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Anastassiadis T, Köhrer C. Ushering in the era of tRNA medicines. J Biol Chem 2023; 299:105246. [PMID: 37703991 PMCID: PMC10583094 DOI: 10.1016/j.jbc.2023.105246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
Long viewed as an intermediary in protein translation, there is a growing awareness that tRNAs are capable of myriad other biological functions linked to human health and disease. These emerging roles could be tapped to leverage tRNAs as diagnostic biomarkers, therapeutic targets, or even as novel medicines. Furthermore, the growing array of tRNA-derived fragments, which modulate an increasingly broad spectrum of cellular pathways, is expanding this opportunity. Together, these molecules offer drug developers the chance to modulate the impact of mutations and to alter cell homeostasis. Moreover, because a single therapeutic tRNA can facilitate readthrough of a genetic mutation shared across multiple genes, such medicines afford the opportunity to define patient populations not based on their clinical presentation or mutated gene but rather on the mutation itself. This approach could potentially transform the treatment of patients with rare and ultrarare diseases. In this review, we explore the diverse biology of tRNA and its fragments, examining the past and present challenges to provide a comprehensive understanding of the molecules and their therapeutic potential.
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Yang M, Mo Y, Ren D, Liu S, Zeng Z, Xiong W. Transfer RNA-derived small RNAs in tumor microenvironment. Mol Cancer 2023; 22:32. [PMID: 36797764 PMCID: PMC9933334 DOI: 10.1186/s12943-023-01742-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Transfer RNAs (tRNAs) are a class of non-coding RNAs responsible for amino acid translocation during protein synthesis and are ubiquitously found in organisms. With certain modifications and under specific conditions, tRNAs can be sheared and fragmented into small non-coding RNAs, also known as tRNA-derived small RNAs (tDRs). With the development of high-throughput sequencing technologies and bioinformatic strategies, more and more tDRs have been identified and their functions in organisms have been characterized. tRNA and it derived tDRs, have been shown to be essential not only for transcription and translation, but also for regulating cell proliferation, apoptosis, metastasis, and immunity. Aberrant expression of tDRs is associated with a wide range of human diseases, especially with tumorigenesis and tumor progression. The tumor microenvironment (TME) is a complex ecosystem consisting of various cellular and cell-free components that are mutually compatible with the tumor. It has been shown that tDRs regulate the TME by regulating cancer stem cells, immunity, energy metabolism, epithelial mesenchymal transition, and extracellular matrix remodeling, playing a pro-tumor or tumor suppressor role. In this review, the biogenesis, classification, and function of tDRs, as well as their effects on the TME and the clinical application prospects will be summarized and discussed based on up to date available knowledge.
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Affiliation(s)
- Mei Yang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Yongzhen Mo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Daixi Ren
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Shun Liu
- Department of Cardiovascular Medicine, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
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Gast M, Nageswaran V, Kuss AW, Tzvetkova A, Wang X, Mochmann LH, Rad PR, Weiss S, Simm S, Zeller T, Voelzke H, Hoffmann W, Völker U, Felix SB, Dörr M, Beling A, Skurk C, Leistner DM, Rauch BH, Hirose T, Heidecker B, Klingel K, Nakagawa S, Poller WC, Swirski FK, Haghikia A, Poller W. tRNA-like Transcripts from the NEAT1-MALAT1 Genomic Region Critically Influence Human Innate Immunity and Macrophage Functions. Cells 2022; 11:cells11243970. [PMID: 36552736 PMCID: PMC9777231 DOI: 10.3390/cells11243970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022] Open
Abstract
The evolutionary conserved NEAT1-MALAT1 gene cluster generates large noncoding transcripts remaining nuclear, while tRNA-like transcripts (mascRNA, menRNA) enzymatically generated from these precursors translocate to the cytosol. Whereas functions have been assigned to the nuclear transcripts, data on biological functions of the small cytosolic transcripts are sparse. We previously found NEAT1-/- and MALAT1-/- mice to display massive atherosclerosis and vascular inflammation. Here, employing selective targeted disruption of menRNA or mascRNA, we investigate the tRNA-like molecules as critical components of innate immunity. CRISPR-generated human ΔmascRNA and ΔmenRNA monocytes/macrophages display defective innate immune sensing, loss of cytokine control, imbalance of growth/angiogenic factor expression impacting upon angiogenesis, and altered cell-cell interaction systems. Antiviral response, foam cell formation/oxLDL uptake, and M1/M2 polarization are defective in ΔmascRNA/ΔmenRNA macrophages, defining first biological functions of menRNA and describing new functions of mascRNA. menRNA and mascRNA represent novel components of innate immunity arising from the noncoding genome. They appear as prototypes of a new class of noncoding RNAs distinct from others (miRNAs, siRNAs) by biosynthetic pathway and intracellular kinetics. Their NEAT1-MALAT1 region of origin appears as archetype of a functionally highly integrated RNA processing system.
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Affiliation(s)
- Martina Gast
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
| | - Vanasa Nageswaran
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 12200 Berlin, Germany
| | - Andreas W Kuss
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Ana Tzvetkova
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Xiaomin Wang
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Liliana H Mochmann
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Pegah Ramezani Rad
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Tanja Zeller
- University Center of Cardiovascular Science, University Heart and Vascular Center, 20246 Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, 20246 Hamburg, Germany
| | - Henry Voelzke
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Wolfgang Hoffmann
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
| | - Stefan B Felix
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Department of Cardiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Marcus Dörr
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Department of Cardiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Antje Beling
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Institute for Biochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10178 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Carsten Skurk
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
| | - David-Manuel Leistner
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Bernhard H Rauch
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Pharmacology, University Medicine Greifswald, 17487 Greifswald, Germany
- Department Human Medicine, Section Pharmacology and Toxicology, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Bettina Heidecker
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Karin Klingel
- Institute for Pathology and Neuropathology, Department of Pathology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama 351-0198, Japan
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Wolfram C Poller
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Filip K Swirski
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arash Haghikia
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Wolfgang Poller
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 13353 Berlin, Germany
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4
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Hou J, Li Q, Wang J, Lu W. tRFs and tRNA Halves: Novel Cellular Defenders in Multiple Biological Processes. Curr Issues Mol Biol 2022; 44:5949-5962. [PMID: 36547066 PMCID: PMC9777342 DOI: 10.3390/cimb44120405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
tRNA fragments derived from angiogenin or Dicer cleavage are referred to as tRNA-derived fragments (tRFs) and tRNA halves. tRFs and tRNA halves have been identified in both eukaryotes and prokaryotes and are precisely cleaved at specific sites on either precursor or mature tRNA transcripts rather than via random degradation. tRFs and tRNA halves are highly involved in regulating transcription and translation in a canonical or non-canonical manner in response to cellular stress. In this review, we summarize the biogenesis and types of tRFs and tRNA halves, clarify the biological functions and molecular mechanisms of tRNA fragments in both physiological and pathological processes with a particular focus on their cytoprotective roles in defending against oxidation and apoptosis, and highlight their potential application as biomarkers in determining cell fate.
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Affiliation(s)
- Jiani Hou
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Qianqing Li
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jun Wang
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.W.); (W.L.); Tel.: +86-0431-84533525; Fax: +861-0431-84533525
| | - Wenfa Lu
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.W.); (W.L.); Tel.: +86-0431-84533525; Fax: +861-0431-84533525
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5
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Gan M, Ma J, Chen L, Zhang S, Niu L, Zhao Y, Li X, Pan H, Zhu L, Shen L. Identification of tRNA-derived small RNAs and their potential roles in porcine skeletal muscle with intrauterine growth restriction. Front Physiol 2022; 13:962278. [PMID: 36388094 PMCID: PMC9662792 DOI: 10.3389/fphys.2022.962278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/10/2022] [Indexed: 07/30/2023] Open
Abstract
Intrauterine growth restriction (IUGR) in humans often manifests as poor growth and delayed intellectual development, whereas in domestic animals it results in increased mortality. As a novel epigenetic regulatory molecule, tRNA-derived small RNAs (tsRNAs) have been reported to be involved in many biological processes. In this study, pigs (35d) were used as a model to characterize tsRNAs by sequencing in normal and IUGR porcine skeletal muscle. A total of 586 tsRNAs were identified, of which 103 were specifically expressed in normal-size pigs and 38 were specifically expressed in IUGR pigs. The tsRNAs formed by splicing before the 5' end anti codon of mature tRNA (tRF-5c) accounted for over 90% of tsRNAs, which were significantly enriched in IUGR pigs than in normal-size pigs. Enriched pathways of differentially expressed tsRNAs target genes mainly included metabolic pathways, Rap1 signaling pathway, endocytosis, mTOR signaling pathway, and AMPK signaling pathway. Regulatory network analysis of target genes revealed that IGF1 was one of the most important molecules of regulatory nodes in IUGR and normal porcine skeletal muscle. In addition, IGF1 was found to be one of the target genes of tRF-Glu-TTC-047, which is a highly expressed tsRNA in IUGR pigs. The findings described herein uncover the role of tsRNAs in IUGR porcine skeletal muscle development, thus providing insights into the prevention and treatment of IUGR in mammals.
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Affiliation(s)
- Mailin Gan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jianfeng Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Lei Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ye Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hongmei Pan
- Key Laboratory of Pig Industry Science of Agriculture Ministry, Chongqing Academy of Animal Science, Chongqing, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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6
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Zhou Y, Cui Q, Zhou Y. Screening and Comprehensive Analysis of Cancer-Associated tRNA-Derived Fragments. Front Genet 2022; 12:747931. [PMID: 35095997 PMCID: PMC8795687 DOI: 10.3389/fgene.2021.747931] [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: 07/27/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
tRNA-derived fragments (tRFs) constitute a novel class of small non-coding RNA cleaved from tRNAs. In recent years, researches have shown the regulatory roles of a few tRFs in cancers, illuminating a new direction for tRF-centric cancer researches. Nonetheless, more specific screening of tRFs related to oncogenesis pathways, cancer progression stages and cancer prognosis is continuously demanded to reveal the landscape of the cancer-associated tRFs. In this work, by combining the clinical information recorded in The Cancer Genome Atlas (TCGA) and the tRF expression profiles curated by MINTbase v2.0, we systematically screened 1,516 cancer-associated tRFs (ca-tRFs) across seven cancer types. The ca-tRF set collectively combined the differentially expressed tRFs between cancer samples and control samples, the tRFs significantly correlated with tumor stage and the tRFs significantly correlated with patient survival. By incorporating our previous tRF-target dataset, we found the ca-tRFs tend to target cancer-associated genes and onco-pathways like ATF6-mediated unfolded protein response, angiogenesis, cell cycle process regulation, focal adhesion, PI3K-Akt signaling pathway, cellular senescence and FoxO signaling pathway across multiple cancer types. And cell composition analysis implies that the expressions of ca-tRFs are more likely to be correlated with T-cell infiltration. We also found the ca-tRF expression pattern is informative to prognosis, suggesting plausible tRF-based cancer subtypes. Together, our systematic analysis demonstrates the potentially extensive involvements of tRFs in cancers, and provides a reasonable list of cancer-associated tRFs for further investigations.
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Affiliation(s)
- Yiran Zhou
- MOE Key Lab of Cardiovascular Sciences, Department of Biomedical Informatics, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- MOE Key Lab of Cardiovascular Sciences, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Qinghua Cui
- MOE Key Lab of Cardiovascular Sciences, Department of Biomedical Informatics, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- MOE Key Lab of Cardiovascular Sciences, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yuan Zhou
- MOE Key Lab of Cardiovascular Sciences, Department of Biomedical Informatics, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- MOE Key Lab of Cardiovascular Sciences, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- *Correspondence: Yuan Zhou,
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Qiu Z, Wang Q, Liu L, Li G, Hao Y, Ning S, Zhang L, Zhang X, Chen Y, Wu J, Wang X, Yang S, Lin Y, Xu S. Riddle of the Sphinx: Emerging Role of Transfer RNAs in Human Cancer. Front Pharmacol 2021; 12:794986. [PMID: 34975491 PMCID: PMC8714751 DOI: 10.3389/fphar.2021.794986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/10/2021] [Indexed: 01/16/2023] Open
Abstract
The dysregulation of transfer RNA (tRNA) expression contributes to the diversity of proteomics, heterogeneity of cell populations, and instability of the genome, which may be related to human cancer susceptibility. However, the relationship between tRNA dysregulation and cancer susceptibility remains elusive because the landscape of cancer-associated tRNAs has not been portrayed yet. Furthermore, the molecular mechanisms of tRNAs involved in tumorigenesis and cancer progression have not been systematically understood. In this review, we detail current knowledge of cancer-related tRNAs and comprehensively summarize the basic characteristics and functions of these tRNAs, with a special focus on their role and involvement in human cancer. This review bridges the gap between tRNAs and cancer and broadens our understanding of their relationship, thus providing new insights and strategies to improve the potential clinical applications of tRNAs for cancer diagnosis and therapy.
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Affiliation(s)
- Zhilin Qiu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Guozheng Li
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yi Hao
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shipeng Ning
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xin Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yihai Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiale Wu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xinheng Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shuai Yang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yaoxin Lin
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, China
- *Correspondence: Yaoxin Lin, ; Shouping Xu,
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Yaoxin Lin, ; Shouping Xu,
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8
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Pandey KK, Madhry D, Ravi Kumar YS, Malvankar S, Sapra L, Srivastava RK, Bhattacharyya S, Verma B. Regulatory roles of tRNA-derived RNA fragments in human pathophysiology. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:161-173. [PMID: 34513302 PMCID: PMC8413677 DOI: 10.1016/j.omtn.2021.06.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hundreds of tRNA genes and pseudogenes are encoded by the human genome. tRNAs are the second most abundant type of RNA in the cell. Advancement in deep-sequencing technologies have revealed the presence of abundant expression of functional tRNA-derived RNA fragments (tRFs). They are either generated from precursor (pre-)tRNA or mature tRNA. They have been found to play crucial regulatory roles during different pathological conditions. Herein, we briefly summarize the discovery and recent advances in deciphering the regulatory role played by tRFs in the pathophysiology of different human diseases.
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Affiliation(s)
- Kush Kumar Pandey
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Deeksha Madhry
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Y S Ravi Kumar
- Department of Biotechnology, M.S. Ramaiah, Institute of Technology, MSR Nagar, Bengaluru, India
| | - Shivani Malvankar
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Leena Sapra
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Rupesh K Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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9
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Fagan SG, Helm M, Prehn JHM. tRNA-derived fragments: A new class of non-coding RNA with key roles in nervous system function and dysfunction. Prog Neurobiol 2021; 205:102118. [PMID: 34245849 DOI: 10.1016/j.pneurobio.2021.102118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 01/12/2023]
Abstract
tRNA-derived small RNAs (tsRNA) are a recently identified family of non-coding RNA that have been associated with a variety of cellular functions including the regulation of protein translation and gene expression. Recent sequencing and bioinformatic studies have identified the broad spectrum of tsRNA in the nervous system and demonstrated that this new class of non-coding RNA is produced from tRNA by specific cleavage events catalysed by ribonucleases such as angiogenin and dicer. Evidence is also accumulating that production of tsRNA is increased during disease processes where they regulate stress responses, proteostasis, and neuronal survival. Mutations to tRNA cleaving and modifying enzymes have been implicated in several neurodegenerative disorders, and tsRNA levels in the blood are advancing as biomarkers for neurological disease. In this review we summarize the physiological importance of tsRNA in the central nervous system and their relevance to neurological disease.
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Affiliation(s)
- Steven G Fagan
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences - IPBS, Johannes Gutenberg-University, 55128, Mainz, Germany
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland.
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10
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Torres AG, Martí E. Toward an Understanding of Extracellular tRNA Biology. Front Mol Biosci 2021; 8:662620. [PMID: 33937338 PMCID: PMC8082309 DOI: 10.3389/fmolb.2021.662620] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Extracellular RNAs (exRNAs) including abundant full length tRNAs and tRNA fragments (tRFs) have recently garnered attention as a promising source of biomarkers and a novel mediator in cell-to-cell communication in eukaryotes. Depending on the physiological state of cells, tRNAs/tRFs are released to the extracellular space either contained in extracellular vesicles (EVs) or free, through a mechanism that is largely unknown. In this perspective article, we propose that extracellular tRNAs (ex-tRNAs) and/or extracellular tRFs (ex-tRFs) are relevant paracrine signaling molecules whose activity depends on the mechanisms of release by source cells and capture by recipient cells. We speculate on how ex-tRNA/ex-tRFs orchestrate the effects in target cells, depending on the type of sequence and the mechanisms of uptake. We further propose that tRNA modifications may be playing important roles in ex-tRNA biology.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulàlia Martí
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Epidemiología y Salud Pública, Madrid, Spain
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11
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Shan N, Li N, Dai Q, Hou L, Yan X, Amei A, Lu L, Wang Z. Interplay of tRNA-Derived Fragments and T Cell Activation in Breast Cancer Patient Survival. Cancers (Basel) 2020; 12:E2230. [PMID: 32785169 PMCID: PMC7466003 DOI: 10.3390/cancers12082230] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/28/2020] [Accepted: 08/07/2020] [Indexed: 01/02/2023] Open
Abstract
Effector CD8+ T cell activation and its cytotoxic function are positively correlated with improved survival in breast cancer. tRNA-derived fragments (tRFs) have recently been found to be involved in gene regulation in cancer progression. However, it is unclear how interactions between expression of tRFs and T cell activation affect breast cancer patient survival. We used Kaplan-Meier survival and multivariate Cox regression models to evaluate the effect of interactions between expression of tRFs and T cell activation on survival in 1081 breast cancer patients. Spearman correlation analysis and weighted gene co-expression network analysis were conducted to identify genes and pathways that were associated with tRFs. tRFdb-5024a, 5P_tRNA-Leu-CAA-4-1, and ts-49 were positively associated with overall survival, while ts-34 and ts-58 were negatively associated with overall survival. Significant interactions were detected between T cell activation and ts-34 and ts-49. In the T cell exhaustion group, patients with a low level of ts-34 or a high level of ts-49 showed improved survival. In contrast, there was no significant difference in the activation group. Breast cancer related pathways were identified for the five tRFs. In conclusion, the identified five tRFs associated with overall survival may serve as therapeutic targets and improve immunotherapy in breast cancer.
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Affiliation(s)
- Nayang Shan
- Center for Statistical Science, Department of Industrial Engineering, Tsinghua University, Beijing 100084, China; (N.S.); (L.H.)
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA; (N.L.); (Q.D.); (X.Y.)
| | - Ningshan Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA; (N.L.); (Q.D.); (X.Y.)
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qile Dai
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA; (N.L.); (Q.D.); (X.Y.)
| | - Lin Hou
- Center for Statistical Science, Department of Industrial Engineering, Tsinghua University, Beijing 100084, China; (N.S.); (L.H.)
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiting Yan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA; (N.L.); (Q.D.); (X.Y.)
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Amei Amei
- Department of Mathematical Sciences, University of Nevada, Las Vegas, NV 89154, USA;
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA; (N.L.); (Q.D.); (X.Y.)
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12
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Zeng T, Hua Y, Sun C, Zhang Y, Yang F, Yang M, Yang Y, Li J, Huang X, Wu H, Fu Z, Li W, Yin Y. Relationship between tRNA-derived fragments and human cancers. Int J Cancer 2020; 147:3007-3018. [PMID: 32427348 DOI: 10.1002/ijc.33107] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
tRNA-derived fragments, a class of small noncoding RNAs (sncRNAs), have been identified in numerous studies in recent years. tRNA-derived fragments are classified into two main groups, including tRNA halves (tiRNAs) and tRNA-derived small RNA fragments (tRFs), according to different cleavage positions of the precursor or mature tRNAs. Instead of random tRNA degradation debris, a growing body of evidence has shown that tRNA-derived fragments are precise products of specific tRNA modifications and play important roles in biological activities, such as regulating protein translation, affecting gene expression, and altering immune signaling. Recently, the relations between tRNA-derived fragments and the occurrence of human diseases, especially cancers, have generated wide interest. It has been demonstrated that tRNA-derived fragments are involved in cancer cell proliferation, metastasis, progression and survival. In this review, we will describe the biogenesis of tRNA-derived fragments, the distinct expression and function of tRNA-derived fragments in the development of cancers, and their emerging roles as diagnostic and prognostic biomarkers and precise targets of future treatments.
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Affiliation(s)
- Tianyu Zeng
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yijia Hua
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chunxiao Sun
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuchen Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fan Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mengzhu Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yiqi Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Wu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ziyi Fu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Nanjing Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated of Nanjing Medical University, Nanjing, China
| | - Wei Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yongmei Yin
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
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13
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Rosace D, López J, Blanco S. Emerging roles of novel small non-coding regulatory RNAs in immunity and cancer. RNA Biol 2020; 17:1196-1213. [PMID: 32186461 DOI: 10.1080/15476286.2020.1737442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The term small non-coding RNAs (ncRNAs) refers to all those RNAs that even without encoding for a protein, can play important functional roles. Transfer RNA and ribosomal RNA-derived fragments (tRFs and rRFs, respectively) are an emerging class of ncRNAs originally considered as simple degradation products, which though play important roles in stress responses, signalling, or gene expression. They control all levels of gene expression regulating transcription and translation and affecting RNA processing and maturation. They have been linked to pivotal cellular processes such as self-renewal, differentiation, and proliferation. For this reason, mis-regulation of this novel class of ncRNAs can lead to various pathological processes such as neurodegenerative and development diseases, metabolism and immune system disorders, and cancer. In this review, we summarise the classification, biogenesis, and functions of tRFs and rRFs with a special focus on their role in immunity and cancer.
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Affiliation(s)
- Domenico Rosace
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| | - Judith López
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| | - Sandra Blanco
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
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14
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Qin C, Xu PP, Zhang X, Zhang C, Liu CB, Yang DG, Gao F, Yang ML, Du LJ, Li JJ. Pathological significance of tRNA-derived small RNAs in neurological disorders. Neural Regen Res 2020; 15:212-221. [PMID: 31552886 PMCID: PMC6905339 DOI: 10.4103/1673-5374.265560] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a type of RNA that is not translated into proteins. Transfer RNAs (tRNAs), a type of ncRNA, are the second most abundant type of RNA in cells. Recent studies have shown that tRNAs can be cleaved into a heterogeneous population of ncRNAs with lengths of 18–40 nucleotides, known as tRNA-derived small RNAs (tsRNAs). There are two main types of tsRNA, based on their length and the number of cleavage sites that they contain: tRNA-derived fragments and tRNA-derived stress-induced RNAs. These RNA species were first considered to be byproducts of tRNA random cleavage. However, mounting evidence has demonstrated their critical functional roles as regulatory factors in the pathophysiological processes of various diseases, including neurological diseases. However, the underlying mechanisms by which tsRNAs affect specific cellular processes are largely unknown. Therefore, this study comprehensively summarizes the following points: (1) The biogenetics of tsRNA, including their discovery, classification, formation, and the roles of key enzymes. (2) The main biological functions of tsRNA, including its miRNA-like roles in gene expression regulation, protein translation regulation, regulation of various cellular activities, immune mediation, and response to stress. (3) The potential mechanisms of pathophysiological changes in neurological diseases that are regulated by tsRNA, including neurodegeneration and neurotrauma. (4) The identification of the functional diversity of tsRNA may provide valuable information regarding the physiological and pathophysiological mechanisms of neurological disorders, thus providing a new reference for the clinical treatment of neurological diseases. Research into tsRNAs in neurological diseases also has the following challenges: potential function and mechanism studies, how to accurately quantify expression, and the exact relationship between tsRNA and miRNA. These challenges require future research efforts.
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Affiliation(s)
- Chuan Qin
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Pei-Pei Xu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Xin Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chao Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chang-Bin Liu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - De-Gang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Feng Gao
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Ming-Liang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Liang-Jie Du
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Jian-Jun Li
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
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15
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Yu C, Wang X, Hong Y, Chen G, Ge J, Cao H, Zhou B. Expression profile of tRNA‑derived fragments and their potential roles in human varicose veins. Mol Med Rep 2019; 20:3191-3201. [PMID: 31432124 PMCID: PMC6755252 DOI: 10.3892/mmr.2019.10544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 06/19/2019] [Indexed: 01/08/2023] Open
Abstract
Varicose veins (VVs) is a common disease presenting with chronic venous insufficiency. tRNA-derived fragments (tRFs) are associated with a variety of pathological conditions. However, the functions of tRFs in VVs have not been elucidated to date. The present study aimed to identify the key tRFs and investigate their potential roles in VVs. Small RNA sequencing (RNA-seq) was performed to investigate the expression of tRFs in tissues of patients with VVs and their matched adjacent normal veins tissues (ANVs). Reverse transcription-quantitative PCR (RT-qPCR) was used to confirm the differential expression of tRFs. A total of 13,789 tRFs were identified by small RNA-seq, including 45 differentially expressed tRFs (DETs), which comprised 14 upregulated and 31 downregulated tRFs in VV tissues compared with ANVs. In addition, DETs were mainly involved in the function of epidermal growth factor receptor and vascular endothelial growth factor receptor signaling pathways in VVs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the target genes of DETs were predominantly involved in Wnt and mitogen-activated protein kinase (MAPK) signaling pathways, as well as calcium signaling. Additionally, two upregulated tRFs (tRF-36-F900BY4D84KRIME and tRF-23-87R8WP9IY) and one downregulated tRF (tRF-40-86J8WPMN1E8Y7Z2R) were further validated by RT-qPCR, and a signaling pathway regulation network of their target genes confirmed their involvement in the calcium, Wnt and MAPK signaling pathways. The results of the present study identified three DETs (tRF-36-F900BY4D84KRIME, tRF-23-87R8WP9IY and tRF-40-86J8WPMN1E8Y7Z2R), which may have crucial roles in the occurrence and progression of VVs by regulating Wnt and MAPK signaling, as well as calcium signaling. The present results may provide a basis for further investigation of the functional roles of tRFs in VVs.
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Affiliation(s)
- Chong Yu
- Department of Vascular Surgery, Shanghai East Hospital Affiliated to Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Xiang Wang
- Department of Vascular Surgery, Shanghai East Hospital Affiliated to Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Yi Hong
- Department of Vascular Surgery, Shanghai East Hospital Affiliated to Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Guojun Chen
- Department of Vascular Surgery, Shanghai East Hospital Affiliated to Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Jin Ge
- Department of Vascular Surgery, Shanghai East Hospital Affiliated to Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Hao Cao
- Department of Cardiovascular Surgery, Shanghai East Hospital Affiliated to Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Bin Zhou
- Department of Vascular Surgery, Shanghai East Hospital Affiliated to Tongji University School of Medicine, Shanghai 200120, P.R. China
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16
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Oberbauer V, Schaefer MR. tRNA-Derived Small RNAs: Biogenesis, Modification, Function and Potential Impact on Human Disease Development. Genes (Basel) 2018; 9:genes9120607. [PMID: 30563140 PMCID: PMC6315542 DOI: 10.3390/genes9120607] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022] Open
Abstract
Transfer RNAs (tRNAs) are abundant small non-coding RNAs that are crucially important for decoding genetic information. Besides fulfilling canonical roles as adaptor molecules during protein synthesis, tRNAs are also the source of a heterogeneous class of small RNAs, tRNA-derived small RNAs (tsRNAs). Occurrence and the relatively high abundance of tsRNAs has been noted in many high-throughput sequencing data sets, leading to largely correlative assumptions about their potential as biologically active entities. tRNAs are also the most modified RNAs in any cell type. Mutations in tRNA biogenesis factors including tRNA modification enzymes correlate with a variety of human disease syndromes. However, whether it is the lack of tRNAs or the activity of functionally relevant tsRNAs that are causative for human disease development remains to be elucidated. Here, we review the current knowledge in regard to tsRNAs biogenesis, including the impact of RNA modifications on tRNA stability and discuss the existing experimental evidence in support for the seemingly large functional spectrum being proposed for tsRNAs. We also argue that improved methodology allowing exact quantification and specific manipulation of tsRNAs will be necessary before developing these small RNAs into diagnostic biomarkers and when aiming to harness them for therapeutic purposes.
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Affiliation(s)
- Vera Oberbauer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
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17
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Li S, Xu Z, Sheng J. tRNA-Derived Small RNA: A Novel Regulatory Small Non-Coding RNA. Genes (Basel) 2018; 9:E246. [PMID: 29748504 PMCID: PMC5977186 DOI: 10.3390/genes9050246] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 05/06/2018] [Accepted: 05/06/2018] [Indexed: 01/15/2023] Open
Abstract
Deep analysis of next-generation sequencing data unveils numerous small non-coding RNAs with distinct functions. Recently, fragments derived from tRNA, named as tRNA-derived small RNA (tsRNA), have attracted broad attention. There are mainly two types of tsRNAs, including tRNA-derived stress-induced RNA (tiRNA) and tRNA-derived fragment (tRF), which differ in the cleavage position of the precursor or mature tRNA transcript. Emerging evidence has shown that tsRNAs are not merely tRNA degradation debris but have been recognized to play regulatory roles in many specific physiological and pathological processes. In this review, we summarize the biogeneses of various tsRNAs, present the emerging concepts regarding functions and mechanisms of action of tsRNAs, highlight the potential application of tsRNAs in human diseases, and put forward the current problems and future research directions.
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Affiliation(s)
- Siqi Li
- Institute of Environmental Health, School of Public Health, Zhejiang University, Hangzhou 310058, China.
| | - Zhengping Xu
- Institute of Environmental Health, School of Public Health, Zhejiang University, Hangzhou 310058, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China.
- Program in Molecular and Cellular Biology, School of Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Jinghao Sheng
- Institute of Environmental Health, School of Public Health, Zhejiang University, Hangzhou 310058, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China.
- Program in Molecular and Cellular Biology, School of Medicine, Zhejiang University, Hangzhou 310058, China.
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18
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Keegan C, Krutzik S, Schenk M, Scumpia PO, Lu J, Pang YLJ, Russell BS, Lim KS, Shell S, Prestwich E, Su D, Elashoff D, Hershberg RM, Bloom BR, Belisle JT, Fortune S, Dedon PC, Pellegrini M, Modlin RL. Mycobacterium tuberculosis Transfer RNA Induces IL-12p70 via Synergistic Activation of Pattern Recognition Receptors within a Cell Network. THE JOURNAL OF IMMUNOLOGY 2018; 200:3244-3258. [PMID: 29610140 DOI: 10.4049/jimmunol.1701733] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/02/2018] [Indexed: 12/14/2022]
Abstract
Upon recognition of a microbial pathogen, the innate and adaptive immune systems are linked to generate a cell-mediated immune response against the foreign invader. The culture filtrate of Mycobacterium tuberculosis contains ligands, such as M. tuberculosis tRNA, that activate the innate immune response and secreted Ags recognized by T cells to drive adaptive immune responses. In this study, bioinformatics analysis of gene-expression profiles derived from human PBMCs treated with distinct microbial ligands identified a mycobacterial tRNA-induced innate immune network resulting in the robust production of IL-12p70, a cytokine required to instruct an adaptive Th1 response for host defense against intracellular bacteria. As validated by functional studies, this pathway contained a feed-forward loop, whereby the early production of IL-18, type I IFNs, and IL-12p70 primed NK cells to respond to IL-18 and produce IFN-γ, enhancing further production of IL-12p70. Mechanistically, tRNA activates TLR3 and TLR8, and this synergistic induction of IL-12p70 was recapitulated by the addition of a specific TLR8 agonist with a TLR3 ligand to PBMCs. These data indicate that M. tuberculosis tRNA activates a gene network involving the integration of multiple innate signals, including types I and II IFNs, as well as distinct cell types to induce IL-12p70.
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Affiliation(s)
- Caroline Keegan
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095.,Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Stephan Krutzik
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Mirjam Schenk
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Philip O Scumpia
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Jing Lu
- Department of Molecular, Cell and Developmental Biology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Brandon S Russell
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kok Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Scarlet Shell
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Erin Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Dan Su
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David Elashoff
- Division of General Internal Medicine, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | | | - Barry R Bloom
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - John T Belisle
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523; and
| | - Sarah Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.,Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore 138602, Singapore
| | - Matteo Pellegrini
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095.,Department of Molecular, Cell and Developmental Biology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Robert L Modlin
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095; .,Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
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19
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Dhahbi JM. 5' tRNA Halves: The Next Generation of Immune Signaling Molecules. Front Immunol 2015; 6:74. [PMID: 25745425 PMCID: PMC4333838 DOI: 10.3389/fimmu.2015.00074] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 02/05/2015] [Indexed: 01/01/2023] Open
Affiliation(s)
- Joseph Mohsen Dhahbi
- Biochemistry Department, University of California Riverside , Riverside, CA , USA ; Center for Genetics, Children's Hospital Oakland Research Institute , Oakland, CA , USA
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20
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Majde JA, Kapás L, Bohnet SG, De A, Krueger JM. Attenuation of the influenza virus sickness behavior in mice deficient in Toll-like receptor 3. Brain Behav Immun 2010; 24:306-15. [PMID: 19861156 PMCID: PMC2818367 DOI: 10.1016/j.bbi.2009.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 10/14/2009] [Accepted: 10/22/2009] [Indexed: 10/20/2022] Open
Abstract
Certain sickness behaviors occur consistently in influenza-infected humans and mice. These include body temperature changes, somnolence, and anorexia. Several cytokines serve as mediators of the influenza acute phase response (APR), including these sickness behaviors, and one likely inducer of these cytokines is dsRNA produced during viral replication. TLR3 is known to be one of the host cellular components capable of recognizing dsRNA and activating cytokine synthesis. To determine the role of TLR3-detected viral dsRNA in the causation of viral symptoms, TLR3-deficient mice (TLR3 knockouts, or KOs) were infected with a marginally-lethal dose of mouse-adapted X-31 influenza virus. TLR3 KOs and their wild-type (WT) controls were monitored for baseline body temperature, locomotor activity, and sleep profiles prior to infection. Both mouse strains were then infected and monitored for changes in these sickness behaviors plus body weight changes and mortality for up to 14days post-infection. Consistent with the observations that influenza pathology is reduced in TLR3 KOs, we showed that hypothermia after post-infection day 5 and the total loss of body weight were attenuated in the TLR3 KOs. Sleep changes characteristic of this infection model [particularly increased non-rapid-eye-movement sleep (NREMS)] were also attenuated in TLR3 KOs and returned to baseline values more rapidly. Locomotor activity suppression was similar in both strains. Therefore virus-associated dsRNA detected by TLR3 appears to play a substantial role in mediating several aspects of the influenza syndrome in mice.
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Affiliation(s)
- Jeannine A. Majde
- Department of VCAPP, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-6520
| | - Levente Kapás
- WWAMI Medical Education Program, Washington State University, Spokane, WA 99210-1495
| | - Stewart G. Bohnet
- Department of VCAPP, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-6520
| | - Alok De
- Department of Obstetrics and Gynecology, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108
| | - James M. Krueger
- Department of VCAPP, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-6520
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21
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Xagorari A, Chlichlia K. Toll-like receptors and viruses: induction of innate antiviral immune responses. Open Microbiol J 2008; 2:49-59. [PMID: 19088911 PMCID: PMC2593046 DOI: 10.2174/1874285800802010049] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 04/30/2008] [Accepted: 05/02/2008] [Indexed: 01/21/2023] Open
Abstract
Induction of antiviral innate immune responses depends on a family of innate immune receptors, the Toll-like receptors (TLR). TLR mediate the antiviral immune responses by recognizing virus infection, activating signaling pathways and inducing the production of antiviral cytokines and chemokines. ssRNA and dsRNA viruses can be recognized by TLR7/8 and TLR3, respectively. TLR receptors are also involved in the recognition of viruses containing genomes rich in CpG DNA motifs as well as envelope glycoproteins. Cytoplasmic recognition of dsRNA by RNA helicases such as RIG-I and MDA5 provides another means of recognizing viral nucleic acid. In order to counteract the innate host immune system viruses evolved mechanisms that block recognition and signaling through pattern recognition receptors, such as TLRs and RNA helicases. Recently, TLR agonists represent a promising approach for the treatment of infectious diseases. This review will focus on the current knowledge of TLR-mediated immune responses to several viral infections.
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Affiliation(s)
- Angeliki Xagorari
- Cell and Gene Therapy Laboratory, Dept. of Hematology/BMT, Gen. Hospital G. Papanikolaou, 57010 Exochi, Thes-saloniki, Greece
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Sensing of viral infection and activation of innate immunity by toll-like receptor 3. Clin Microbiol Rev 2008; 21:13-25. [PMID: 18202435 DOI: 10.1128/cmr.00022-07] [Citation(s) in RCA: 233] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Toll-like receptors (TLRs) form a major group of transmembrane receptors that are involved in the detection of invading pathogens. Double-stranded RNA is a marker for viral infection that is recognized by TLR3. TLR3 triggering activates specific signaling pathways that culminate in the activation of NF-kappaB and IRF3 transcription factors, as well as apoptosis, enabling the host to mount an effective innate immune response through the induction of cytokines, chemokines, and other proinflammatory mediators. In this review, we describe the paradoxical role of TLR3 in innate immunity against different viruses and in viral pathogenesis but also the evidence for TLR3 as a "danger" receptor in nonviral diseases. We also discuss the structure and cellular localization of TLR3, as well as the complex signaling and regulatory events that contribute to TLR3-mediated immune responses.
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Abstract
Leptospirosis is a serious infection disease caused by pathogenic strains of the Leptospira spirochetes, which affects not only humans but also animals. It has long been expected to find an effective vaccine to prevent leptospirosis through immunization of high risk humans or animals. Although some leptospirosis vaccines have been obtained, the vaccination is relatively unsuccessful in clinical application despite decades of research and millions of dollars spent. In this review, the recent advancements of recombinant outer membrane protein (OMP) vaccines, lipopolysaccharide (LPS) vaccines, inactivated vaccines, attenuated vaccines and DNA vaccines against leptospirosis are reviewed. A comparison of these vaccines may lead to development of new potential methods to combat leptospirosis and facilitate the leptospirosis vaccine research. Moreover, a vaccine ontology database was built for the scientists working on the leptospirosis vaccines as a starting tool.
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Affiliation(s)
- Zhijun Wang
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, PR China.
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24
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Greidinger EL. Immune Effects of Autoantigen-Associated RNA. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 598:293-308. [PMID: 17892220 DOI: 10.1007/978-0-387-71767-8_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Eric L Greidinger
- University of Miami Miller School of Medicine, Division of Rheumatology, Miami Department of Veterans Affairs Medical Center, FL 33136, USA.
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25
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Wang Z, Yuan Z, Xiang L, Shao J, Węgrzyn G. tRNA-dependent cleavage of the ColE1 plasmid-encoded RNA I. MICROBIOLOGY-SGM 2007; 152:3467-3476. [PMID: 17159198 DOI: 10.1099/mic.0.29134-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Effects of tRNA(Ala)(UGC) and its derivative devoid of the 3'-ACCA motif [tRNA(Ala)(UGC)DeltaACCA] on the cleavage of the ColE1-like plasmid-derived RNA I were analysed in vivo and in vitro. In an amino-acid-starved relA mutant, in which uncharged tRNAs occur in large amounts, three products of specific cleavage of RNA I were observed, in contrast to an otherwise isogenic relA(+) host. Overexpression of tRNA(Ala)(UGC), which under such conditions occurs in Escherichia coli mostly in an uncharged form, induced RNA I cleavage and resulted in an increase in ColE1-like plasmid DNA copy number. Such effects were not observed during overexpression of the 3'-ACCA-truncated tRNA(Ala)(UGC). Moreover, tRNA(Ala)(UGC), but not tRNA(Ala)(UGC)DeltaACCA, caused RNA I cleavage in vitro in the presence of MgCl(2). These results strongly suggest that tRNA-dependent RNA I cleavage occurs in ColE1-like plasmid-bearing E. coli, and demonstrate that tRNA(Ala)(UGC) participates in specific degradation of RNA I in vivo and in vitro. This reaction is dependent on the presence of the 3'-ACCA motif of tRNA(Ala)(UGC).
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MESH Headings
- Bacteriocin Plasmids/genetics
- Base Sequence
- Blotting, Northern
- Coenzymes/pharmacology
- DNA, Bacterial/biosynthesis
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Magnesium Chloride/pharmacology
- Models, Biological
- Molecular Sequence Data
- RNA Stability
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Catalytic/metabolism
- RNA, Transfer, Ala/metabolism
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Affiliation(s)
- Zhijun Wang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca 14853, NY, USA
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 200032, Shanghai, People's Republic of China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 200032, Shanghai, People's Republic of China
| | - Li Xiang
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 200032, Shanghai, People's Republic of China
| | - Junjie Shao
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 200032, Shanghai, People's Republic of China
| | - Grzegorz Węgrzyn
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, Św. Wojciecha 5, 81-347 Gdynia, Poland
- Department of Molecular Biology, University of Gdańsk, 80-822, Gdańsk, Poland
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