151
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Gu X, Ma S, Liang B, Ju S. Serum hsa_tsr016141 as a Kind of tRNA-Derived Fragments Is a Novel Biomarker in Gastric Cancer. Front Oncol 2021; 11:679366. [PMID: 34055648 PMCID: PMC8155501 DOI: 10.3389/fonc.2021.679366] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/20/2021] [Indexed: 12/13/2022] Open
Abstract
Background Gastric cancer (GC) is one of the most common malignant tumors globally and the third leading cause of cancer-related death. Currently, the sensitivity and specificity of diagnostic markers for GC are low, so it is urgent to find new biomarkers with higher sensitivity and specificity. tRNA-derived small RNAs are a kind of small non-coding RNAs derived from tRNAs. It is abundant in cancer cells and body fluids. Our goal is to find the differentially expressed tRNA-derived small RNAs in GC to explore their potential as a GC biomarker. Methods Quantitative real-time PCR was used to detect the expression level of hsa_tsr016141. The molecular characteristics of hsa_tsr016141 were verified by agarose gel electrophoresis, Sanger sequencing, Actinomycin D Assay, and Nuclear and Cytoplasmic RNA Separation Assay. The diagnostic efficiency of hsa_tsr016141 was analyzed through receiver operating characteristic. Results The expression level of hsa_tsr016141 in GC tissues and serum was significantly increased. The serum expression level showed a gradient change between GC patients, gastritis patients, and healthy donors and was positively correlated with the degree of lymph node metastasis and tumor grade. ROC analysis showed that the serum expression level of hsa_tsr016141 could significantly distinguish GC patients from healthy donors or gastritis patients. Besides, the expression level of hsa_tsr016141 in GC patients decreased significantly after the operation (P<0.0001). Conclusions Serum hsa_tsr016141 has good stability and specificity and can be used for dynamic monitoring of GC patients, suggesting that serum hsa_tsr016141 can be a novel biomarker for GC diagnosis and postoperative monitoring.
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Affiliation(s)
- Xinliang Gu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China.,Medical School of Nantong University, Nantong University, Nantong, China
| | - Shuo Ma
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China.,Medical School of Nantong University, Nantong University, Nantong, China
| | - Bo Liang
- Department of Medical Ultrasonics, Affiliated Hospital of Nantong University, Nantong, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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152
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Guan L, Grigoriev A. Computational meta-analysis of ribosomal RNA fragments: potential targets and interaction mechanisms. Nucleic Acids Res 2021; 49:4085-4103. [PMID: 33772581 PMCID: PMC8053083 DOI: 10.1093/nar/gkab190] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
The most abundant cellular RNA species, ribosomal RNA (rRNA), appears to be a source of massive amounts of non-randomly generated fragments. We found rRNA fragments (rRFs) in immunoprecipitated Argonaute (Ago-IP) complexes in human and mouse cells and in small RNA sequencing datasets. In human Ago1-IP, guanine-rich rRFs were preferentially cut in single-stranded regions of mature rRNAs between pyrimidines and adenosine, and non-randomly paired with cellular transcripts in crosslinked chimeras. Numerous identical rRFs were found in the cytoplasm and nucleus in mouse Ago2-IP. We report specific interaction motifs enriched in rRF-target pairs. Locations of such motifs on rRFs were compatible with the Ago structural features and patterns of the Ago-RNA crosslinking in both species. Strikingly, many of these motifs may bind to double-stranded regions on target RNAs, suggesting a potential pathway for regulating translation by unwinding mRNAs. Occurring on either end of rRFs and matching intronic, untranslated or coding regions in targets, such interaction sites extend the concept of microRNA seed regions. Targeting both borders of certain short introns, rRFs may be involved in their biogenesis or function, facilitated by Ago. Frequently dismissed as noise, rRFs are poised to greatly enrich the known functional spectrum of small RNA regulation.
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Affiliation(s)
- Lingyu Guan
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA
| | - Andrey Grigoriev
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA
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153
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Gong S, Gaccioli F, Dopierala J, Sovio U, Cook E, Volders PJ, Martens L, Kirk PDW, Richardson S, Smith GCS, Charnock-Jones DS. The RNA landscape of the human placenta in health and disease. Nat Commun 2021; 12:2639. [PMID: 33976128 PMCID: PMC8113443 DOI: 10.1038/s41467-021-22695-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
The placenta is the interface between mother and fetus and inadequate function contributes to short and long-term ill-health. The placenta is absent from most large-scale RNA-Seq datasets. We therefore analyze long and small RNAs (~101 and 20 million reads per sample respectively) from 302 human placentas, including 94 cases of preeclampsia (PE) and 56 cases of fetal growth restriction (FGR). The placental transcriptome has the seventh lowest complexity of 50 human tissues: 271 genes account for 50% of all reads. We identify multiple circular RNAs and validate 6 of these by Sanger sequencing across the back-splice junction. Using large-scale mass spectrometry datasets, we find strong evidence of peptides produced by translation of two circular RNAs. We also identify novel piRNAs which are clustered on Chr1 and Chr14. PE and FGR are associated with multiple and overlapping differences in mRNA, lincRNA and circRNA but fewer consistent differences in small RNAs. Of the three protein coding genes differentially expressed in both PE and FGR, one encodes a secreted protein FSTL3 (follistatin-like 3). Elevated serum levels of FSTL3 in pregnant women are predictive of subsequent PE and FGR. To aid visualization of our placenta transcriptome data, we develop a web application ( https://www.obgyn.cam.ac.uk/placentome/ ).
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Affiliation(s)
- Sungsam Gong
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Francesca Gaccioli
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Justyna Dopierala
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Functional Genomics, GlaxoSmithKline Limited, Stevenage, Hertfordshire, UK
| | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Emma Cook
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Pieter-Jan Volders
- Computational Omics and Systems Biology Group, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lennart Martens
- Computational Omics and Systems Biology Group, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Paul D W Kirk
- MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sylvia Richardson
- MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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154
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Jacovetti C, Bayazit MB, Regazzi R. Emerging Classes of Small Non-Coding RNAs With Potential Implications in Diabetes and Associated Metabolic Disorders. Front Endocrinol (Lausanne) 2021; 12:670719. [PMID: 34040585 PMCID: PMC8142323 DOI: 10.3389/fendo.2021.670719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/20/2021] [Indexed: 11/13/2022] Open
Abstract
Most of the sequences in the human genome do not code for proteins but generate thousands of non-coding RNAs (ncRNAs) with regulatory functions. High-throughput sequencing technologies and bioinformatic tools significantly expanded our knowledge about ncRNAs, highlighting their key role in gene regulatory networks, through their capacity to interact with coding and non-coding RNAs, DNAs and proteins. NcRNAs comprise diverse RNA species, including amongst others PIWI-interacting RNAs (piRNAs), involved in transposon silencing, and small nucleolar RNAs (snoRNAs), which participate in the modification of other RNAs such as ribosomal RNAs and transfer RNAs. Recently, a novel class of small ncRNAs generated from the cleavage of tRNAs or pre-tRNAs, called tRNA-derived small RNAs (tRFs) has been identified. tRFs have been suggested to regulate protein translation, RNA silencing and cell survival. While for other ncRNAs an implication in several pathologies is now well established, the potential involvement of piRNAs, snoRNAs and tRFs in human diseases, including diabetes, is only beginning to emerge. In this review, we summarize fundamental aspects of piRNAs, snoRNAs and tRFs biology. We discuss their biogenesis while emphasizing on novel sequencing technologies that allow ncRNA discovery and annotation. Moreover, we give an overview of genomic approaches to decrypt their mechanisms of action and to study their functional relevance. The review will provide a comprehensive landscape of the regulatory roles of these three types of ncRNAs in metabolic disorders by reporting their differential expression in endocrine pancreatic tissue as well as their contribution to diabetes incidence and diabetes-underlying conditions such as inflammation. Based on these discoveries we discuss the potential use of piRNAs, snoRNAs and tRFs as promising therapeutic targets in metabolic disorders.
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Affiliation(s)
- Cécile Jacovetti
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Mustafa Bilal Bayazit
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
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155
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Meseguer S. MicroRNAs and tRNA-Derived Small Fragments: Key Messengers in Nuclear-Mitochondrial Communication. Front Mol Biosci 2021; 8:643575. [PMID: 34026824 PMCID: PMC8138316 DOI: 10.3389/fmolb.2021.643575] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondria are not only important as energy suppliers in cells but also participate in other biological processes essential for cell growth and survival. They arose from α-proteobacterial predecessors through endosymbiosis and evolved transferring a large part of their genome to the host cell nucleus. Such a symbiotic relationship has been reinforced over time through increasingly complex signaling mechanisms between the host cell and mitochondria. So far, we do not have a complete view of the mechanisms that allow the mitochondria to communicate their functional status to the nucleus and trigger adaptive and compensatory responses. Recent findings place two classes of small non-coding RNAs (sncRNAs), microRNAs (miRNAs), and tRNA-derived small fragments, in such a scenario, acting as key pieces in the mitochondria-nucleus cross-talk. This review highlights the emerging roles and the interrelation of these sncRNAs in different signaling pathways between mitochondria and the host cell. Moreover, we describe in what way alterations of these complex regulatory mechanisms involving sncRNAs lead to diseases associated with mitochondrial dysfunction. In turn, these discoveries provide novel prognostic biomarker candidates and/or potential therapeutic targets.
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Affiliation(s)
- Salvador Meseguer
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
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156
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Li J, Jin L, Gao Y, Gao P, Ma L, Zhu B, Yin X, Sui S, Chen S, Jiang Z, Zhu C. Low expression of tRF-Pro-CGG predicts poor prognosis in pancreatic ductal adenocarcinoma. J Clin Lab Anal 2021; 35:e23742. [PMID: 33675071 PMCID: PMC8128309 DOI: 10.1002/jcla.23742] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/29/2021] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND & AIMS tRFs (tRNA-derived RNA fragments) have been reported to facilitate cancer progression in multiple cancers. However, their role in pancreatic ductal adenocarcinoma (PDAC) remains to be determined. In this study, we mainly investigated the expression of tRF-Pro-CGG in pancreatic ductal adenocarcinoma and evaluated its relationship with the clinicopathology and survival time of patients. METHODS 37 cases of pancreatic ductal adenocarcinoma, and 15 cases of normal pancreatic tissues were collected which were resected by surgery from January 2017 to June 2020 from the Department of Hepatobiliary and Pancreatic surgery of Changzhou second people's Hospital. The expression of tRF-Pro-CGG in paraffin-embedded tissues was detected by fluorescence in situ hybridization (FISH). The clinical data including age, sex, tumor location, tumor diameter, tumor clinical stage (TNM stage), depth of invasion, regional lymph node metastasis, serum CA199, and serum CEA were collected and analyzed retrospectively, whether the expression tRF-Pro-CGG was correlation with the pathological parameters and clinical outcomes of patients. RESULTS The expression level of tRF-Pro-CGG was significantly downregulated in PDAC and associated with an advanced TNM stage (P=0.000) and the N stage (P=0.000) of patients. More importantly, low tRF-Pro-CGG expression predicted poor survival in PDAC patients (P=0.003). CONCLUSIONS TRF-Pro-CGG is under-expressed in PDAC and is associated with short clinical survival and poor prognosis. tRF-Pro-CGG is an independent prognostic factor, which highlights its role as a potential biomarker for PDAC progression and therapy.
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Affiliation(s)
- Jun Li
- Dalian Medical UniversityDalianChina
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Lei Jin
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Yuan Gao
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Peng Gao
- Dalian Medical UniversityDalianChina
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Le Ma
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Bei Zhu
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Xu Yin
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Shizhen Sui
- Dalian Medical UniversityDalianChina
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Shuai Chen
- Dalian Medical UniversityDalianChina
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | | | - Chunfu Zhu
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
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157
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Lakshmanan V, Sujith TN, Bansal D, Shivaprasad PV, Palakodeti D, Krishna S. Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs). RNA (NEW YORK, N.Y.) 2021; 27:477-495. [PMID: 33446492 PMCID: PMC7962491 DOI: 10.1261/rna.077701.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
tRNA-derived fragments (tRFs) have recently gained a lot of scientific interest due to their diverse regulatory roles in several cellular processes. However, their function in dynamic biological processes such as development and regeneration remains unexplored. Here, we show that tRFs are dynamically expressed during planarian regeneration, suggesting a possible role for these small RNAs in the regulation of regeneration. In order to characterize planarian tRFs, we first annotated 457 tRNAs in S. mediterranea combining two tRNA prediction algorithms. Annotation of tRNAs facilitated the identification of three main species of tRFs in planarians-the shorter tRF-5s and itRFs, and the abundantly expressed 5'-tsRNAs. Spatial profiling of tRFs in sequential transverse sections of planarians revealed diverse expression patterns of these small RNAs, including those that are enriched in the head and pharyngeal regions. Expression analysis of these tRF species revealed dynamic expression of these small RNAs over the course of regeneration suggesting an important role in planarian anterior and posterior regeneration. Finally, we show that 5'-tsRNA in planaria interact with all three SMEDWI proteins and an involvement of AGO1 in the processing of itRFs. In summary, our findings implicate a novel role for tRFs in planarian regeneration, highlighting their importance in regulating complex systemic processes. Our study adds to the catalog of posttranscriptional regulatory systems in planaria, providing valuable insights on the biogenesis and the function of tRFs in neoblasts and planarian regeneration.
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MESH Headings
- Algorithms
- Animals
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Base Pairing
- Base Sequence
- Gene Expression Regulation
- Helminth Proteins/genetics
- Helminth Proteins/metabolism
- Molecular Sequence Annotation
- Nucleic Acid Conformation
- Planarians/genetics
- Planarians/metabolism
- RNA, Helminth/chemistry
- RNA, Helminth/classification
- RNA, Helminth/genetics
- RNA, Helminth/metabolism
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/classification
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Regeneration/genetics
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Affiliation(s)
- Vairavan Lakshmanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
- SASTRA University, 613401 Thanjavur, India
| | - T N Sujith
- National Centre for Biological Sciences (NCBS), 560065 Bangalore, India
| | - Dhiru Bansal
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
| | | | - Dasaradhi Palakodeti
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
| | - Srikar Krishna
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
- SASTRA University, 613401 Thanjavur, India
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158
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Shi J, Zhang Y, Tan D, Zhang X, Yan M, Zhang Y, Franklin R, Shahbazi M, Mackinlay K, Liu S, Kuhle B, James ER, Zhang L, Qu Y, Zhai Q, Zhao W, Zhao L, Zhou C, Gu W, Murn J, Guo J, Carrell DT, Wang Y, Chen X, Cairns BR, Yang XL, Schimmel P, Zernicka-Goetz M, Cheloufi S, Zhang Y, Zhou T, Chen Q. PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nat Cell Biol 2021; 23:424-436. [PMID: 33820973 PMCID: PMC8236090 DOI: 10.1038/s41556-021-00652-7] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/23/2021] [Indexed: 02/06/2023]
Abstract
Although high-throughput RNA sequencing (RNA-seq) has greatly advanced small non-coding RNA (sncRNA) discovery, the currently widely used complementary DNA library construction protocol generates biased sequencing results. This is partially due to RNA modifications that interfere with adapter ligation and reverse transcription processes, which prevent the detection of sncRNAs bearing these modifications. Here, we present PANDORA-seq (panoramic RNA display by overcoming RNA modification aborted sequencing), employing a combinatorial enzymatic treatment to remove key RNA modifications that block adapter ligation and reverse transcription. PANDORA-seq identified abundant modified sncRNAs-mostly transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs)-that were previously undetected, exhibiting tissue-specific expression across mouse brain, liver, spleen and sperm, as well as cell-specific expression across embryonic stem cells (ESCs) and HeLa cells. Using PANDORA-seq, we revealed unprecedented landscapes of microRNA, tsRNA and rsRNA dynamics during the generation of induced pluripotent stem cells. Importantly, tsRNAs and rsRNAs that are downregulated during somatic cell reprogramming impact cellular translation in ESCs, suggesting a role in lineage differentiation.
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Affiliation(s)
- Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Yunfang Zhang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Dongmei Tan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Xudong Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Menghong Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
- Pudong Medical Center, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Reuben Franklin
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, USA
| | - Marta Shahbazi
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Kirsty Mackinlay
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Shichao Liu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Emma R James
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Liwen Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yongcun Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qiwei Zhai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Wenxin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Changcheng Zhou
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Weifeng Gu
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, USA
| | - Jernej Murn
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, USA
| | - Jingtao Guo
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Douglas T Carrell
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sihem Cheloufi
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, USA.
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- The Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA.
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159
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Pan X, Geng X, Liu Y, Yu M, Mishra MK, Xu X, Ding X, Liu P, Liang M. Transfer RNA Fragments in the Kidney in Hypertension. Hypertension 2021; 77:1627-1637. [PMID: 33775129 DOI: 10.1161/hypertensionaha.121.16994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Xiaoqing Pan
- Department of Mathematics, Shanghai Normal University, China (X.P.).,Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Xuemei Geng
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.).,Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Mengqian Yu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China (M.Y., P.L.)
| | - Manoj K Mishra
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Xialian Xu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.).,Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China (M.Y., P.L.)
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
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160
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Pereira M, Ribeiro DR, Pinheiro MM, Ferreira M, Kellner S, Soares AR. m 5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs. Int J Mol Sci 2021; 22:ijms22062941. [PMID: 33799331 PMCID: PMC8001983 DOI: 10.3390/ijms22062941] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/15/2023] Open
Abstract
Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification and tsRNA formation. More specifically, m5U54 hypomodification is followed by overexpression of the ribonuclease angiogenin (ANG) that cleaves tRNAs near the anticodon, resulting in accumulation of 5′tRNA-derived stress-induced RNAs (5′tiRNAs), namely 5′tiRNA-GlyGCC and 5′tiRNA-GluCTC, among others. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tiRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tiRNA formation in mammalian cells. These results establish a link between tRNA hypomethylation and ANG-dependent tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.
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Affiliation(s)
- Marisa Pereira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Diana R. Ribeiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Miguel M. Pinheiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Margarida Ferreira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, 81377 Munich, Germany;
- Institute of Pharmaceutical Chemistry, Goethe-University, 60438 Frankfurt, Germany
| | - Ana R. Soares
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
- Correspondence:
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161
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Chukrallah LG, Badrinath A, Seltzer K, Snyder EM. Of rodents and ruminants: a comparison of small noncoding RNA requirements in mouse and bovine reproduction. J Anim Sci 2021; 99:6156131. [PMID: 33677580 DOI: 10.1093/jas/skaa388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/01/2020] [Indexed: 01/03/2023] Open
Abstract
Ruminants are major producers of meat and milk, thus managing their reproductive potential is a key element in cost-effective, safe, and efficient food production. Of particular concern, defects in male germ cells and female germ cells may lead to significantly reduced live births relative to fertilization. However, the underlying molecular drivers of these defects are unclear. Small noncoding RNAs, such as piRNAs and miRNAs, are known to be important regulators of germ-cell physiology in mouse (the best-studied mammalian model organism) and emerging evidence suggests that this is also the case in a range of ruminant species, in particular bovine. Similarities exist between mouse and bovids, especially in the case of meiotic and postmeiotic male germ cells. However, fundamental differences in small RNA abundance and metabolism between these species have been observed in the female germ cell, differences that likely have profound impacts on their physiology. Further, parentally derived small noncoding RNAs are known to influence early embryos and significant species-specific differences in germ-cell born small noncoding RNAs have been observed. These findings demonstrate the mouse to be an imperfect model for understanding germ-cell small noncoding RNA biology in ruminants and highlight the need to increase research efforts in this underappreciated aspect of animal reproduction.
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Affiliation(s)
| | - Aditi Badrinath
- Department of Animal Science, Rutgers University, New Brunswick, NJ
| | - Kelly Seltzer
- Department of Animal Science, Rutgers University, New Brunswick, NJ
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162
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Luan N, Mu Y, Mu J, Chen Y, Ye X, Zhou Q, Xu M, Deng Q, Hu Y, Tang Z, Wang J. Dicer1 Promotes Colon Cancer Cell Invasion and Migration Through Modulation of tRF-20-MEJB5Y13 Expression Under Hypoxia. Front Genet 2021; 12:638244. [PMID: 33763118 PMCID: PMC7982525 DOI: 10.3389/fgene.2021.638244] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/15/2021] [Indexed: 01/01/2023] Open
Abstract
Hypoxia plays a key role in colorectal cancer (CRC) metastasis, but its underlying mechanism remains largely unknown. Dicer1, an RNase, has been considered as a tumor regulator in many tumors. However, whether Dicer1 affects CRC progression under hypoxia remains uncertain. In this study, we found that Dicer1 expression was induced by hypoxia in CRC cells and it mediates hypoxia-induced CRC cell progression. Furthermore, we found that the expression of tRF-20-MEJB5Y13, a small non-coding RNA derived from tRNA, was increased under hypoxic conditions, and its upregulation by Dicer1 resulted in hypoxia-induced CRC cell invasion and migration. These results advance the current understanding of the role of Dicer1 in regulating hypoxia signals and provide a new pathway for the development of therapeutic interventions for inhibiting cancer progression.
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Affiliation(s)
- Na Luan
- Department of Colorectal Surgery, 4th Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Department of Colorectal Surgery and Oncology, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yali Mu
- Department of Colorectal Surgery, 4th Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Department of Colorectal Surgery and Oncology, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiayi Mu
- Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Department of Colorectal Surgery and Oncology, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiquan Chen
- Department of Colorectal Surgery, 4th Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Department of Colorectal Surgery and Oncology, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xun Ye
- Department of Colorectal Surgery, 4th Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Department of Colorectal Surgery and Oncology, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qin Zhou
- Department of Colorectal Surgery, 4th Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Department of Colorectal Surgery and Oncology, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Miaorong Xu
- Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Department of Colorectal Surgery and Oncology, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qun Deng
- Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Department of Colorectal Surgery and Oncology, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yeting Hu
- Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Department of Colorectal Surgery and Oncology, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhe Tang
- Department of Surgery, 4th Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Surgery, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianwei Wang
- Department of Colorectal Surgery, 4th Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Department of Colorectal Surgery and Oncology, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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163
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Berg MD, Brandl CJ. Transfer RNAs: diversity in form and function. RNA Biol 2021; 18:316-339. [PMID: 32900285 PMCID: PMC7954030 DOI: 10.1080/15476286.2020.1809197] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022] Open
Abstract
As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
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Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Canada
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164
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Xiao Q, Gao P, Huang X, Chen X, Chen Q, Lv X, Fu Y, Song Y, Wang Z. tRFTars: predicting the targets of tRNA-derived fragments. J Transl Med 2021; 19:88. [PMID: 33632236 PMCID: PMC7908658 DOI: 10.1186/s12967-021-02731-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 01/29/2021] [Indexed: 12/30/2022] Open
Abstract
Background tRNA-derived fragments (tRFs) are 14–40-nucleotide-long, small non-coding RNAs derived from specific tRNA cleavage events with key regulatory functions in many biological processes. Many studies have shown that tRFs are associated with Argonaute (AGO) complexes and inhibit gene expression in the same manner as miRNAs. However, there are currently no tools for accurately predicting tRF target genes. Methods We used tRF-mRNA pairs identified by crosslinking, ligation, and sequencing of hybrids (CLASH) and covalent ligation of endogenous AGO-bound RNAs (CLEAR)-CLIP to assess features that may participate in tRF targeting, including the sequence context of each site and tRF-mRNA interactions. We applied genetic algorithm (GA) to select key features and support vector machine (SVM) to construct tRF prediction models. Results We first identified features that globally influenced tRF targeting. Among these features, the most significant were the minimum free folding energy (MFE), position 8 match, number of bases paired in the tRF-mRNA duplex, and length of the tRF, which were consistent with previous findings. Our constructed model yielded an area under the receiver operating characteristic (ROC) curve (AUC) = 0.980 (0.977–0.983) in the training process and an AUC = 0.847 (0.83–0.861) in the test process. The model was applied to all the sites with perfect Watson–Crick complementarity to the seed in the 3′ untranslated region (3′-UTR) of the human genome. Seven of nine target/nontarget genes of tRFs confirmed by reporter assay were predicted. We also validated the predictions via quantitative real-time PCR (qRT-PCR). Thirteen potential target genes from the top of the predictions were significantly down-regulated at the mRNA levels by overexpression of the tRFs (tRF-3001a, tRF-3003a or tRF-3009a). Conclusions Predictions can be obtained online, tRFTars, freely available at http://trftars.cmuzhenninglab.org:3838/tar/, which is the first tool to predict targets of tRFs in humans with a user-friendly interface.
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Affiliation(s)
- Qiong Xiao
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang, 110001, China
| | - Peng Gao
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang, 110001, China
| | - Xuanzhang Huang
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang, 110001, China
| | - Xiaowan Chen
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang, 110001, China
| | - Quan Chen
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang, 110001, China
| | - Xinger Lv
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang, 110001, China
| | - Yu Fu
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang, 110001, China
| | - Yongxi Song
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang, 110001, China.
| | - Zhenning Wang
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang, 110001, China.
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165
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López-Jiménez E, Andrés-León E. The Implications of ncRNAs in the Development of Human Diseases. Noncoding RNA 2021; 7:17. [PMID: 33668203 PMCID: PMC8006041 DOI: 10.3390/ncrna7010017] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/14/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022] Open
Abstract
The mammalian genome comprehends a small minority of genes that encode for proteins (barely 2% of the total genome in humans) and an immense majority of genes that are transcribed into RNA but not encoded for proteins (ncRNAs). These non-coding genes are intimately related to the expression regulation of protein-coding genes. The ncRNAs subtypes differ in their size, so there are long non-coding genes (lncRNAs) and other smaller ones, like microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs). Due to their important role in the maintenance of cellular functioning, any deregulation of the expression profiles of these ncRNAs can dissemble in the development of different types of diseases. Among them, we can highlight some of high incidence in the population, such as cancer, neurodegenerative, or cardiovascular disorders. In addition, thanks to the enormous advances in the field of medical genomics, these same ncRNAs are starting to be used as possible drugs, approved by the FDA, as an effective treatment for diseases.
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Affiliation(s)
- Elena López-Jiménez
- Centre for Haematology, Immunology and Inflammation Department, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Eduardo Andrés-León
- Unidad de Bioinformática, Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, 18016 Granada, Spain
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166
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Tao EW, Wang HL, Cheng WY, Liu QQ, Chen YX, Gao QY. A specific tRNA half, 5'tiRNA-His-GTG, responds to hypoxia via the HIF1α/ANG axis and promotes colorectal cancer progression by regulating LATS2. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:67. [PMID: 33588913 PMCID: PMC7885485 DOI: 10.1186/s13046-021-01836-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023]
Abstract
Background Currently, tRNA-derived small RNAs (tsRNAs) are recognized as a novel and potential type of non-coding RNAs (ncRNAs), which participate in various cellular processes and play an essential role in cancer progression. However, tsRNAs involvement in colorectal cancer (CRC) progression remains unclear. Methods Sequencing analyses were performed to explore the tsRNAs with differential expression in CRC. Gain- and loss-of functions of 5’tiRNA-His-GTG were performed in CRC cells and xenograft tumor to discover its role in the progression of CRC. Hypoxia culture and hypoxia inducible factor 1 subunit alpha (HIF1α) inhibitors were performed to uncover the biogenesis of 5’tiRNA-His-GTG. The regulation of 5’tiRNA-His-GTG for large tumor suppressor kinase 2 (LATS2) were identified by luciferase reporter assay, western blot, and rescue experiments. Results Here, our study uncovered the profile of tsRNAs in human CRC tissues and confirmed a specific tRNA half, 5’tiRNA-His-GTG, is upregulated in CRC tissues. Then, in vitro and in vivo experiments revealed the oncogenic role of 5’tiRNA-His-GTG in CRC and found that targeting 5’tiRNA-His-GTG can induce cell apoptosis. Mechanistically, the generation of 5’tiRNA-His-GTG seems to be a responsive process of tumor hypoxic microenvironment, and it is regulated via the HIF1α/angiogenin (ANG) axis. Remarkably, LATS2 was found to be an important and major target of 5’tiRNA-His-GTG, which renders 5’tiRNA-His-GTG to “turn off” hippo signaling pathway and finally promotes the expression of pro-proliferation and anti-apoptosis related genes. Conclusions In summary, the findings revealed a specific 5’tiRNA-His-GTG-engaged pathway in CRC progression and provided clues to design a novel therapeutic target in CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01836-7.
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Affiliation(s)
- En-Wei Tao
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine, Renji Hospital, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Hao-Lian Wang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine, Renji Hospital, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Wing Yin Cheng
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Qian-Qian Liu
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine, Renji Hospital, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine, Renji Hospital, 145 Middle Shandong Road, 200001, Shanghai, China.
| | - Qin-Yan Gao
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine, Renji Hospital, 145 Middle Shandong Road, 200001, Shanghai, China.
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167
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Baptista B, Riscado M, Queiroz JA, Pichon C, Sousa F. Non-coding RNAs: Emerging from the discovery to therapeutic applications. Biochem Pharmacol 2021; 189:114469. [PMID: 33577888 DOI: 10.1016/j.bcp.2021.114469] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023]
Abstract
The knowledge about non-coding RNAs (ncRNAs) is rapidly increasing with new data continuously emerging, regarding their diverse types, applications, and roles. Particular attention has been given to ncRNA with regulatory functions, which may have a critical role both in biological and pathological conditions. As a result of the diversity of ncRNAs and their ubiquitous involvement in several biologic processes, ncRNA started to be considered in the biomedical field, with immense potential to be exploited either as biomarkers or as therapeutic agents in certain pathologies. Indeed, ncRNA-based therapeutics have been proposed in many disorders and some even reached clinical trials. However, to prepare an RNA product suitable for pharmacological applications, certain criteria must be fulfilled, and it has to be guaranteed RNA purity, stability, and bioactivity. So, in this review, the different types of ncRNAs are identified and characterized, by describing their biogenesis, functions, and applications. A perspective on the main challenges and innovative approaches for the future and broad therapeutic application of RNA is also presented.
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Affiliation(s)
- B Baptista
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - M Riscado
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - J A Queiroz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - C Pichon
- Centre de Biophysique Moléculaire (CBM), UPR 4301 CNRS & University of Orléans Orléans, France
| | - F Sousa
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal.
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168
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Zuo Y, Zhu L, Guo Z, Liu W, Zhang J, Zeng Z, Wu Q, Cheng J, Fu X, Jin Y, Zhao Y, Peng Y. tsRBase: a comprehensive database for expression and function of tsRNAs in multiple species. Nucleic Acids Res 2021; 49:D1038-D1045. [PMID: 33068436 PMCID: PMC7778983 DOI: 10.1093/nar/gkaa888] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/18/2020] [Accepted: 09/29/2020] [Indexed: 02/05/2023] Open
Abstract
tRNA-derived small RNAs (tsRNAs) are a class of novel small RNAs, ubiquitously present in prokaryotes and eukaryotes. It has been reported that tsRNAs exhibit spatiotemporal expression patterns and can function as regulatory molecules in many biological processes. Current tsRNA databases only cover limited organisms and ignore tsRNA functional characteristics. Thus, integrating more relevant tsRNA information is helpful for further exploration. Here, we present a tsRNA database, named tsRBase, which integrates the expression pattern and functional information of tsRNAs in multiple species. In tsRBase, we identified 121 942 tsRNAs by analyzing more than 14 000 publicly available small RNA-seq data covering 20 species. This database collects samples from different tissues/cell-lines, or under different treatments and genetic backgrounds, thus helps depict specific expression patterns of tsRNAs under different conditions. Importantly, to enrich our understanding of biological significance, we collected tsRNAs experimentally validated from published literatures, obtained protein-binding tsRNAs from CLIP/RIP-seq data, and identified targets of tsRNAs from CLASH and CLEAR-CLIP data. Taken together, tsRBase is the most comprehensive and systematic tsRNA repository, exhibiting all-inclusive information of tsRNAs from diverse data sources of multiple species. tsRBase is freely available at http://www.tsrbase.org.
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Affiliation(s)
- Yuanli Zuo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of life Sciences, Sichuan University, Chengdu 610041, China
| | - Lei Zhu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Zhixin Guo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Wenrong Liu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Jiting Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of life Sciences, Sichuan University, Chengdu 610041, China
| | - Zhen Zeng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of life Sciences, Sichuan University, Chengdu 610041, China
| | - Qingbin Wu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Jian Cheng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Xin Fu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yang Jin
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yun Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of life Sciences, Sichuan University, Chengdu 610041, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
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Rousselle T, Bardhi E, Maluf DG, Mas VR. Epigenetic modifications and the development of kidney graft fibrosis. Curr Opin Organ Transplant 2021; 26:1-9. [PMID: 33315766 PMCID: PMC8059991 DOI: 10.1097/mot.0000000000000839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW To outline recent discoveries in epigenetic regulatory mechanisms that have potential implications in the development of renal fibrosis following kidney transplantation. RECENT FINDINGS The characterization of renal fibrosis following kidney transplantation has shown TGFβ/Smad signaling to play a major role in the progression to chronic allograft dysfunction. The onset of unregulated proinflammatory pathways are only exacerbated by the decline in regulatory mechanisms lost with progressive patient age and comorbidities such as hypertension and diabetes. However, significant developments in the recognition of epigenetic regulatory markers upstream of aberrant TGFβ-signaling has significant clinical potential to provide therapeutic targets for the treatment of renal fibrosis. In addition, discoveries in extracellular vesicles and the characterization of their cargo has laid new framework for the potential to evaluate patient outcomes independent of invasive biopsies. SUMMARY The current review summarizes the main findings in epigenetic machinery specific to the development of renal fibrosis and highlights therapeutic options that have significant potential to translate into clinical practice.
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Affiliation(s)
- Thomas Rousselle
- Surgical Sciences Division, Department of Surgery, School
of Medicine, University of Maryland
| | - Elissa Bardhi
- Surgical Sciences Division, Department of Surgery, School
of Medicine, University of Maryland
| | - Daniel G. Maluf
- Surgical Sciences Division, Department of Surgery, School
of Medicine, University of Maryland
- Program in Transplantation, School of Medicine, University
of Maryland
| | - Valeria R. Mas
- Division of Transplant, Department of Surgery, School of
Medicine, University of Maryland
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170
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Ozkocer SE, Konac E. The current perspective on genetic and epigenetic factors in sperm maturation in the epididymis. Andrologia 2021; 53:e13989. [PMID: 33491190 DOI: 10.1111/and.13989] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/11/2022] Open
Abstract
Male infertility affects approximately 30% of infertile couples. As spermatozoa mature in the epididymal lumen, their potential for mobility increases, and their protein, lipid and small RNA (sRNA) content changes, whereas capacitation and fertilisation take place in the female reproductive tract. Both of the latter processes are affected by maturation, because impaired maturation causes premature capacitation and fertilization. The epididymis produces a suitable environment for sperm maturation via ion transport, vesicle secretion and protein matrix formation. The microenvironment for sperm maturation varies in three broad segments: the caput, the corpus and the cauda epididymis. Epididymosomes transfer proteins, lipids and sRNAs from the epididymal epithelium to spermatozoa and genetic alterations of epididymal genes can lead to decreased sperm motility, morphological abnormalities of spermatozoa and subfertility. Genetic factors are involved in all aetiological categories in male infertility. However, studies conducted on the genes involved in epididymal functions are limited. The sRNA content of spermatozoa changes during epididymal migration, and these sRNAs play a role in embryo development and epigenetic inheritance. This review aims to clarify the role of the epididymal epithelium in the maturation of spermatozoa in light of the current molecular genomic knowledge.
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Affiliation(s)
- Suheyla Esra Ozkocer
- Faculty of Medicine, Department of Medical Biology and Genetics, Gazi University, Besevler, Ankara, Turkey.,Faculty of Medicine, Department of Histology and Embryology, Gazi University, Besevler, Ankara, Turkey
| | - Ece Konac
- Faculty of Medicine, Department of Medical Biology and Genetics, Gazi University, Besevler, Ankara, Turkey
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171
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Li N, Shan N, Lu L, Wang Z. tRFtarget: a database for transfer RNA-derived fragment targets. Nucleic Acids Res 2021; 49:D254-D260. [PMID: 33035346 PMCID: PMC7779015 DOI: 10.1093/nar/gkaa831] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/10/2020] [Accepted: 09/17/2020] [Indexed: 12/22/2022] Open
Abstract
Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs and play important roles in biological and physiological processes. Prediction of tRF target genes and binding sites is crucial in understanding the biological functions of tRFs in the molecular mechanisms of human diseases. We developed a publicly accessible web-based database, tRFtarget (http://trftarget.net), for tRF target prediction. It contains the computationally predicted interactions between tRFs and mRNA transcripts using the two state-of-the-art prediction tools RNAhybrid and IntaRNA, including location of the binding sites on the target, the binding region, and free energy of the binding stability with graphic illustration. tRFtarget covers 936 tRFs and 135 thousand predicted targets in eight species. It allows researchers to search either target genes by tRF IDs or tRFs by gene symbols/transcript names. We also integrated the manually curated experimental evidence of the predicted interactions into the database. Furthermore, we provided a convenient link to the DAVID® web server to perform downstream functional pathway analysis and gene ontology annotation on the predicted target genes. This database provides useful information for the scientific community to experimentally validate tRF target genes and facilitate the investigation of the molecular functions and mechanisms of tRFs.
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Affiliation(s)
- Ningshan Li
- 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.,Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA
| | - Nayang Shan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA.,Center for Statistical Science, Department of Industrial Engineering, Tsinghua University, Beijing 100084, China
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA
| | - Zuoheng Wang
- 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
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172
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Huh D, Passarelli MC, Gao J, Dusmatova SN, Goin C, Fish L, Pinzaru AM, Molina H, Ren Z, McMillan EA, Asgharian H, Goodarzi H, Tavazoie SF. A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression. EMBO J 2021; 40:e106696. [PMID: 33346941 PMCID: PMC7809793 DOI: 10.15252/embj.2020106696] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic transfer RNAs can become selectively fragmented upon various stresses, generating tRNA-derived small RNA fragments. Such fragmentation has been reported to impact a small fraction of the tRNA pool and thus presumed to not directly impact translation. We report that oxidative stress can rapidly generate tyrosine-tRNAGUA fragments in human cells-causing significant depletion of the precursor tRNA. Tyrosine-tRNAGUA depletion impaired translation of growth and metabolic genes enriched in cognate tyrosine codons. Depletion of tyrosine tRNAGUA or its translationally regulated targets USP3 and SCD repressed proliferation-revealing a dedicated tRNA-regulated growth-suppressive pathway for oxidative stress response. Tyrosine fragments are generated in a DIS3L2 exoribonuclease-dependent manner and inhibit hnRNPA1-mediated transcript destabilization. Moreover, tyrosine fragmentation is conserved in C. elegans. Thus, tRNA fragmentation can coordinately generate trans-acting small RNAs and functionally deplete a tRNA. Our findings reveal the existence of an underlying adaptive codon-based regulatory response inherent to the genetic code.
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Affiliation(s)
- Doowon Huh
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Maria C Passarelli
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Jenny Gao
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | | | - Clara Goin
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Lisa Fish
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | | | - Henrik Molina
- Proteome Resource CenterThe Rockefeller UniversityNew YorkNYUSA
| | - Zhiji Ren
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | | | - Hosseinali Asgharian
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Hani Goodarzi
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
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173
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tRNA Biology in the Pathogenesis of Diabetes: Role of Genetic and Environmental Factors. Int J Mol Sci 2021; 22:ijms22020496. [PMID: 33419045 PMCID: PMC7825315 DOI: 10.3390/ijms22020496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 02/07/2023] Open
Abstract
The global rise in type 2 diabetes results from a combination of genetic predisposition with environmental assaults that negatively affect insulin action in peripheral tissues and impair pancreatic β-cell function and survival. Nongenetic heritability of metabolic traits may be an important contributor to the diabetes epidemic. Transfer RNAs (tRNAs) are noncoding RNA molecules that play a crucial role in protein synthesis. tRNAs also have noncanonical functions through which they control a variety of biological processes. Genetic and environmental effects on tRNAs have emerged as novel contributors to the pathogenesis of diabetes. Indeed, altered tRNA aminoacylation, modification, and fragmentation are associated with β-cell failure, obesity, and insulin resistance. Moreover, diet-induced tRNA fragments have been linked with intergenerational inheritance of metabolic traits. Here, we provide a comprehensive review of how perturbations in tRNA biology play a role in the pathogenesis of monogenic and type 2 diabetes.
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174
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Analysis of tRNA-derived RNA fragments (tRFs) in Cryptococcus spp.: RNAi-independent generation and possible compensatory effects in a RNAi-deficient genotype. Fungal Biol 2021; 125:389-399. [PMID: 33910680 DOI: 10.1016/j.funbio.2020.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/30/2020] [Accepted: 12/18/2020] [Indexed: 01/03/2023]
Abstract
Small RNAs (sRNAs) are key factors in the regulation of gene expression. Recently, a new class of regulatory sRNAs derived from tRNAs was described, the tRNA-derived RNA fragments (tRFs). Such RNAs range in length from 14 to 30 nucleotides and are produced from both mature and primary tRNA transcripts, with very specific cleavage sites along the tRNA sequence. Although several mechanisms have been proposed for how tRFs mediate regulation of gene expression, the exact mechanism of tRF biogenesis and its dependency upon the RNAi pathway remain unclear. Cryptococcus gattii and Cryptococcus neoformans are basidiomycetous yeasts and important human pathogens. While C. neoformans is RNAi proficient, C. gattii VGII has lost essential RNAi genes. Here, we sought to identify the tRF production profile in C. gattii VGII and C. neoformans in order to assess the RNAi-dependency of tRF production in these fungal species. We developed a RNA-sequencing-based tRF prediction workflow designed to improve the currently available prediction tools. Using this methodology, we were able to identify tRFs in both organisms. Despite the loss of the RNAi pathway, C. gattii VGII displayed a number of identified tRFs that did not differ significantly from those observed in C. neoformans. The analysis of predicted tRF targets revealed that a higher number of targets was found for C. gattii VGII tRFs compared to C. neoformans tRFs. These results support the idea that tRFs are at least partially independent of the canonical RNAi machinery, raising questions about possible compensatory roles of alternative regulatory RNAs in the absence of a functional RNAi pathway.
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175
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Yu X, Xie Y, Zhang S, Song X, Xiao B, Yan Z. tRNA-derived fragments: Mechanisms underlying their regulation of gene expression and potential applications as therapeutic targets in cancers and virus infections. Am J Cancer Res 2021; 11:461-469. [PMID: 33391486 PMCID: PMC7681095 DOI: 10.7150/thno.51963] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
tRNA-derived fragments (tRFs) are a new category of regulatory noncoding RNAs with distinct biological functions in cancers and stress-induced diseases. Herein, we first summarize the classification and biogenesis of tRFs. tRFs are produced from pre-tRNAs or mature tRNAs. Based on the incision loci, tRFs are classified into several types: tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF. Some tRFs participate in posttranscriptional regulation through microRNA-like actions or by displacing RNA binding proteins and regulating protein translation by promoting ribosome biogenesis or interfering with translation initiation. Other tRFs prevent cell apoptosis by binding to cytochrome c or promoting virus replication. More importantly, the dysregulation of tRFs has important clinical implications. They are potential diagnostic and prognostic biomarkers of gastric cancer, liver cancer, breast cancer, prostate cancer, and chronic lymphocytic leukemia. tRFs may become new therapeutic targets for the treatment of diseases such as hepatocellular carcinoma and respiratory syncytial virus infection. Finally, we point out the existing problems and future research directions associated with tRFs. In conclusion, the current progress in the research of tRFs reveals that they have important clinical implications and may constitute novel molecular therapeutic targets for modulating pathological processes.
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176
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Avcilar-Kucukgoze I, Kashina A. Hijacking tRNAs From Translation: Regulatory Functions of tRNAs in Mammalian Cell Physiology. Front Mol Biosci 2020; 7:610617. [PMID: 33392265 PMCID: PMC7773854 DOI: 10.3389/fmolb.2020.610617] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Transfer tRNAs (tRNAs) are small non-coding RNAs that are highly conserved in all kingdoms of life. Originally discovered as the molecules that deliver amino acids to the growing polypeptide chain during protein synthesis, tRNAs have been believed for a long time to play exclusive role in translation. However, recent studies have identified key roles for tRNAs and tRNA-derived small RNAs in multiple other processes, including regulation of transcription and translation, posttranslational modifications, stress response, and disease. These emerging roles suggest that tRNAs may be central players in the complex machinery of biological regulatory pathways. Here we overview these non-canonical roles of tRNA in normal physiology and disease, focusing largely on eukaryotic and mammalian systems.
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Affiliation(s)
- Irem Avcilar-Kucukgoze
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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177
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Zhang ZY, Zhang CH, Yang JJ, Xu PP, Yi PJ, Hu ML, Peng WJ. Genome-wide analysis of hippocampal transfer RNA-derived small RNAs identifies new potential therapeutic targets of Bushen Tiansui formula against Alzheimer's disease. JOURNAL OF INTEGRATIVE MEDICINE-JIM 2020; 19:135-143. [PMID: 33334712 DOI: 10.1016/j.joim.2020.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Bushen Tiansui formula (BSTSF), a traditional Chinese medicine prescription, has been widely used to treat Alzheimer's disease (AD). However, the mechanisms underlying its effects remain largely unknown. In this study, a rat AD model was used to study the effects of BSTSF on cognitive performance and expression of transfer RNA-derived small RNAs (tsRNAs) in the hippocampus, to determine whether treatment of AD with BSTSF could regulate the expression of tsRNAs, a novel small non-coding RNA. METHODS To generate a validated AD model, oligomeric amyloid-β1-42 (Aβ1-42) was injected intracerebroventricularly into rats. The Morris water maze (MWM) test was used to evaluate rat cognitive performance, and tsRNA-sequencing was conducted to examine tsRNA expression in the rat hippocampus. Potential targets were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Bioinformatic analyses were conducted to investigate the biological function of candidate tsRNAs. RESULTS The learning and memory deficits of Aβ1-42-induced AD rats, assessed by MWM tests, were clearly ameliorated by BSTSF treatment. A total of 387 tsRNAs were detected in the rat hippocampus. Among them, 13 were significantly dysregulated in AD rats compared with sham control rats, while 57 were markedly altered by BSTSF treatment, relative to untreated AD rats (fold change ≥ 2 and P < 0.05). Moreover, six BSTSF treatment-related tsRNAs were identified and validated by qRT-PCR. Bioinformatic analyses indicated that the six treatment-related tsRNAs had potential therapeutic roles, via multiple signaling pathways and Gene Ontology biological functions, including cyclic adenosine monophosphate and retrograde endocannabinoid signaling. CONCLUSION This study identified a previously uncharacterized mechanism underlying the effects of BSTSF in alleviating the learning and memory deficits in Aβ1-42-induced AD rats, demonstrating that tsRNAs are potential therapeutic targets of BSTSF in the treatment of AD.
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Affiliation(s)
- Zhe-Yu Zhang
- Department of Integrated Traditional Chinese & Western Medicine, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, China
| | - Chun-Hu Zhang
- Department of Integrated Traditional Chinese & Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Jing-Jing Yang
- Department of Integrated Traditional Chinese & Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Pan-Pan Xu
- Department of Integrated Traditional Chinese & Western Medicine, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, China
| | - Peng-Ji Yi
- Department of Integrated Traditional Chinese & Western Medicine, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, China
| | - Mu-Li Hu
- Department of Scientific Research, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, China
| | - Wei-Jun Peng
- Department of Integrated Traditional Chinese & Western Medicine, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, China.
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178
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Bogard B, Francastel C, Hubé F. Multiple information carried by RNAs: total eclipse or a light at the end of the tunnel? RNA Biol 2020; 17:1707-1720. [PMID: 32559119 PMCID: PMC7714488 DOI: 10.1080/15476286.2020.1783868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/06/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
The findings that an RNA is not necessarily either coding or non-coding, or that a precursor RNA can produce different types of mature RNAs, whether coding or non-coding, long or short, have challenged the dichotomous view of the RNA world almost 15 years ago. Since then, and despite an increasing number of studies, the diversity of information that can be conveyed by RNAs is rarely searched for, and when it is known, it remains largely overlooked in further functional studies. Here, we provide an update with prominent examples of multiple functions that are carried by the same RNA or are produced by the same precursor RNA, to emphasize their biological relevance in most living organisms. An important consequence is that the overall function of their locus of origin results from the balance between various RNA species with distinct functions and fates. The consideration of the molecular basis of this multiplicity of information is obviously crucial for downstream functional studies when the targeted functional molecule is often not the one that is believed.
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Affiliation(s)
- Baptiste Bogard
- Université De Paris, Epigenetics and Cell Fate, CNRS, Paris, France
| | | | - Florent Hubé
- Université De Paris, Epigenetics and Cell Fate, CNRS, Paris, France
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179
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Abstract
As one of the most abundant and conserved RNA species, transfer RNAs (tRNAs) are well known for their role in reading the codons on messenger RNAs and translating them into proteins. In this review, we discuss the noncanonical functions of tRNAs. These include tRNAs as precursors to novel small RNA molecules derived from tRNAs, also called tRNA-derived fragments, that are abundant across species and have diverse functions in different biological processes, including regulating protein translation, Argonaute-dependent gene silencing, and more. Furthermore, the role of tRNAs in biosynthesis and other regulatory pathways, including nutrient sensing, splicing, transcription, retroelement regulation, immune response, and apoptosis, is reviewed. Genome organization and sequence variation of tRNA genes are also discussed in light of their noncanonical functions. Lastly, we discuss the recent applications of tRNAs in genome editing and microbiome sequencing.
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Affiliation(s)
- Zhangli Su
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia 22901, USA; , , ,
| | - Briana Wilson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia 22901, USA; , , ,
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia 22901, USA; , , ,
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia 22901, USA; , , ,
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180
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The Importance of AGO 1 and 4 in Post-Transcriptional Gene Regulatory Function of tRF5-GluCTC, an Respiratory Syncytial Virus-Induced tRNA-Derived RNA Fragment. Int J Mol Sci 2020; 21:ijms21228766. [PMID: 33233493 PMCID: PMC7699471 DOI: 10.3390/ijms21228766] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/18/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection in infants, the elderly, and immune-compromised patients. It is also a significant contributor to upper respiratory tract infection in the pediatric population. However, its disease mechanisms are still largely unknown. We have recently shown that a tRNA-derived RNA fragment (tRF) from the 5′-end of mature tRNA encoding GluCTC (tRF5-GluCTC), a recently discovered non-coding RNA, is functionally important for RSV replication and host gene regulation at the post-transcriptional level. However, how tRF5-GluCTC carries out the gene regulation is not fully known. In this study, we found that tRF5-GluCTC has impaired gene trans-silencing function in cells deficient of AGO1 or 4, while AGO2 and 3 seem not involved in tRF5-GluCTC-mediated gene regulation. By pulling down individual AGO protein, we discovered that tRF5-GluCTC is detectable only in the AGO4 complex, confirming the essential role of AGO4 in gene regulation and also suggesting that AGO1 contributes to the gene trans-silencing activity of tRF5-GluCTC in an atypical way. We also found that the P protein of RSV is associated with both AGO1 and 4 and AGO4 deficiency leads to reduced infectious viral particles. In summary, this study demonstrates the importance of AGO1 and 4 in mediating the gene trans-silencing function of tRF5-GluCTC.
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181
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Park MS, Sim G, Kehling AC, Nakanishi K. Human Argonaute2 and Argonaute3 are catalytically activated by different lengths of guide RNA. Proc Natl Acad Sci U S A 2020; 117:28576-28578. [PMID: 33122430 PMCID: PMC7682322 DOI: 10.1073/pnas.2015026117] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA interfering is a eukaryote-specific gene silencing by 20∼23-nucleotide (nt) microRNAs and small interfering RNAs that recruit Argonaute proteins to complementary RNAs for degradation. In humans, Argonaute2 (AGO2) has been known as the only slicer while Argonaute3 (AGO3) barely cleaves RNAs. Therefore, the intrinsic slicing activity of AGO3 remains controversial and a long-standing question. Here, we report 14-nt 3' end-shortened variants of let-7a, miR-27a, and specific miR-17-92 families that make AGO3 an extremely competent slicer, increasing target cleavage up to ∼82-fold in some instances. These RNAs, named cleavage-inducing tiny guide RNAs (cityRNAs), conversely lower the activity of AGO2, demonstrating that AGO2 and AGO3 have different optimum guide lengths for target cleavage. Our study sheds light on the role of tiny guide RNAs.
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Affiliation(s)
- Mi Seul Park
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - GeunYoung Sim
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH 43210
| | - Audrey C Kehling
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210;
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH 43210
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182
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Li PF, Guo SC, Liu T, Cui H, Feng D, Yang A, Cheng Z, Luo J, Tang T, Wang Y. Integrative analysis of transcriptomes highlights potential functions of transfer-RNA-derived small RNAs in experimental intracerebral hemorrhage. Aging (Albany NY) 2020; 12:22794-22813. [PMID: 33203799 PMCID: PMC7746353 DOI: 10.18632/aging.103938] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/01/2020] [Indexed: 12/16/2022]
Abstract
Transfer-RNA-derived small RNAs (tsRNAs) are a novel class of short non-coding RNAs, that possess regulatory functions. However, their biological roles in hemorrhagic stroke are not understood. In this study, by RNA sequencing, we investigated the tsRNA expression profiles of intracerebral hemorrhagic rat brains in the chronic phase. A total of 331 tsRNAs were identified (308 in sham and 309 in intracerebral hemorrhage). Among them, the validation revealed that 7 tsRNAs (1 up-regulated and 6 down-regulated) were significantly changed. Subsequently, we predicted the target mRNAs of the 7 tsRNAs. Through integrative analysis, the predicted targets were validated by mRNA microarray data. Moreover, we confirmed the functions of tsRNAs targeting mRNAs in vitro. Furthermore, using bioinformatics tools and databases, we developed a tsRNA-mRNA-pathway interaction network to visualize their potential functions. Bioinformatics analyses and confirmatory experiments indicated that the altered genes were mainly enriched in several signaling pathways. These pathways were interrelated with intracerebral hemorrhage, such as response to oxidative stress, endocytosis, and regulation of G protein-coupled receptor signaling pathway. In summary, this study systematically revealed the profiles of tsRNAs after an experimental intracerebral hemorrhage. These results may provide novel therapeutic targets following a hemorrhagic stroke in the chronic phase.
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Affiliation(s)
- Peng-Fei Li
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,Henan Key Laboratory for Pharmacology of Liver Diseases, Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Shi-Chao Guo
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Tao Liu
- Department of Gerontology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi 830011, China
| | - Hanjin Cui
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Dandan Feng
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ali Yang
- Department of Neurology, Henan Province People’s Hospital, Zhengzhou 450003, China
| | - Zhe Cheng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.,Henan Key Laboratory for Pharmacology of Liver Diseases, Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Jiekun Luo
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Tao Tang
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yang Wang
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
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Gu X, Wang L, Coates PJ, Boldrup L, Fåhraeus R, Wilms T, Sgaramella N, Nylander K. Transfer-RNA-Derived Fragments Are Potential Prognostic Factors in Patients with Squamous Cell Carcinoma of the Head and Neck. Genes (Basel) 2020; 11:genes11111344. [PMID: 33202812 PMCID: PMC7698123 DOI: 10.3390/genes11111344] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 12/25/2022] Open
Abstract
Transfer-RNA-derived fragments (tRFs) are a class of small non-coding RNAs that are functionally different from their parental transfer RNAs (tRNAs). tRFs can regulate gene expression by several mechanisms, and are involved in a variety of pathological processes. Here, we aimed at understanding the composition and abundance of tRFs in squamous cell carcinoma of the head and neck (SCCHN), and evaluated the potential of tRFs as prognostic markers in this cancer type. We obtained tRF expression data from The Cancer Genome Atlas (TCGA) HNSC cohort (523 patients) using MINTbase v2.0, and correlated to available TCGA clinical data. RNA-binding proteins were predicted according to the calculated Position Weight Matrix (PWM) score from the RNA-Binding Protein DataBase (RBPDB). A total of 10,158 tRFs were retrieved and a high diversity in expression levels was seen. Fifteen tRFs were found to be significantly associated with overall survival (Kaplan-Meier survival analysis, log rank test p-value < 0.01). The top prognostic marker, tRF-20-S998LO9D (p < 0.001), was further measured in tumor and tumor-free samples from 16 patients with squamous cell carcinoma of the oral tongue and 12 healthy controls, and was significantly upregulated in tumor compared to matched tumor-free tongue (p < 0.001). Results suggest that tRFs are useful prognostic markers in SCCHN.
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Affiliation(s)
- Xiaolian Gu
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden; (L.W.); (L.B.); (R.F.); (N.S.); (K.N.)
- Correspondence: ; Tel.: +46-(0)-702-086-036
| | - Lixiao Wang
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden; (L.W.); (L.B.); (R.F.); (N.S.); (K.N.)
| | - Philip J. Coates
- Regional Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 65653 Brno, Czech Republic;
| | - Linda Boldrup
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden; (L.W.); (L.B.); (R.F.); (N.S.); (K.N.)
| | - Robin Fåhraeus
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden; (L.W.); (L.B.); (R.F.); (N.S.); (K.N.)
- Regional Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 65653 Brno, Czech Republic;
- Institute of Molecular Genetics, University Paris 7, St. Louis Hospital, 75010 Paris, France
| | - Torben Wilms
- Department of Clinical Sciences/ENT, Umeå University, 90185 Umeå, Sweden;
| | - Nicola Sgaramella
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden; (L.W.); (L.B.); (R.F.); (N.S.); (K.N.)
| | - Karin Nylander
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden; (L.W.); (L.B.); (R.F.); (N.S.); (K.N.)
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184
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Magee R, Rigoutsos I. On the expanding roles of tRNA fragments in modulating cell behavior. Nucleic Acids Res 2020; 48:9433-9448. [PMID: 32890397 PMCID: PMC7515703 DOI: 10.1093/nar/gkaa657] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
The fragments that derive from transfer RNAs (tRNAs) are an emerging category of regulatory RNAs. Known as tRFs, these fragments were reported for the first time only a decade ago, making them a relatively recent addition to the ever-expanding pantheon of non-coding RNAs. tRFs are short, 16-35 nucleotides (nts) in length, and produced through cleavage of mature and precursor tRNAs at various positions. Both cleavage positions and relative tRF abundance depend strongly on context, including the tissue type, tissue state, and disease, as well as the sex, population of origin, and race/ethnicity of an individual. These dependencies increase the urgency to understand the regulatory roles of tRFs. Such efforts are gaining momentum, and comprise experimental and computational approaches. System-level studies across many tissues and thousands of samples have produced strong evidence that tRFs have important and multi-faceted roles. Here, we review the relevant literature on tRF biology in higher organisms, single cell eukaryotes, and prokaryotes.
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Affiliation(s)
- Rogan Magee
- Computational Medicine Center, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Isidore Rigoutsos
- To whom correspondence should be addressed. Tel: +1 215 503 4219; Fax: +1 215 503 0466;
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185
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Liu W, Liu Y, Pan Z, Zhang X, Qin Y, Chen X, Li M, Chen X, Zheng Q, Liu X, Li D. Systematic Analysis of tRNA-Derived Small RNAs Discloses New Therapeutic Targets of Caloric Restriction in Myocardial Ischemic Rats. Front Cell Dev Biol 2020; 8:568116. [PMID: 33224944 PMCID: PMC7670042 DOI: 10.3389/fcell.2020.568116] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
Caloric restriction (CR) is a novel dietary therapy that has a protective effect on myocardial ischemia. However, the mechanisms underlying the therapeutic effect of CR remain unclear. Transfer RNA-derived small RNAs (tsRNAs) are a novel type of short non-coding RNAs that have potential regulatory functions in various physiological and pathological processes. In this study, we explored new therapeutic targets of CR through tsRNA sequencing. Rats were randomly divided into three groups: a normal control group (norm group), isoproterenol (ISO)-induced myocardial ischemic group (MI group), and CR pretreatment plus ISO-induced myocardial ischemic group (CR + MI group). Triphenyl tetrazolium chloride staining, terminal deoxynucleotidyl transferase dUTP nick-end labeling staining, serum creatine kinase (CK) and lactic acid dehydrogenase activity detection kits, and creatine kinase isoenzyme 1 levels were used to measure the degree of myocardial ischemic injury. These indicators of myocardial ischemia were significantly improved in the CR + MI group compared with those in the MI group. In the ischemic myocardial tissue of the MI group, a total of 708 precisely matched tsRNAs were identified, and 302 tsRNAs (fold change >1.5, P < 0.05) were significantly changed when compared with those in the norm group. Furthermore, 55 tsRNAs were significantly regulated by CR pretreatment, among which five tsRNAs (tiRNA-His-GTG-004, tRF-Gly-TCC-018, tRF-Cys-GCA-022, tRF-Lys-CTT-026, tRF-Met-CAT-008) were randomly selected and verified by quantitative real-time polymerase chain reaction. In addition, predictions of target genes and bioinformatics analysis indicated that these tsRNAs may play a therapeutic role through the regulation of macromolecular metabolism. In conclusion, our findings reveal that tsRNAs are potential therapeutic targets for CR pre-pretreatment to improve myocardial ischemic injury. This study provides new ideas for future research on elucidating the mechanisms of CR pretreatment in ameliorating myocardial ischemic injury.
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Affiliation(s)
- Wenjing Liu
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Yang Liu
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhaohai Pan
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Xin Zhang
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Yao Qin
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Xiaojie Chen
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Minjing Li
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Xiaoyu Chen
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Qiusheng Zheng
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China.,Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Ministry of Education, School of Pharmacy, Shihezi University, Shihezi, China
| | - Xiaona Liu
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Defang Li
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
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186
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Contribution of miRNAs, tRNAs and tRFs to Aberrant Signaling and Translation Deregulation in Lung Cancer. Cancers (Basel) 2020; 12:cancers12103056. [PMID: 33092114 PMCID: PMC7593945 DOI: 10.3390/cancers12103056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary The profiles of miRNAs, tRNA-derived fragments and tRNAs from lung cancer biopsy specimens indicate involvement of gene networks that modulate signaling and translation initiation. The current study highlights the important role of several regulatory small non-coding RNAs in aberrant signaling and translation deregulation in lung cancer. Abstract Transcriptomics profiles of miRNAs, tRNAs or tRFs are used as biomarkers, after separate examination of several cancer cell lines, blood samples or biopsies. However, the possible contribution of all three profiles on oncogenic signaling and translation as a net regulatory effect, is under investigation. The present analysis of miRNAs and tRFs from lung cancer biopsies indicated putative targets, which belong to gene networks involved in cell proliferation, transcription and translation regulation. In addition, we observed differential expression of specific tRNAs along with several tRNA-related genes with possible involvement in carcinogenesis. Transfection of lung adenocarcinoma cells with two identified tRFs and subsequent NGS analysis indicated gene targets that mediate signaling and translation regulation. Broader analysis of all major signaling and translation factors in several biopsy specimens revealed a crosstalk between the PI3K/AKT and MAPK pathways and downstream activation of eIF4E and eEF2. Subsequent polysome profile analysis and 48S pre-initiation reconstitution experiments showed increased global translation rates and indicated that aberrant expression patterns of translation initiation factors could contribute to elevated protein synthesis. Overall, our results outline the modulatory effects that possibly correlate the expression of important regulatory non-coding RNAs with aberrant signaling and translation deregulation in lung cancer.
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187
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Sun X, Yang J, Yu M, Yao D, Zhou L, Li X, Qiu Q, Lin W, Lu B, Chen E, Wang P, Chen W, Tao S, Xu H, Williams A, Liu Y, Pan X, Cowley AW, Lu W, Liang M, Liu P, Lu Y. Global identification and characterization of tRNA-derived RNA fragment landscapes across human cancers. NAR Cancer 2020; 2:zcaa031. [PMID: 34316691 PMCID: PMC8210304 DOI: 10.1093/narcan/zcaa031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/24/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Transfer RNA-derived RNA fragments (tRFs) are a class of small non-coding RNAs that are abundant in many organisms, but their role in cancer has not been fully explored. Here, we report a functional genomic landscape of tRFs in 8118 specimens across 15 cancer types from The Cancer Genome Atlas. These tRFs exhibited characteristics of widespread expression, high sequence conservation, cytoplasmic localization, specific patterns of tRNA cleavage and conserved cleavage in tissues. A cross-tumor analysis revealed significant commonality among tRF expression subtypes from distinct tissues of origins, characterized by upregulation of a group of tRFs with similar size and activation of cancer-associated signaling. One of the largest superclusters was composed of 22 nt 3'-tRFs upregulated in 13 cancer types, all of which share the activation of Ras/MAPK, RTK and TSC/mTOR signaling. tRF-based subgrouping provided clinically relevant stratifications and significantly improved outcome prediction by incorporating clinical variables. Additionally, we discovered 11 cancer driver tRFs using an effective approach for accurately exploring cross-tumor and platform trends. As a proof of concept, we performed comprehensive functional assays on a non-microRNA driver tRF, 5'-IleAAT-8-1-L20, and validated its oncogenic roles in lung cancer in vitro and in vivo. Our study also provides a valuable tRF resource for identifying diagnostic and prognostic biomarkers, developing cancer therapy and studying cancer pathogenesis.
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Affiliation(s)
- Xiwei Sun
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Juze Yang
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Mengqian Yu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
| | - Dongxia Yao
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
| | - Liyuan Zhou
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Xufan Li
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Qiongzi Qiu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
| | - Weiqiang Lin
- The First Affiliated Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Bingjian Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
| | - Enguo Chen
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Ping Wang
- The First Affiliated Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Wantao Chen
- Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200011, China
| | - Sifeng Tao
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Haiming Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Anna Williams
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Xiaoqing Pan
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Allen W Cowley
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Weiguo Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Pengyuan Liu
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
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188
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Molla-Herman A, Angelova MT, Ginestet M, Carré C, Antoniewski C, Huynh JR. tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation. Front Genet 2020; 11:518949. [PMID: 33193603 PMCID: PMC7586317 DOI: 10.3389/fgene.2020.518949] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/03/2020] [Indexed: 01/16/2023] Open
Abstract
tRNA fragments (tRFs) are a class of small non-coding RNAs (sncRNAs) derived from tRNAs. tRFs are highly abundant in many cell types including stem cells and cancer cells, and are found in all domains of life. Beyond translation control, tRFs have several functions ranging from transposon silencing to cell proliferation control. However, the analysis of tRFs presents specific challenges and their biogenesis is not well understood. They are very heterogeneous and highly modified by numerous post-transcriptional modifications. Here we describe a bioinformatic pipeline (tRFs-Galaxy) to study tRFs populations and shed light onto tRNA fragments biogenesis in Drosophila melanogaster. Indeed, we used small RNAs Illumina sequencing datasets extracted from wild type and mutant ovaries affecting two different highly conserved steps of tRNA biogenesis: 5'pre-tRNA processing (RNase-P subunit Rpp30) and tRNA 2'-O-methylation (dTrm7_34 and dTrm7_32). Using our pipeline, we show how defects in tRNA biogenesis affect nuclear and mitochondrial tRFs populations and other small non-coding RNAs biogenesis, such as small nucleolar RNAs (snoRNAs). This tRF analysis workflow will advance the current understanding of tRFs biogenesis, which is crucial to better comprehend tRFs roles and their implication in human pathology.
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Affiliation(s)
- Anahi Molla-Herman
- Collège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, France
| | - Margarita T. Angelova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Maud Ginestet
- Collège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, France
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Christophe Antoniewski
- ARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Jean-René Huynh
- Collège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, France
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189
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Zhou Y, Peng H, Cui Q, Zhou Y. tRFTar: Prediction of tRF-target gene interactions via systemic re-analysis of Argonaute CLIP-seq datasets. Methods 2020; 187:57-67. [PMID: 33045361 DOI: 10.1016/j.ymeth.2020.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/04/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022] Open
Abstract
tRNA-derived fragments (tRFs), which by definition are cleaved from tRNAs, comprise a novel class of regulatory small non-coding RNAs. Recent evidence has revealed that tRFs can be loaded onto Argonaute (AGO) family proteins to perform post-transcriptional regulations via substantial tRF-target gene interactions (TGIs). However, there is no resource that systematically profiles potential AGO-mediated TGIs. To this end, we performed a systemic computational screening of potential AGO-mediated TGIs by a re-analysis of 146 crosslinking-immunoprecipitation and high-throughput sequencing (CLIP-seq) datasets in which 920,690 TGIs between 12,102 tRFs and 5,688 target genes were identified. The predicted TGIs have superior signal-to-noise ratio and good consistency with TGIs identified from an orthogonal technique. AGO-bound tRFs are not evenly distributed, where the 5'-tRF and 3'-tRF are enriched and some commonly expressed tRFs are also overrepresented. The tRFs tend to target conserved regions of transcripts and co-express with their target genes. Filtering TGIs with consistent co-expression with target genes results in a set of regulatory TGIs that contains 25,281 tRF-target pairs. Together, our results unveiled the extensive regulatory interactions between tRFs and target genes. Finally, the CLIP-derived TGIs were incorporated in a user-friendly online platform termed as tRFTar, where various functions like custom searching, co-expressed TGI filtering, genome browser and TGI-based tRF functional enrichment analysis are enabled to help users to investigate the functions of tRFs. The tRFTar is freely available at http://www.rnanut.net/tRFTar/.
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Affiliation(s)
- Yiran Zhou
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Haoran Peng
- School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Qinghua Cui
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Center of Bioinformatics, Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Yuan Zhou
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing 100191, China.
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190
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Tolstyko EA, Lezzhov AA, Morozov SY, Solovyev AG. Phloem transport of structured RNAs: A widening repertoire of trafficking signals and protein factors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110602. [PMID: 32900440 DOI: 10.1016/j.plantsci.2020.110602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/20/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
The conducting sieve tubes of the phloem consist of sieve elements (SEs), which are enucleate cells incapable of transcription and translation. Nevertheless, SEs contain a large variety of RNAs, and long-distance RNA trafficking via the phloem has been documented. The phloem transport of certain RNAs, as well as the further unloading of these RNAs at target tissues, is essential for plant individual development and responses to environmental cues. The translocation of such RNAs via the phloem is believed to be directed by RNA structural elements serving as phloem transport signals (PTSs), which are recognized by proteins that direct the PTS-containing RNAs into the phloem translocation pathway. The ability of phloem transport has been reported for several classes of structured RNAs including viroids, genuine tRNAs, mRNAs with tRNA sequences embedded into mRNA untranslated regions, tRNA-like structures in the genomic RNAs of plant viruses, and micro-RNA (miRNA) precursors (pri-miRNA). Here, three distinct types of such RNAs are discussed, along with the proteins that may specifically interact with these structures in the phloem. Three-dimensional (3D) motifs, which are characteristic of imperfect RNA duplexes, are discussed as elements of phloem-mobile structured RNAs specifically recognized by proteins involved in phloem transport, thus serving as PTSs.
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Affiliation(s)
- Eugeny A Tolstyko
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia
| | - Alexander A Lezzhov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119991, Russia
| | - Sergey Y Morozov
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia
| | - Andrey G Solovyev
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia.
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191
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Li Y, Baptista RP, Kissinger JC. Noncoding RNAs in Apicomplexan Parasites: An Update. Trends Parasitol 2020; 36:835-849. [DOI: 10.1016/j.pt.2020.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/26/2020] [Accepted: 07/18/2020] [Indexed: 12/16/2022]
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192
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Yu AM, Choi YH, Tu MJ. RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. Pharmacol Rev 2020; 72:862-898. [PMID: 32929000 PMCID: PMC7495341 DOI: 10.1124/pr.120.019554] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.
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MESH Headings
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Betacoronavirus
- COVID-19
- Chemistry Techniques, Analytical/methods
- Chemistry Techniques, Analytical/standards
- Clustered Regularly Interspaced Short Palindromic Repeats
- Coronavirus Infections/drug therapy
- Drug Delivery Systems/methods
- Drug Development/organization & administration
- Drug Discovery
- Humans
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Pandemics
- Pneumonia, Viral/drug therapy
- RNA/adverse effects
- RNA/drug effects
- RNA/pharmacology
- RNA, Antisense/pharmacology
- RNA, Antisense/therapeutic use
- RNA, Messenger/drug effects
- RNA, Messenger/pharmacology
- RNA, Ribosomal/drug effects
- RNA, Ribosomal/pharmacology
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
- RNA, Viral/drug effects
- Ribonucleases/metabolism
- Riboswitch/drug effects
- SARS-CoV-2
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Young Hee Choi
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
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193
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Yan Y, Chang C, Su J, Venø MT, Kjems J. Osteoblastogenesis Alters Small RNA Profiles in EVs Derived from Bone Marrow Stem Cells (BMSCs) and Adipose Stem Cells (ASCs). Biomedicines 2020; 8:biomedicines8100387. [PMID: 32998458 PMCID: PMC7599808 DOI: 10.3390/biomedicines8100387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022] Open
Abstract
Multipotent stem cells (MSCs) are used in various therapeutic applications based on their paracrine secretion activity. Here, we set out to identify and characterize the paracrine factors released during osteoblastogenesis, with a special focus on small non-coding RNAs released in extracellular vesicles (EVs). Bone marrow stem cells (BMSCs) and adipose stem cells (ASCs) from healthy human donors were used as representatives of MSCs. We isolated EVs secreted before and after induction of osteoblastic differentiation and found that the EVs contained a specific subset of microRNAs (miRNAs) and tRNA-derived small RNAs (tsRNA) compared to their parental cells. Osteoblastic differentiation had a larger effect on the small RNA profile of BMSC-EVs relative to ASC-EVs. Our data showed that EVs from different MSC origin exhibited distinct expression profiles of small RNA profiles when undergoing osteoblastogenesis, a factor that should be taken into consideration for stem cell therapy.
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Affiliation(s)
- Yan Yan
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark; (Y.Y.); (C.C.); (J.S.); (M.T.V.)
- Omiics ApS, Åbogade 15, 8200 Aarhus N, Denmark
| | - Clare Chang
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark; (Y.Y.); (C.C.); (J.S.); (M.T.V.)
| | - Junyi Su
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark; (Y.Y.); (C.C.); (J.S.); (M.T.V.)
| | - Morten T. Venø
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark; (Y.Y.); (C.C.); (J.S.); (M.T.V.)
- Omiics ApS, Åbogade 15, 8200 Aarhus N, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark; (Y.Y.); (C.C.); (J.S.); (M.T.V.)
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Correspondence: ; Tel.: +45-289-920-86
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194
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Park J, Ahn SH, Shin MG, Kim HK, Chang S. tRNA-Derived Small RNAs: Novel Epigenetic Regulators. Cancers (Basel) 2020; 12:cancers12102773. [PMID: 32992597 PMCID: PMC7599909 DOI: 10.3390/cancers12102773] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Cells must synthesize new proteins to maintain its life and tRNA (transfer RNA) is an essential component of the translation process. tRNA-derived small RNA (tsRNA) is a relatively uncharacterized small RNA, derived from enzymatic cleavage of the tRNAs. Accumulating evidences suggest that tsRNA is an abundant, highly modified, dynamically regulated small-RNA and interacts with other types of RNAs or proteins. Moreover, it is abnormally expressed in multiple human diseases including systemic lupus, neurological disorder, metabolic disorder and cancer, implying its diverse function in the initiation or progression of such diseases. In this review, we summarize the classification of tsRNA and its role focused on the epigenetic regulation. Further, we discuss the limitation of current knowledge about the tsRNA and its potential applications. Abstract An epigenetic change is a heritable genetic alteration that does not involve any nucleotide changes. While the methylation of specific DNA regions such as CpG islands or histone modifications, including acetylation or methylation, have been investigated in detail, the role of small RNAs in epigenetic regulation is largely unknown. Among the many types of small RNAs, tRNA-derived small RNAs (tsRNAs) represent a class of noncoding small RNAs with multiple roles in diverse physiological processes, including neovascularization, sperm maturation, immune modulation, and stress response. Regarding these roles, several pioneering studies have revealed that dysregulated tsRNAs are associated with human diseases, such as systemic lupus, neurological disorder, metabolic disorder, and cancer. Moreover, recent findings suggest that tsRNAs regulate the expression of critical genes linked with these diseases by a variety of mechanisms, including epigenetic regulation. In this review, we will describe different classes of tsRNAs based on their biogenesis and will focus on their role in epigenetic regulation.
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Affiliation(s)
- Joonhyeong Park
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (J.P.); (M.G.S.)
| | - Se Hee Ahn
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea;
| | - Myung Geun Shin
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (J.P.); (M.G.S.)
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (J.P.); (M.G.S.)
- Correspondence: (H.K.K.); (S.C.); Tel.: +82-2-820-5197 (H.K.K.); +82-2-3010-2095 (S.C.)
| | - Suhwan Chang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea;
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea
- Correspondence: (H.K.K.); (S.C.); Tel.: +82-2-820-5197 (H.K.K.); +82-2-3010-2095 (S.C.)
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195
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Kiltschewskij DJ, Cairns MJ. Transcriptome-Wide Analysis of Interplay between mRNA Stability, Translation and Small RNAs in Response to Neuronal Membrane Depolarization. Int J Mol Sci 2020; 21:ijms21197086. [PMID: 32992958 PMCID: PMC7582590 DOI: 10.3390/ijms21197086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/19/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023] Open
Abstract
Experience-dependent changes to neural circuitry are shaped by spatially-restricted activity-dependent mRNA translation. Although the complexity of mRNA translation in neuronal cells is widely appreciated, translational profiles associated with neuronal excitation remain largely uncharacterized, and the associated regulatory mechanisms are poorly understood. Here, we employed ribosome profiling, mRNA sequencing and small RNA sequencing to profile transcriptome-wide changes in mRNA translation after whole cell depolarization of differentiated neuroblast cultures, and investigate the contribution of sequence-specific regulatory mechanisms. Immediately after depolarization, a functional partition between transcriptional and translational responses was uncovered, in which many mRNAs were subjected to significant changes in abundance or ribosomal occupancy, but not both. After an extended (2 h) post-stimulus rest phase, however, these changes became synchronized, suggesting that there are different layers of post-transcriptional regulation which are temporally separated but become coordinated over time. Globally, changes in mRNA abundance and translation were found to be associated with a number of intrinsic mRNA features, including mRNA length, GC% and secondary structures; however, the effect of these factors differed between both post-depolarization time-points. Furthermore, small RNA sequencing revealed that miRNAs and tRNA-derived small RNA fragments were subjected to peak changes in expression immediately after stimulation, during which these molecules were predominantly associated with fluctuations in mRNA abundance, consistent with known regulatory mechanisms. These data suggest that excitation-associated neuronal translation is subjected to extensive temporal coordination, with substantial contributions from a number of sequence-dependent regulatory mechanisms.
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Affiliation(s)
- Dylan J. Kiltschewskij
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan 2308, Australia;
- Centre for Brain and Mental Health Research, Hunter Medical Research Institute, New Lambton 2305, Australia
| | - Murray J. Cairns
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan 2308, Australia;
- Centre for Brain and Mental Health Research, Hunter Medical Research Institute, New Lambton 2305, Australia
- Schizophrenia Research Institute, Randwick 2031, Australia
- Correspondence: ; Tel.: +61-02-4921-8670
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196
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Looney MM, Lu Y, Karakousis PC, Halushka MK. Mycobacterium tuberculosis Infection Drives Mitochondria-Biased Dysregulation of Host Transfer RNA-Derived Fragments. J Infect Dis 2020; 223:1796-1805. [PMID: 32959876 DOI: 10.1093/infdis/jiaa596] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/17/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis, causes 10 million infections and 1.5 million deaths per year worldwide. The success of Mtb as a human pathogen is directly related to its ability to suppress host responses, which are critical for clearing intracellular pathogens. Emerging evidence suggests that key response pathways may be regulated by a novel class of small noncoding RNA, called transfer RNA (tRNA)-derived fragments (tRFs). tRFs can complex with Argonaute proteins to target and degrade messenger RNA targets, similarly to micro RNAs, but have thus far been overlooked in the context of bacterial infections. METHODS We generated a novel miRge2.0-based tRF-analysis tool, tRFcluster, and used it to analyze independently generated and publicly available RNA-sequencing datasets to assess tRF dysregulation in host cells following infection with Mtb and other intracellular bacterial pathogens. RESULTS We found that Mtb and Listeria monocytogenes drive dramatic tRF dysregulation, whereas other bacterial pathogens do not. Interestingly, Mtb infection uniquely increased the expression of mitochondria-derived tRFs rather than genomic-derived tRFs, suggesting an association with mitochondrial damage in Mtb infection. CONCLUSIONS tRFs are dysregulated in some, but not all, bacterial infections. Biased dysregulation of mitochondria-derived tRFs in Mtb infection suggests a link between mitochondrial distress and tRF production.
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Affiliation(s)
- Monika M Looney
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yin Lu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Petros C Karakousis
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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197
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Cao J, Cowan DB, Wang DZ. tRNA-Derived Small RNAs and Their Potential Roles in Cardiac Hypertrophy. Front Pharmacol 2020; 11:572941. [PMID: 33041815 PMCID: PMC7527594 DOI: 10.3389/fphar.2020.572941] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/28/2020] [Indexed: 12/21/2022] Open
Abstract
Transfer RNAs (tRNAs) are abundantly expressed, small non-coding RNAs that have long been recognized as essential components of the protein translation machinery. The tRNA-derived small RNAs (tsRNAs), including tRNA halves (tiRNAs), and tRNA fragments (tRFs), were unexpectedly discovered and have been implicated in a variety of important biological functions such as cell proliferation, cell differentiation, and apoptosis. Mechanistically, tsRNAs regulate mRNA destabilization and translation, as well as retro-element reverse transcriptional and post-transcriptional processes. Emerging evidence has shown that tsRNAs are expressed in the heart, and their expression can be induced by pathological stress, such as hypertrophy. Interestingly, cardiac pathophysiological conditions, such as oxidative stress, aging, and metabolic disorders can be viewed as inducers of tsRNA biogenesis, which further highlights the potential involvement of tsRNAs in these conditions. There is increasing enthusiasm for investigating the molecular and biological functions of tsRNAs in the heart and their role in cardiovascular disease. It is anticipated that this new class of small non-coding RNAs will offer new perspectives in understanding disease mechanisms and may provide new therapeutic targets to treat cardiovascular disease.
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Affiliation(s)
- Jun Cao
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Douglas B Cowan
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
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198
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Mo X, Du S, Chen X, Wang Y, Liu X, Zhang C, Zhu C, Ding L, Li Y, Tong Y, Ju Q, Qu D, Tan F, Wei F, Cai Q. Lactate Induces Production of the tRNA His Half to Promote B-lymphoblastic Cell Proliferation. Mol Ther 2020; 28:2442-2457. [PMID: 32966775 DOI: 10.1016/j.ymthe.2020.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/27/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022] Open
Abstract
High plasma lactate is emerging as a critical regulator in development and progression of many human malignancies. Small RNAs derived from cleavage of mature tRNAs have been implicated in many cellular stresses, but the detailed mechanisms that respond to lactic acid (LA; acidic lactate) are not well defined. Here, using an Epstein-Barr virus (EBV)-immortalized B lymphoblastic cell line (LCL) as a model, we report that LA induces cleavage of mature tRNA at the anticodon loop, particularly production of three 5'-tRNA halves (5'-HisGUG, 5'-ValAAC, and 5'-GlyGCC), along with increased expression of RNA polymerase III and angiogenin (ANG). Of these, only the 5'-HisGUG half binds to the chromatin regulator argonaute-2 (AGO2) instead of the AGO1 protein for stability. Notably, the levels of ANG and 5'-HisGUG half expression in peripheral blood mononuclear cells from B cell lymphoma patients are tightly correlated with lactate dehydrogenase (LDH; a lactate indicator) in plasma. Silencing production of the 5'-HisGUG half by small interfering RNA or inhibition of ANG significantly reduces colony formation and growth of LA-induced tumor cells in vitro and in vivo using a murine xenograft model. Overall, our findings identify a novel molecular therapeutic target for the diagnosis and treatment of B cell lymphoma.
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Affiliation(s)
- Xiaohui Mo
- Department of Dermatology, Renji Hospital, School of Medicine & ShengYushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; MOE & NHC & CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Science, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China; Central Laboratory, Shanghai Dermatology Hospital, Shanghai 200443, P.R. China
| | - Shujuan Du
- MOE & NHC & CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Science, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Xiaoting Chen
- MOE & NHC & CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Science, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yuyan Wang
- MOE & NHC & CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Science, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Xiaoqing Liu
- MOE & NHC & CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Science, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Chongqi Zhang
- Department of Dermatology, Renji Hospital, School of Medicine & ShengYushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Caixia Zhu
- MOE & NHC & CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Science, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Ling Ding
- MOE & NHC & CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Science, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Ying Li
- Division of Hematology, Shanghai First People's Hospital, Shanghai Jiao Tong University, Shanghai 200080, P.R. China
| | - Yin Tong
- Division of Hematology, Shanghai First People's Hospital, Shanghai Jiao Tong University, Shanghai 200080, P.R. China
| | - Qiang Ju
- Department of Dermatology, Renji Hospital, School of Medicine & ShengYushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Di Qu
- MOE & NHC & CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Science, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Fei Tan
- Central Laboratory, Shanghai Dermatology Hospital, Shanghai 200443, P.R. China.
| | - Fang Wei
- Department of Dermatology, Renji Hospital, School of Medicine & ShengYushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.
| | - Qiliang Cai
- MOE & NHC & CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Science, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China; Expert Workstation, Baoji Central Hospital, Baoji 721008, P.R. China.
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199
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Kim HK, Yeom JH, Kay MA. Transfer RNA-Derived Small RNAs: Another Layer of Gene Regulation and Novel Targets for Disease Therapeutics. Mol Ther 2020; 28:2340-2357. [PMID: 32956625 DOI: 10.1016/j.ymthe.2020.09.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/23/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Decades after identification as essential for protein synthesis, transfer RNAs (tRNAs) have been implicated in various cellular processes beyond translation. tRNA-derived small RNAs (tsRNAs), referred to as tRNA-derived fragments (tRFs) or tRNA-derived, stress-induced RNAs (tiRNAs), are produced by cleavage at different sites from mature or pre-tRNAs. They are classified into six major types representing potentially thousands of unique sequences and have been implicated to play a wide variety of regulatory roles in maintaining normal homeostasis, cancer cell viability, tumorigenesis, ribosome biogenesis, chromatin remodeling, translational regulation, intergenerational inheritance, retrotransposon regulation, and viral replication. However, the detailed mechanisms governing these processes remain unknown. Aberrant expression of tsRNAs is found in various human disease conditions, suggesting that a further understanding of the regulatory role of tsRNAs will assist in identifying novel biomarkers, potential therapeutic targets, and gene-regulatory tools. Here, we highlight the classification, biogenesis, and biological role of tsRNAs in regulatory mechanisms of normal and disease states.
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Affiliation(s)
- Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Mark A Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA.
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200
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Yu M, Lu B, Zhang J, Ding J, Liu P, Lu Y. tRNA-derived RNA fragments in cancer: current status and future perspectives. J Hematol Oncol 2020; 13:121. [PMID: 32887641 PMCID: PMC7487644 DOI: 10.1186/s13045-020-00955-6] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/24/2020] [Indexed: 01/02/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have been the focus of many studies over the last few decades, and their fundamental roles in human diseases have been well established. Transfer RNAs (tRNAs) are housekeeping ncRNAs that deliver amino acids to ribosomes during protein biosynthesis. tRNA fragments (tRFs) are a novel class of small ncRNAs produced through enzymatic cleavage of tRNAs and have been shown to play key regulatory roles similar to microRNAs. Development and application of high-throughput sequencing technologies has provided accumulating evidence of dysregulated tRFs in cancer. Aberrant expression of tRFs has been found to participate in cell proliferation, invasive metastasis, and progression in several human malignancies. These newly identified functional tRFs also have great potential as new biomarkers and therapeutic targets for cancer treatment. In this review, we focus on the major biological functions of tRFs including RNA silencing, translation regulation, and epigenetic regulation; summarize recent research on the roles of tRFs in different types of cancer; and discuss the potential of using tRFs as clinical biomarkers for cancer diagnosis and prognosis and as therapeutic targets for cancer treatment.
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Affiliation(s)
- Mengqian Yu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Bingjian Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Jisong Zhang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Jinwang Ding
- Department of Head and Neck Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, China
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China.,Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.
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