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The Upregulation of HAS2-AS1 Relates to the Granulosa Cell Dysfunction by Repressing TGF-β Signaling and Upregulating HAS2. Mol Cell Biol 2022; 42:e0010722. [PMID: 35938797 PMCID: PMC9476914 DOI: 10.1128/mcb.00107-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HAS2 antisense RNA 1 (HAS2-AS1) is a long noncoding RNA that has increased expression in mature granulosa cells (GCs) and contributes to cumulus expansion by regulating HAS2 expression. However, the roles of HAS2-AS1 during the pathological process of polycystic ovary syndrome (PCOS) are still unclear. This study investigated the roles of HAS2-AS1 in patients with PCOS. Here, a significant upregulation of HAS2-AS1 was found in the primary GCs from patients with PCOS, which was positively correlated with the level of the protein HAS2. The knockdown of HAS2 restored the upregulation of HAS2-AS1 in promoting migration but could not restore the effects of HAS2-AS1 overexpression in promoting proliferation and repressing apoptosis. Transforming growth factor β (TGF-β) upregulated HAS2-AS1 levels, while HAS2-AS1 functioned as a feedback inhibition factor repressing TGF-β signaling by inhibiting TGF-β receptor type 2 (TGFBR2) expression. HAS2-AS1 bonded with EZH2 and guided the polycomb complex 2 to the TGFBR2 promoter region. HAS2-AS1 overexpression induced H3K27 hypermethylation in the TGFBR2 promoter region and then repressed TGFBR2 transcription in KGN cells and primary GCs. In conclusion, we identified for the first time that HAS2-AS1 is upregulated in patients with PCOS and represses TGF-β signaling via inducing TGFBR2 promoter region hypermethylation, which allowed us to explore the pathological processes of PCOS.
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152
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Zheng AJL, Thermou A, Daskalogianni C, Malbert-Colas L, Karakostis K, Le Sénéchal R, Trang Dinh V, Tovar Fernandez MC, Apcher S, Chen S, Blondel M, Fahraeus R. The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA. Nucleic Acids Res 2022; 50:10110-10122. [PMID: 36107769 PMCID: PMC9508830 DOI: 10.1093/nar/gkac751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/10/2022] [Indexed: 11/20/2022] Open
Abstract
Protein aggregates and abnormal proteins are toxic and associated with neurodegenerative diseases. There are several mechanisms to help cells get rid of aggregates but little is known on how cells prevent aggregate-prone proteins from being synthesised. The EBNA1 of the Epstein-Barr virus (EBV) evades the immune system by suppressing its own mRNA translation initiation in order to minimize the production of antigenic peptides for the major histocompatibility (MHC) class I pathway. Here we show that the emerging peptide of the disordered glycine–alanine repeat (GAr) within EBNA1 dislodges the nascent polypeptide-associated complex (NAC) from the ribosome. This results in the recruitment of nucleolin to the GAr-encoding mRNA and suppression of mRNA translation initiation in cis. Suppressing NAC alpha (NACA) expression prevents nucleolin from binding to the GAr mRNA and overcomes GAr-mediated translation inhibition. Taken together, these observations suggest that EBNA1 exploits a nascent protein quality control pathway to regulate its own rate of synthesis that is based on sensing the nascent GAr peptide by NAC followed by the recruitment of nucleolin to the GAr-encoding RNA sequence.
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Affiliation(s)
- Alice J L Zheng
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
| | - Aikaterini Thermou
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
- ICCVS, University of Gdańsk , Science, ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Chrysoula Daskalogianni
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
- ICCVS, University of Gdańsk , Science, ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Laurence Malbert-Colas
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
| | - Konstantinos Karakostis
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
| | - Ronan Le Sénéchal
- Inserm UMR 1078, Université de Bretagne Occidentale (UBO), Etablissement Français du Sang (EFS) Bretagne, CHRU Brest , 29200 , Brest , France
| | - Van Trang Dinh
- Inserm UMR 1078, Université de Bretagne Occidentale (UBO), Etablissement Français du Sang (EFS) Bretagne, CHRU Brest , 29200 , Brest , France
| | - Maria C Tovar Fernandez
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
- ICCVS, University of Gdańsk , Science, ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Sébastien Apcher
- Institut Gustave Roussy, Université Paris Sud, Unité 1015 département d’immunologie , 114, rue Edouard Vaillant , 94805 Villejuif , France
| | - Sa Chen
- Department of Medical Biosciences, Building 6M, Umeå University , 901 85 Umeå , Sweden
| | - Marc Blondel
- Inserm UMR 1078, Université de Bretagne Occidentale (UBO), Etablissement Français du Sang (EFS) Bretagne, CHRU Brest , 29200 , Brest , France
| | - Robin Fahraeus
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
- Department of Medical Biosciences, Building 6M, Umeå University , 901 85 Umeå , Sweden
- RECAMO, Masaryk Memorial Cancer Institute , Zluty kopec 7 , 65653 Brno , Czech Republic
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153
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Abstract
An effective innate immune response to virus infection requires the induction of type I interferons and up-regulation of hundreds of interferon-stimulated genes (ISGs) that instruct antiviral functions and immune regulation. Deciphering the regulatory mechanisms that direct expression of the ISG network is critical for understanding the fundamental organization of the innate immune response and the development of antiviral therapies. We define a regulatory role for the primate-specific long noncoding RNA CHROMR in coordinating ISG transcription. CHROMR sequesters the interferon regulatory factor (IRF)-2/IRF2BP2 complex that restrains ISG transcription and thus is required to restrict influenza virus replication. These data identify a novel regulator of the antiviral gene program in humans and provide insights into the multilayered regulatory network that controls the innate immune response. Long noncoding RNAs (lncRNAs) have emerged as critical regulators of gene expression, yet their contribution to immune regulation in humans remains poorly understood. Here, we report that the primate-specific lncRNA CHROMR is induced by influenza A virus and SARS-CoV-2 infection and coordinates the expression of interferon-stimulated genes (ISGs) that execute antiviral responses. CHROMR depletion in human macrophages reduces histone acetylation at regulatory regions of ISG loci and attenuates ISG expression in response to microbial stimuli. Mechanistically, we show that CHROMR sequesters the interferon regulatory factor (IRF)-2-dependent transcriptional corepressor IRF2BP2, thereby licensing IRF-dependent signaling and transcription of the ISG network. Consequently, CHROMR expression is essential to restrict viral infection of macrophages. Our findings identify CHROMR as a key arbitrator of antiviral innate immune signaling in humans.
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154
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Bhogadia M, Stone B, Del Villar Guerra R, Muskett FW, Ghosh S, Taladriz-Sender A, Burley GA, Eperon IC, Hudson AJ, Dominguez C. Biophysical characterisation of the Bcl-x pre-mRNA and binding specificity of the ellipticine derivative GQC-05: Implication for alternative splicing regulation. Front Mol Biosci 2022; 9:943105. [PMID: 36060245 PMCID: PMC9428248 DOI: 10.3389/fmolb.2022.943105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
The BCL2L1 gene expresses two isoforms of Bcl-x protein via the use of either of two alternative 5′ splice sites (5′ss) in exon 2. These proteins have antagonistic actions, Bcl-XL being anti-apoptotic and Bcl-XS pro-apoptotic. In a number of cancers the Bcl-XL isoform is over-expressed, resulting in cancer cell survival and growth, so switching splicing to the Xs isoform could have therapeutic benefits. We have previously proposed that a putative G-quadruplex (G4) exists downstream of the XS 5′ss and shown that the ellipticine derivative GQC-05, a previously identified DNA G4-specific ligand, induces an increase in the XS/XL ratio both in vitro and in cells. Here, we demonstrate that this G4 forms in vitro and that the structure is stabilised in the presence of GQC-05. We also show that GQC-05 binds RNA non-specifically in buffer conditions, but selectively to the Bcl-x G4 in the presence of nuclear extract, highlighting the limitations of biophysical measurements taken outside of a functional environment. We also demonstrate that GQC-05 is able to shift the equilibrium between competing G4 and duplex structures towards the G4 conformation, leading to an increase in accessibility of the XS 5′ss, supporting our previous model on the mechanism of action of GQC-05.
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Affiliation(s)
- Mohammed Bhogadia
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Beth Stone
- The Leicester Institute of Structural and Chemical Biology, Department of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Rafael Del Villar Guerra
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Frederick W. Muskett
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Sudipta Ghosh
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Andrea Taladriz-Sender
- Department of Pure Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Glenn A. Burley
- Department of Pure Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Ian C. Eperon
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
- *Correspondence: Ian C. Eperon, ; Andrew J. Hudson, ; Cyril Dominguez,
| | - Andrew J. Hudson
- The Leicester Institute of Structural and Chemical Biology, Department of Chemistry, University of Leicester, Leicester, United Kingdom
- *Correspondence: Ian C. Eperon, ; Andrew J. Hudson, ; Cyril Dominguez,
| | - Cyril Dominguez
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
- *Correspondence: Ian C. Eperon, ; Andrew J. Hudson, ; Cyril Dominguez,
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155
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Vannutelli A, Schell L, Perreault JP, Ouangraoua A. GAIA: G-quadruplexes in alive creature database. Nucleic Acids Res 2022; 51:D135-D140. [PMID: 35971612 PMCID: PMC9825426 DOI: 10.1093/nar/gkac657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/08/2022] [Accepted: 08/08/2022] [Indexed: 01/29/2023] Open
Abstract
G-quadruplexes (G4) are 3D structures that are found in both DNA and RNA. Interest in this structure has grown over the past few years due to both its implication in diverse biological mechanisms and its potential use as a therapeutic target, to name two examples. G4s in humans have been widely studied; however, the level of their study in other species remains relatively minimal. That said, progress in this field has resulted in the prediction of G4s structures in various species, ranging from bacteria to eukaryotes. These predictions were analysed in a previous study which revealed that G4s are present in all living kingdoms. To date, eleven different databases have grouped the various G4s depending on either their structures, on the proteins that might bind them, or on their location in the various genomes. However, none of these databases contains information on their location in the transcriptome of many of the implicated species. The GAIA database was designed so as to make this data available online in a user-friendly manner. Through its web interface, users can query GAIA to filter G4s, which, we hope, will help the research in this field. GAIA is available at: https://gaia.cobius.usherbrooke.ca.
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Affiliation(s)
- Anaïs Vannutelli
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada,Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC J1K 2R1, Canada
| | | | - Jean-Pierre Perreault
- Correspondence may also be addressed to Jean-Pierre Perreault. Tel: +1 819 821 8000 (Ext 75310);
| | - Aïda Ouangraoua
- To whom correspondence should be addressed. Tel: +1 819 821 8000 (Ext 62014);
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156
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Cheng EL, Cardle II, Kacherovsky N, Bansia H, Wang T, Zhou Y, Raman J, Yen A, Gutierrez D, Salipante SJ, des Georges A, Jensen MC, Pun SH. Discovery of a Transferrin Receptor 1-Binding Aptamer and Its Application in Cancer Cell Depletion for Adoptive T-Cell Therapy Manufacturing. J Am Chem Soc 2022; 144:13851-13864. [PMID: 35875870 PMCID: PMC10024945 DOI: 10.1021/jacs.2c05349] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The clinical manufacturing of chimeric antigen receptor (CAR) T cells includes cell selection, activation, gene transduction, and expansion. While the method of T-cell selection varies across companies, current methods do not actively eliminate the cancer cells in the patient's apheresis product from the healthy immune cells. Alarmingly, it has been found that transduction of a single leukemic B cell with the CAR gene can confer resistance to CAR T-cell therapy and lead to treatment failure. In this study, we report the identification of a novel high-affinity DNA aptamer, termed tJBA8.1, that binds transferrin receptor 1 (TfR1), a receptor broadly upregulated by cancer cells. Using competition assays, high resolution cryo-EM, and de novo model building of the aptamer into the resulting electron density, we reveal that tJBA8.1 shares a binding site on TfR1 with holo-transferrin, the natural ligand of TfR1. We use tJBA8.1 to effectively deplete B lymphoma cells spiked into peripheral blood mononuclear cells with minimal impact on the healthy immune cell composition. Lastly, we present opportunities for affinity improvement of tJBA8.1. As TfR1 expression is broadly upregulated in many cancers, including difficult-to-treat T-cell leukemias and lymphomas, our work provides a facile, universal, and inexpensive approach for comprehensively removing cancerous cells from patient apheresis products for safe manufacturing of adoptive T-cell therapies.
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Affiliation(s)
- Emmeline L Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Ian I Cardle
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States.,Seattle Children's Therapeutics, Seattle, Washington 98101, United States
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Harsh Bansia
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States
| | - Tong Wang
- Nanoscience Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States
| | - Yunshi Zhou
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Jai Raman
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Albert Yen
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Dominique Gutierrez
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York (CUNY), New York, New York 10016, United States
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195-7110, United States
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States.,Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,Department of Chemistry and Biochemistry, City College of New York, New York, New York 10031, United States
| | - Michael C Jensen
- Seattle Children's Therapeutics, Seattle, Washington 98101, United States.,Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
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157
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Nam H, Gupta A, Nam H, Lee S, Cho HS, Park C, Park S, Park SJ, Hwang I. JULGI-mediated increment in phloem transport capacity relates to fruit yield in tomato. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1533-1545. [PMID: 35478430 PMCID: PMC9342617 DOI: 10.1111/pbi.13831] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
The continuous growth of the global population and the increase in the amount of arid land has severely constrained agricultural crop production. To solve this problem, many researchers have attempted to increase productivity through the efficient distribution of energy; however, the direct relationship between the plant vasculature, specifically phloem development, and crop yield is not well established. Here, we demonstrate that an optimum increase in phloem-transportation capacity by reducing SIJUL expression leads to improved sink strength in tomato (Solanum lycopersicum L.). SIJUL, a negative regulator of phloem development, suppresses the translation of a positive regulator of phloem development, SlSMXL5. The suppression of SlJUL increases the number of phloem cells and sucrose transport, but only an optimal reduction of SlJUL function greatly enhances sink strength in tomato, improving fruit setting, and yield contents by 37% and 60%, respectively. We show that the increment in phloem cell number confers spare transport capacity. Our results suggest that the control of phloem-transport capacity within the threshold could enhance the commitment of photosynthates to instigate yield improvement.
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Affiliation(s)
- Hoyoung Nam
- Department of Life SciencesPOSTECH Biotech CenterPohang University of Science and TechnologyPohangKorea
| | - Aarti Gupta
- Department of Life SciencesPOSTECH Biotech CenterPohang University of Science and TechnologyPohangKorea
| | - Heejae Nam
- Department of Life SciencesPOSTECH Biotech CenterPohang University of Science and TechnologyPohangKorea
| | - Seungchul Lee
- Department of Life SciencesPOSTECH Biotech CenterPohang University of Science and TechnologyPohangKorea
| | - Hyun Seob Cho
- Department of Life SciencesPOSTECH Biotech CenterPohang University of Science and TechnologyPohangKorea
| | - Chanyoung Park
- Department of Life SciencesPOSTECH Biotech CenterPohang University of Science and TechnologyPohangKorea
| | - Soyoung Park
- Department of Life SciencesPOSTECH Biotech CenterPohang University of Science and TechnologyPohangKorea
| | - Soon Ju Park
- Division of Biological Sciences and Research Institute for Basic ScienceWonkwang UniversityIksanKorea
| | - Ildoo Hwang
- Department of Life SciencesPOSTECH Biotech CenterPohang University of Science and TechnologyPohangKorea
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158
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de Arriba MDC, Fernández G, Chacón-Solano E, Mataix M, Martínez-Santamaría L, Illera N, Carrión-Marchante R, Martín ME, Larcher F, González VM, Del Río M, Carretero M. FPR2 DNA Aptamers for Targeted Therapy of Wound Repair. J Invest Dermatol 2022; 142:2238-2248.e8. [PMID: 34979109 DOI: 10.1016/j.jid.2021.12.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 02/05/2023]
Abstract
Chronic wounds represent a major health problem worldwide. Some of the available therapies based on recombinant proteins usually fail owing to the hostile environment found at the wound bed. Aptamers appear as an attractive alternative to recombinant factors owing in part to their stability, sensitivity, specificity, and low-cost production. In this study, the Cell-Systematic Evolution of Ligands by EXponential Enrichment technology was employed to generate aptamers that specifically recognize and modulate the function of the FPR2, a receptor expressed in a variety of cells involved in wound repair. Three aptamers were obtained that specifically bound to FPR2 stable transfectants generated in HaCaT cells. The targeted aptamers were shown to act as FPR2 agonists in different in vitro functional assays, including wound healing assays, and elicited a similar pattern of response to that obtained with other known FPR2 peptide agonists, such as the human LL37 cathelicidin. We have also obtained in vivo evidence for the prohealing activities of one of these FPR2 aptamers in a skin-humanized mouse model developed by us, previously shown to accurately recreate the main phases of physiological human wound repair process. In conclusion, we provide evidence of the potential therapeutic value of FPR2 aptamers for cutaneous repair.
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Affiliation(s)
- María Del Carmen de Arriba
- Department of Bioengineering and Aerospace, University Carlos III of Madrid, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), CB06/07/0019, ISCIII, Madrid, Spain; Biomedical Research Institute Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | | | - Esteban Chacón-Solano
- Department of Bioengineering and Aerospace, University Carlos III of Madrid, Madrid, Spain; Biomedical Research Institute Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Manuel Mataix
- Epithelial Biomedicine Division, Centre for Energy, Environment and Technology Research (CIEMAT), Madrid, Spain
| | - Lucía Martínez-Santamaría
- Department of Bioengineering and Aerospace, University Carlos III of Madrid, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), CB06/07/0019, ISCIII, Madrid, Spain; Biomedical Research Institute Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Nuria Illera
- Biomedical Research Institute Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain; Epithelial Biomedicine Division, Centre for Energy, Environment and Technology Research (CIEMAT), Madrid, Spain
| | | | | | - Fernando Larcher
- Department of Bioengineering and Aerospace, University Carlos III of Madrid, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), CB06/07/0019, ISCIII, Madrid, Spain; Biomedical Research Institute Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain; Epithelial Biomedicine Division, Centre for Energy, Environment and Technology Research (CIEMAT), Madrid, Spain
| | - Victor M González
- Aptus Biotech SL, Madrid, Spain; Aptamer Group, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Marcela Del Río
- Department of Bioengineering and Aerospace, University Carlos III of Madrid, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), CB06/07/0019, ISCIII, Madrid, Spain; Biomedical Research Institute Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Marta Carretero
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), CB06/07/0019, ISCIII, Madrid, Spain; Biomedical Research Institute Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain; Epithelial Biomedicine Division, Centre for Energy, Environment and Technology Research (CIEMAT), Madrid, Spain.
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159
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Makhoul M, Chawla HS, Wittkop B, Stahl A, Voss-Fels KP, Zetzsche H, Snowdon RJ, Obermeier C. Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:942461. [PMID: 36420025 PMCID: PMC9676936 DOI: 10.3389/fpls.2022.942461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/03/2022] [Indexed: 05/26/2023]
Abstract
The gene VERNALIZATION1 (VRN1) is a key controller of vernalization requirement in wheat. The genome of hexaploid wheat (Triticum aestivum) harbors three homoeologous VRN1 loci on chromosomes 5A, 5B, and 5D. Structural sequence variants including small and large deletions and insertions and single nucleotide polymorphisms (SNPs) in the three homoeologous VRN1 genes not only play an important role in the control of vernalization requirement, but also have been reported to be associated with other yield related traits of wheat. Here we used single-molecule sequencing of barcoded long-amplicons to assay the full-length sequences (∼13 kbp plus 700 bp from the promoter sequence) of the three homoeologous VRN1 genes in a panel of 192 predominantly European winter wheat cultivars. Long read sequences revealed previously undetected duplications, insertions and single-nucleotide polymorphisms in the three homoeologous VRN1 genes. All the polymorphisms were confirmed by Sanger sequencing. Sequence analysis showed the predominance of the winter alleles vrn-A1, vrn-B1, and vrn-D1 across the investigated cultivars. Associations of SNPs and structural variations within the three VRN1 genes with 20 economically relevant traits including yield, nodal root-angle index and quality related traits were evaluated at the levels of alleles, haplotypes, and copy number variants. Cultivars carrying structural variants within VRN1 genes showed lower grain yield, protein yield and biomass compared to those with intact genes. Cultivars carrying a single vrn-A1 copy and a unique haplotype with a high number of SNPs were found to have elevated grain yield, kernels per spike and kernels per m2 along with lower grain sedimentation values. In addition, we detected a novel SNP polymorphism within the G-quadruplex region of the promoter of vrn-A1 that was associated with deeper roots in winter wheat. Our findings show that multiplex, single-molecule long-amplicon sequencing is a useful tool for detecting variants in target genes within large plant populations, and can be used to simultaneously assay sequence variants among target multiple gene homoeologs in polyploid crops. Numerous novel VRN1 haplotypes and alleles were identified that showed significantly associations to economically important traits. These polymorphisms were converted into PCR or KASP assays for use in marker-assisted breeding.
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Affiliation(s)
- Manar Makhoul
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Harmeet S. Chawla
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Kai Peter Voss-Fels
- Institute for Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Holger Zetzsche
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
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160
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Barshai M, Aubert A, Orenstein Y. G4detector: Convolutional Neural Network to Predict DNA G-Quadruplexes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1946-1955. [PMID: 33872156 DOI: 10.1109/tcbb.2021.3073595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
G-quadruplexes (G4s) are nucleic acid secondary structures that form within guanine-rich DNA or RNA sequences. G4 formation can affect chromatin architecture and gene regulation, and has been associated with genomic instability, genetic diseases, and cancer progression. The experimental data produced by the G4-seq experiment provides unprecedented details on G4 formation in the genome. Still, running the experimental protocol on a whole genome is an expensive and time-consuming process. Thus, it is highly desirable to have a computational method to predict G4 formation in new DNA sequences or whole genomes. Here, we present G4detector, a new method based on a convolutional neural network to predict G4s from DNA sequences. On top of the sequence information, we improved prediction accuracy by the addition of RNA secondary structure information. To train and test G4detector, we compiled novel high-throughput benchmarks over multiple species genomes measured by the G4-seq protocol. We show that G4detector outperforms extant methods for the same task on all benchmark datasets, can detect G4s genome-wide with high accuracy, and is able to extrapolate human-trained measurements to various non-human species. The code and benchmarks are publicly available on github.com/OrensteinLab/G4detector.
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Kusumawati A, Mustopa AZ, Wibawan IWT, Setiyono A, Sudarwanto MB. A sequential toggle cell-SELEX DNA aptamer for targeting Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli bacteria. J Genet Eng Biotechnol 2022; 20:95. [PMID: 35776386 PMCID: PMC9249959 DOI: 10.1186/s43141-022-00374-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/02/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND Mastitis is an inflammation of the mammary glands caused by a microbial infection. The common bacteria causing this infection in dairy farms are Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli. The aptamer is a new biosensor platform for detecting pathogens; however, its use for simultaneous detection of S. aureus, S. agalactiae, and E. coli bacteria has not been reported. This study's objective is to isolate and characterize polyclonal DNA aptamer with broad reactivity to the mastitis bacteria S. aureus, S. agalactiae, and E. coli using a sequential toggle cell-SELEX. METHODS AND RESULTS The DNA aptamer pool from SELEX 15 was inserted into the pGEM-T easy plasmid. Furthermore, the transformant clones were selected by PCR colony, plasmid isolation, and sequencing. Six DNA aptamers, consisting of S15K3, S15K4, S15K6, S15K13, S15K15, and S15K20 with a constant region and the right size of 81 bp were derived from the sequencing analysis. The secondary structure of the DNA was predicted using Mfold software. The DNA was analyzed with binding characteristics, including binding capacity and affinity (Kd), using qPCR. The results indicated aptamer S15K15 has the highest binding ability into S. agalactiae, while S15K13 performed binding capacity most to E. coli EPEC 4, and S15K3 has the highest capacity of binding to S. aureus BPA-12. CONCLUSION Aptamer S15K3 has the best binding characteristics on all three bacterial targets.
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Affiliation(s)
- Arizah Kusumawati
- Study Program of Veterinary Public Health, IPB Graduate School, IPB University, Bogor, Indonesia
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Cibinong, Bogor, 16911 Indonesia
| | - Apon Zaenal Mustopa
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Cibinong, Bogor, 16911 Indonesia
| | - I. Wayan Teguh Wibawan
- Department of Animal Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, IPB University, Bogor, Indonesia
- Division of Medical Microbiology, Department of Animal Infectious Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, IPB University, Agatis Street, Dramaga, Bogor, West Java 16680 Indonesia
| | - Agus Setiyono
- Department of Veterinary Clinic Reproduction and Pathology, Faculty of Veterinary Medicine, IPB University, Bogor, Indonesia
| | - Mirnawati Bachrum Sudarwanto
- Department of Animal Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, IPB University, Bogor, Indonesia
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Shankar U, Mishra SK, Jain N, Tawani A, Yadav P, Kumar A. Ni +2 permease system of Helicobacter pylori contains highly conserved G-quadruplex motifs. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105298. [PMID: 35526824 DOI: 10.1016/j.meegid.2022.105298] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
The genome of a micro-organism contains all the information required for its survival inside its host cells. The guanine rich regions of the genome can form stable G-quadruplex structures that act as the regulators of gene expression. Herein, the completely sequenced genomes of Helicobacter pylori were explored for the identification and characterization of the conserved G-quadruplex motifs in this gastrointestinal pathogen. Initial in silico analysis revealed the presence of ~8241 GQ motifs in the H. pylori genome. Metal binding proteins of H. pylori are significantly enriched in the GQ motifs. Our study emphasizes the identification and characterization of four highly conserved G-quadruplex forming motifs (HPGQs) in the nickel transporter genes (nixA, niuB1, niuB2, and niuD) of the H. pylori. Nickel is a virulence determinant in H. pylori and is required as a co-factor for the urease and [NiFe] hydrogenase enzymes that are crucial for its survival in the stomach lining of humans. The presence of GQ motifs in these nickel transporter genes can affect their expression and may alter the functioning of Urease and [NiFe] hydrogenase. Similar to human and virus G-quadruplexes, targeting these conserved PGQs with bioactive molecules may represent a novel therapeutic avenue for combating infection of H. pylori. The identified HPGQs were characterized in-vitro by using CD spectroscopy, electrophoresis technique, and NMR spectroscopy at both acidic (4.5) and neutral pH (7.0). ITC revealed the specific interaction of these HPGQs with high affinity to the known G-quadruplex binding ligand, TMPyP4. The mTFP based reporter assay showed decrease in the gene expression of mTFP in the TMPyP4 treated cells as compared to the untreated and further affirmed the formation of stable G-quadruplex structures in the HPGQ motifs in vivo. This is the first report for characterizing G-quadruplex motifs in nickel transport-associated genes in the H. pylori bacterium.
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Affiliation(s)
- Uma Shankar
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Subodh Kumar Mishra
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Neha Jain
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Arpita Tawani
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India.
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Mora A, Huang X, Jauhari S, Jiang Q, Li X. Chromatin Hubs: A biological and computational outlook. Comput Struct Biotechnol J 2022; 20:3796-3813. [PMID: 35891791 PMCID: PMC9304431 DOI: 10.1016/j.csbj.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/02/2022] [Accepted: 07/02/2022] [Indexed: 11/20/2022] Open
Abstract
This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromolecules such as RNA polymerase or lncRNAs, and hubs around nuclear bodies such as the nucleolus or nuclear speckles. The second part reviews existing computational methods, including enhancer–promoter interaction prediction, network analysis, chromatin domain callers, transcription factory predictors, and multi-way interaction analysis. We introduce an integrated model that makes sense of the existing evidence. Understanding chromatin hubs may allow us (i) to explain long-unsolved biological questions such as interaction specificity and redundancy of mechanisms, (ii) to develop more realistic kinetic and functional predictions, and (iii) to explain the etiology of genomic disease.
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Affiliation(s)
- Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
- Corresponding authors.
| | - Xiaowei Huang
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Shaurya Jauhari
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Qin Jiang
- Affiliated Eye Hospital of Nanjing Medical University, Nanjing 210000, PR China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, and Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China
- Corresponding authors.
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Rahman MM, Young CKJ, Goffart S, Pohjoismäki JLO, Young MJ. Heterozygous p.Y955C mutation in DNA polymerase γ leads to alterations in bioenergetics, complex I subunit expression, and mtDNA replication. J Biol Chem 2022; 298:102196. [PMID: 35760101 PMCID: PMC9307957 DOI: 10.1016/j.jbc.2022.102196] [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: 01/23/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
In human cells, ATP is generated using oxidative phosphorylation machinery, which is inoperable without proteins encoded by mitochondrial DNA (mtDNA). The DNA polymerase gamma (Polγ) repairs and replicates the multicopy mtDNA genome in concert with additional factors. The Polγ catalytic subunit is encoded by the POLG gene, and mutations in this gene cause mtDNA genome instability and disease. Barriers to studying the molecular effects of disease mutations include scarcity of patient samples and a lack of available mutant models; therefore, we developed a human SJCRH30 myoblast cell line model with the most common autosomal dominant POLG mutation, c.2864A>G/p.Y955C, as individuals with this mutation can present with progressive skeletal muscle weakness. Using on-target sequencing, we detected a 50% conversion frequency of the mutation, confirming heterozygous Y955C substitution. We found mutated cells grew slowly in a glucose-containing medium and had reduced mitochondrial bioenergetics compared with the parental cell line. Furthermore, growing Y955C cells in a galactose-containing medium to obligate mitochondrial function enhanced these bioenergetic deficits. Also, we show complex I NDUFB8 and ND3 protein levels were decreased in the mutant cell line, and the maintenance of mtDNA was severely impaired (i.e., lower copy number, fewer nucleoids, and an accumulation of Y955C-specific replication intermediates). Finally, we show the mutant cells have increased sensitivity to the mitochondrial toxicant 2′-3′-dideoxycytidine. We expect this POLG Y955C cell line to be a robust system to identify new mitochondrial toxicants and therapeutics to treat mitochondrial dysfunction.
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Affiliation(s)
- Md Mostafijur Rahman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Carolyn K J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, 80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, 80101 Joensuu, Finland
| | - Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901.
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Vo T, Brownmiller T, Hall K, Jones TL, Choudhari S, Grammatikakis I, Ludwig K, Caplen N. HNRNPH1 destabilizes the G-quadruplex structures formed by G-rich RNA sequences that regulate the alternative splicing of an oncogenic fusion transcript. Nucleic Acids Res 2022; 50:6474-6496. [PMID: 35639772 PMCID: PMC9226515 DOI: 10.1093/nar/gkac409] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/07/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the presence of physiological monovalent cations, thousands of RNA G-rich sequences can form parallel G-quadruplexes (G4s) unless RNA-binding proteins inhibit, destabilize, or resolve the formation of such secondary RNA structures. Here, we have used a disease-relevant model system to investigate the biophysical properties of the RNA-binding protein HNRNPH1's interaction with G-rich sequences. We demonstrate the importance of two EWSR1-exon 8 G-rich regions in mediating the exclusion of this exon from the oncogenic EWS-FLI1 transcripts expressed in a subset of Ewing sarcomas, using complementary analysis of tumor data, long-read sequencing, and minigene studies. We determined that HNRNPH1 binds the EWSR1-exon 8 G-rich sequences with low nM affinities irrespective of whether in a non-G4 or G4 state but exhibits different kinetics depending on RNA structure. Specifically, HNRNPH1 associates and dissociates from G4-folded RNA faster than the identical sequences in a non-G4 state. Importantly, we demonstrate using gel shift and spectroscopic assays that HNRNPH1, particularly the qRRM1-qRRM2 domains, destabilizes the G4s formed by the EWSR1-exon 8 G-rich sequences in a non-catalytic fashion. Our results indicate that HNRNPH1's binding of G-rich sequences favors the accumulation of RNA in a non-G4 state and that this contributes to its regulation of RNA processing.
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Affiliation(s)
- Tam Vo
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tayvia Brownmiller
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine Hall
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tamara L Jones
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sulbha Choudhari
- CCR-SF Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Ioannis Grammatikakis
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Katelyn R Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Liu H, Chu Z, Yang X. A Key Molecular Regulator, RNA G-Quadruplex and Its Function in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:926953. [PMID: 35783953 PMCID: PMC9242502 DOI: 10.3389/fpls.2022.926953] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
RNA structure plays key roles in plant growth, development, and adaptation. One of the complex RNA structures is the RNA G-quadruplex (RG4) where guanine-rich sequences are folded into two or more layers of G-quartets. Previous computational predictions of RG4 revealed that it is widespread across the whole transcriptomes in many plant species, raising the hypothesis that RG4 is likely to be an important regulatory motif in plants. Recently, with the advances in both high-throughput sequencing and cell imaging technologies, RG4 can be detected in living cells as well as at the genome-wide scale. Here, we provide a comprehensive review of recent developments in new methods for detecting RG4 in plants. We also summarize the new functions of RG4 in regulating plant growth and development. We then discuss the possible role of RG4 in adapting to environmental conditions along with evolutionary perspectives.
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Affiliation(s)
- Haifeng Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Zhaohui Chu
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaofei Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Shanghai, China
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167
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Yu Y, Liu M, Choi VNT, Cheung YW, Tanner JA. Selection and characterization of DNA aptamers inhibiting a druggable target of osteoarthritis, ADAMTS-5. Biochimie 2022; 201:168-176. [PMID: 35700850 DOI: 10.1016/j.biochi.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 01/15/2023]
Abstract
There is a critical need for the development of more potent inhibitors for osteoarthritis (OA) therapy given the poor life quality of arthritis patients. Aggrecanase ADAMTS-5 (a disintegrin and metalloproteinase with thrombospondin motifs 5) is an established drug target identified for osteoarthritis. In this study, we evolved and characterized two new DNA aptamer inhibitors of ADAMTS-5, namely apt21 and apt25. The aptamers exhibited nanomolar binding affinity and high specificity against ADAMTS-5. KD values of apt21 and apt25 were determined by the Enzyme-linked Oligonucleotide Assay (ELONA) at 1.54 ± 0.16 nM and 1.79 ± 0.08 nM, respectively. Circular Dichroism (CD) analysis demonstrated that both aptamers formed monovalent cation dependent G-quadruplex structures. Calcium ions did not affect the binding of the aptamers to ADAMTS-5. The inhibitory effects of apt21 and apt25 on ADAMTS-5 were evaluated by the Förster Resonance Energy Transfer (FRET) assay, in which IC50 values of apt21 and apt25 were estimated at 52.76 ± 6.70 μM and 61.14 ± 9.67 μM, respectively. These two aptamers are the first DNA G-quadruplex aptamers demonstrated to inhibit ADAMTS-5 and could have value for OA therapy.
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Affiliation(s)
- Yuanyuan Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, PR China
| | - Mengping Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China
| | - Vanessa N T Choi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China
| | - Yee-Wai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China
| | - Julian A Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, PR China.
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Lockd promotes myoblast proliferation and muscle regeneration via binding with DHX36 to facilitate 5' UTR rG4 unwinding and Anp32e translation. Cell Rep 2022; 39:110927. [PMID: 35675771 DOI: 10.1016/j.celrep.2022.110927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/10/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
Adult muscle stem cells, also known as satellite cells (SCs), play pivotal roles in muscle regeneration, and long non-coding RNA (lncRNA) functions in SCs remain largely unknown. Here, we identify a lncRNA, Lockd, which is induced in activated SCs upon acute muscle injury. We demonstrate that Lockd promotes SC proliferation; deletion of Lockd leads to cell-cycle arrest, and in vivo repression of Lockd in mouse muscles hinders regeneration process. Mechanistically, we show that Lockd directly interacts with RNA helicase DHX36 and the 5'end of Lockd possesses the strongest binding with DHX36. Furthermore, we demonstrate that Lockd stabilizes the interaction between DHX36 and EIF3B proteins; synergistically, this complex unwinds the RNA G-quadruplex (rG4) structure formed at Anp32e mRNA 5' UTR and promotes the translation of ANP32E protein, which is required for myoblast proliferation. Altogether, our findings identify a regulatory Lockd/DHX36/Anp32e axis that promotes myoblast proliferation and acute-injury-induced muscle regeneration.
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169
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Edwards M, Huang M, Joseph S. The Fragile X Protein Disordered Regions Bind a Novel RNA Target. Biochemistry 2022; 61:1199-1212. [PMID: 35653700 DOI: 10.1021/acs.biochem.2c00228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fragile X proteins (FXPs) are a family of RNA-binding proteins that regulate mRNA translation to promote proper neural development and cognition in mammals. Of particular interest to researchers is the fragile X mental retardation protein (FMRP), as its absence leads to a neurodevelopmental disorder: fragile X syndrome (FXS), the leading monogenetic cause of autism spectrum disorders. A primary focus of research has been to determine mRNA targets of the FXPs in vivo through pull-down techniques, and to validate them through in vitro binding studies; another approach has been to perform in vitro selection experiments to identify RNA sequence and structural targets. These mRNA targets can be further investigated as potential targets for FXS therapeutics. The most established RNA structural target of this family of proteins is the G-quadruplex. In this article, we report a 99 nucleotide RNA target that is bound by all three FXPs with nanomolar equilibrium constants. Furthermore, we determined that the last 102 amino acids of FMRP, which includes the RGG motif, were necessary and sufficient to bind this RNA target. To the best of our knowledge, this is one of only a few examples of non-G-quadruplex, non-homopolymer RNAs bound by the RGG motif/C-termini of FMRP.
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Affiliation(s)
- Madison Edwards
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0314 United States
| | - Molly Huang
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0314 United States
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0314 United States
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Zhang A, Sun Y, Jing H, Liu J, Duan E, Ke W, Tao R, Li Y, Wang J, Cao S, Zhao P, Wang H, Zhang Y. Interaction of HnRNP F with the guanine-rich segments in viral antigenomic RNA enhances porcine reproductive and respiratory syndrome virus-2 replication. Virol J 2022; 19:82. [PMID: 35570267 PMCID: PMC9107676 DOI: 10.1186/s12985-022-01811-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/05/2022] [Indexed: 11/12/2022] Open
Abstract
Background Heterogeneous nuclear ribonucleoprotein (HnRNP) F is a member of HnRNP family proteins that participate in splicing of cellular newly synthesized mRNAs by specifically recognizing tandem guanine-tracts (G-tracts) RNA sequences. Whether HnRNP F could recognize viral-derived tandem G-tracts and affect virus replication remain poorly defined. Methods The effect of HnRNP F on porcine reproductive and respiratory syndrome virus (PRRSV) propagation was evaluated by real-time PCR, western blotting, and plaque-forming unit assay. The association between HnRNP F and PRRSV guanine-rich segments (GRS) were analyzed by RNA pulldown and RNA immunoprecipitation. The expression pattern of HnRNP F was investigated by western blotting and nuclear and cytoplasmic fractionation. Results Knockdown of endogenous HnRNP F effectively blocks the synthesis of viral RNA and nucleocapsid (N) protein. Conversely, overexpression of porcine HnRNP F has the opposite effect. Moreover, RNA pulldown and RNA immunoprecipitation assays reveal that the qRMM1 and qRRM2 domains of HnRNP F recognize the GRS in PRRSV antigenomic RNA. Finally, HnRNP F is redistributed into the cytoplasm and forms a complex with guanine-quadruplex (G4) helicase DHX36 during PRRSV infection. Conclusions These findings elucidate the potential functions of HnRNP F in regulating the proliferation of PRRSV and contribute to a better molecular understanding of host-PRRSV interactions.
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Maekawa K, Yamada S, Sharma R, Chaudhuri J, Keeney S. Triple-helix potential of the mouse genome. Proc Natl Acad Sci U S A 2022; 119:e2203967119. [PMID: 35503911 PMCID: PMC9171763 DOI: 10.1073/pnas.2203967119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/30/2022] [Indexed: 01/14/2023] Open
Abstract
Certain DNA sequences, including mirror-symmetric polypyrimidine•polypurine runs, are capable of folding into a triple-helix–containing non–B-form DNA structure called H-DNA. Such H-DNA–forming sequences occur frequently in many eukaryotic genomes, including in mammals, and multiple lines of evidence indicate that these motifs are mutagenic and can impinge on DNA replication, transcription, and other aspects of genome function. In this study, we show that the triplex-forming potential of H-DNA motifs in the mouse genome can be evaluated using S1-sequencing (S1-seq), which uses the single-stranded DNA (ssDNA)–specific nuclease S1 to generate deep-sequencing libraries that report on the position of ssDNA throughout the genome. When S1-seq was applied to genomic DNA isolated from mouse testis cells and splenic B cells, we observed prominent clusters of S1-seq reads that appeared to be independent of endogenous double-strand breaks, that coincided with H-DNA motifs, and that correlated strongly with the triplex-forming potential of the motifs. Fine-scale patterns of S1-seq reads, including a pronounced strand asymmetry in favor of centrally positioned reads on the pyrimidine-containing strand, suggested that this S1-seq signal is specific for one of the four possible isomers of H-DNA (H-y5). By leveraging the abundance and complexity of naturally occurring H-DNA motifs across the mouse genome, we further defined how polypyrimidine repeat length and the presence of repeat-interrupting substitutions modify the structure of H-DNA. This study provides an approach for studying DNA secondary structure genome-wide at high spatial resolution.
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Affiliation(s)
- Kaku Maekawa
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shintaro Yamada
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Rahul Sharma
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- HHMI, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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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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173
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Chen Y, Niu K, Song Q, Feng Q. Effect of G-quadruplex loop mutations on the G-quadruplex formation, protein binding and transcription of BmPOUM2 in Bombyx mori. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 110:e21876. [PMID: 35220618 DOI: 10.1002/arch.21876] [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: 01/23/2022] [Revised: 01/30/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
A G-quadruplex (G4) was identified in the promoter of transcription factor BmPOUM2 in Bombyx mori. This G4 structure contains three loops and is bound by transcription factor BmLARK, facilitating the transcription of BmPOUM2. However, the relationship between the structure and function of the BmPOUM2 G4 remains to be clarified. In this study, loop mutants of the BmPOUM2 G4 structure were generated to study the function of the structure in transcription regulation. The results revealed that mutations of Loops A and B could not completely suppress G4 formation, but affected the binding of the G4 structure with BmLARK and the promoter activity. The mutation (C-to-T) of the one-nucleotide-loop, Loop C, enhanced the G4 formation, its binding with BmLARK and the transcription activity of the BmPOUM2 promoter. It is speculated that the binding site of BmLARK probably is on the G-quartet planes, rather than on the loops, which may assist the maintenance and modification of the G4 structure and its protein binding activity.
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Affiliation(s)
- Yanfei Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, South China Normal University, Guangzhou, China
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, South China Normal University, Guangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, South China Normal University, Guangzhou, China
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174
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Modulation of Aptamer-Ligand-Binding by Complementary Oligonucleotides: A G-Quadruplex Anti-Ochratoxin A Aptamer Case Study. Int J Mol Sci 2022; 23:ijms23094876. [PMID: 35563267 PMCID: PMC9103105 DOI: 10.3390/ijms23094876] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 11/16/2022] Open
Abstract
Short oligonucleotides are widely used for the construction of aptamer-based sensors and logical bioelements to modulate aptamer-ligand binding. However, relationships between the parameters (length, location of the complementary region) of oligonucleotides and their influence on aptamer-ligand interactions remain unclear. Here, we addressed this task by comparing the effects of short complementary oligonucleotides (ssDNAs) on the structure and ligand-binding ability of an aptamer and identifying ssDNAs' features that determine these effects. Within this, the interactions between the OTA-specific G-quadruplex aptamer 1.12.2 (5'-GATCGGGTGTGGGTGGCGTAAAGGGA GCATCGGACA-3') and 21 single-stranded DNA (ssDNA) oligonucleotides complementary to different regions of the aptamer were studied. Two sets of aptamer-ssDNA dissociation constants were obtained in the absence and in the presence of OTA by isothermal calorimetry and fluorescence anisotropy, respectively. In both sets, the binding constants depend on the number of hydrogen bonds formed in the aptamer-ssDNA complex. The ssDNAs' having more than 23 hydrogen bonds with the aptamer have a lower aptamer dissociation constant than for aptamer-OTA interactions. The ssDNAs' having less than 18 hydrogen bonds did not affect the aptamer-OTA affinity. The location of ssDNA's complementary site in the aptamer affeced the kinetics of the interaction and retention of OTA-binding in aptamer-ssDNA complexes. The location of the ssDNA site in the aptamer G-quadruplex led to its unfolding. In the presence of OTA, the unfolding process was longer and takes from 20 to 70 min. The refolding in the presence of OTA was possible and depends on the length and location of the ssDNA's complementary site. The location of the ssDNA site in the tail region led to its rapid displacement and wasn't affecting the G-qaudruplex's integrity. It makes the tail region more perspective for the development of ssDNA-based tools using this aptamer.
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175
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Laugel M, Lecomte E, Ayuso E, Adjali O, Mével M, Penaud-Budloo M. The Diversity of Parvovirus Telomeres. Vet Med Sci 2022. [DOI: 10.5772/intechopen.102684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Parvoviridae are small viruses composed of a 4–6 kb linear single-stranded DNA protected by an icosahedral capsid. The viral genes coding non-structural (NS), capsid, and accessory proteins are flanked by intriguing sequences, namely the telomeres. Telomeres are essential for parvovirus genome replication, encapsidation, and integration. Similar (homotelomeric) or different (heterotelomeric) at the two ends, they all contain imperfect palindromes that fold into hairpin structures. Up to 550 nucleotides in length, they harbor a wide variety of motifs and structures known to be recognized by host cell factors. Our study aims to comprehensively analyze parvovirus ends to better understand the role of these particular sequences in the virus life cycle. Forty Parvoviridae terminal repeats (TR) were publicly available in databases. The folding and specific DNA secondary structures, such as G4 and triplex, were systematically analyzed. A principal component analysis was carried out from the prediction data to determine variables signing parvovirus groups. A special focus will be put on adeno-associated virus (AAV) inverted terminal repeats (ITR), a member of the genus Dependoparvovirus used as vectors for gene therapy. This chapter highlights the diversity of the Parvoviridae telomeres regarding shape and secondary structures, providing information that could be relevant for virus-host interactions studies.
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176
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Nanoparticle-Mediated Signaling for Aptamer-Based Multiplexed Detection of Cortisol and Neuropeptide Y in Serum. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10050153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Multiplexed profiling of the expression of neurochemical biomarkers of stress, for periodic assessment to enable augmentation of human performance, requires wash-free detection platforms that exhibit reproducible signals from samples in biological matrices. However, alterations in aptamer conformation after binding to targets, such as cortisol, are minimal based on NMR spectra, and the methylene blue signaling is blocked by serum proteins. Hence, in this study, we explore aptamer derivatization with magnetic nanoparticles that are conjugated with multiple methylene blue moieties, to amplify signals and alter the net charge configuration for repulsing serum proteins, so that the aptamer conformation upon target recognition can lead to a signal ON assay in serum media. Based on this, a microchip platform with addressable electrodes that are immobilized with selective aptamer receptors is developed for multiplexed detection of cortisol (1–700 ng/mL) and neuropeptide Y (5–1000 pg/mL) in patient-derived serum samples, which is validated by immunoassays. We envision the application of this sensor for profiling a wider array of human performance biomarkers under stress-related events to develop stress augmentation methodologies.
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177
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Characterization of G-Quadruplexes in Enterovirus A71 Genome and Their Interaction with G-Quadruplex Ligands. Microbiol Spectr 2022; 10:e0046022. [PMID: 35446122 PMCID: PMC9241713 DOI: 10.1128/spectrum.00460-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human enteroviruses cause many diseases; however, there is no specific therapeutic drug. G-quadruplex is an atypical secondary structure formed in the guanine rich region of DNA or RNA, which can exist in the viral genome. The different positions of G-quadruplex play an important role in the regulation of virus replication and infection. Whether G-quadruplexes are present in human enteroviruses is unknown. In current study, we analyzed the potential quadruplex forming sequences of human enteroviruses, especially EV-A71 virus, which causes hand, foot, and mouth disease. The results showed that there were a certain number of potential quadruplex-forming sequences in human enteroviruses. Through a variety of experimental methods, we evaluated the formation potential of EV-A71 encoded G-quadruplex and analyzed the binding ability of G-quadruplex ligands, including BRACO-19, pyridostatin and TMPyP4 to virus encoded G-quadruplexes. G-quadruplex ligands BRACO-19, PDS and TMPyP4 could inhibit the transcription of constructs containing EV-A71 G-quadruplex sequences. Moreover, we found that BRACO-19 was able to inhibit the replication of EV-A71, suggesting that targeting G-quadruplexes in EV-A71 genome by G-quadruplex ligands could be a novel antiviral way against EV-A71. Our finding not only uncovered the G-quadruplexes in human enteroviruses, but also would provide a new strategy for human enteroviruses therapy. IMPORTANCE G-quadruplex is a stable nucleic acid secondary structure formed by the folding of guanine rich nucleic acid. The important regulatory function of G-quadruplex makes it an attractive target of antiviral effect. Human enteroviruses cause a variety of human diseases, including common cold, nervous system diseases, cardiovascular damage, and diabetes. Enterovirus A71 (EV-A71) is one of pathogens causing hand, foot, and mouth disease; however, whether G-quadruplexes are present in the genomes of human enteroviruses is unknown. The function of G-quadruplexes in the EV-A71 genomes is not clear. We predicted and characterized G-quadruplex sequences in EV-A71. G-quadruplex ligands were identified to stabilize EV-A71 G-quadruplexes with high affinities. We also demonstrated G-quadruplex ligand BRACO-19 inhibited EV-A71 replication. Our studies provide a framework for targeting G-quadruplexes in the enteroviruses genome, which will be a new way to develop antiviral agents against human enteroviruses.
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178
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Umar MI, Chan CY, Kwok CK. Development of RNA G-quadruplex (rG4)-targeting L-RNA aptamers by rG4-SELEX. Nat Protoc 2022; 17:1385-1414. [PMID: 35444329 DOI: 10.1038/s41596-022-00679-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
RNA G-quadruplex (rG4)-SELEX is a method that generates L-RNA aptamers to target an rG4 structure of interest, which can be applied to inhibit G-quadruplex-mediated interactions that have important roles in gene regulation and function. Here we present a Protocol Extension substantially modifying an existing SELEX protocol to describe in detail the procedures involved in performing rG4-SELEX to identify rG4-specific binders that can effectively suppress rG4-peptide and rG4-protein associations. This Protocol Extension improves the speed of aptamer discovery and identification, offering a suite of techniques to characterize the aptamer secondary structure and monitor binding affinity and specificity, and demonstrating the utility of the L-RNA aptamer. The previous protocol mainly describes the identification of RNA aptamers against proteins of interest, whereas in this Protocol Extension we present the development of an unnatural RNA aptamer against an RNA structure of interest, with the potential to be applicable to other nucleic acid motifs or biomolecules. rG4-SELEX starts with a random D-RNA library incubated with the L-rG4 target of interest, followed by binding, washing and elution of the library. Enriched D-aptamer candidates are sequenced and structurally characterized. Then, the L-aptamer is synthesized and used for different applications. rG4-SELEX can be carried out by an experienced molecular biologist with a basic understanding of nucleic acids. The development of rG4-targeting L-RNA aptamers expands the current rG4 toolkit to explore innovative rG4-related applications, and opens new doors to discovering novel rG4 biology in the near future. The duration of each selection cycle as outlined in the protocol is ~2 d.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,RNA Molecular Biology Group, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD, USA
| | - Chun-Yin Chan
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universtität München, Munich, Germany
| | - 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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179
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Vacacela J, Schaap‐Johansen A, Manikova P, Marcatili P, Prado M, Sun Y, Ashley J. The Protein‐Templated Synthesis of Enzyme‐Generated Aptamers. Angew Chem Int Ed Engl 2022; 61:e202201061. [PMID: 35167174 PMCID: PMC9314878 DOI: 10.1002/anie.202201061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Indexed: 01/15/2023]
Abstract
Inspired by the chemical synthesis of molecularly imprinted polymers, we demonstrated for the first time, the protein‐target mediated synthesis of enzyme‐generated aptamers (EGAs). We prepared pre‐polymerisation mixtures containing different ratios of nucleotides, an initiator sequence and protein template and incubated each mixture with terminal deoxynucleotidyl transferase (TdT). Upon purification and rebinding of the EGAs against the target, we observed an enhancement in binding of templated‐EGAs towards the target compared to a non‐templated control. These results demonstrate the presence of two primary mechanisms for the formation of EGAs, namely, the binding of random sequences to the target as observed in systematic evolution of ligands by exponential enrichment (SELEX) and the dynamic competition between TdT enzyme and the target protein for binding of EGAs during synthesis. The latter mechanism serves to increase the stringency of EGA‐based screening and represents a new way to develop aptamers that relies on rational design.
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Affiliation(s)
- Julio Vacacela
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
| | - Anna‐Lisa Schaap‐Johansen
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
| | - Patricia Manikova
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
| | - Paolo Marcatili
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
| | - Marta Prado
- International Iberian Nanotechnology Laboratory (INL) Av. Mestre José Veiga Braga 4715-330 Portugal
| | - Yi Sun
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
| | - Jon Ashley
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
- School of Pharmacy and Biomolecular Sciences Liverpool John Moores University Byrom Street Liverpool L3 3AF UK
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180
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Holoubek J, Bednářová K, Haviernik J, Huvarová I, Dvořáková Z, Černý J, Outlá M, Salát J, Konkol'ová E, Boura E, Růžek D, Vorlíčková M, Eyer L, Renčiuk D. Guanine quadruplexes in the RNA genome of the tick-borne encephalitis virus: their role as a new antiviral target and in virus biology. Nucleic Acids Res 2022; 50:4574-4600. [PMID: 35420134 PMCID: PMC9071444 DOI: 10.1093/nar/gkac225] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/11/2022] Open
Abstract
We have identified seven putative guanine quadruplexes (G4) in the RNA genome of tick-borne encephalitis virus (TBEV), a flavivirus causing thousands of human infections and numerous deaths every year. The formation of G4s was confirmed by biophysical methods on synthetic oligonucleotides derived from the predicted TBEV sequences. TBEV-5, located at the NS4b/NS5 boundary and conserved among all known flaviviruses, was tested along with its mutated variants for interactions with a panel of known G4 ligands, for the ability to affect RNA synthesis by the flaviviral RNA-dependent RNA polymerase (RdRp) and for effects on TBEV replication fitness in cells. G4-stabilizing TBEV-5 mutations strongly inhibited RdRp RNA synthesis and exhibited substantially reduced replication fitness, different plaque morphology and increased sensitivity to G4-binding ligands in cell-based systems. In contrast, strongly destabilizing TBEV-5 G4 mutations caused rapid reversion to the wild-type genotype. Our results suggest that there is a threshold of stability for G4 sequences in the TBEV genome, with any deviation resulting in either dramatic changes in viral phenotype or a rapid return to this optimal level of G4 stability. The data indicate that G4s are critical elements for efficient TBEV replication and are suitable targets to tackle TBEV infection.
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Affiliation(s)
- Jiří Holoubek
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Klára Bednářová
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
| | - Jan Haviernik
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Ivana Huvarová
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic
| | - Zuzana Dvořáková
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
| | - Jiří Černý
- Faculty of Tropical Agrisciences, Czech University of Life Sciences Prague, CZ-16500 Prague, Czech Republic
| | - Martina Outlá
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Jiří Salát
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Eva Konkol'ová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy ofSciences, CZ-16000 Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy ofSciences, CZ-16000 Prague, Czech Republic
| | - Daniel Růžek
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Michaela Vorlíčková
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
| | - Luděk Eyer
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Daniel Renčiuk
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
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181
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Trinh KH, Kadam US, Rampogu S, Cho Y, Yang KA, Kang CH, Lee KW, Lee KO, Chung WS, Hong JC. Development of novel fluorescence-based and label-free noncanonical G4-quadruplex-like DNA biosensor for facile, specific, and ultrasensitive detection of fipronil. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:127939. [PMID: 34893377 DOI: 10.1016/j.jhazmat.2021.127939] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Fipronil is a broad-spectrum insecticide widely used in agriculture and residential areas; its indiscriminate use leads to environmental pollution and poses health hazards. Early detection of fipronil is critical to prevent the deleterious effects. However, current insecticide analysis methods such as HPLC, LC/MS, and GC/MS are incompetent; they are costly, immobile, time-consuming, laborious, and need skilled technicians. Hence, a sensitive, specific, and cheap biosensor are essential to containing the contamination. Here, we designed two novel biosensors-the first design relied on fluorescent labeling/quenching, while the second sensor focused on label-free detection using Thioflavin T displacement. Altogether, we identified four candidate aptamers, predicted secondary structures, and performed 3D molecular modeling to predict the binding pocket of fipronil in FiPA6B aptamer. Furthermore, the aptameric sensors showed high sensitivity to fipronil of sub-ppb level LOD, attributed to stringent experimental design. The biosensors displayed high specificity against other phenylpyrazole insecticides and demonstrated robust sensitivity for fipronil in real samples like cabbage and cucumber. Notably, to the best of our knowledge, this is the first demonstration of noncanonical G4-quadruplex-like aptamer binding to fipronil, verified using CD spectroscopy. Such aptasensors possess considerable potential for real-time measurements of hazardous insecticides as point-of-care technology.
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Affiliation(s)
- Kien Hong Trinh
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi City 12400, Vietnam
| | - Ulhas Sopanrao Kadam
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Shailima Rampogu
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Yuhan Cho
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Kyung-Ae Yang
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Chang Ho Kang
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Keun-Woo Lee
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Kyun Oh Lee
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Woo Sik Chung
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Plant Sciences, University of Missouri, Columbia, Missouri, MO 65211, USA.
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182
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Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. [G-quadruplex structures in bacteria: functional properties and prospects for use as biotargets]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:93-103. [PMID: 35485483 DOI: 10.18097/pbmc20226802093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
G-quadruplexes (G4), non-canonical secondary DNA structures, are intensively investigated for a long time. In eukaryotic organisms they play an important role in the regulation of gene expression and DNA repair. G4 have also been found in the genomes of numerous bacteria and archaea, but their functional role has not yet been fully explored. Nevertheless, their participation in the formation of antigenic variability, pathogenicity, antibiotic resistance and survival in extreme conditions has been established. Currently, many tools have been developed to detect potential G4 sequences and confirm their formation ability. Since the controlled formation and resolution of the quadruplex are significant means for the regulation of genes critical for survival, a promising direction is the search for ligands - compounds that can have a stabilizing effect on the quadruplex structure and thereby alter gene expression. Currently, a number of ligands are already known, their use stops the growth of pathogenic microorganisms. G4 ligands are of interest as potential antibiotics, which are extremely relevant due to the wide spread of drug resistant pathogens.
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Affiliation(s)
- E A Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - D A Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - I N Bodoev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - M V Zaychikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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183
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Zhou R, Gao Y, Yang C, Zhang X, Hu B, Zhao L, Guo H, Sun M, Wang L, Jiao B. A Novel SELEX Based on Immobilizing Libraries Enables Screening of Saxitoxin Aptamers for BLI Aptasensor Applications. Toxins (Basel) 2022; 14:228. [PMID: 35324725 PMCID: PMC8955768 DOI: 10.3390/toxins14030228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/18/2022] [Indexed: 12/20/2022] Open
Abstract
Saxitoxin (STX) is one of the potent marine biotoxins that has high rate of lethality. However, there are no effective treatments at present, and the existing detection methods need to be further explored because of ethical problems or technical limitations. In this work, oligonucleotide aptamers toward STX were screened based on immobilizing libraries on Immobilized Metal-Chelate (IMC), such as Ni-NTA Sepharose, and the IMC-SELEX was conducted by the G-quadruplex library and the random library, respectively. Aptamer 45e (from the G-quadruplex library) and aptamer 75a were obtained after optimization, and aptamer 45e turned out to have a higher affinity toward STX. Furthermore, it was found that the hydrogen bonding and the van der Waals forces (VDW) played major roles in the high efficiency and specificity between STX and 45e by means of molecular docking and dynamics simulation. Based on this, aptamer 45e-1 with the Kd value of 19 nM was obtained by further optimization, which was then used to construct a simple, label-free and real-time optical BLI aptasensor for the detection of STX. This aptasensor showed good reproducibility and stability. In summary, with the advantages of screening aptamers of high efficiency and specificity toward the targets, the proposed IMC-SELEX provides a promising screening strategy for discovering aptamers, which could be used as the potential molecular recognition elements in the fields of biomedicine, food safety and environmental monitoring.
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Affiliation(s)
- Rong Zhou
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Yun Gao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Chengfang Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Xiaojuan Zhang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
- College of Medicine, Shaoxing University, 900th Chengnan Avenue, Shaoxing 312000, China
| | - Bo Hu
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center of PLA, Navy Medical University, Shanghai 200433, China;
| | - Luming Zhao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Han Guo
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Mingjuan Sun
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Lianghua Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Binghua Jiao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
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184
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Maiti AK. Identification of G-quadruplex DNA sequences in SARS-CoV2. Immunogenetics 2022; 74:455-463. [PMID: 35303126 PMCID: PMC8931451 DOI: 10.1007/s00251-022-01257-6] [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: 01/17/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
G-quadruplex structure or Putative Quadruplex Sequences (PQSs) are abundant in human, microbial, DNA, or RNA viral genomes. These sequences in RNA viral genome play critical roles in integration into human genome as LTR (Long Terminal Repeat), genome replication, chromatin rearrangements, gene regulation, antigen variation (Av), and virulence. Here, we investigated whether the genome of SARS-CoV2, an RNA virus, contained such potential G-quadruplex structures. Using bioinformatic tools, we searched for such sequences and found thirty-seven (forward strand (twenty-five) + reverse strand (Twelve)) QGRSs (Quadruplex forming G-Rich Sequences)/PQSs in SARS-CoV2 genome. These sequences are dispersed mainly in the upstream of SARS-CoV2 genes. We discuss whether existing PQS/QGRS ligands could inhibit the SARS-CoV2 replication and gene transcription as has been observed in other RNA viruses. Further experimental validation would determine the role of these G-quadruplex sequences in SARS-CoV2 genome function to survive in the host cells and identify therapeutic agents to destabilize these PQSs/QGRSs.
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Affiliation(s)
- Amit K Maiti
- Mydnavar, Department of Genetics and Genomics, 2645 Somerset Boulevard, Troy, MI, 48084, USA.
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185
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to have devastating consequences worldwide. Recently, great efforts have been made to identify SARS-CoV-2 host factors, but the regulatory mechanisms of these host molecules, as well as the virus per se, remain elusive. Here we report a role of RNA G-quadruplex (RG4) in SARS-CoV-2 infection. Combining bioinformatics, biochemical and biophysical assays, we demonstrate the presence of RG4s in both SARS-CoV-2 genome and host factors. The biological and pathological importance of these RG4s is then exemplified by a canonical 3-quartet RG4 within Tmprss2, which can inhibit Tmprss2 translation and prevent SARS-CoV-2 entry. Intriguingly, G-quadruplex (G4)-specific stabilizers attenuate SARS-CoV-2 infection in pseudovirus cell systems and mouse models. Consistently, the protein level of TMPRSS2 is increased in lungs of COVID-19 patients. Our findings reveal a previously unknown mechanism underlying SARS-CoV-2 infection and suggest RG4 as a potential target for COVID-19 prevention and treatment. Understanding the mechanisms of SARS-CoV-2 infection is important to control the pandemic. Here the authors show the biological and pathological role of RNA G-quadruplex structure in both SARS-CoV-2 genome and host factors, particularly TMPRSS2.
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186
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Stability and context of intercalated motifs (i-motifs) for biological applications. Biochimie 2022; 198:33-47. [PMID: 35259471 DOI: 10.1016/j.biochi.2022.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 11/24/2022]
Abstract
DNA is naturally dynamic and can self-assemble into alternative secondary structures including the intercalated motif (i-motif), a four-stranded structure formed in cytosine-rich DNA sequences. Until recently, i-motifs were thought to be unstable in physiological cellular environments. Studies demonstrating their existence in the human genome and role in gene regulation are now shining light on their biological relevance. Herein, we review the effects of epigenetic modifications on i-motif structure and stability, and biological factors that affect i-motif formation within cells. Furthermore, we highlight recent progress in targeting i-motifs with structure-specific ligands for biotechnology and therapeutic purposes.
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187
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Vacacela J, Schaap‐Johansen A, Manikova P, Marcatili P, Prado M, Sun Y, Ashley J. The Protein‐Templated Synthesis of Enzyme‐Generated Aptamers. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julio Vacacela
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
| | - Anna‐Lisa Schaap‐Johansen
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
| | - Patricia Manikova
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
| | - Paolo Marcatili
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
| | - Marta Prado
- International Iberian Nanotechnology Laboratory (INL) Av. Mestre José Veiga Braga 4715-330 Portugal
| | - Yi Sun
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
| | - Jon Ashley
- Department of Health Technology Technical University of Denmark Ørsteds Pl. 345C Kgs. Lyngby 2800 Denmark
- School of Pharmacy and Biomolecular Sciences Liverpool John Moores University Byrom Street Liverpool L3 3AF UK
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188
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Levy S, Somasundaram L, Raj IX, Ic-Mex D, Phal A, Schmidt S, Ng WI, Mar D, Decarreau J, Moss N, Alghadeer A, Honkanen H, Sarthy J, Vitanza N, Hawkins RD, Mathieu J, Wang Y, Baker D, Bomsztyk K, Ruohola-Baker H. dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region. Cell Rep 2022; 38:110457. [PMID: 35235780 PMCID: PMC8984963 DOI: 10.1016/j.celrep.2022.110457] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 11/23/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Bifurcation of cellular fates, a critical process in development, requires histone 3 lysine 27 methylation (H3K27me3) marks propagated by the polycomb repressive complex 2 (PRC2). However, precise chromatin loci of functional H3K27me3 marks are not yet known. Here, we identify critical PRC2 functional sites at high resolution. We fused a computationally designed protein, EED binder (EB), which competes with EZH2 and thereby inhibits PRC2 function, to dCas9 (EBdCas9) to allow for PRC2 inhibition at a precise locus using gRNA. Targeting EBdCas9 to four different genes (TBX18, p16, CDX2, and GATA3) results in precise H3K27me3 and EZH2 reduction, gene activation, and functional outcomes in the cell cycle (p16) or trophoblast transdifferentiation (CDX2 and GATA3). In the case of TBX18, we identify a PRC2-controlled, functional TATA box >500 bp upstream of the TBX18 transcription start site (TSS) using EBdCas9. Deletion of this TATA box eliminates EBdCas9-dependent TATA binding protein (TBP) recruitment and transcriptional activation. EBdCas9 technology may provide a broadly applicable tool for epigenomic control of gene regulation.
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Affiliation(s)
- Shiri Levy
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Logeshwaran Somasundaram
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Infencia Xavier Raj
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Diego Ic-Mex
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Ashish Phal
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, School of Medicine, Seattle, WA 98105, USA
| | - Sven Schmidt
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Weng I Ng
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Daniel Mar
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA 98195, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Moss
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Division of Medical Genetics, Department of Medicine, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ammar Alghadeer
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98109, USA; Department of Biomedical Dental Sciences, Imam Abdulrahman Bin Faisal University, College of Dentistry, Dammam 31441, Saudi Arabia
| | - Henrik Honkanen
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Jay Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorder Center, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Nicholas Vitanza
- The Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - R David Hawkins
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Division of Medical Genetics, Department of Medicine, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Karol Bomsztyk
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA 98195, USA
| | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, School of Medicine, Seattle, WA 98105, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98109, USA.
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189
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A comparative study on regulation of HLA-G expression in bad obstetric history and in head and neck squamous cell carcinoma from Northeast India. Hum Immunol 2022; 83:453-457. [DOI: 10.1016/j.humimm.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/17/2022] [Accepted: 02/20/2022] [Indexed: 11/17/2022]
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190
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Pratihar S, Agrawal R, Pal VK, Singh A, Govindaraju T. Reliable Fluorometric Detection of SARS-CoV-2 by Targeting the G-Quadruplex through pH-Triggered Conformational Polymorphism. ACS Sens 2022; 7:453-459. [PMID: 35084824 DOI: 10.1021/acssensors.1c02113] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Unravelling unique molecular targets specific to viruses is challenging yet critical for diagnosing emerging viral diseases. Nucleic acids and proteins are the major targets in diagnostic assays of viral pathogens. Identification of novel sequences and conformations of nucleic acids as targets is desirable for developing diagnostic assays specific to a virus of interest. Here, we disclose the identification and characterization of a highly conserved antiparallel G-quadruplex (GQ)-forming DNA sequence present within the SARS-CoV-2 genome. The two-quartet GQ with unique loop compositions formed a distinct recognition motif. Design, synthesis, and fine tuning of structure-activity of a set of small molecules led to the identification of a benzobisthiazole-based fluorogenic probe which unambiguously recognizes the target SARS-CoV-2 GQ DNA. A robust cost-effective assay was developed through thermal cycler PCR-based amplification of the antiparallel GQ-forming ORF1ab region of the SARS-CoV-2 genome and endpoint fluorescence detection with the probe. An exclusive pH window (3.5-4) helped trigger reliable conformational polymorphism (RCP) involving DNA duplex to GQ transformation, which aided the development of a GQ-RCP platform for the diagnosis of SARS-CoV-2 clinical samples. This general strategy can be adapted for the development of specific diagnostic assays targeting different noncanonical nucleic acid sequences.
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Affiliation(s)
- Sumon Pratihar
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru, Karnataka 560064, India
| | - Ragini Agrawal
- Department of Microbiology and Cell Biology, and Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Virender Kumar Pal
- Department of Microbiology and Cell Biology, and Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, and Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru, Karnataka 560064, India
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191
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Hoque ME, Mahendran T, Basu S. Reversal of G-Quadruplexes' Role in Translation Control When Present in the Context of an IRES. Biomolecules 2022; 12:314. [PMID: 35204814 PMCID: PMC8869680 DOI: 10.3390/biom12020314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
G-quadruplexes (GQs) are secondary nucleic acid structures that play regulatory roles in various cellular processes. G-quadruplex-forming sequences present within the 5' UTR of mRNAs can function not only as repressors of translation but also as elements required for optimum function. Based upon previous reports, the majority of the 5' UTR GQ structures inhibit translation, presumably by blocking the ribosome scanning process that is essential for detection of the initiation codon. However, there are certain mRNAs containing GQs that have been identified as positive regulators of translation, as they are needed for translation initiation. While most cellular mRNAs utilize the 5' cap structure to undergo cap-dependent translation initiation, many rely on cap-independent translation under certain conditions in which the cap-dependent initiation mechanism is not viable or slowed down, for example, during development, under stress and in many diseases. Cap-independent translation mainly occurs via Internal Ribosomal Entry Sites (IRESs) that are located in the 5' UTR of mRNAs and are equipped with structural features that can recruit the ribosome or other factors to initiate translation without the need for a 5' cap. In this review, we will focus only on the role of RNA GQs present in the 5' UTR of mRNAs, where they play a critical role in translation initiation, and discuss the potential mechanism of this phenomenon, which is yet to be fully delineated.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA; (M.E.H.); (T.M.)
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192
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He K, Sun L, Wang L, Li W, Hu G, Ji X, Zhang Y, Xu X. Engineering DNA G-quadruplex assembly for label-free detection of Ochratoxin A in colorimetric and fluorescent dual modes. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:126962. [PMID: 34464866 DOI: 10.1016/j.jhazmat.2021.126962] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Colorimetric and fluorescent methods for Ochratoxin A (OTA) detection are convenient and well received. However, the pigments and autofluorescence originated from food matrices often interfere with detection signals. We have developed a strategy with colorimetric and fluorescent dual modes to solve this challenge. In the colorimetric mode, OTA aptamer (AP9) was assembled into a DNA triple-helix switch with a specially designed signal-amplifying sequence. The OTA-induced G-quadruplex (G4) of AP9 would open the switch and release the signal-amplifying sequence for colorimetric signal amplification. The G4 structures of AP9 were further utilized to combine with the fluorogenic dye ThT for fluorescent mode. By skillfully engineering DNA G4 assembly for signal amplification, there was no need for any DNA amplification or nanomaterials labeling. Detections could be carried out in a wide temperature range (22-37 ℃) and finished rapidly (colorimetric mode, 60 min; fluorescent mode, 15 min). Broad linear ranges (colorimetric mode, 10-1.5 ×103 μg/kg; fluorescent mode, 0.05-1.0 ×103 μg/kg) were achieved. The limit of detection for colorimetric and fluorescent modes were 4 μg/kg and 0.01 μg/kg, respectively. The two modes have been successfully applied to detect OTA in samples with intrinsic pigments and autofluorescence, showing their applicability and reliability.
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Affiliation(s)
- Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Liping Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wang Li
- College of Food Science & Engineering, Central South University of Forestry & Technology, Changsha 410004, China
| | - Guixian Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofeng Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yiming Zhang
- School of Agriculture and Food Science, Zhejiang A&F University, Hangzhou 311300, China.
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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193
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Víglaský V. Hidden Information Revealed Using the Orthogonal System of Nucleic Acids. Int J Mol Sci 2022; 23:ijms23031804. [PMID: 35163723 PMCID: PMC8836696 DOI: 10.3390/ijms23031804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 11/25/2022] Open
Abstract
In this study, the organization of genetic information in nucleic acids is defined using a novel orthogonal representation. Clearly defined base pairing in DNA allows the linear base chain and sequence to be mathematically transformed into an orthogonal representation where the G–C and A–T pairs are displayed in different planes that are perpendicular to each other. This form of base allocation enables the evaluation of any nucleic acid and predicts the likelihood of a particular region to form non-canonical motifs. The G4Hunter algorithm is currently a popular method of identifying G-quadruplex forming sequences in nucleic acids, and offers promising scores despite its lack of a substantial rational basis. The orthogonal representation described here is an effort to address this incongruity. In addition, the orthogonal display facilitates the search for other sequences that are capable of adopting non-canonical motifs, such as direct and palindromic repeats. The technique can also be used for various RNAs, including any aptamers. This powerful tool based on an orthogonal system offers considerable potential for a wide range of applications.
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Affiliation(s)
- Viktor Víglaský
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, Pavol Jozef Šafárik University, 04001 Košice, Slovakia
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Torres-Vázquez B, María de Lucas A, García-Crespo C, Antonio García-Martín J, Fragoso A, Fernández-Algar M, Perales C, Domingo E, Moreno M, Briones C. In vitro selection of high affinity DNA and RNA aptamers that detect hepatitis C virus core protein of genotypes 1 to 4 and inhibit virus production in cell culture. J Mol Biol 2022; 434:167501. [DOI: 10.1016/j.jmb.2022.167501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023]
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195
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Vergara-Barberán M, Lerma-García MJ, Simó-Alfonso EF, García-Hernández M, Martín ME, García-Sacristán A, González VM, Herrero-Martínez JM. Selection and characterization of DNA aptamers for highly selective recognition of the major allergen of olive pollen Ole e 1. Anal Chim Acta 2022; 1192:339334. [PMID: 35057930 DOI: 10.1016/j.aca.2021.339334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 02/05/2023]
Abstract
In this study, single-stranded DNA aptamers with binding affinity to Ole e 1, the major allergen of olive pollen, were selected using systematic evolution of ligands by exponential enrichment (SELEX) method. Binding of the aptamers was firstly established by enzyme-linked oligonucleotide assay (ELONA) and aptaprecipitation assays. Additionally, aptamer-modified monolithic capillary chromatography was used in order to evaluate the recognition of this allergenic protein against other non-target proteins. The results indicated that AptOle1#6 was the aptamer that provided the highest affinity for Ole e 1. The selected aptamer showed good selective recognition of this protein, being not able to retain other non-target proteins (HSA, cyt c, and other pollen protein such as Ole e 9). The feasibility of the affinity monolithic column was demonstrated by selective recognition of Ole e 1 in an allergy skin test. The stability and reproducibility of this monolithic column was suitable, with relative standard deviations (RSDs) in retention times and peak area values of 7.8 and 9.3%, respectively (column-to-column reproducibility). This is the first study that describes the design of an efficient DNA aptamer for this relevant allergen.
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Affiliation(s)
- María Vergara-Barberán
- Department of Analytical Chemistry, University of Valencia, C. Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain
| | - María Jesús Lerma-García
- Department of Analytical Chemistry, University of Valencia, C. Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain
| | - Ernesto F Simó-Alfonso
- Department of Analytical Chemistry, University of Valencia, C. Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain
| | - Marta García-Hernández
- Grupo de Aptámeros. Departamento de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal (IRYCIS), Carretera de Colmenar Viejo Km.9.100, CP-28034, Madrid, Spain
| | - M Elena Martín
- Grupo de Aptámeros. Departamento de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal (IRYCIS), Carretera de Colmenar Viejo Km.9.100, CP-28034, Madrid, Spain
| | | | - Víctor M González
- Grupo de Aptámeros. Departamento de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal (IRYCIS), Carretera de Colmenar Viejo Km.9.100, CP-28034, Madrid, Spain; Aptus Biotech SL, Av. Cardenal Herrera Oria 298, CP-28035, Madrid, Spain
| | - José Manuel Herrero-Martínez
- Department of Analytical Chemistry, University of Valencia, C. Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain.
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196
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Shokri E, Hosseini M, Boldaji MN, Shahsavar K, amiri-Sadeghan A, Nasiri N, Bahmani A, Ganjali MR, Saboury AA. A novel DNA/hemin complex with enzyme-like activity selected from a hairpin DNAs library at zero H2O2 concentration. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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197
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Santos T, Miranda A, Imbert L, Jardim A, Caneira CRF, Chu V, Conde JP, Campello MPC, Paulo A, Salgado G, Cabrita EJ, Cruz C. Pre-miRNA-149 G-quadruplex as a molecular agent to capture nucleolin. Eur J Pharm Sci 2022; 169:106093. [PMID: 34922315 DOI: 10.1016/j.ejps.2021.106093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/14/2021] [Accepted: 12/04/2021] [Indexed: 02/07/2023]
Abstract
One of the most significant challenges in capturing and detecting biomarkers is the choice of an appropriate biomolecular receptor. Recently, RNA G-quadruplexes emerged as plausible receptors due to their ability to recognize with high-affinity proteins. Herein, we have unveiled and characterized the capability of the precursor microRNA 149 to form a G-quadruplex structure and determined the role that some ligands may have in its folding and binding capacity to nucleolin. The G-quadruplex formation was induced by K+ ions and stabilized by ligands, as demonstrated by nuclear magnetic resonance and circular dichroism experiments. Surface plasmon resonance measurements showed a binding affinity of precursor microRNA 149 towards ligands in the micromolar range (10-5-10-6 M) and a strong binding affinity to nucleolin RNA-binding domains 1 and 2 (8.38 × 10-10 M). Even in the presence of the ligand PhenDC3, the binding remains almost identical and in the same order of magnitude (4.46 × 10-10 M). The molecular interactions of the RNA G-quadruplex motif found in precursor miRNA 149 (5'-GGGAGGGAGGGACGGG- 3') and nucleolin RNA-binding domains 1 and 2 were explored by means of molecular docking and molecular dynamics studies. The results showed that RNA G-quadruplex binds to a cavity between domains 1 and 2 of the protein. Then, complex formation was also evaluated through polyacrylamide gel electrophoresis. The results suggest that precursor microRNA 149/ligands and precursor microRNA 149/nucleolin RNA-binding domains 1 and 2 form stable molecular complexes. The in vitro co-localization of precursor microRNA 149 and nucleolin in PC3 cells was demonstrated using confocal microscopy. Finally, a rapid and straightforward microfluidic strategy was employed to check the ability of precursor microRNA 149 to capture nucleolin RNA-binding domains 1 and 2. The results revealed that precursor microRNA 149 can capture nucleolin RNA-binding domains 1 and 2 labeled with Fluorescein 5-isothiocyanate in a concentration-dependent manner, but PhenDC3 complexation seems to decrease the ability of precursor microRNA 149 to capture the protein. Overall, our results proved the formation of the G-quadruplex structure in the precursor microRNA 149 and the ability to recognize and detect nucleolin. This proof-of-concept study could open up a new framework for developing new strategies to design improved molecular receptors for capture and detection of nucleolin in complex biological samples.
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Affiliation(s)
- Tiago Santos
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - André Miranda
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Lionel Imbert
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France; Univ. Grenoble Alpes, CNRS, CEA, EMBL Integrated Structural Biology Grenoble (ISBG), Grenoble, France
| | - Andreia Jardim
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - Catarina R F Caneira
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - Virgínia Chu
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - João P Conde
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Paula Cabral Campello
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 1397), 2695-066 Bobadela LRS, Portugal; DECN -Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - António Paulo
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 1397), 2695-066 Bobadela LRS, Portugal; DECN -Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Gilmar Salgado
- Univ. Bordeaux, ARNA Laboratory INSERM, U1212, CNRS UMR 5320, IECB, Pessac, France
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal.
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198
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The Fragile X Proteins Differentially Regulate Translation of Reporter mRNAs with G-quadruplex Structures. J Mol Biol 2022; 434:167396. [PMID: 34896112 PMCID: PMC8892671 DOI: 10.1016/j.jmb.2021.167396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/29/2021] [Accepted: 12/01/2021] [Indexed: 02/01/2023]
Abstract
Fragile X Syndrome, as well as some manifestations of autism spectrum disorder, results from improper RNA regulation due to a deficiency of fragile X mental retardation protein (FMRP). FMRP and its autosomal paralogs, fragile X related proteins 1 & 2 (FXR1P/2P), have been implicated in many aspects of RNA regulation, from protein synthesis to mRNA stability and decay. The literature on the fragile X related proteins' (FXPs) role in mRNA regulation and their potential mRNA targets is vast. Therefore, we developed an approach to investigate the function of FXPs in translational control using three potential mRNA targets. Briefly, we first selected top mRNA candidates found to be associated with the FXPs and whose translation are influenced by one or more of the FXPs. We then narrowed down the FXPs' binding site(s) within the mRNA, analyzed the strength of this binding in vitro, and determined how each FXP affects the translation of a minimal reporter mRNA with the binding site. Overall, all FXPs bound with high affinity to RNAs containing G-quadruplexes, such as Cyclin Dependent Kinase Inhibitor p21 and FMRP's own coding region. Interestingly, FMRP inhibited the translation of each mRNA distinctly and in a manner that appears to correlate with its binding to each mRNA. In contrast, FXR1P/2P inhibited all mRNAs tested. Finally, although binding of our RNAs was due to the RGG (arginine-glycine-glycine) motif-containing C-terminal region of the FXPs, this region was not sufficient to cause inhibition of translation.
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199
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Lv L, Cui H, Chen Z, Zhou Y, Zhang L. G‐quadruplex ligands inhibit chikungunya virus replication. J Med Virol 2022; 94:2519-2527. [PMID: 35075669 DOI: 10.1002/jmv.27622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/27/2021] [Accepted: 01/21/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Lu Lv
- Department of Clinical Laboratory MedicineThe First Affifiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan HospitalJinanShandongChina
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Haoran Cui
- Department of Clinical Laboratory MedicineThe First Affifiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan HospitalJinanShandongChina
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Zhiyang Chen
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Yixuan Zhou
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Leiliang Zhang
- Department of Clinical Laboratory MedicineThe First Affifiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan HospitalJinanShandongChina
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
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200
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Gockert M, Schmid M, Jakobsen L, Jens M, Andersen JS, Jensen TH. Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation. Nucleic Acids Res 2022; 50:1583-1600. [PMID: 35048984 PMCID: PMC8860595 DOI: 10.1093/nar/gkac001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/13/2021] [Accepted: 01/05/2022] [Indexed: 12/15/2022] Open
Abstract
Turnover of nucleoplasmic transcripts by the mammalian multi-subunit RNA exosome is mediated by two adaptors: the Nuclear EXosome Targeting (NEXT) complex and the Poly(A) tail eXosome Targeting (PAXT) connection. Functional analyses of NEXT and PAXT have largely utilized long-term factor depletion strategies, facilitating the appearance of indirect phenotypes. Here, we rapidly deplete NEXT, PAXT and core exosome components, uncovering the direct consequences of their acute losses. Generally, proteome changes are sparse and largely dominated by co-depletion of other exosome and adaptor subunits, reflecting possible subcomplex compositions. While parallel high-resolution 3′ end sequencing of newly synthesized RNA confirms previously established factor specificities, it concomitantly demonstrates an inflation of long-term depletion datasets by secondary effects. Most strikingly, a general intron degradation phenotype, observed in long-term NEXT depletion samples, is undetectable upon short-term depletion, which instead emphasizes NEXT targeting of snoRNA-hosting introns. Further analysis of these introns uncovers an unusual mode of core exosome-independent RNA decay. Our study highlights the accumulation of RNAs as an indirect result of long-term decay factor depletion, which we speculate is, at least partly, due to the exhaustion of alternative RNA decay pathways.
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Affiliation(s)
- Maria Gockert
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Marvin Jens
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, 68-271A, Cambridge, MA 02139-4307, USA
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
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