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Hou YM, Xu BH, Zhang QT, Cheng J, Zhang X, Yang HR, Wang ZY, Wang P, Zhang MX. Deficiency of smooth muscle cell ILF3 alleviates intimal hyperplasia via HMGB1 mRNA degradation-mediated regulation of the STAT3/DUSP16 axis. J Mol Cell Cardiol 2024; 190:62-75. [PMID: 38583797 DOI: 10.1016/j.yjmcc.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Intimal hyperplasia is a complicated pathophysiological phenomenon attributable to in-stent restenosis, and the underlying mechanism remains unclear. Interleukin enhancer-binding factor 3 (ILF3), a double-stranded RNA-binding protein involved in regulating mRNA stability, has been recently demonstrated to assume a crucial role in cardiovascular disease; nevertheless, its impact on intimal hyperplasia remains unknown. In current study, we used samples of human restenotic arteries and rodent models of intimal hyperplasia, we found that vascular smooth muscle cell (VSMC) ILF3 expression was markedly elevated in human restenotic arteries and murine ligated carotid arteries. SMC-specific ILF3 knockout mice significantly suppressed injury induced neointimal formation. In vitro, platelet-derived growth factor type BB (PDGF-BB) treatment elevated the level of VSMC ILF3 in a dose- and time-dependent manner. ILF3 silencing markedly inhibited PDGF-BB-induced phenotype switching, proliferation, and migration in VSMCs. Transcriptome sequencing and RNA immunoprecipitation sequencing depicted that ILF3 maintained its stability upon binding to the mRNA of the high-mobility group box 1 protein (HMGB1), thereby exerting an inhibitory effect on the transcription of dual specificity phosphatase 16 (DUSP16) through enhanced phosphorylation of signal transducer and activator of transcription 3 (STAT3). Therefore, the results both in vitro and in vivo indicated that the loss of ILF3 in VSMC ameliorated neointimal hyperplasia by regulating the STAT3/DUSP16 axis through the degradation of HMGB1 mRNA. Our findings revealed that vascular injury activates VSMC ILF3, which in turn promotes intima formation. Consequently, targeting specific VSMC ILF3 may present a potential therapeutic strategy for ameliorating cardiovascular restenosis.
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Affiliation(s)
- Ya-Min Hou
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Bo-Han Xu
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Qiu-Ting Zhang
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Jie Cheng
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Xu Zhang
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Hong-Rui Yang
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Ze-Ying Wang
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Peng Wang
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Ming-Xiang Zhang
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China.
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2
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Cao Y, Wu J, Hu Y, Chai Y, Song J, Duan J, Zhang S, Xu X. Virus-induced lncRNA-BTX allows viral replication by regulating intracellular translocation of DHX9 and ILF3 to induce innate escape. Cell Rep 2023; 42:113262. [PMID: 37864796 DOI: 10.1016/j.celrep.2023.113262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/26/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023] Open
Abstract
The roles of long noncoding RNA (lncRNA) and RNA-binding proteins (RBPs) in antiviral innate response warrant further investigation. Here, we identify an lncRNA, termed lncRNA-BTX (between Tbk1 and Xpot), which is upregulated upon viral infection via an IRF3-type I interferon-independent pathway, promoting viral innate immune escape. Deletion of lncRNA-BTX in cells or mice significantly reduces viral load in vitro or in vivo, respectively. Mechanistically, lncRNA-BTX strengthens the interactions between DHX9 or ILF3 (two RBPs that have opposite functions in regulating the replication of RNA virus) and their respective partner, JMJD6 or ILF2, which regulates intracellular translocations of DHX9 and ILF3 from the nucleus to the cytoplasm. Put simply, lncRNA-BTX facilitates DHX9's return to the cytoplasm and retains ILF3 within the nucleus, promoting viral replication. This work unveils a strategy developed by the virus to bypass host innate immunity, thus providing a potential target for antiviral therapeutics.
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Affiliation(s)
- Yang Cao
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiacheng Wu
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Ye Hu
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yangyang Chai
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jiaying Song
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jiaqi Duan
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Song Zhang
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiaoqing Xu
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China; Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China.
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3
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Smith MR, Costa G. RNA-binding proteins and translation control in angiogenesis. FEBS J 2022; 289:7788-7809. [PMID: 34796614 DOI: 10.1111/febs.16286] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/17/2021] [Accepted: 11/17/2021] [Indexed: 01/14/2023]
Abstract
Tissue vascularization through the process of angiogenesis ensures adequate oxygen and nutrient supply during development and regeneration. The complex morphogenetic events involved in new blood vessel formation are orchestrated by a tightly regulated crosstalk between extra and intracellular factors. In this context, RNA-binding protein (RBP) activity and protein translation play fundamental roles during the cellular responses triggered by particular environmental cues. A solid body of work has demonstrated that key RBPs (such as HuR, TIS11 proteins, hnRNPs, NF90, QKIs and YB1) are implicated in both physiological and pathological angiogenesis. These RBPs are critical for the metabolism of messenger (m)RNAs encoding angiogenic modulators and, importantly, strong evidence suggests that RBP-mRNA interactions can be altered in disease. Lesser known, but not less important, the mechanistic aspects of protein synthesis can also regulate the generation of new vessels. In this review, we outline the key findings demonstrating the implications of RBP-mediated RNA regulation and translation control in angiogenesis. Furthermore, we highlight how these mechanisms of post-transcriptional control of gene expression have led to promising therapeutic strategies aimed at targeting undesired blood vessel formation.
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Affiliation(s)
- Madeleine R Smith
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, UK
| | - Guilherme Costa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, UK
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4
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Gao X, Fang D, Liang Y, Deng X, Chen N, Zeng M, Luo M. Circular RNAs as emerging regulators in COVID-19 pathogenesis and progression. Front Immunol 2022; 13:980231. [PMID: 36439162 PMCID: PMC9681929 DOI: 10.3389/fimmu.2022.980231] [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: 06/28/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), an infectious acute respiratory disease caused by a newly emerging RNA virus, is a still-growing pandemic that has caused more than 6 million deaths globally and has seriously threatened the lives and health of people across the world. Currently, several drugs have been used in the clinical treatment of COVID-19, such as small molecules, neutralizing antibodies, and monoclonal antibodies. In addition, several vaccines have been used to prevent the spread of the pandemic, such as adenovirus vector vaccines, inactivated vaccines, recombinant subunit vaccines, and nucleic acid vaccines. However, the efficacy of vaccines and the onset of adverse reactions vary among individuals. Accumulating evidence has demonstrated that circular RNAs (circRNAs) are crucial regulators of viral infections and antiviral immune responses and are heavily involved in COVID-19 pathologies. During novel coronavirus infection, circRNAs not only directly affect the transcription process and interfere with viral replication but also indirectly regulate biological processes, including virus-host receptor binding and the immune response. Consequently, understanding the expression and function of circRNAs during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will provide novel insights into the development of circRNA-based methods. In this review, we summarize recent progress on the roles and underlying mechanisms of circRNAs that regulate the inflammatory response, viral replication, immune evasion, and cytokines induced by SARS-CoV-2 infection, and thus highlighting the diagnostic and therapeutic challenges in the treatment of COVID-19 and future research directions.
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Affiliation(s)
- Xiaojun Gao
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Dan Fang
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yu Liang
- College of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Traditional Chinese Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Xin Deng
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Ni Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Min Zeng
- Department of Pharmacy, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Mao Luo
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- College of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Traditional Chinese Medicine, Southwest Medical University, Luzhou, Sichuan, China
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5
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The Polyvalent Role of NF90 in RNA Biology. Int J Mol Sci 2022; 23:ijms232113584. [DOI: 10.3390/ijms232113584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
Double-stranded RNA-binding proteins (dsRBPs) are major players in the regulation of gene expression patterns. Among them, Nuclear Factor 90 (NF90) has a plethora of well-known functions in viral infection, transcription, and translation as well as RNA stability and degradation. In addition, NF90 has been identified as a regulator of microRNA (miRNA) maturation by competing with Microprocessor for the binding of pri-miRNAs in the nucleus. NF90 was recently shown to control the biogenesis of a subset of human miRNAs, which ultimately influences, not only the abundance, but also the expression of the host gene and the fate of the mRNA target repertoire. Moreover, recent evidence suggests that NF90 is also involved in RNA-Induced Silencing Complex (RISC)-mediated silencing by binding to target mRNAs and controlling their translation and degradation. Here, we review the many, and growing, functions of NF90 in RNA biology, with a focus on the miRNA pathway and RISC-mediated gene silencing.
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6
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Moghimi S, Viktorova EG, Gabaglio S, Zimina A, Budnik B, Wynn BG, Sztul E, Belov GA. A Proximity biotinylation assay with a host protein bait reveals multiple factors modulating enterovirus replication. PLoS Pathog 2022; 18:e1010906. [PMID: 36306280 PMCID: PMC9645661 DOI: 10.1371/journal.ppat.1010906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/09/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
As ultimate parasites, viruses depend on host factors for every step of their life cycle. On the other hand, cells evolved multiple mechanisms of detecting and interfering with viral replication. Yet, our understanding of the complex ensembles of pro- and anti-viral factors is very limited in virtually every virus-cell system. Here we investigated the proteins recruited to the replication organelles of poliovirus, a representative of the genus Enterovirus of the Picornaviridae family. We took advantage of a strict dependence of enterovirus replication on a host protein GBF1, and established a stable cell line expressing a truncated GBF1 fused to APEX2 peroxidase that effectively supported viral replication upon inhibition of the endogenous GBF1. This construct biotinylated multiple host and viral proteins on the replication organelles. Among the viral proteins, the polyprotein cleavage intermediates were overrepresented, suggesting that the GBF1 environment is linked to viral polyprotein processing. The proteomics characterization of biotinylated host proteins identified multiple proteins previously associated with enterovirus replication, as well as more than 200 new factors recruited to the replication organelles. RNA metabolism proteins, many of which normally localize in the nucleus, constituted the largest group, underscoring the massive release of nuclear factors into the cytoplasm of infected cells and their involvement in viral replication. Functional analysis of several newly identified proteins revealed both pro- and anti-viral factors, including a novel component of infection-induced stress granules. Depletion of these proteins similarly affected the replication of diverse enteroviruses indicating broad conservation of the replication mechanisms. Thus, our data significantly expand the knowledge of the composition of enterovirus replication organelles, provide new insights into viral replication, and offer a novel resource for identifying targets for anti-viral interventions.
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Affiliation(s)
- Seyedehmahsa Moghimi
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Ekaterina G. Viktorova
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Samuel Gabaglio
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Anna Zimina
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource Laboratory (MSPRL), FAS Division of Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - Bridge G. Wynn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - George A. Belov
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
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7
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Grasso G, Akkawi C, Franckhauser C, Nait-Saidi R, Bello M, Barbier J, Kiernan R. NF90 interacts with components of RISC and modulates association of Ago2 with mRNA. BMC Biol 2022; 20:194. [PMID: 36050755 PMCID: PMC9438302 DOI: 10.1186/s12915-022-01384-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 08/05/2022] [Indexed: 01/14/2023] Open
Abstract
Background Nuclear factor 90 (NF90) is a double-stranded RNA-binding protein involved in a multitude of different cellular mechanisms such as transcription, translation, viral infection, and mRNA stability. Recent data suggest that NF90 might influence the abundance of target mRNAs in the cytoplasm through miRNA- and Argonaute 2 (Ago2)-dependent activity. Results Here, we identified the interactome of NF90 in the cytoplasm, which revealed several components of the RNA-induced silencing complex (RISC) and associated factors. Co-immunoprecipitation analysis confirmed the interaction of NF90 with the RISC-associated RNA helicase, Moloney leukemia virus 10 (MOV10), and other proteins involved in RISC-mediated silencing, including Ago2. Furthermore, NF90 association with MOV10 and Ago2 was found to be RNA-dependent. Glycerol gradient sedimentation of NF90 immune complexes indicates that these proteins occur in the same protein complex. At target RNAs predicted to bind both NF90 and MOV10 in their 3′ UTRs, NF90 association was increased upon loss of MOV10 and vice versa. Interestingly, loss of NF90 led to an increase in association of Ago2 as well as a decrease in the abundance of the target mRNA. Similarly, during hypoxia, the binding of Ago2 to vascular endothelial growth factor (VEGF) mRNA increased after loss of NF90, while the level of VEGF mRNA decreased. Conclusions These findings reveal that, in the cytoplasm, NF90 can associate with components of RISC such as Ago2 and MOV10. In addition, the data indicate that NF90 and MOV10 may compete for the binding of common target mRNAs, suggesting a role for NF90 in the regulation of RISC-mediated silencing by stabilizing target mRNAs, such as VEGF, during cancer-induced hypoxia. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01384-2.
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Affiliation(s)
- Giuseppa Grasso
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Charbel Akkawi
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Celine Franckhauser
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Rima Nait-Saidi
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Maxime Bello
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Jérôme Barbier
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Rosemary Kiernan
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France.
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8
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Wang XW, Liu CX, Chen LL, Zhang QC. RNA structure probing uncovers RNA structure-dependent biological functions. Nat Chem Biol 2021; 17:755-766. [PMID: 34172967 DOI: 10.1038/s41589-021-00805-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/23/2021] [Indexed: 01/22/2023]
Abstract
RNA molecules fold into complex structures that enable their diverse functions in cells. Recent revolutionary innovations in transcriptome-wide RNA structural probing of living cells have ushered in a new era in understanding RNA functions. Here, we summarize the latest technological advances for probing RNA secondary structures and discuss striking discoveries that have linked RNA regulation and biological processes through interrogation of RNA structures. In particular, we highlight how different long noncoding RNAs form into distinct secondary structures that determine their modes of interactions with protein partners to realize their unique functions. These dynamic structures mediate RNA regulatory functions through altering interactions with proteins and other RNAs. We also outline current methodological hurdles and speculate about future directions for development of the next generation of RNA structure-probing technologies of higher sensitivity and resolution, which could then be applied in increasingly physiologically relevant studies.
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Affiliation(s)
- Xi-Wen Wang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Chu-Xiao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, China. .,School of Life Sciences, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China. .,Tsinghua-Peking Center for Life Sciences, Beijing, China.
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9
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Dou S, Li G, Li G, Hou C, Zheng Y, Tang L, Gao Y, Mo R, Li Y, Wang R, Shen B, Zhang J, Han G. Ubiquitination and degradation of NF90 by Tim-3 inhibits antiviral innate immunity. eLife 2021; 10:66501. [PMID: 34110282 PMCID: PMC8225388 DOI: 10.7554/elife.66501] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022] Open
Abstract
Nuclear factor 90 (NF90) is a novel virus sensor that serves to initiate antiviral innate immunity by triggering stress granule (SG) formation. However, the regulation of the NF90-SG pathway remains largely unclear. We found that Tim-3, an immune checkpoint inhibitor, promotes the ubiquitination and degradation of NF90 and inhibits NF90-SG-mediated antiviral immunity. Vesicular stomatitis virus (VSV) infection induces the up-regulation and activation of Tim-3 in macrophages, which in turn recruit the E3 ubiquitin ligase TRIM47 to the zinc finger domain of NF90 and initiate a proteasome-dependent degradation via K48-linked ubiquitination at Lys297. Targeted inactivation of Tim-3 enhances the NF90 downstream SG formation by selectively increasing the phosphorylation of protein kinase R and eukaryotic translation initiation factor 2α, the expression of SG markers G3BP1 and TIA-1, and protecting mice from VSV challenge. These findings provide insights into the crosstalk between Tim-3 and other receptors in antiviral innate immunity and its related clinical significance.
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Affiliation(s)
- Shuaijie Dou
- Beijing Institute of Basic Medical Sciences, Beijing, China.,Anhui Medical University, Hefei, China
| | - Guoxian Li
- Beijing Institute of Basic Medical Sciences, Beijing, China.,Institute of Immunology, Medical School of Henan University, Kaifeng, China
| | - Ge Li
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chunmei Hou
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yang Zheng
- Department of Oncology, First Hospital of Jilin University, Changchun, China
| | - Lili Tang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yang Gao
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Rongliang Mo
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yuxiang Li
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Renxi Wang
- Beijing Institute of Basic Medical Sciences, Beijing, China.,Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Beifen Shen
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jun Zhang
- Institute of Immunology, Medical School of Henan University, Kaifeng, China
| | - Gencheng Han
- Beijing Institute of Basic Medical Sciences, Beijing, China
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10
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Emerging functions of circular RNA in aging. Trends Genet 2021; 37:819-829. [PMID: 34016449 DOI: 10.1016/j.tig.2021.04.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/05/2021] [Accepted: 04/22/2021] [Indexed: 01/22/2023]
Abstract
Circular RNA (circRNA) is a closed, single-stranded transcript widely detected in eukaryotes. Recent studies indicate that the levels of circRNAs change with age in various tissues in multiple species, ranging from nematodes to mammals. Here we discuss the functional roles of circRNAs in animal aging and longevity. We review studies regarding the differential expression of circRNAs that contributes to cellular senescence and the pathogenesis of aging-associated diseases. We explore the features of aging-associated circRNAs by discussing their potential as biomarkers of aging, tissue specificity, physiological roles, action mechanisms, and evolutionarily conserved characteristics. Our review provides insights into current progress in circRNA research and their significant functions in the aging process.
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11
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Razavi ZS, Asgarpour K, Mahjoubin-Tehran M, Rasouli S, Khan H, Shahrzad MK, Hamblin MR, Mirzaei H. Angiogenesis-related non-coding RNAs and gastrointestinal cancer. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:220-241. [PMID: 34095461 PMCID: PMC8141508 DOI: 10.1016/j.omto.2021.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gastrointestinal (GI) cancers are among the main reasons for cancer death globally. The deadliest types of GI cancer include colon, stomach, and liver cancers. Multiple lines of evidence have shown that angiogenesis has a key role in the growth and metastasis of all GI tumors. Abnormal angiogenesis also has a critical role in many non-malignant diseases. Therefore, angiogenesis is considered to be an important target for improved cancer treatment. Despite much research, the mechanisms governing angiogenesis are not completely understood. Recently, it has been shown that angiogenesis-related non-coding RNAs (ncRNAs) could affect the development of angiogenesis in cancer cells and tumors. The broad family of ncRNAs, which include long non-coding RNAs, microRNAs, and circular RNAs, are related to the development, promotion, and metastasis of GI cancers, especially in angiogenesis. This review discusses the role of ncRNAs in mediating angiogenesis in various types of GI cancers and looks forward to the introduction of mimetics and antagonists as possible therapeutic agents.
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Affiliation(s)
| | - Kasra Asgarpour
- Department of Medicine, University of Western Ontario, London, ON, Canada
| | - Maryam Mahjoubin-Tehran
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Susan Rasouli
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mohammad Karim Shahrzad
- Department of Internal Medicine and Endocrinology, Shohadae Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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12
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Fang N, Ding GW, Ding H, Li J, Liu C, Lv L, Shi YJ. Research Progress of Circular RNA in Gastrointestinal Tumors. Front Oncol 2021; 11:665246. [PMID: 33937077 PMCID: PMC8082141 DOI: 10.3389/fonc.2021.665246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/15/2021] [Indexed: 01/17/2023] Open
Abstract
circular RNA (circRNA) is a closed ring structure formed by cyclic covalent bonds connecting the 5’-end and 3’-end of pre-mRNA. circRNA is widely distributed in eukaryotic cells. Recent studies have shown that circRNA is involved in the pathogenesis and development of multiple types of diseases, including tumors. circRNA is specifically expressed in tissues. And the stability of circRNA is higher than that of linear RNA, which can play biological roles through sponge adsorption of miRNA, interaction with RNA binding protein, regulation of gene transcription, the mRNA and protein translation brake, and translation of protein and peptides. These characteristics render circRNAs as biomarkers and therapeutic targets of tumors. Gastrointestinal tumors are common malignancies worldwide, which seriously threaten human health. In this review, we summarize the generation and biological characteristics of circRNA, molecular regulation mechanism and related effects of circRNA in gastrointestinal tumors.
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Affiliation(s)
- Na Fang
- Department of Oncology, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Guo-Wen Ding
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Hao Ding
- Department of Respiratory, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Juan Li
- Department of Oncology, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Chao Liu
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Lu Lv
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Yi-Jun Shi
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
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13
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Zhang XO, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annu Rev Genomics Hum Genet 2021; 22:199-218. [PMID: 33792357 DOI: 10.1146/annurev-genom-111620-100736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Short interspersed nuclear elements (SINEs) are nonautonomous retrotransposons that occupy approximately 13% of the human genome. They are transcribed by RNA polymerase III and can be retrotranscribed and inserted back into the genome with the help of other autonomous retroelements. Because they are preferentially located close to or within gene-rich regions, they can regulate gene expression by various mechanisms that act at both the DNA and the RNA levels. In this review, we summarize recent findings on the involvement of SINEs in different types of gene regulation and discuss the potential regulatory functions of SINEs that are in close proximity to genes, Pol III-transcribed SINE RNAs, and embedded SINE sequences within Pol II-transcribed genes in the human genome. These discoveries illustrate how the human genome has exapted some SINEs into functional regulatory elements.
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Affiliation(s)
- Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; .,Current affiliation: School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Henry Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
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14
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McKellar J, Rebendenne A, Wencker M, Moncorgé O, Goujon C. Mammalian and Avian Host Cell Influenza A Restriction Factors. Viruses 2021; 13:522. [PMID: 33810083 PMCID: PMC8005160 DOI: 10.3390/v13030522] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022] Open
Abstract
The threat of a new influenza pandemic is real. With past pandemics claiming millions of lives, finding new ways to combat this virus is essential. Host cells have developed a multi-modular system to detect incoming pathogens, a phenomenon called sensing. The signaling cascade triggered by sensing subsequently induces protection for themselves and their surrounding neighbors, termed interferon (IFN) response. This response induces the upregulation of hundreds of interferon-stimulated genes (ISGs), including antiviral effectors, establishing an antiviral state. As well as the antiviral proteins induced through the IFN system, cells also possess a so-called intrinsic immunity, constituted of antiviral proteins that are constitutively expressed, creating a first barrier preceding the induction of the interferon system. All these combined antiviral effectors inhibit the virus at various stages of the viral lifecycle, using a wide array of mechanisms. Here, we provide a review of mammalian and avian influenza A restriction factors, detailing their mechanism of action and in vivo relevance, when known. Understanding their mode of action might help pave the way for the development of new influenza treatments, which are absolutely required if we want to be prepared to face a new pandemic.
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Affiliation(s)
- Joe McKellar
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Antoine Rebendenne
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Mélanie Wencker
- Centre International de Recherche en Infectiologie, INSERM/CNRS/UCBL1/ENS de Lyon, 69007 Lyon, France;
| | - Olivier Moncorgé
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Caroline Goujon
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
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15
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Meier T, Timm M, Montani M, Wilkens L. Gene networks and transcriptional regulators associated with liver cancer development and progression. BMC Med Genomics 2021; 14:41. [PMID: 33541355 PMCID: PMC7863452 DOI: 10.1186/s12920-021-00883-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 01/24/2021] [Indexed: 12/14/2022] Open
Abstract
Background Treatment options for hepatocellular carcinoma (HCC) are limited, and overall survival is poor. Despite the high frequency of this malignoma, its basic disease mechanisms are poorly understood. Therefore, the aim of this study was to use different methodological approaches and combine the results to improve our knowledge on the development and progression of HCC. Methods Twenty-three HCC samples were characterized by histological, morphometric and cytogenetic analyses, as well as comparative genomic hybridization (aCGH) and genome-wide gene expression followed by a bioinformatic search for potential transcriptional regulators and master regulatory molecules of gene networks. Results Histological evaluation revealed low, intermediate and high-grade HCCs, and gene expression analysis split them into two main sets: GE1-HCC and GE2-HCC, with a low and high proliferation gene expression signature, respectively. Array-based comparative genomic hybridization demonstrated a high level of chromosomal instability, with recurrent chromosomal gains of 1q, 6p, 7q, 8q, 11q, 17q, 19p/q and 20q in both HCC groups and losses of 1p, 4q, 6q, 13q and 18q characteristic for GE2-HCC. Gene expression and bioinformatics analyses revealed that different genes and gene regulatory networks underlie the distinct biological features observed in GE1-HCC and GE2-HCC. Besides previously reported dysregulated genes, the current study identified new candidate genes with a putative role in liver cancer, e.g. C1orf35, PAFAH1B3, ZNF219 and others. Conclusion Analysis of our findings, in accordance with the available published data, argues in favour of the notion that the activated E2F1 signalling pathway, which can be responsible for both inappropriate cell proliferation and initial chromosomal instability, plays a pivotal role in HCC development and progression. A dedifferentiation switch that manifests in exaggerated gene expression changes might be due to turning on transcriptional co-regulators with broad impact on gene expression, e.g. POU2F1 (OCT1) and NFY, as a response to accumulating cell stress during malignant development. Our findings point towards the necessity of different approaches for the treatment of HCC forms with low and high proliferation signatures and provide new candidates for developing appropriate HCC therapies.
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Affiliation(s)
- Tatiana Meier
- Institute of Pathology, Nordstadtkrankenhaus, Hanover, Germany.
| | - Max Timm
- Institute of Pathology, Nordstadtkrankenhaus, Hanover, Germany.,Clinic for Laryngology, Rhinology and Otology, Medical School Hanover, Hanover, Germany
| | - Matteo Montani
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Ludwig Wilkens
- Institute of Pathology, Nordstadtkrankenhaus, Hanover, Germany.,Institute of Human Genetics, Medical School Hanover, Hanover, Germany
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16
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Rajappa A, Banerjee S, Sharma V, Khandelia P. Circular RNAs: Emerging Role in Cancer Diagnostics and Therapeutics. Front Mol Biosci 2020; 7:577938. [PMID: 33195421 PMCID: PMC7655967 DOI: 10.3389/fmolb.2020.577938] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
Circular RNAs (circRNAs) are rapidly coming to the fore as major regulators of gene expression and cellular functions. They elicit their influence via a plethora of diverse molecular mechanisms. It is not surprising that aberrant circRNA expression is common in cancers and they have been implicated in multiple aspects of cancer pathophysiology such as apoptosis, invasion, migration, and proliferation. We summarize the emerging role of circRNAs as biomarkers and therapeutic targets in cancer.
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Affiliation(s)
| | | | - Vivek Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Hyderabad, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Hyderabad, India
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17
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Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
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18
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Nitschko V, Kunzelmann S, Fröhlich T, Arnold GJ, Förstemann K. Trafficking of siRNA precursors by the dsRBD protein Blanks in Drosophila. Nucleic Acids Res 2020; 48:3906-3921. [PMID: 32025726 PMCID: PMC7144943 DOI: 10.1093/nar/gkaa072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 01/03/2023] Open
Abstract
RNA interference targets aberrant transcripts with cognate small interfering RNAs, which derive from double-stranded RNA precursors. Several functional screens have identified Drosophila blanks/lump (CG10630) as a facilitator of RNAi, yet its molecular function has remained unknown. The protein carries two dsRNA binding domains (dsRBD) and blanks mutant males have a spermatogenesis defect. We demonstrate that blanks selectively boosts RNAi triggered by dsRNA of nuclear origin. Blanks binds dsRNA via its second dsRBD in vitro, shuttles between nucleus and cytoplasm and the abundance of siRNAs arising at many sites of convergent transcription is reduced in blanks mutants. Since features of nascent RNAs - such as introns and transcription beyond the polyA site – contribute to the small RNA pool, we propose that Blanks binds dsRNA formed by cognate nascent RNAs in the nucleus and fosters its export to the cytoplasm for dicing. We refer to the resulting small RNAs as blanks exported siRNAs (bepsiRNAs). While bepsiRNAs were fully dependent on RNA binding to the second dsRBD of blanks in transgenic flies, male fertility was not. This is consistent with a previous report that linked fertility to the first dsRBD of Blanks. The role of blanks in spermatogenesis appears thus unrelated to its role in dsRNA export.
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Affiliation(s)
- Volker Nitschko
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Stefan Kunzelmann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Thomas Fröhlich
- Laboratory of Functional Genome Analysis, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Georg J Arnold
- Laboratory of Functional Genome Analysis, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Klaus Förstemann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
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19
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The expanding regulatory mechanisms and cellular functions of circular RNAs. Nat Rev Mol Cell Biol 2020; 21:475-490. [PMID: 32366901 DOI: 10.1038/s41580-020-0243-y] [Citation(s) in RCA: 791] [Impact Index Per Article: 197.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
Many protein-coding genes in higher eukaryotes can produce circular RNAs (circRNAs) through back-splicing of exons. CircRNAs differ from mRNAs in their production, structure and turnover and thereby have unique cellular functions and potential biomedical applications. In this Review, I discuss recent progress in our understanding of the biogenesis of circRNAs and the regulation of their abundance and of their biological functions, including in transcription and splicing, sequestering or scaffolding of macromolecules to interfere with microRNA activities or signalling pathways, and serving as templates for translation. I further discuss the emerging roles of circRNAs in regulating immune responses and cell proliferation, and the possibilities of applying circRNA technologies in biomedical research.
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20
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Watson SF, Bellora N, Macias S. ILF3 contributes to the establishment of the antiviral type I interferon program. Nucleic Acids Res 2020; 48:116-129. [PMID: 31701124 PMCID: PMC7145544 DOI: 10.1093/nar/gkz1060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/21/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Upon detection of viral infections, cells activate the expression of type I interferons (IFNs) and pro-inflammatory cytokines to control viral dissemination. As part of their antiviral response, cells also trigger the translational shutoff response which prevents translation of viral mRNAs and cellular mRNAs in a non-selective manner. Intriguingly, mRNAs encoding for antiviral factors bypass this translational shutoff, suggesting the presence of additional regulatory mechanisms enabling expression of the self-defence genes. Here, we identified the dsRNA binding protein ILF3 as an essential host factor required for efficient translation of the central antiviral cytokine, IFNB1, and a subset of interferon-stimulated genes. By combining polysome profiling and next-generation sequencing, ILF3 was also found to be necessary to establish the dsRNA-induced transcriptional and translational programs. We propose a central role for the host factor ILF3 in enhancing expression of the antiviral defence mRNAs in cellular conditions where cap-dependent translation is compromised.
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Affiliation(s)
- Samir F Watson
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, UK
| | | | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, UK
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21
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Patop IL, Wüst S, Kadener S. Past, present, and future of circRNAs. EMBO J 2019; 38:e100836. [PMID: 31343080 PMCID: PMC6694216 DOI: 10.15252/embj.2018100836] [Citation(s) in RCA: 730] [Impact Index Per Article: 146.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 05/15/2019] [Accepted: 06/03/2019] [Indexed: 12/28/2022] Open
Abstract
Exonic circular RNAs (circRNAs) are covalently closed RNA molecules generated by a process named back-splicing. circRNAs are highly abundant in eukaryotes, and many of them are evolutionary conserved. In metazoans, circular RNAs are expressed in a tissue-specific manner, are highly stable, and accumulate with age in neural tissues. circRNA biogenesis can regulate the production of the linear RNA counterpart in cis as back-splicing competes with linear splicing. Recent reports also demonstrate functions for some circRNAs in trans: Certain circRNAs interact with microRNAs, some are translated, and circRNAs have been shown to regulate immune responses and behavior. Here, we review current knowledge about animal circRNAs and summarize new insights into potential circRNA functions, concepts of their origin, and possible future directions in the field.
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Affiliation(s)
| | - Stas Wüst
- Department of BiologyBrandeis UniversityWalthamMAUSA
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22
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Jia R, Ajiro M, Yu L, McCoy P, Zheng ZM. Oncogenic splicing factor SRSF3 regulates ILF3 alternative splicing to promote cancer cell proliferation and transformation. RNA (NEW YORK, N.Y.) 2019; 25:630-644. [PMID: 30796096 PMCID: PMC6467003 DOI: 10.1261/rna.068619.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/21/2019] [Indexed: 05/28/2023]
Abstract
Alternative RNA splicing is an important focus in molecular and clinical oncology. We report here that SRSF3 regulates alternative RNA splicing of interleukin enhancer binding factor 3 (ILF3) and production of this double-strand RNA-binding protein. An increased coexpression of ILF3 isoforms and SRSF3 was found in various types of cancers. ILF3 isoform-1 and isoform-2 promote cell proliferation and transformation. Tumor cells with reduced SRSF3 expression produce aberrant isoform-5 and -7 of ILF3. By binding to RNA sequence motifs, SRSF3 regulates the production of various ILF3 isoforms by exclusion/inclusion of ILF3 exon 18 or by selection of an alternative 3' splice site within exon 18. ILF3 isoform-5 and isoform-7 suppress tumor cell proliferation and the isoform-7 induces cell apoptosis. Our data indicate that ILF3 isoform-1 and isoform-2 are two critical factors for cell proliferation and transformation. The increased SRSF3 expression in cancer cells plays an important role in maintaining the steady status of ILF3 isoform-1 and isoform-2.
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Affiliation(s)
- Rong Jia
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Ke Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Masahiko Ajiro
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Lulu Yu
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Philip McCoy
- Flow Cytometry Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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23
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Garcia-Moreno M, Järvelin AI, Castello A. Unconventional RNA-binding proteins step into the virus-host battlefront. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1498. [PMID: 30091184 PMCID: PMC7169762 DOI: 10.1002/wrna.1498] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 12/15/2022]
Abstract
The crucial participation of cellular RNA‐binding proteins (RBPs) in virtually all steps of virus infection has been known for decades. However, most of the studies characterizing this phenomenon have focused on well‐established RBPs harboring classical RNA‐binding domains (RBDs). Recent proteome‐wide approaches have greatly expanded the census of RBPs, discovering hundreds of proteins that interact with RNA through unconventional RBDs. These domains include protein–protein interaction platforms, enzymatic cores, and intrinsically disordered regions. Here, we compared the experimentally determined census of RBPs to gene ontology terms and literature, finding that 472 proteins have previous links with viruses. We discuss what these proteins are and what their roles in infection might be. We also review some of the pioneering examples of unorthodox RBPs whose RNA‐binding activity has been shown to be critical for virus infection. Finally, we highlight the potential of these proteins for host‐based therapies against viruses. This article is categorized under:
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
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Affiliation(s)
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, Oxford, UK
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24
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Fernández-Ponce C, Durán-Ruiz MC, Narbona-Sánchez I, Muñoz-Miranda JP, Arbulo-Echevarria MM, Serna-Sanz A, Baumann C, Litrán R, Aguado E, Bloch W, García-Cozar F. Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells. Front Microbiol 2018; 8:2595. [PMID: 29354102 PMCID: PMC5758585 DOI: 10.3389/fmicb.2017.02595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus core protein is a highly basic viral protein that multimerizes with itself to form the viral capsid. When expressed in CD4+ T lymphocytes, it can induce modifications in several essential cellular and biological networks. To shed light on the mechanisms underlying the alterations caused by the viral protein, we have analyzed HCV-core subcellular localization and its associations with host proteins in Jurkat T cells. In order to investigate the intracellular localization of Hepatitis C virus core protein, we have used a lentiviral system to transduce Jurkat T cells and subsequently localize the protein using immunoelectron microscopy techniques. We found that in Jurkat T cells, Hepatitis C virus core protein mostly localizes in the nucleus and specifically in the nucleolus. In addition, we performed pull-down assays combined with Mass Spectrometry Analysis, to identify proteins that associate with Hepatitis C virus core in Jurkat T cells. We found proteins such as NOLC1, PP1γ, ILF3, and C1QBP implicated in localization and/or traffic to the nucleolus. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4+ T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. Thus, in the current work, we show the ultrastructural localization of Hepatitis C virus core and the first profile of HCV core associated proteins in T cells, and we discuss the functions and interconnections of these proteins in molecular networks where relevant biological modifications have been described upon the expression of Hepatitis C virus core protein. Thereby, the current work constitutes a necessary step toward understanding the mechanisms underlying HCV core mediated alterations that had been described in relevant biological processes in CD4+ T cells.
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Affiliation(s)
- Cecilia Fernández-Ponce
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Maria C Durán-Ruiz
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Isaac Narbona-Sánchez
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Juan P Muñoz-Miranda
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Mikel M Arbulo-Echevarria
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | | | | | - Rocío Litrán
- Department of Condensed Matter Physics, University of Cádiz, Puerto Real, Spain
| | - Enrique Aguado
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Wilhelm Bloch
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiovascular Research and Sport Medicine, German Sport University Cologne, Cologne, Germany
| | - Francisco García-Cozar
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
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25
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Patzina C, Botting CH, García-Sastre A, Randall RE, Hale BG. Human interactome of the influenza B virus NS1 protein. J Gen Virol 2017; 98:2267-2273. [PMID: 28869005 PMCID: PMC5656757 DOI: 10.1099/jgv.0.000909] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
NS1 proteins of influenza A and B viruses share limited sequence homology, yet both are potent manipulators of host cell processes, particularly interferon (IFN) induction. Although many cellular partners are reported for A/NS1, only a few (e.g. PKR and ISG15) have been identified for B/NS1. Here, affinity-purification and mass spectrometry were used to expand the known host interactome of B/NS1. We identified 22 human proteins as new putative targets for B/NS1, validating several, including DHX9, ILF3, YBX1 and HNRNPC. Consistent with two RNA-binding domains in B/NS1, many of the identified factors bind RNA and some interact with B/NS1 in an RNA-dependent manner. Functional characterization of several B/NS1 interactors identified SNRNP200 as a potential positive regulator of host IFN responses, while ILF3 exhibited dual roles in both IFN induction and influenza B virus replication. These data provide a resource for future investigations into the mechanisms underpinning host cell modulation by influenza B virus NS1.
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Affiliation(s)
- Corinna Patzina
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Catherine H. Botting
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife, KY16 9ST, UK
| | - Adolfo García-Sastre
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Richard E. Randall
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife, KY16 9ST, UK
| | - Benjamin G. Hale
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- *Correspondence: Benjamin G. Hale,
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26
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Li X, Liu CX, Xue W, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L, Chen LL. Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection. Mol Cell 2017. [PMID: 28625552 DOI: 10.1016/j.molcel.2017.05.023] [Citation(s) in RCA: 428] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Circular RNAs (circRNAs) generated via back-splicing are enhanced by flanking complementary sequences. Expression levels of circRNAs vary under different conditions, suggesting participation of protein factors in their biogenesis. Using genome-wide siRNA screening that targets all human unique genes and an efficient circRNA expression reporter, we identify double-stranded RNA-binding domain containing immune factors NF90/NF110 as key regulators in circRNA biogenesis. NF90/NF110 promote circRNA production in the nucleus by associating with intronic RNA pairs juxtaposing the circRNA-forming exon(s); they also interact with mature circRNAs in the cytoplasm. Upon viral infection, circRNA expression is decreased, in part owing to the nuclear export of NF90/NF110 to the cytoplasm. Meanwhile, NF90/NF110 released from circRNP complexes bind to viral mRNAs as part of their functions in antiviral immune response. Our results therefore implicate a coordinated regulation of circRNA biogenesis and function by NF90/NF110 in viral infection.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Chu-Xiao Liu
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Wei Xue
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yang Zhang
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shan Jiang
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Qing-Fei Yin
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jia Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Run-Wen Yao
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Li Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
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27
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Zhu X, Zelmer A, Wellmann S. Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay. J Vis Exp 2017. [PMID: 28117799 DOI: 10.3791/55218] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Protein-protein interactions are involved in thousands of cellular processes and occur in distinct spatial context. Traditionally, co-immunoprecipitation is a popular technique to detect protein-protein interactions. Subsequent Western blot analysis is the most common method to visualize co-immunoprecipitated proteins. Recently, the proximity ligation assay has become a powerful tool to visualize protein-protein interactions in situ and provides the possibility to quantify protein-protein interactions by this method. Similar to conventional immunocytochemistry, the proximity ligation assay technique is also based on the accessibility of primary antibodies to the antigens, but in contrast, proximity ligation assay detects protein-protein interactions with a unique technique involving rolling-circle PCR, while conventional immunocytochemistry only shows co-localization of proteins. Nuclear factor 90 (NF90) and RNA-binding motif protein 3 (RBM3) have been previously demonstrated as interacting partners. They are predominantly localized in the nucleus, but also migrate into the cytoplasm and regulate signaling pathways in the cytoplasmic compartment. Here, we compared NF90-RBM3 interaction in both the nucleus and the cytoplasm by co-immunoprecipitation and proximity ligation assay. In addition, we discussed the advantages and limitations of these two techniques in visualizing protein-protein interactions in respect to spatial distribution and the properties of protein-protein interactions.
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Affiliation(s)
- Xinzhou Zhu
- University Children's Hospital Basel (UKBB), University of Basel;
| | - Andrea Zelmer
- University Children's Hospital Basel (UKBB), University of Basel
| | - Sven Wellmann
- University Children's Hospital Basel (UKBB), University of Basel; Department of Clinical Research, University of Basel
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28
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Zhou Q, Zhu Y, Wei X, Zhou J, Chang L, Sui H, Han Y, Piao D, Sha R, Bai Y. MiR-590-5p inhibits colorectal cancer angiogenesis and metastasis by regulating nuclear factor 90/vascular endothelial growth factor A axis. Cell Death Dis 2016; 7:e2413. [PMID: 27735951 PMCID: PMC5133975 DOI: 10.1038/cddis.2016.306] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 08/16/2016] [Accepted: 08/31/2016] [Indexed: 12/19/2022]
Abstract
Altered expression of microRNA-590-5p (miR-590-5p) is involved in tumorigenesis, however, its role in colorectal cancer (CRC) remains to be determined. In this study, we focused on examining the effects of different expression levels of miR-590-5p in cancer cells and normal cells. Results showed that there are lower expression levels of miR-590-5p in human CRC cells and tissues than in normal control cells and tissues. Similarly, in our xenograft mouse model, knockdown of miR-590-5p promoted the progression of CRC. However, an overexpression of miR-590-5p in the mice inhibited angiogenesis, tumor growth, and lung metastasis. Nuclear factor 90 (NF90), a positive regulator of vascular endothelial growth factor (VEGF) mRNA stability and protein synthesis, was shown to be a direct target of miR-590-5p. The overexpression of NF90 restored VEGFA expression and rescued the loss of tumor angiogenesis caused by miR-590-5p. Conversely, the NF90-shRNA attenuated the increased tumor progression caused by the miR-590-5p inhibitor. Clinically, the levels of miR-590-5p were inversely correlated with those of NF90 and VEGFA in CRC tissues. Furthermore, knockdown of NF90 lead to a reduction of pri-miR-590 and an increase of mature miR-590-5p, suggesting a negative feedback loop between miR-590-5p and NF90. Collectively, these data establish miR-590-5p as an anti-onco-miR that inhibits CRC angiogenesis and metastasis through a new mechanism involving NF90/VEGFA signaling axis, highlighting the potential of miR-590-5p as a target for human CRC therapy.
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Affiliation(s)
- Qingxin Zhou
- Department of Gastrointestinal Oncology, The Third Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yuekun Zhu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoli Wei
- Department of Gastrointestinal Oncology, The Third Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jianhua Zhou
- Department of Gastrointestinal Oncology, The Third Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Liang Chang
- Department of Neurosurgery, The Third Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Hong Sui
- Department of Gastrointestinal Oncology, The Third Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yu Han
- Department of Gastrointestinal Oncology, The Third Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Daxun Piao
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ruihua Sha
- Department of Digestive Disease, Hongqi Hospital, Mudanjiang Medical University, Mudanjiang, China
| | - Yuxian Bai
- Department of Gastrointestinal Oncology, The Third Affiliated Hospital, Harbin Medical University, Harbin, China
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29
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Li T, Li X, Zhu W, Wang H, Mei L, Wu S, Lin X, Han X. NF90 is a novel influenza A virus NS1-interacting protein that antagonizes the inhibitory role of NS1 on PKR phosphorylation. FEBS Lett 2016; 590:2797-810. [PMID: 27423063 DOI: 10.1002/1873-3468.12311] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 12/24/2022]
Abstract
NF90 is a novel host antiviral factor that regulates PKR activation and stress granule formation in influenza A virus (IAV)-infected cells, but the precise mechanisms by which it operates remain unclear. We identified NF90 as a novel interacting protein of IAV nonstructural protein 1 (NS1). The interaction was dependent on the RNA-binding properties of NS1. NS1 associated with NF90 and PKR simultaneously; however, the interaction between NF90 and PKR was restricted by NS1. Knockdown of NF90 promoted inhibition of PKR phosphorylation induced by NS1, while coexpression of NF90 impeded reduction of PKR phosphorylation and stress granule formation triggered by NS1. In summary, NF90 exerts its antiviral activity by antagonizing the inhibitory role of NS1 on PKR phosphorylation.
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Affiliation(s)
- Ting Li
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - Xi Li
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - WenFei Zhu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, China
| | - HuiYu Wang
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - Lin Mei
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - ShaoQiang Wu
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - XiangMei Lin
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - XueQing Han
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
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30
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Murphy J, Hall WW, Ratner L, Sheehy N. Novel interactions between the HTLV antisense proteins HBZ and APH-2 and the NFAR protein family: Implications for the HTLV lifecycles. Virology 2016; 494:129-42. [PMID: 27110706 DOI: 10.1016/j.virol.2016.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/17/2023]
Abstract
The human T-cell leukaemia virus type 1 and type 2 (HTLV-1/HTLV-2) antisense proteins HBZ and APH-2 play key roles in the HTLV lifecycles and persistence in the host. Nuclear Factors Associated with double-stranded RNA (NFAR) proteins NF90/110 function in the lifecycles of several viruses and participate in host innate immunity against infection and oncogenesis. Using GST pulldown and co-immunoprecipitation assays we demonstrate specific novel interactions between HBZ/APH-2 and NF90/110 and characterised the protein domains involved. Moreover we show that NF90/110 significantly enhance Tax mediated LTR activation, an effect that was abolished by HBZ but enhanced by APH-2. Additionally we found that HBZ and APH-2 modulate the promoter activity of survivin and are capable of antagonising NF110-mediated survivin activation. Thus interactions between HTLV antisense proteins and the NFAR protein family have an overall positive impact on HTLV infection. Hence NFARs may represent potential therapeutic targets in HTLV infected cells.
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Affiliation(s)
- Jane Murphy
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - William W Hall
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Lee Ratner
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Noreen Sheehy
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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31
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Li Y, Belshan M. NF45 and NF90 Bind HIV-1 RNA and Modulate HIV Gene Expression. Viruses 2016; 8:v8020047. [PMID: 26891316 PMCID: PMC4776202 DOI: 10.3390/v8020047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/27/2016] [Accepted: 02/04/2016] [Indexed: 01/03/2023] Open
Abstract
A previous proteomic screen in our laboratory identified nuclear factor 45 (NF45) and nuclear factor 90 (NF90) as potential cellular factors involved in human immunodeficiency virus type 1 (HIV-1) replication. Both are RNA binding proteins that regulate gene expression; and NF90 has been shown to regulate the expression of cyclin T1 which is required for Tat-dependent trans-activation of viral gene expression. In this study the roles of NF45 and NF90 in HIV replication were investigated through overexpression studies. Ectopic expression of either factor potentiated HIV infection, gene expression, and virus production. Deletion of the RNA binding domains of NF45 and NF90 diminished the enhancement of HIV infection and gene expression. Both proteins were found to interact with the HIV RNA. RNA decay assays demonstrated that NF90, but not NF45, increased the half-life of the HIV RNA. Overall, these studies indicate that both NF45 and NF90 potentiate HIV infection through their RNA binding domains.
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Affiliation(s)
- Yan Li
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178, USA.
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178, USA.
- The Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583, USA.
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32
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Zhou H, Li J, Jian Y, Chen T, Deng H, Zhang J, Zeng H, Shan Z, Chen W. Effects and mechanism of arsenic trioxide in combination with rmhTRAIL in multiple myeloma. Exp Hematol 2016; 44:125-131.e11. [DOI: 10.1016/j.exphem.2015.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/24/2015] [Accepted: 10/14/2015] [Indexed: 12/31/2022]
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33
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Jayachandran U, Grey H, Cook AG. Nuclear factor 90 uses an ADAR2-like binding mode to recognize specific bases in dsRNA. Nucleic Acids Res 2015; 44:1924-36. [PMID: 26712564 PMCID: PMC4770229 DOI: 10.1093/nar/gkv1508] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/10/2015] [Indexed: 02/06/2023] Open
Abstract
Nuclear factors 90 and 45 (NF90 and NF45) form a protein complex involved in the post-transcriptional control of many genes in vertebrates. NF90 is a member of the dsRNA binding domain (dsRBD) family of proteins. RNA binding partners identified so far include elements in 3′ untranslated regions of specific mRNAs and several non-coding RNAs. In NF90, a tandem pair of dsRBDs separated by a natively unstructured segment confers dsRNA binding activity. We determined a crystal structure of the tandem dsRBDs of NF90 in complex with a synthetic dsRNA. This complex shows surprising similarity to the tandem dsRBDs from an adenosine-to-inosine editing enzyme, ADAR2 in complex with a substrate RNA. Residues involved in unusual base-specific recognition in the minor groove of dsRNA are conserved between NF90 and ADAR2. These data suggest that, like ADAR2, underlying sequences in dsRNA may influence how NF90 recognizes its target RNAs.
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Affiliation(s)
- Uma Jayachandran
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Heather Grey
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Atlanta G Cook
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
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