-motifs at low pH. All these helicases directly act on and efficiently resolve i-motifs into intermediates independent of ATP, although they poorly unwind G4 or duplex at low pH. Owing to the extreme sensitivity to helicases and no need for ATP, i-motif may be applied as a probe for helicase sensing both in vitro and in vivo.
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Affiliation(s)
- Bo Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Ya-Ting Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Ai-Min Su
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
- LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Gif-sur-Yvette, France
| | - Xi-Miao Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Corresponding author
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21
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Miyashita E, Komatsu KR, Saito H. Large-Scale Analysis of RNA-Protein Interactions for Functional RNA Motif Discovery Using FOREST. Methods Mol Biol 2022; 2509:279-290. [PMID: 35796970 DOI: 10.1007/978-1-0716-2380-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
RNA transcripts can form a variety of higher-order structures. We developed a large-scale affinity analysis system, FOREST (Folded RNA Element Profiling with Structure Library), to investigate the function of these RNA structures on transcriptome-wide scale. Here we describe a protocol to analyze RNA-protein interactions using FOREST . Users of the protocol prepare an RNA structure library comprised of diverse species of transcripts and perform high-throughput characterization of the RNA-protein interactions to obtain quantitative and comprehensive information on the binding affinities and specificities. Moreover, we demonstrate how FOREST can be used to analyze a non-canonical structure, the RNA G-quadruplex, without sequencing bias, because the quantification is performed directly on a microarray without sequence amplification. FOREST will contribute to the discovery of RNA structure motifs that determine RNA-protein interactions.
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Affiliation(s)
- Emi Miyashita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- xFOREST Therapeutics Co., Ltd., Kyoto, Japan
| | | | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.
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22
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Paul T, Liou W, Cai X, Opresko PL, Myong S. TRF2 promotes dynamic and stepwise looping of POT1 bound telomeric overhang. Nucleic Acids Res 2021; 49:12377-12393. [PMID: 34850123 PMCID: PMC8643667 DOI: 10.1093/nar/gkab1123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/20/2021] [Accepted: 11/18/2021] [Indexed: 11/12/2022] Open
Abstract
Human telomeres are protected by shelterin proteins, but how telomeres maintain a dynamic structure remains elusive. Here, we report an unexpected activity of POT1 in imparting conformational dynamics of the telomere overhang, even at a monomer level. Strikingly, such POT1-induced overhang dynamics is greatly enhanced when TRF2 engages with the telomere duplex. Interestingly, TRF2, but not TRF2ΔB, recruits POT1-bound overhangs to the telomere ds/ss junction and induces a discrete stepwise movement up and down the axis of telomere duplex. The same steps are observed regardless of the length of the POT1-bound overhang, suggesting a tightly regulated conformational dynamic coordinated by TRF2 and POT1. TPP1 and TIN2 which physically connect POT1 and TRF2 act to generate a smooth movement along the axis of the telomere duplex. Our results suggest a plausible mechanism wherein telomeres maintain a dynamic structure orchestrated by shelterin.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Wilson Liou
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xinyi Cai
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, Hillman Cancer Center, 5117 Centre Avenue, Suite 2.6a, Pittsburgh, PA 15213, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
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23
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Liu Y, Zhu X, Wang K, Zhang B, Qiu S. The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans. Front Mol Biosci 2021; 8:783889. [PMID: 34912850 PMCID: PMC8667583 DOI: 10.3389/fmolb.2021.783889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/02/2021] [Indexed: 01/19/2023] Open
Abstract
G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.
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Affiliation(s)
- Yang Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Xinting Zhu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Shuyi Qiu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
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24
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Varshney D, Cuesta SM, Herdy B, Abdullah UB, Tannahill D, Balasubramanian S. RNA G-quadruplex structures control ribosomal protein production. Sci Rep 2021; 11:22735. [PMID: 34815422 PMCID: PMC8611094 DOI: 10.1038/s41598-021-01847-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Four-stranded G-quadruplex (G4) structures form from guanine-rich tracts, but the extent of their formation in cellular RNA and details of their role in RNA biology remain poorly defined. Herein, we first delineate the presence of endogenous RNA G4s in the human cytoplasmic transcriptome via the binding sites of G4-interacting proteins, DDX3X (previously published), DHX36 and GRSF1. We demonstrate that a sub-population of these RNA G4s are reliably detected as folded structures in cross-linked cellular lysates using the G4 structure-specific antibody BG4. The 5' UTRs of protein coding mRNAs show significant enrichment in folded RNA G4s, particularly those for ribosomal proteins. Mutational disruption of G4s in ribosomal protein UTRs alleviates translation in vitro, whereas in cells, depletion of G4-resolving helicases or treatment with G4-stabilising small molecules inhibit the translation of ribosomal protein mRNAs. Our findings point to a common mode for translational co-regulation mediated by G4 structures. The results reveal a potential avenue for therapeutic intervention in diseases with dysregulated translation, such as cancer.
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Affiliation(s)
- Dhaval Varshney
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Sergio Martinez Cuesta
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge, UK
| | - Barbara Herdy
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ummi Binti Abdullah
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David Tannahill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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25
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Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy. Biomolecules 2021; 11:biom11111579. [PMID: 34827577 PMCID: PMC8615981 DOI: 10.3390/biom11111579] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 12/19/2022] Open
Abstract
G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety of topologies and have complex folding/unfolding dynamics. Determining the dynamics of G4s and their regulation by proteins remains challenging due to the coexistence of multiple structures in a heterogeneous sample. Here, in this mini-review, we introduce the application of single-molecule force-spectroscopy methods, such as magnetic tweezers, optical tweezers, and atomic force microscopy, to characterize the polymorphism and folding/unfolding dynamics of G4s. We also briefly introduce recent studies using single-molecule force spectroscopy to study the molecular mechanisms of G4-interacting proteins.
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26
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Marilovtseva EV, Studitsky VM. Guanine Quadruplexes in Cell Nucleus Metabolism. Mol Biol 2021. [DOI: 10.1134/s0026893321040075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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28
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Lyu K, Chow EYC, Mou X, Chan TF, Kwok CK. RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res 2021; 49:5426-5450. [PMID: 33772593 PMCID: PMC8191793 DOI: 10.1093/nar/gkab187] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago. Over the years, these four-stranded structural motifs have been demonstrated to have significant regulatory roles in diverse biological processes, but challenges remain in detecting them globally and reliably. Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently. In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and important functions of rG4 being discovered in vivo across the tree of life, and discuss the key biological questions to be addressed in the near future.
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Affiliation(s)
- Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Eugene Yui-Ching Chow
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xi Mou
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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29
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Cui Y, Li Z, Cao J, Lane J, Birkin E, Dong X, Zhang L, Jiang WG. The G4 Resolvase DHX36 Possesses a Prognosis Significance and Exerts Tumour Suppressing Function Through Multiple Causal Regulations in Non-Small Cell Lung Cancer. Front Oncol 2021; 11:655757. [PMID: 33987090 PMCID: PMC8111079 DOI: 10.3389/fonc.2021.655757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is one of the most prevalent cancers in both men and women worldwide. The nucleic acid G4 structures have been implicated in the transcriptional programmes of cancer-related genes in some cancers such as lung cancer. However, the role of the dominant G4 resolvase DHX36 in the progression of lung cancer remains unknown. In this study, by bioinformatic analysis of public datasets (TCGA and GEO), we find DHX36 is an independent prognosis indicator in non-small-cell lung carcinoma (NSCLC) with subtype dependence. The stable lentiviral knockdown of the DHX36 results in accelerated migration and aggregation of the S-phase subpopulation in lung cancer cells. The reduction of DHX36 level de-sensitises the proliferation response of lung cancer cells to chemotherapeutic drugs such as paclitaxel with cell dependence. The knockdown of this helicase leads to promoted tumour growth, demonstrated by a 3D fluorescence spheroid lung cancer model, and the stimulation of cell colony formation as shown by single-cell cultivation. High throughput proteomic array indicates that DHX36 functions in lung cancer cells through regulating multiple signalling pathways including activation of protein activity, protein autophosphorylation, Fc-receptor signalling pathway, response to peptide hormone and stress-activated protein kinase signalling cascade. A causal transcriptomic analysis suggests that DHX36 is significantly associated with mRNA surveillance, RNA degradation, DNA replication and Myc targets. Therefore, we unveil that DHX36 presents clinical significance and plays a role in tumour suppression in lung cancer, and propose a potentially new concept for an anti-cancer therapy based on helicase-specific targeting.
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Affiliation(s)
- Yuxin Cui
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Zhilei Li
- Department of Pharmacy, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Junxia Cao
- Biotherapy Center, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Jane Lane
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Emily Birkin
- Cardiff & Vale University Health Board, University Hospital of Wales, Cardiff, United Kingdom
| | - Xuefei Dong
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Lijian Zhang
- Department of Thoracic Surgery, Peking University Cancer Hospital, Beijing, China
| | - Wen G Jiang
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff, United Kingdom
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30
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Liu H, Lu YN, Paul T, Periz G, Banco MT, Ferré-D'Amaré AR, Rothstein JD, Hayes LR, Myong S, Wang J. A Helicase Unwinds Hexanucleotide Repeat RNA G-Quadruplexes and Facilitates Repeat-Associated Non-AUG Translation. J Am Chem Soc 2021; 143:7368-7379. [PMID: 33855846 DOI: 10.1021/jacs.1c00131] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The expansion of a hexanucleotide repeat GGGGCC (G4C2) in the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The G4C2 expansion leads to repeat-associated non-AUG (RAN) translation and the production of toxic dipeptide repeat (DPR) proteins, but the mechanisms of RAN translation remain enigmatic. Here, we report that the RNA helicase DHX36 is a robust positive regulator of C9orf72 RAN translation. DHX36 has a high affinity for the G4C2 repeat RNA, preferentially binds to the repeat RNA's G-quadruplex conformation, and efficiently unwinds the G4C2 G-quadruplex structures. Native DHX36 interacts with the G4C2 repeat RNA and is essential for effective RAN translation in the cell. In induced pluripotent stem cells and differentiated motor neurons derived from C9orf72-linked ALS patients, reducing DHX36 significantly decreased the levels of endogenous DPR proteins. DHX36 is also aberrantly upregulated in tissues of C9orf72-linked ALS patients. These results indicate that DHX36 facilitates C9orf72 RAN translation by resolving repeat RNA G-quadruplex structures and may be a potential target for therapeutic intervention.
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Affiliation(s)
- Honghe Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Yu-Ning Lu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Goran Periz
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Michael T Banco
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, United States
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, United States
| | - Jeffrey D Rothstein
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Lindsey R Hayes
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
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31
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The Long Linker Region of Telomere-Binding Protein TRF2 Is Responsible for Interactions with Lamins. Int J Mol Sci 2021; 22:ijms22073293. [PMID: 33804854 PMCID: PMC8036907 DOI: 10.3390/ijms22073293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/15/2022] Open
Abstract
Telomere-binding factor 2 (TRF2) is part of the shelterin protein complex found at chromosome ends. Lamin A/C interacts with TRF2 and influences telomere position. TRF2 has an intrinsically disordered region between the ordered dimerization and DNA-binding domains. This domain is referred to as the long linker region of TRF2, or udTRF2. We suggest that udTRF2 might be involved in the interaction between TRF2 and lamins. The recombinant protein corresponding to the udTRF2 region along with polyclonal antibodies against this region were used in co-immunoprecipitation with purified lamina and nuclear extracts. Co-immunoprecipitation followed by Western blots and mass spectrometry indicated that udTRF2 interacts with lamins, preferably lamins A/C. The interaction did not involve any lamin-associated proteins, was not dependent on the post-translation modification of lamins, nor did it require their higher-order assembly. Besides lamins, a number of other udTRF2-interacting proteins were identified by mass spectrometry, including several heterogeneous nuclear ribonucleoproteins (hnRNP A2/B1, hnRNPA1, hnRNP A3, hnRNP K, hnRNP L, hnRNP M), splicing factors (SFPQ, NONO, SRSF1, and others), helicases (DDX5, DHX9, and Eif4a3l1), topoisomerase I, and heat shock protein 71, amongst others. Some of the identified interactors are known to be involved in telomere biology; the roles of the others remain to be investigated. Thus, the long linker region of TRF2 (udTRF2) is a regulatory domain responsible for the association between TRF2 and lamins and is involved in interactions with other proteins.
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32
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Paul T, Ha T, Myong S. Regeneration of PEG slide for multiple rounds of single-molecule measurements. Biophys J 2021; 120:1788-1799. [PMID: 33675764 DOI: 10.1016/j.bpj.2021.02.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022] Open
Abstract
Single-molecule fluorescence detection of protein and other biomolecules requires a polyethylene glycol (PEG)-passivated surface. Individual channels on a PEG-passivated slide are typically used only a few times, limiting the number of experiments per slide. Here, we report several strategies for regenerating PEG surfaces for multiple rounds of experiments. First, we show regeneration of DNA- or RNA-tethered surfaces by washing out the bound protein by 0.1% sodium dodecyl sulfate, which is significantly more effective than 6 M urea, 6 M GdmCl, or 100 μM proteinase K. Strikingly, 10 consecutive experiments in five different systems produced indistinguishable results both in molecule count and protein activity. Second, duplexed DNA unwound by helicase or denatured by 50 mM NaOH was reannealed with a complementary strand to regenerate the duplexed substrate with an exceptionally high recovery rate. Third, the biotin-PEG layer was regenerated by using 7 M NaOH to strip off NeutrAvidin, which can be reapplied for additional experiments. We demonstrate five cycles of regenerating antibody immobilized surface by which three different protein activity was measured. Altogether, our methods represent reliable and reproducible yet simple and rapid strategies that will enhance the efficiency of single-molecule experiments.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, Maryland
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois.
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33
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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34
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Meier-Stephenson V, Badmalia MD, Mrozowich T, Lau KCK, Schultz SK, Gemmill DL, Osiowy C, van Marle G, Coffin CS, Patel TR. Identification and characterization of a G-quadruplex structure in the pre-core promoter region of hepatitis B virus covalently closed circular DNA. J Biol Chem 2021; 296:100589. [PMID: 33774051 PMCID: PMC8094906 DOI: 10.1016/j.jbc.2021.100589] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023] Open
Abstract
Approximately 250 million people worldwide are chronically infected with the hepatitis B virus (HBV) and are at increased risk of developing cirrhosis and hepatocellular carcinoma. The HBV genome persists as covalently closed circular DNA (cccDNA), which serves as the template for all HBV mRNA transcripts. Current nucleos(t)ide analogs used to treat HBV do not directly target the HBV cccDNA genome and thus cannot eradicate HBV infection. Here, we report the discovery of a unique G-quadruplex structure in the pre-core promoter region of the HBV genome that is conserved among nearly all genotypes. This region is central to critical steps in the viral life cycle, including the generation of pregenomic RNA, synthesis of core and polymerase proteins, and genome encapsidation; thus, an increased understanding of the HBV pre-core region may lead to the identification of novel anti-HBV cccDNA targets. We utilized biophysical methods (circular dichroism and small-angle X-ray scattering) to characterize the HBV G-quadruplex and the effect of three distinct G to A mutants. We also used microscale thermophoresis to quantify the binding affinity of G-quadruplex and its mutants with a known quadruplex-binding protein (DHX36). To investigate the physiological relevance of HBV G-quadruplex, we employed assays using DHX36 to pull-down cccDNA and compared HBV infection in HepG2 cells transfected with wild-type and mutant HBV plasmids by monitoring the levels of genomic DNA, pregenomic RNA, and antigens. Further evaluation of this critical host-protein interaction site in the HBV cccDNA genome may facilitate the development of novel anti-HBV therapeutics against the resilient cccDNA template.
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Affiliation(s)
- Vanessa Meier-Stephenson
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada; Department of Medicine, Cumming School of Medicine, Calgary, Alberta, Canada
| | - Maulik D Badmalia
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Tyler Mrozowich
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Keith C K Lau
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Sarah K Schultz
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Darren L Gemmill
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Carla Osiowy
- Viral Hepatitis and Bloodborne Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Guido van Marle
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Carla S Coffin
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada; Department of Medicine, Cumming School of Medicine, Calgary, Alberta, Canada.
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada; DiscoveryLab, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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35
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You H, Zhou Y, Yan J. Using Magnetic Tweezers to Unravel the Mechanism of the G-quadruplex Binding and Unwinding Activities of DHX36 Helicase. Methods Mol Biol 2021; 2209:175-191. [PMID: 33201470 DOI: 10.1007/978-1-0716-0935-4_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule manipulation methods are useful techniques to probe the interactions of proteins and nucleic acid structures. Here, we describe the magnetic tweezers-based single-molecule investigation of the binding of helicases to G-quadruplex structures and their ATP-dependent unwinding activity, using DHX36 (also known as RHAU and G4R1) helicase and a DNA G-quadruplex structure for an example. We specifically emphasize on the principle and method to probe the interactions between DHX36 and the DNA G-quadruplex in different intermediate states during an ATPase cycle of DHX36, based on detecting the DHX36-induced changes in the lifetime of the DNA G-quadruplex under tension. The principle of the measurement can be broadly extended to the studies of other DNA or RNA G-quadruplex helicases.
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Affiliation(s)
- Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhou
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
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36
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Kharel P, Becker G, Tsvetkov V, Ivanov P. Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back. Nucleic Acids Res 2020; 48:12534-12555. [PMID: 33264409 PMCID: PMC7736831 DOI: 10.1093/nar/gkaa1126] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
Guanine-quadruplexes (G4s) are non-canonical four-stranded structures that can be formed in guanine (G) rich nucleic acid sequences. A great number of G-rich sequences capable of forming G4 structures have been described based on in vitro analysis, and evidence supporting their formation in live cells continues to accumulate. While formation of DNA G4s (dG4s) within chromatin in vivo has been supported by different chemical, imaging and genomic approaches, formation of RNA G4s (rG4s) in vivo remains a matter of discussion. Recent data support the dynamic nature of G4 formation in the transcriptome. Such dynamic fluctuation of rG4 folding-unfolding underpins the biological significance of these structures in the regulation of RNA metabolism. Moreover, rG4-mediated functions may ultimately be connected to mechanisms underlying disease pathologies and, potentially, provide novel options for therapeutics. In this framework, we will review the landscape of rG4s within the transcriptome, focus on their potential impact on biological processes, and consider an emerging connection of these functions in human health and disease.
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Affiliation(s)
- Prakash Kharel
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gertraud Becker
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vladimir Tsvetkov
- Computational Oncology Group, I. M. Sechenov First Moscow State Medical University, Moscow 119146, Russia
- Federal Research and Clinical Center for Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow 117912, Russia
| | - Pavel Ivanov
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
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37
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Russon MP, Westerhouse KM, Tran EJ. Transcription, translation, and DNA repair: new insights from emerging noncanonical substrates of RNA helicases. Biol Chem 2020; 402:637-644. [PMID: 33857360 DOI: 10.1515/hsz-2020-0333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/23/2020] [Indexed: 11/15/2022]
Abstract
RNA helicases are enzymes that exist in all domains of life whose canonical functions include ATP-dependent remodeling of RNA structures and displacement of proteins from ribonucleoprotein complexes (RNPs). These enzymes play roles in virtually all processes of RNA metabolism, including pre-mRNA splicing, rRNA processing, nuclear mRNA export, translation and RNA decay. Here we review emerging noncanonical substrates of RNA helicases including RNA-DNA hybrids (R-loops) and RNA and DNA G-quadruplexes and discuss their biological significance.
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Affiliation(s)
- Matthew P Russon
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN, 47907, USA
| | - Kirsten M Westerhouse
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN, 47907, USA
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN, 47907, USA.,Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN, 47907, USA
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38
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RNA structure-wide discovery of functional interactions with multiplexed RNA motif library. Nat Commun 2020; 11:6275. [PMID: 33293523 PMCID: PMC7723054 DOI: 10.1038/s41467-020-19699-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/16/2020] [Indexed: 12/30/2022] Open
Abstract
Biochemical assays and computational analyses have discovered RNA structures throughout various transcripts. However, the roles of these structures are mostly unknown. Here we develop folded RNA element profiling with structure library (FOREST), a multiplexed affinity assay system to identify functional interactions from transcriptome-wide RNA structure datasets. We generate an RNA structure library by extracting validated or predicted RNA motifs from gene-annotated RNA regions. The RNA structure library with an affinity enrichment assay allows for the comprehensive identification of target-binding RNA sequences and structures in a high-throughput manner. As a proof-of-concept, FOREST discovers multiple RNA-protein interaction networks with quantitative scores, including translational regulatory elements that function in living cells. Moreover, FOREST reveals different binding landscapes of RNA G-quadruplex (rG4) structures-binding proteins and discovers rG4 structures in the terminal loops of precursor microRNAs. Overall, FOREST serves as a versatile platform to investigate RNA structure-function relationships on a large scale. Structured RNA motifs can be obtained by structure probing, duplex capture, and motif prediction. Here the authors develop a multiplexed affinity assay system to identify functional protein interactors from an RNA structure library with validated or predicted RNA motifs.
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39
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Dumas L, Herviou P, Dassi E, Cammas A, Millevoi S. G-Quadruplexes in RNA Biology: Recent Advances and Future Directions. Trends Biochem Sci 2020; 46:270-283. [PMID: 33303320 DOI: 10.1016/j.tibs.2020.11.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
RNA G-quadruplexes (RG4s) are four-stranded structures known to control gene expression mechanisms, from transcription to protein synthesis, and DNA-related processes. Their potential impact on RNA biology allows these structures to shape cellular processes relevant to disease development, making their targeting for therapeutic purposes an attractive option. We review here the current knowledge on RG4s, focusing on the latest breakthroughs supporting the notion of transient structures that fluctuate dynamically in cellulo, their interplay with RNA modifications, their role in cell compartmentalization, and their deregulation impacting the host immune response. We emphasize RG4-binding proteins as determinants of their transient conformation and effectors of their biological functions.
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Affiliation(s)
- Leïla Dumas
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III - Paul Sabatier, 31330 Toulouse, France
| | - Pauline Herviou
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III - Paul Sabatier, 31330 Toulouse, France
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, (TN), Italy
| | - Anne Cammas
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III - Paul Sabatier, 31330 Toulouse, France
| | - Stefania Millevoi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III - Paul Sabatier, 31330 Toulouse, France.
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40
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Schult P, Paeschke K. The DEAH helicase DHX36 and its role in G-quadruplex-dependent processes. Biol Chem 2020; 402:581-591. [PMID: 33021960 DOI: 10.1515/hsz-2020-0292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023]
Abstract
DHX36 is a member of the DExD/H box helicase family, which comprises a large number of proteins involved in various cellular functions. Recently, the function of DHX36 in the regulation of G-quadruplexes (G4s) was demonstrated. G4s are alternative nucleic acid structures, which influence many cellular pathways on a transcriptional and post-transcriptional level. In this review we provide an overview of the current knowledge about DHX36 structure, substrate specificity, and mechanism of action based on the available models and crystal structures. Moreover, we outline its multiple functions in cellular homeostasis, immunity, and disease. Finally, we discuss the open questions and provide potential directions for future research.
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Affiliation(s)
- Philipp Schult
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, D-53127Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, D-53127Bonn, Germany
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41
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Richardson A, Zentz ZA, Chambers AE, Sandwith SN, Reisinger MA, Saunders DW, Tompkins JD, Riggs AD, Routh ED, Rubenstein EM, Smaldino MA, Vaughn JP, Haney RA, Smaldino PJ. G-Quadruplex Helicase DHX36/G4R1 Engages Nuclear Lamina Proteins in Quiescent Breast Cancer Cells. ACS OMEGA 2020; 5:24916-24926. [PMID: 33015511 PMCID: PMC7528498 DOI: 10.1021/acsomega.0c03723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
G-quadruplexes (G4s) are nucleic acid structures found enriched within gene regulatory sequences. G4s control fundamental cellular processes, including replication, transcription, and translation. Proto-oncogenes are enriched with G4 sequences, while tumor-suppressor genes are depleted, suggesting roles for G4s in cell survival and proliferation. Specialized helicases participate in G4-mediated gene regulation via enzymatic unwinding activity. One such enzyme, DHX36/G4R1, is the major G4-helicase and is a master regulator of G4-DNAs and mRNAs. G4-resolution promotes the expression of proproliferative genes; as such, DHX36/G4R1 promotes cell proliferation. Little is known about how DHX36/G4R1 itself is regulated in nondividing cells. We hypothesized that DHX36/G4R1 protein binding partners are altered when a cell transitions from a dividing to a quiescent state. We found that DHX36/G4R1 co-purifies with a distinct set of proteins under quiescent conditions, which may represent a novel complex that regulates DHX36/G4R1 during cell cycle transitions and have implications for development and cancer.
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Affiliation(s)
- Adam.
E. Richardson
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Zachary. A. Zentz
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Antonio E. Chambers
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Siara N. Sandwith
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Michael A. Reisinger
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Destinee W. Saunders
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Joshua D. Tompkins
- Department
of Diabetes Complications and Metabolism, City of Hope, Duarte, California 91010, United States
| | - Arthur D. Riggs
- Department
of Diabetes Complications and Metabolism, City of Hope, Duarte, California 91010, United States
| | - Eric D. Routh
- Lineberger
Comprehensive Cancer Center, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eric M. Rubenstein
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Melissa A. Smaldino
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - James P. Vaughn
- NanoMedica
LLC, Winston-Salem, North Carolina 27101, United States
| | - Robert A. Haney
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Philip J. Smaldino
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
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42
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Maltby CJ, Schofield JPR, Houghton SD, O’Kelly I, Vargas-Caballero M, Deinhardt K, Coldwell MJ. A 5' UTR GGN repeat controls localisation and translation of a potassium leak channel mRNA through G-quadruplex formation. Nucleic Acids Res 2020; 48:9822-9839. [PMID: 32870280 PMCID: PMC7515701 DOI: 10.1093/nar/gkaa699] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/28/2020] [Indexed: 12/18/2022] Open
Abstract
RNA G-quadruplexes (G4s) are secondary structures proposed to function as regulators of post-transcriptional mRNA localisation and translation. G4s within some neuronal mRNAs are known to control distal localisation and local translation, contributing to distinct local proteomes that facilitate the synaptic remodelling attributed to normal cellular function. In this study, we characterise the G4 formation of a (GGN)13 repeat found within the 5' UTR of the potassium 2-pore domain leak channel Task3 mRNA. Biophysical analyses show that this (GGN)13 repeat forms a parallel G4 in vitro exhibiting the stereotypical potassium specificity of G4s, remaining thermostable under physiological ionic conditions. Through mouse brain tissue G4-RNA immunoprecipitation, we further confirm that Task3 mRNA forms a G4 structure in vivo. The G4 is inhibitory to translation of Task3 in vitro and is overcome through activity of a G4-specific helicase DHX36, increasing K+ leak currents and membrane hyperpolarisation in HEK293 cells. Further, we observe that this G4 is fundamental to ensuring delivery of Task3 mRNA to distal primary cortical neurites. It has been shown that aberrant Task3 expression correlates with neuronal dysfunction, we therefore posit that this G4 is important in regulated local expression of Task3 leak channels that maintain K+ leak within neurons.
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Affiliation(s)
- Connor J Maltby
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - James P R Schofield
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Steven D Houghton
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Ita O’Kelly
- Centre for Human Development, Stem Cells and Regeneration, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | | | - Katrin Deinhardt
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Mark J Coldwell
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
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43
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Masai H, Tanaka T. G-quadruplex DNA and RNA: Their roles in regulation of DNA replication and other biological functions. Biochem Biophys Res Commun 2020; 531:25-38. [PMID: 32826060 DOI: 10.1016/j.bbrc.2020.05.132] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/19/2022]
Abstract
G-quadruplex is one of the best-studied non-B type DNA that is now known to be prevalently present in the genomes of almost all the biological species. Recent studies reveal roles of G-quadruplex (G4) structures in various nucleic acids and chromosome transactions. In this short article, we will first describe recent findings on the roles of G4 in regulation of DNA replication. G4 is involved in regulation of spatio-temporal regulation of DNA replication through interaction with a specific binding protein, Rif1. This regulation is at least partially mediated by generation of specific chromatin architecture through Rif1-G4 interactions. We will also describe recent studies showing the potential roles of G4 in initiation of DNA replication. Next, we will present showcases of highly diversified roles of DNA G4 and RNA G4 in regulation of nucleic acid and chromosome functions. Finally, we will discuss how the formation of cellular G4 could be regulated.
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Affiliation(s)
- Hisao Masai
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | - Taku Tanaka
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
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44
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Varshney D, Spiegel J, Zyner K, Tannahill D, Balasubramanian S. The regulation and functions of DNA and RNA G-quadruplexes. Nat Rev Mol Cell Biol 2020; 21:459-474. [PMID: 32313204 PMCID: PMC7115845 DOI: 10.1038/s41580-020-0236-x] [Citation(s) in RCA: 579] [Impact Index Per Article: 144.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
DNA and RNA can adopt various secondary structures. Four-stranded G-quadruplex (G4) structures form through self-recognition of guanines into stacked tetrads, and considerable biophysical and structural evidence exists for G4 formation in vitro. Computational studies and sequencing methods have revealed the prevalence of G4 sequence motifs at gene regulatory regions in various genomes, including in humans. Experiments using chemical, molecular and cell biology methods have demonstrated that G4s exist in chromatin DNA and in RNA, and have linked G4 formation with key biological processes ranging from transcription and translation to genome instability and cancer. In this Review, we first discuss the identification of G4s and evidence for their formation in cells using chemical biology, imaging and genomic technologies. We then discuss possible functions of DNA G4s and their interacting proteins, particularly in transcription, telomere biology and genome instability. Roles of RNA G4s in RNA biology, especially in translation, are also discussed. Furthermore, we consider the emerging relationships of G4s with chromatin and with RNA modifications. Finally, we discuss the connection between G4 formation and synthetic lethality in cancer cells, and recent progress towards considering G4s as therapeutic targets in human diseases.
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Affiliation(s)
- Dhaval Varshney
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jochen Spiegel
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Katherine Zyner
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - David Tannahill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK.
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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45
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Paul T, Voter AF, Cueny RR, Gavrilov M, Ha T, Keck J, Myong S. E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands. Nucleic Acids Res 2020; 48:6640-6653. [PMID: 32449930 PMCID: PMC7337899 DOI: 10.1093/nar/gkaa442] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/24/2020] [Accepted: 05/21/2020] [Indexed: 11/30/2022] Open
Abstract
G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that Rep and Rep-X (an enhanced version of Rep) display G4 unwinding activities in vitro that are significantly higher than the closely related UvrD helicase. G4 unwinding mediated by Rep involves repetitive cycles of G4 unfolding and refolding fueled by ATP hydrolysis. Rep-X and Rep also dislodge G4-stabilizing ligands, in agreement with our in vivo G4-ligand sensitivity result. We further demonstrate that RecA filaments disrupt G4 structures and remove G4 ligands in vitro, consistent with its role in countering cellular toxicity of G4-stabilizing ligands. Together, our study reveals novel genome caretaking functions for Rep and RecA in resolving deleterious G4 structures.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew F Voter
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Rachel R Cueny
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Momčilo Gavrilov
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
- Howard Hughes Medical Institute, Johns Hopkins University, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
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46
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Reina C, Cavalieri V. Epigenetic Modulation of Chromatin States and Gene Expression by G-Quadruplex Structures. Int J Mol Sci 2020; 21:E4172. [PMID: 32545267 PMCID: PMC7312119 DOI: 10.3390/ijms21114172] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes are four-stranded helical nucleic acid structures formed by guanine-rich sequences. A considerable number of studies have revealed that these noncanonical structural motifs are widespread throughout the genome and transcriptome of numerous organisms, including humans. In particular, G-quadruplexes occupy strategic locations in genomic DNA and both coding and noncoding RNA molecules, being involved in many essential cellular and organismal functions. In this review, we first outline the fundamental structural features of G-quadruplexes and then focus on the concept that these DNA and RNA structures convey a distinctive layer of epigenetic information that is critical for the complex regulation, either positive or negative, of biological activities in different contexts. In this framework, we summarize and discuss the proposed mechanisms underlying the functions of G-quadruplexes and their interacting factors. Furthermore, we give special emphasis to the interplay between G-quadruplex formation/disruption and other epigenetic marks, including biochemical modifications of DNA bases and histones, nucleosome positioning, and three-dimensional organization of chromatin. Finally, epigenetic roles of RNA G-quadruplexes in post-transcriptional regulation of gene expression are also discussed. Undoubtedly, the issues addressed in this review take on particular importance in the field of comparative epigenetics, as well as in translational research.
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Affiliation(s)
- Chiara Reina
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, 90127 Palermo, Italy;
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
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47
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Herbert A. ALU non-B-DNA conformations, flipons, binary codes and evolution. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200222. [PMID: 32742689 PMCID: PMC7353975 DOI: 10.1098/rsos.200222] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/18/2020] [Indexed: 05/08/2023]
Abstract
ALUs contribute to genetic diversity by altering DNA's linear sequence through retrotransposition, recombination and repair. ALUs also have the potential to form alternative non-B-DNA conformations such as Z-DNA, triplexes and quadruplexes that alter the read-out of information from the genome. I suggest here these structures enable the rapid reprogramming of cellular pathways to offset DNA damage and regulate inflammation. The experimental data supporting this form of genetic encoding is presented. ALU sequence motifs that form non-B-DNA conformations under physiological conditions are called flipons. Flipons are binary switches. They are dissipative structures that trade energy for information. By efficiently targeting cellular machines to active genes, flipons expand the repertoire of RNAs compiled from a gene. Their action greatly increases the informational capacity of linearly encoded genomes. Flipons are programmable by epigenetic modification, synchronizing cellular events by altering both chromatin state and nucleosome phasing. Different classes of flipon exist. Z-flipons are based on Z-DNA and modify the transcripts compiled from a gene. T-flipons are based on triplexes and localize non-coding RNAs that direct the assembly of cellular machines. G-flipons are based on G-quadruplexes and sense DNA damage, then trigger the appropriate protective responses. Flipon conformation is dynamic, changing with context. When frozen in one state, flipons often cause disease. The propagation of flipons throughout the genome by ALU elements represents a novel evolutionary innovation that allows for rapid change. Each ALU insertion creates variability by extracting a different set of information from the neighbourhood in which it lands. By elaborating on already successful adaptations, the newly compiled transcripts work with the old to enhance survival. Systems that optimize flipon settings through learning can adapt faster than with other forms of evolution. They avoid the risk of relying on random and irreversible codon rewrites.
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Cooperative Analysis of Structural Dynamics in RNA-Protein Complexes by Single-Molecule Förster Resonance Energy Transfer Spectroscopy. Molecules 2020; 25:molecules25092057. [PMID: 32354083 PMCID: PMC7248720 DOI: 10.3390/molecules25092057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/13/2020] [Indexed: 12/24/2022] Open
Abstract
RNA-protein complexes (RNPs) are essential components in a variety of cellular processes, and oftentimes exhibit complex structures and show mechanisms that are highly dynamic in conformation and structure. However, biochemical and structural biology approaches are mostly not able to fully elucidate the structurally and especially conformationally dynamic and heterogeneous nature of these RNPs, to which end single molecule Förster resonance energy transfer (smFRET) spectroscopy can be harnessed to fill this gap. Here we summarize the advantages of strategic smFRET studies to investigate RNP dynamics, complemented by structural and biochemical data. Focusing on recent smFRET studies of three essential biological systems, we demonstrate that investigation of RNPs on a single molecule level can answer important functional questions that remained elusive with structural or biochemical approaches alone: The complex structural rearrangements throughout the splicing cycle, unwinding dynamics of the G-quadruplex (G4) helicase RHAU, and aspects in telomere maintenance regulation and synthesis.
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49
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Masuzawa T, Oyoshi T. Roles of the RGG Domain and RNA Recognition Motif of Nucleolin in G-Quadruplex Stabilization. ACS OMEGA 2020; 5:5202-5208. [PMID: 32201808 PMCID: PMC7081427 DOI: 10.1021/acsomega.9b04221] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/20/2020] [Indexed: 05/14/2023]
Abstract
G-quadruplexes have important biologic functions that are regulated by G-quadruplex-binding proteins. In particular, G-quadruplex structures are folded or unfolded by their binding proteins and affect transcription and other biologic functions. Here, we investigated the effect of the RNA recognition motif (RRM) and arginine-glycine-glycine repeat (RGG) domain of nucleolin on G-quadruplex formation. Our findings indicate that Phe in the RGG domain of nucleolin is responsible for G-quadruplex binding and folding. Moreover, the RRM of nucleolin potentially binds to a guanine-rich single strand and folds the G-quadruplex with a 5'-terminal and 3'-terminal single strand containing guanine. Our findings contribute to our understanding of how the RRM and RGG domains contribute to G-quadruplex folding and unfolding.
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Affiliation(s)
- Tatsuki Masuzawa
- Department of Chemistry,
Graduate School of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Takanori Oyoshi
- Department of Chemistry,
Graduate School of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
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50
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Srinivasan S, Liu Z, Chuenchor W, Xiao TS, Jankowsky E. Function of Auxiliary Domains of the DEAH/RHA Helicase DHX36 in RNA Remodeling. J Mol Biol 2020; 432:2217-2231. [PMID: 32087197 DOI: 10.1016/j.jmb.2020.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 01/06/2023]
Abstract
The DEAH/RHA helicase DHX36 has been linked to cellular RNA and DNA quadruplex structures and to AU-rich RNA elements. In vitro, DHX36 remodels DNA and RNA quadruplex structures and unwinds DNA duplexes in an ATP-dependent manner. DHX36 contains the superfamily 2 helicase core and several auxiliary domains that are conserved in orthologs of the enzyme. The role of these auxiliary domains for the enzymatic function of DHX36 is not well understood. Here, we combine structural and biochemical studies to define the function of three auxiliary domains that contact nucleic acid. We first report the crystal structure of mouse DHX36 bound to ADP. The structure reveals an overall architecture of mouse DHX36 that is similar to previously reported architectures of fly and bovine DHX36. In addition, our structure shows conformational changes that accompany stages of the ATP-binding and hydrolysis cycle. We then examine the roles of the DHX36-specific motif (DSM), the OB-fold, and a conserved β-hairpin (β-HP) in mouse DHX36 in the remodeling of RNA structures. We demonstrate and characterize RNA duplex unwinding for DHX36 and examine the remodeling of inter- and intramolecular RNA quadruplex structures. We find that the DSM not only functions as a quadruplex binding adaptor but also promotes the remodeling of RNA duplex and quadruplex structures. The OB-fold and the β-HP contribute to RNA binding. Both domains are also essential for remodeling RNA quadruplex and duplex structures. Our data reveal roles of auxiliary domains for multiple steps of the nucleic acid remodeling reactions.
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Affiliation(s)
| | - Zhonghua Liu
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Tsan Sam Xiao
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, USA; Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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