51
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Li X, Peng J, Yi C. The epitranscriptome of small non-coding RNAs. Noncoding RNA Res 2021; 6:167-173. [PMID: 34820590 PMCID: PMC8581453 DOI: 10.1016/j.ncrna.2021.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
Small non-coding RNAs are short RNA molecules and involved in many biological processes, including cell proliferation and differentiation, immune response, cell death, epigenetic regulation, metabolic control. A diversity of RNA modifications have been identified in these small non-coding RNAs, including transfer RNAs (tRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nuclear RNA (snRNA), small nucleolar RNAs (snoRNAs), and tRNA-derived small RNAs (tsRNAs). These post-transcriptional modifications are involved in the biogenesis and function of these small non-coding RNAs. In this review, we will summarize the existence of RNA modifications in the small non-coding RNAs and the emerging roles of these epitranscriptomic marks.
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Affiliation(s)
- Xiaoyu Li
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.,Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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52
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Chen L, Xu W, Liu K, Jiang Z, Han Y, Jin H, Zhang L, Shen W, Jia S, Sun Q, Meng A. 5' Half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos. SCIENCE ADVANCES 2021; 7:eabh0494. [PMID: 34797706 PMCID: PMC8604414 DOI: 10.1126/sciadv.abh0494] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
5′tRFls are small transfer RNA (tRNA) fragments derived from 5′ half of mature tRNAs. However, it is unknown whether 5′tRFls could feed back to regulate tRNA biogenesis. Here, we show that 5′tRFlGly/GCC and 5′tRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis, dynamics of 5′tRFlGly/GCC and 5′tRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino-mediated knockdown of 5′tRFlGly/GCC or 5′tRFlGlu/CTC down-regulates tRNAGly/GCC or tRNAGlu/CTC levels, respectively, and causes embryonic lethality that is efficiently rescued by coinjection of properly refolded corresponding tRNA. In zebrafish embryos, tRNA:DNA and 5′tRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically, unstable 5′tRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA gene transcription. The uncovered mechanism may be implicated in other physiological and pathological processes.
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Affiliation(s)
- Luxi Chen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kunpeng Liu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zheng Jiang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yang Han
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongbin Jin
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lin Zhang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shunji Jia
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Guangzhou Laboratory, Guangzhou 510320, Guangdong Province, China
- Corresponding author.
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53
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Dannfald A, Favory JJ, Deragon JM. Variations in transfer and ribosomal RNA epitranscriptomic status can adapt eukaryote translation to changing physiological and environmental conditions. RNA Biol 2021; 18:4-18. [PMID: 34159889 PMCID: PMC8677040 DOI: 10.1080/15476286.2021.1931756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 01/27/2023] Open
Abstract
The timely reprogramming of gene expression in response to internal and external cues is essential to eukaryote development and acclimation to changing environments. Chemically modifying molecular receptors and transducers of these signals is one way to efficiently induce proper physiological responses. Post-translation modifications, regulating protein biological activities, are central to many well-known signal-responding pathways. Recently, messenger RNA (mRNA) chemical (i.e. epitranscriptomic) modifications were also shown to play a key role in these processes. In contrast, transfer RNA (tRNA) and ribosomal RNA (rRNA) chemical modifications, although critical for optimal function of the translation apparatus, and much more diverse and quantitatively important compared to mRNA modifications, were until recently considered as mainly static chemical decorations. We present here recent observations that are challenging this view and supporting the hypothesis that tRNA and rRNA modifications dynamically respond to various cell and environmental conditions and contribute to adapt translation to these conditions.
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Affiliation(s)
- Arnaud Dannfald
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Jacques Favory
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Marc Deragon
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
- Institut Universitaire de France, Paris, France
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54
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Chen Q, Zhang X, Shi J, Yan M, Zhou T. Origins and evolving functionalities of tRNA-derived small RNAs. Trends Biochem Sci 2021; 46:790-804. [PMID: 34053843 PMCID: PMC8448906 DOI: 10.1016/j.tibs.2021.05.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are among the most ancient small RNAs in all domains of life and are generated by the cleavage of tRNAs. Emerging studies have begun to reveal the versatile roles of tsRNAs in fundamental biological processes, including gene silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, which are rooted in tsRNA sequence conservation, RNA modifications, and protein-binding abilities. We summarize the mechanisms of tsRNA biogenesis and the impact of RNA modifications, and propose how thinking of tsRNA functionality from an evolutionary perspective urges the expansion of tsRNA research into a wider spectrum, including cross-tissue/cross-species regulation and harnessing of the 'tsRNA code' for precision medicine.
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Affiliation(s)
- Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA.
| | - Xudong Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Menghong Yan
- Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China; Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
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55
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Emerging Functions for snoRNAs and snoRNA-Derived Fragments. Int J Mol Sci 2021; 22:ijms221910193. [PMID: 34638533 PMCID: PMC8508363 DOI: 10.3390/ijms221910193] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022] Open
Abstract
The widespread implementation of mass sequencing has revealed a diverse landscape of small RNAs derived from larger precursors. Whilst many of these are likely to be byproducts of degradation, there are nevertheless metabolically stable fragments derived from tRNAs, rRNAs, snoRNAs, and other non-coding RNA, with a number of examples of the production of such fragments being conserved across species. Coupled with specific interactions to RNA-binding proteins and a growing number of experimentally reported examples suggesting function, a case is emerging whereby the biological significance of small non-coding RNAs extends far beyond miRNAs and piRNAs. Related to this, a similarly complex picture is emerging of non-canonical roles for the non-coding precursors, such as for snoRNAs that are also implicated in such areas as the silencing of gene expression and the regulation of alternative splicing. This is in addition to a body of literature describing snoRNAs as an additional source of miRNA-like regulators. This review seeks to highlight emerging roles for such non-coding RNA, focusing specifically on “new” roles for snoRNAs and the small fragments derived from them.
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56
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Chai Y, Lu Y, Yang L, Qiu J, Qin C, Zhang J, Zhang Y, Wang X, Qi G, Liu C, Zhang X, Li D, Zhu H. Identification and potential functions of tRNA-derived small RNAs (tsRNAs) in irritable bowel syndrome with diarrhea. Pharmacol Res 2021; 173:105881. [PMID: 34509631 DOI: 10.1016/j.phrs.2021.105881] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/17/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023]
Abstract
IBS-D is a functional bowel disease without clear diagnostic markers and exact pathogenesis. Studies have proved that non-coding RNAs participate in IBS-D. However, tRNA-derived small RNAs (tsRNAs), as a new type of non-coding RNAs that are more suitable as markers, remain to be clarified in IBS-D. Hence, we focused on the identification and potential functions of tsRNAs in IBS-D. Intestinal biopsies were obtained from IBS-D patients and healthy volunteers, and twenty-eight differential tsRNAs were screened by high-throughput sequencing. The changes of tiRNA-His-GTG-001, tRF-Ser-GCT-113, and tRF-Gln-TTG-035 by q-PCR in expanded samples were consistent with the sequencing results. Meanwhile, target gene prediction and bioinformatics showed that the three differential tsRNAs may be involved in some key signal pathways, such as GABAergic synapse, tumor necrosis factor-α (TNF-α), etc. Their regulation on target genes were demonstrated through cell experiments and luciferase reporter assays. In addition, the receiver-operating characteristic (ROC) analysis showed that the three tsRNAs all could be used as candidate markers of IBS-D. The correlation analysis indicated they were related to the degree of abdominal pain, abdominal distension, and stool morphology. So, we believe that the abnormal tiRNA-His-GTG-001, tRF-Ser-GCT-113, and tRF-Gln-TTG-035 are related to the clinical symptoms of IBS-D, and can target regulate the important molecules of the brain-gut axis, even could be expected as potential biomarkers for the diagnosis and treatment of IBS-D.
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Affiliation(s)
- Yuna Chai
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.
| | - Yaoyao Lu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Limin Yang
- Digestive department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jianli Qiu
- Department of Pediatrics, First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450052, China
| | - Chongzhen Qin
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jingmin Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ying Zhang
- Hip Disease Research and Treatment Center, Luoyang Orthopedic Hospital, Luoyang, Henan 471002, China
| | - Xinru Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Guangzhao Qi
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Chengye Liu
- Department of Orthopedics, The Third Affiliated Hospital of Henan University of Science and Technology, Luoyang Dongfang Hospital, Luoyang, Henan 471003, China
| | - Xiaojian Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.
| | - Duolu Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.
| | - He Zhu
- Pharmaceutical Department, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China.
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57
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Wang Y, Zhang Y, Kong L, Song C, Chen X, Fang X, Zhang C. tRNA-derived RNA fragments in the exosomes of bovine milk and colostrum. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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58
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Cao Y, Liu K, Xiong Y, Zhao C, Liu L. Increased expression of fragmented tRNA promoted neuronal necrosis. Cell Death Dis 2021; 12:823. [PMID: 34462418 PMCID: PMC8405691 DOI: 10.1038/s41419-021-04108-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 06/26/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
Neuronal necrosis induced by excessive glutamate release is well known to contribute morbidity and mortality in ischemic stroke. Over the past decades, strategies on targeting glutamate receptor did not achieve desirable clinical outcomes. Finding the downstream mechanism of the glutamate receptor activation may provide new targets to suppress the cell death. Previously, our study demonstrated that the increase of H3K4 trimethylation (H3K4me3) played a key detrimental role on neuronal necrosis; however, the mechanism of this histone modification is unclear. Through a genome-wide small RNA sequencing, we identified several tRNA-derived fragments (tRFs) and piwi-interacting RNA (piRNAs) species were enriched in glutamate-induced neuronal necrosis in rat primary neuron cultures, and this enrichment was dependent on the H3K4me3 increase. Strikingly, when we transfected several synthesized tRFs and piRNA species into neurons, the tRFs but not the piRNAs induced neuron swelling and death. The cell death morphology recapitulated neuronal necrosis induced by glutamate. For the cytotoxic effect of tRFs, our data suggested that protein synthesis was inhibited likely through induction of ribosomal stalling. By proteomic analysis of tRFs effect, the most affected pathway was enriched in the mitochondrial metabolism. Consistently, mitochondrial fragmentation was increased in neuronal necrosis, and suppression of mitochondrial fission by genetic manipulation or drug rescued neuronal necrosis. Using our previously established Drosophila model of neuronal necrosis, we found that inhibition of small RNA transcription, blocking RNA transport from nucleus to cytosol, or knocking down Ago1/2 to suppress the RNA interference effect, all rescued the fly death, suggesting transcription and processing of small RNAs contribute to neuronal necrosis. Together, these results indicate that the abnormal transcription of tRFs may play a key role downstream of the H3K4me3 increase. This provides a potential new strategy to suppress neuronal necrosis.
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Affiliation(s)
- Yanyan Cao
- grid.24696.3f0000 0004 0369 153XDepartment of Biochemistry and Molecular Biology School of Basic Medicine, Capital Medical University, Youanmen, Beijing, China ,grid.453074.10000 0000 9797 0900Department of Neurology, First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Kai Liu
- grid.49470.3e0000 0001 2331 6153College of Life Sciences, Wuhan University, Wuhan, China
| | - Ying Xiong
- grid.24696.3f0000 0004 0369 153XDepartment of Biochemistry and Molecular Biology School of Basic Medicine, Capital Medical University, Youanmen, Beijing, China
| | - Chunyue Zhao
- grid.64939.310000 0000 9999 1211Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, China
| | - Lei Liu
- grid.24696.3f0000 0004 0369 153XDepartment of Biochemistry and Molecular Biology School of Basic Medicine, Capital Medical University, Youanmen, Beijing, China
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59
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Kouvela A, Zaravinos A, Stamatopoulou V. Adaptor Molecules Epitranscriptome Reprograms Bacterial Pathogenicity. Int J Mol Sci 2021; 22:8409. [PMID: 34445114 PMCID: PMC8395126 DOI: 10.3390/ijms22168409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 11/16/2022] Open
Abstract
The strong decoration of tRNAs with post-transcriptional modifications provides an unprecedented adaptability of this class of non-coding RNAs leading to the regulation of bacterial growth and pathogenicity. Accumulating data indicate that tRNA post-transcriptional modifications possess a central role in both the formation of bacterial cell wall and the modulation of transcription and translation fidelity, but also in the expression of virulence factors. Evolutionary conserved modifications in tRNA nucleosides ensure the proper folding and stability redounding to a totally functional molecule. However, environmental factors including stress conditions can cause various alterations in tRNA modifications, disturbing the pathogen homeostasis. Post-transcriptional modifications adjacent to the anticodon stem-loop, for instance, have been tightly linked to bacterial infectivity. Currently, advances in high throughput methodologies have facilitated the identification and functional investigation of such tRNA modifications offering a broader pool of putative alternative molecular targets and therapeutic avenues against bacterial infections. Herein, we focus on tRNA epitranscriptome shaping regarding modifications with a key role in bacterial infectivity including opportunistic pathogens of the human microbiome.
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Affiliation(s)
- Adamantia Kouvela
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece;
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 2404, Cyprus
- Cancer Genetics, Genomics and Systems Biology Group, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus
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60
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Yuan Y, Li J, He Z, Fan X, Mao X, Yang M, Yang D. tRNA-derived fragments as New Hallmarks of Aging and Age-related Diseases. Aging Dis 2021; 12:1304-1322. [PMID: 34341710 PMCID: PMC8279533 DOI: 10.14336/ad.2021.0115] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/15/2021] [Indexed: 01/02/2023] Open
Abstract
tRNA-derived fragments (tRFs), which are non-coding RNAs produced via tRNA cleavage with lengths of 14 to 50 nucleotides, originate from precursor tRNAs or mature tRNAs and exist in a wide range of organisms. tRFs are produced not by random fracture of tRNAs but by specific mechanisms. Considerable evidence shows that tRFs are detectable in model organisms of different ages and are associated with age-related diseases in humans, such as cancer and neurodegenerative diseases. In this literature review, the origin and classification of tRFs and the regulatory mechanisms of tRFs in aging and age-related diseases are summarized. We also describe the available tRF databases and research techniques and lay a foundation for the exploration of tRFs as biomarkers for the diagnosis and treatment of aging and age-related diseases.
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Affiliation(s)
- Ya Yuan
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Jiamei Li
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Zhi He
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiaolan Fan
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xueping Mao
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Mingyao Yang
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Deying Yang
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
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61
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Polacek N, Ivanov P. The regulatory world of tRNA fragments beyond canonical tRNA biology. RNA Biol 2021; 17:1057-1059. [PMID: 32715957 DOI: 10.1080/15476286.2020.1785196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Norbert Polacek
- Department of Chemistry and Biochemistry, University of Bern , Bern, Switzerland
| | - Pavel Ivanov
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital , Boston, MA, USA.,Department of Medicine, Harvard Medical School , Boston, MA, USA
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62
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Fagan SG, Helm M, Prehn JHM. tRNA-derived fragments: A new class of non-coding RNA with key roles in nervous system function and dysfunction. Prog Neurobiol 2021; 205:102118. [PMID: 34245849 DOI: 10.1016/j.pneurobio.2021.102118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 01/12/2023]
Abstract
tRNA-derived small RNAs (tsRNA) are a recently identified family of non-coding RNA that have been associated with a variety of cellular functions including the regulation of protein translation and gene expression. Recent sequencing and bioinformatic studies have identified the broad spectrum of tsRNA in the nervous system and demonstrated that this new class of non-coding RNA is produced from tRNA by specific cleavage events catalysed by ribonucleases such as angiogenin and dicer. Evidence is also accumulating that production of tsRNA is increased during disease processes where they regulate stress responses, proteostasis, and neuronal survival. Mutations to tRNA cleaving and modifying enzymes have been implicated in several neurodegenerative disorders, and tsRNA levels in the blood are advancing as biomarkers for neurological disease. In this review we summarize the physiological importance of tsRNA in the central nervous system and their relevance to neurological disease.
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Affiliation(s)
- Steven G Fagan
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences - IPBS, Johannes Gutenberg-University, 55128, Mainz, Germany
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland.
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63
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Reuther J, Schneider L, Iacovache I, Pircher A, Gharib WH, Zuber B, Polacek N. A small ribosome-associated ncRNA globally inhibits translation by restricting ribosome dynamics. RNA Biol 2021; 18:2617-2632. [PMID: 34121604 PMCID: PMC8632108 DOI: 10.1080/15476286.2021.1935573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ribosome-associated non-coding RNAs (rancRNAs) have been recognized as an emerging class of regulatory molecules capable of fine-tuning translation in all domains of life. RancRNAs are ideally suited for allowing a swift response to changing environments and are therefore considered pivotal during the first wave of stress adaptation. Previously, we identified an mRNA-derived 18 nucleotides long rancRNA (rancRNA_18) in Saccharomyces cerevisiae that rapidly downregulates protein synthesis during hyperosmotic stress. However, the molecular mechanism of action remained enigmatic. Here, we combine biochemical, genetic, transcriptome-wide and structural evidence, thus revealing rancRNA_18 as global translation inhibitor by targeting the E-site region of the large ribosomal subunit. Ribosomes carrying rancRNA_18 possess decreased affinity for A-site tRNA and impaired structural dynamics. Cumulatively, these discoveries reveal the mode of action of a rancRNA involved in modulating protein biosynthesis at a thus far unequalled precision.
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Affiliation(s)
- Julia Reuther
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Lukas Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Ioan Iacovache
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Andreas Pircher
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Walid H Gharib
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Benoît Zuber
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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64
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Zacharjasz J, Mleczko AM, Bąkowski P, Piontek T, Bąkowska-Żywicka K. Small Noncoding RNAs in Knee Osteoarthritis: The Role of MicroRNAs and tRNA-Derived Fragments. Int J Mol Sci 2021; 22:5711. [PMID: 34071929 PMCID: PMC8198041 DOI: 10.3390/ijms22115711] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Knee osteoarthritis (OA) is a degenerative knee joint disease that results from the breakdown of joint cartilage and underlying bone, affecting about 3.3% of the world's population. As OA is a multifactorial disease, the underlying pathological process is closely associated with genetic changes in articular cartilage and bone. Many studies have focused on the role of small noncoding RNAs in OA and identified numbers of microRNAs that play important roles in regulating bone and cartilage homeostasis. The connection between other types of small noncoding RNAs, especially tRNA-derived fragments and knee osteoarthritis is still elusive. The observation that there is limited information about small RNAs different than miRNAs in knee OA was very surprising to us, especially given the fact that tRNA fragments are known to participate in a plethora of human diseases and a portion of them are even more abundant than miRNAs. Inspired by these findings, in this review we have summarized the possible involvement of microRNAs and tRNA-derived fragments in the pathology of knee osteoarthritis.
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Affiliation(s)
- Julian Zacharjasz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland;
| | - Anna M. Mleczko
- Center for Advanced Technology, Adam Mickiewicz University in Poznań, 61-614 Poznan, Poland;
| | - Paweł Bąkowski
- Department of Orthopedic Surgery, Rehasport Clinic, 60-201 Poznan, Poland; (P.B.); (T.P.)
| | - Tomasz Piontek
- Department of Orthopedic Surgery, Rehasport Clinic, 60-201 Poznan, Poland; (P.B.); (T.P.)
- Department of Spine Disorders and Pediatric Orthopedics, University of Medical Sciences Poznan, 61-854 Poznan, Poland
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65
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Li J, Zhu L, Cheng J, Peng Y. Transfer RNA-derived small RNA: A rising star in oncology. Semin Cancer Biol 2021; 75:29-37. [PMID: 34029740 DOI: 10.1016/j.semcancer.2021.05.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 02/05/2023]
Abstract
Transfer RNAs (tRNAs) participate in protein synthesis through delivering amino acids to the ribosome. Nevertheless, recent studies revealed that tRNAs can undergo cleavage by endoribonucleases to generate a heterogeneous class of small RNAs, designated as tRNA-derived small RNAs (tsRNAs). Accumulating evidence demonstrates that tsRNAs play an important role in many biological processes, and their dysregulation is associated with the progression of diseases including cancer. Abnormally expressed tsRNAs contribute to tumor initiation and development through distinct mechanisms, such as transcriptional regulation and RNA interference. In this review, we briefly summarize the current knowledge regarding classification, biogenesis and biological function of tsRNAs. Moreover, we highlight the dysregulation and critical roles of tsRNAs in cancer and discuss their potentials as diagnostic and prognostic biomarkers or therapeutic targets.
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Affiliation(s)
- Jiao Li
- 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
| | - 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
| | - 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
| | - 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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66
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Li Z, Stanton BA. Transfer RNA-Derived Fragments, the Underappreciated Regulatory Small RNAs in Microbial Pathogenesis. Front Microbiol 2021; 12:687632. [PMID: 34079534 PMCID: PMC8166272 DOI: 10.3389/fmicb.2021.687632] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 01/20/2023] Open
Abstract
In eukaryotic organisms, transfer RNA (tRNA)-derived fragments have diverse biological functions. Considering the conserved sequences of tRNAs, it is not surprising that endogenous tRNA fragments in bacteria also play important regulatory roles. Recent studies have shown that microbes secrete extracellular vesicles (EVs) containing tRNA fragments and that the EVs deliver tRNA fragments to eukaryotic hosts where they regulate gene expression. Here, we review the literature describing microbial tRNA fragment biogenesis and how the fragments secreted in microbial EVs suppress the host immune response, thereby facilitating chronic infection. Also, we discuss knowledge gaps and research challenges for understanding the pathogenic roles of microbial tRNA fragments in regulating the host response to infection.
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Affiliation(s)
- Zhongyou Li
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
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67
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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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68
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Dwivedi SKD, Rao G, Dey A, Mukherjee P, Wren JD, Bhattacharya R. Small Non-Coding-RNA in Gynecological Malignancies. Cancers (Basel) 2021; 13:1085. [PMID: 33802524 PMCID: PMC7961667 DOI: 10.3390/cancers13051085] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
Gynecologic malignancies, which include cancers of the cervix, ovary, uterus, vulva, vagina, and fallopian tube, are among the leading causes of female mortality worldwide, with the most prevalent being endometrial, ovarian, and cervical cancer. Gynecologic malignancies are complex, heterogeneous diseases, and despite extensive research efforts, the molecular mechanisms underlying their development and pathology remain largely unclear. Currently, mechanistic and therapeutic research in cancer is largely focused on protein targets that are encoded by about 1% of the human genome. Our current understanding of 99% of the genome, which includes noncoding RNA, is limited. The discovery of tens of thousands of noncoding RNAs (ncRNAs), possessing either structural or regulatory functions, has fundamentally altered our understanding of genetics, physiology, pathophysiology, and disease treatment as they relate to gynecologic malignancies. In recent years, it has become clear that ncRNAs are relatively stable, and can serve as biomarkers for cancer diagnosis and prognosis, as well as guide therapy choices. Here we discuss the role of small non-coding RNAs, i.e., microRNAs (miRs), P-Element induced wimpy testis interacting (PIWI) RNAs (piRNAs), and tRNA-derived small RNAs in gynecological malignancies, specifically focusing on ovarian, endometrial, and cervical cancer.
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Affiliation(s)
- Shailendra Kumar Dhar Dwivedi
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Geeta Rao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
| | - Anindya Dey
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Priyabrata Mukherjee
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jonathan D. Wren
- Biochemistry and Molecular Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
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69
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Krishna S, Raghavan S, DasGupta R, Palakodeti D. tRNA-derived fragments (tRFs): establishing their turf in post-transcriptional gene regulation. Cell Mol Life Sci 2021; 78:2607-2619. [PMID: 33388834 PMCID: PMC11073306 DOI: 10.1007/s00018-020-03720-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Transfer RNA (tRNA)-derived fragments (tRFs) are an emerging class of conserved small non-coding RNAs that play important roles in post-transcriptional gene regulation. High-throughput sequencing of multiple biological samples have identified heterogeneous species of tRFs with distinct functionalities. These small RNAs have garnered a lot of scientific attention due to their ubiquitous expression and versatility in regulating various biological processes. In this review, we highlight our current understanding of tRF biogenesis and their regulatory functions. We summarize the diverse modes of biogenesis through which tRFs are generated and discuss the mechanism through which different tRF species regulate gene expression and the biological implications. Finally, we conceptualize research areas that require focus to strengthen our understanding of the biogenesis and function of tRFs.
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Affiliation(s)
- Srikar Krishna
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Srikala Raghavan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.
| | - Ramanuj DasGupta
- Precision Oncology, Genome Institute of Singapore, Singapore City, Singapore.
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70
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Raad N, Luidalepp H, Fasnacht M, Polacek N. Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs in E. coli. Int J Mol Sci 2021; 22:1703. [PMID: 33567722 PMCID: PMC7914890 DOI: 10.3390/ijms22041703] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 12/13/2022] Open
Abstract
Almost two-thirds of the microbiome's biomass has been predicted to be in a non-proliferating, and thus dormant, growth state. It is assumed that dormancy goes hand in hand with global downregulation of gene expression. However, it remains largely unknown how bacteria manage to establish this resting phenotype at the molecular level. Recently small non-protein-coding RNAs (sRNAs or ncRNAs) have been suggested to be involved in establishing the non-proliferating state in bacteria. Here, we have deep sequenced the small transcriptome of Escherichia coli in the exponential and stationary phases and analyzed the resulting reads by a novel biocomputational pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 12,000 small transcripts enriched during both growth stages. Differential expression analysis reveals distinct sRNAs enriched in the stationary phase that originate from various genomic regions, including transfer RNA (tRNA) fragments. Furthermore, expression profiling by Northern blot and RT-qPCR analyses confirms the growth phase-dependent expression of several enriched sRNAs. Our study adds to the existing repertoire of bacterial sRNAs and suggests a role for some of these small molecules in establishing and maintaining stationary phase as well as the bacterial stress response. Functional characterization of these detected sRNAs has the potential of unraveling novel regulatory networks central for stationary phase biology.
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Affiliation(s)
- Nicole Raad
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (N.R.); (H.L.); (M.F.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Hannes Luidalepp
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (N.R.); (H.L.); (M.F.)
| | - Michel Fasnacht
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (N.R.); (H.L.); (M.F.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (N.R.); (H.L.); (M.F.)
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71
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Choi EJ, Wu W, Zhang K, Lee I, Kim IH, Lee YS, Bao X. ELAC2, an Enzyme for tRNA Maturation, Plays a Role in the Cleavage of a Mature tRNA to Produce a tRNA-Derived RNA Fragment During Respiratory Syncytial Virus Infection. Front Mol Biosci 2021; 7:609732. [PMID: 33604354 PMCID: PMC7884774 DOI: 10.3389/fmolb.2020.609732] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/21/2020] [Indexed: 11/24/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection in young children. However, effective treatment against RSV is unavailable. tRNA-derived RNA fragments (tRFs) are a recently discovered family of non-coding RNAs. We made an early observation that RSV infection causes significant induction of tRFs, which are mainly derived from the 5’-end of mature tRNAs (tRF5). However, their functions and biogenesis mechanism are not fully understood. Herein, we identified an enzyme responsible for the induction of a functional tRF5 derived from tRNA-Gln-CTG (tRF5-GlnCTG). We found that tRF5-GlnCTG promotes RSV replication and its induction, assessed by Northern blot and a new qRT-PCR-based method, is regulated by ribonuclease ELAC2. ELAC2-mediated tRF5 induction has never been reported. We also found that ELAC2 is associated with RSV N and NS1 proteins. Given the fact that tRF5-GlnCTG plays a role in RSV replication, the identification of ELAC2 being responsible for tRF5-GlnCTG induction could provide new insights into therapeutic strategy development against RSV infection.
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Affiliation(s)
- Eun-Jin Choi
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Wenzhe Wu
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Ke Zhang
- Department of Chemistry, The University of Houston Clear Lake, Clear Lake, TX, United States
| | - Inhan Lee
- miRcore, Ann Arbor, MI, United States
| | - In-Hoo Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Xiaoyong Bao
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States.,Sealy Center for Molecular Medicine, The University of Texas Medical Branch, Galveston, TX, United States.,The Institute of Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States.,The Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, United States
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Pinel-Marie ML, Brielle R, Riffaud C, Germain-Amiot N, Polacek N, Felden B. RNA antitoxin SprF1 binds ribosomes to attenuate translation and promote persister cell formation in Staphylococcus aureus. Nat Microbiol 2021; 6:209-220. [PMID: 33398097 DOI: 10.1038/s41564-020-00819-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/20/2020] [Indexed: 01/28/2023]
Abstract
Persister cells are a subpopulation of transiently antibiotic-tolerant bacteria associated with chronic infection and antibiotic treatment failure. Toxin-antitoxin systems have been linked to persister cell formation but the molecular mechanisms leading to bacterial persistence are mostly unknown. Here, we show that SprF1, a type I antitoxin, associates with translating ribosomes from the major human pathogen Staphylococcus aureus to reduce the pathogen's overall protein synthesis during growth. Under hyperosmotic stress, SprF1 levels increase due to enhanced stability, accumulate on polysomes and attenuate protein synthesis. Using an internal 6-nucleotide sequence on its 5'-end, SprF1 binds ribosomes and interferes with initiator transfer RNA binding, thus reducing translation initiation. An excess of messenger RNA displaces the ribosome-bound antitoxin, freeing the ribosomes for new translation cycles; however, this RNA antitoxin can also displace ribosome-bound mRNA. This translation attenuation mechanism, mediated by an RNA antitoxin, promotes antibiotic persister cell formation. The untranslated SprF1 is a dual-function RNA antitoxin that represses toxin expression by its 3'-end and fine-tunes overall bacterial translation via its 5'-end. These findings demonstrate a general function for a bacterial RNA antitoxin beyond protection from toxicity. They also highlight an RNA-guided molecular process that influences antibiotic persister cell formation.
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Affiliation(s)
- Marie-Laure Pinel-Marie
- Institut National de la Santé et de la Recherche Médicale, Bacterial Regulatory RNAs and Medicine UMR_S 1230, Rennes, France.
| | - Régine Brielle
- Institut National de la Santé et de la Recherche Médicale, Bacterial Regulatory RNAs and Medicine UMR_S 1230, Rennes, France
| | - Camille Riffaud
- Institut National de la Santé et de la Recherche Médicale, Bacterial Regulatory RNAs and Medicine UMR_S 1230, Rennes, France
| | - Noëlla Germain-Amiot
- Institut National de la Santé et de la Recherche Médicale, Bacterial Regulatory RNAs and Medicine UMR_S 1230, Rennes, France
| | - Norbert Polacek
- Department of Chemistry and Biochemistry, Bern University, Bern, Switzerland
| | - Brice Felden
- Institut National de la Santé et de la Recherche Médicale, Bacterial Regulatory RNAs and Medicine UMR_S 1230, Rennes, France.
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Wang ZS, Zhou HC, Wei CY, Wang ZH, Hao X, Zhang LH, Li JZ, Wang ZL, Wang H. Global survey of miRNAs and tRNA-derived small RNAs from the human parasitic protist Trichomonas vaginalis. Parasit Vectors 2021; 14:87. [PMID: 33514387 PMCID: PMC7844918 DOI: 10.1186/s13071-020-04570-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/28/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Small non-coding RNAs play critical regulatory roles in post-transcription. However, their characteristics in Trichomonas vaginalis, the causative agent of human sexually transmitted trichomoniasis, still remain to be determined. METHODS Small RNA transcriptomes from Trichomonas trophozoites were deep sequenced using the Illumina NextSeq 500 system and comprehensively analyzed to identify Trichomonas microRNAs (miRNAs) and transfer RNA (tRNA)-derived small RNAs (tsRNAs). The tsRNA candidates were confirmed by stem-loop quantitative reverse transcription-PCR, and motifs to guide the cleavage of tsRNAs were predicted using the GLAM2 algorithm. RESULTS The miRNAs were found to be present in T. vaginalis but at an extremely low abundance (0.0046%). Three categories of endogenous Trichomonas tsRNAs were identified, namely 5'tritsRNAs, mid-tritsRNAs and 3'tritsRNAs, with the 5'tritsRNAs constituting the dominant category (67.63%) of tsRNAs. Interestingly, the cleavage site analysis verified both conventional classes of tRNA-derived fragments (tRFs) and tRNA-halves in tritsRNAs, indicating the expression of tRNA-halves in the non-stress condition. A total of 25 tritsRNAs were experimentally confirmed, accounting for 78.1% of all tested candidates. Three motifs were predicted to guide the production of tritsRNAs. The results prove the expression of tRFs and tRNA-halves in the T. vaginalis transcriptome. CONCLUSIONS This is the first report of genome-wide investigation of small RNAs, particularly tsRNAs and miRNAs, from Trichomonas parasites. Our findings demonstrate the expression profile of tsRNAs in T. vaginalis, while miRNA was barely detected. These results may promote further research aimed at gaining a better understanding of the evolution of small non-coding RNA in T. vaginalis and their functions in the pathogenesis of trichomoniasis.
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Affiliation(s)
- Zhen-Sheng Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China.,NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Hong-Chang Zhou
- School of Medicine, Huzhou University and Huzhou Central Hospital, Huzhou, 313000, Zhejiang province, China
| | - Chun-Yan Wei
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Zhi-Hua Wang
- Department of Immunology, Guilin Medical University, Guilin, 541000, Guangxi province, China
| | - Xiao Hao
- Blood Chamber, Blood Station of Jinan, Jinan, 250000, Shandong province, China
| | - Lian-Hui Zhang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Jing-Zhong Li
- NHC Key Laboratory of Echinococcosis Prevention and Control, #21 linkuo North Road, Chengguan District, Lhasa, 850000, Tibet Autonomous Region, People's Republic of China
| | - Zeng-Lei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
| | - Heng Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China.
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Zong T, Yang Y, Zhao H, Li L, Liu M, Fu X, Tang G, Zhou H, Aung LHH, Li P, Wang J, Wang Z, Yu T. tsRNAs: Novel small molecules from cell function and regulatory mechanism to therapeutic targets. Cell Prolif 2021; 54:e12977. [PMID: 33507586 PMCID: PMC7941233 DOI: 10.1111/cpr.12977] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022] Open
Abstract
tsRNAs are small fragments of RNAs with specific lengths that are generated by particular ribonucleases, such as dicer and angiogenin (ANG), clipping on the rings of transfer RNAs (tRNAs) in specific cells and tissues under specific conditions. Depending on where the splicing site is, tsRNAs can be segmented into two main types, tRNA‐derived stress‐induced RNAs (tiRNAs) and tRNA‐derived fragments (tRFs). Many studies have shown that tsRNAs are functional molecules, not the random degradative products of tRNAs. Notably, due to their regulatory mechanism in regulating mRNA stability, transcription, ribosomal RNA (rRNA) synthesis and RNA reverse transcription, tsRNAs are significantly involved in the cell function, such as cell proliferation, migration, cycle and apoptosis, as well as the occurrence and development of a variety of diseases. In addition, tsRNAs may represent a new generation of clinical biomarkers or therapeutic targets because of their stable structures, high conservation and widely distribution, particularly in the peripheral tissues, bodily fluids and exosomes. In this review, we describe the generation, function and mechanism of tsRNAs and illustrate the current research progress of tsRNAs in various diseases, highlight their potentials as biomarkers and therapeutic targets in clinical application. Although our understanding of tsRNAs is still in infancy, the application prospects shown in this field deserve further exploration.
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Affiliation(s)
- Tingyu Zong
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yanyan Yang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Hui Zhao
- Department of Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lin Li
- Department of Vascular surgery, Qingdao Hiser Medical Center, Qingdao, China
| | - Meixin Liu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiuxiu Fu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guozhang Tang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hong Zhou
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lynn Htet Htet Aung
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jianxun Wang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Zhibin Wang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Tao Yu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China.,Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
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75
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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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76
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Cao Z, Rosenkranz D, Wu S, Liu H, Pang Q, Zhang X, Liu B, Zhao B. Different classes of small RNAs are essential for head regeneration in the planarian Dugesia japonica. BMC Genomics 2020; 21:876. [PMID: 33287698 PMCID: PMC7722302 DOI: 10.1186/s12864-020-07234-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Planarians reliably regenerate all body parts after injury, including a fully functional head and central nervous system. But until now, the expression dynamics and functional role of miRNAs and other small RNAs during the process of head regeneration are not well understood. Furthermore, little is known about the evolutionary conservation of the relevant small RNAs pathways, rendering it difficult to assess whether insights from planarians will apply to other taxa. RESULTS In this study, we applied high throughput sequencing to identify miRNAs, tRNA fragments and piRNAs that are dynamically expressed during head regeneration in Dugesia japonica. We further show that knockdown of selected small RNAs, including three novel Dugesia-specific miRNAs, during head regeneration induces severe defects including abnormally small-sized eyes, cyclopia and complete absence of eyes. CONCLUSIONS Our findings suggest that a complex pool of small RNAs takes part in the process of head regeneration in Dugesia japonica and provide novel insights into global small RNA expression profiles and expression changes in response to head amputation. Our study reveals the evolutionary conserved role of miR-124 and brings further promising candidate small RNAs into play that might unveil new avenues for inducing restorative programs in non-regenerative organisms via small RNA mimics based therapies.
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Affiliation(s)
- Zhonghong Cao
- grid.412509.b0000 0004 1808 3414School of Life Sciences, Shandong University of Technology, 266 Xincun Western Road, Zibo, 255049 People’s Republic of China
| | - David Rosenkranz
- grid.5802.f0000 0001 1941 7111Institute of Organismic and Molecular Evolution (iOME), Anthropology, Anselm-Franz-von-Bentzel-Weg 7, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Suge Wu
- grid.412509.b0000 0004 1808 3414School of Life Sciences, Shandong University of Technology, 266 Xincun Western Road, Zibo, 255049 People’s Republic of China
| | - Hongjin Liu
- grid.412509.b0000 0004 1808 3414School of Life Sciences, Shandong University of Technology, 266 Xincun Western Road, Zibo, 255049 People’s Republic of China
| | - Qiuxiang Pang
- grid.412509.b0000 0004 1808 3414School of Life Sciences, Shandong University of Technology, 266 Xincun Western Road, Zibo, 255049 People’s Republic of China
| | - Xiufang Zhang
- grid.412509.b0000 0004 1808 3414School of Life Sciences, Shandong University of Technology, 266 Xincun Western Road, Zibo, 255049 People’s Republic of China
| | - Baohua Liu
- grid.412509.b0000 0004 1808 3414School of Life Sciences, Shandong University of Technology, 266 Xincun Western Road, Zibo, 255049 People’s Republic of China
| | - Bosheng Zhao
- grid.412509.b0000 0004 1808 3414School of Life Sciences, Shandong University of Technology, 266 Xincun Western Road, Zibo, 255049 People’s Republic of China
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tRNA-Derived Fragments (tRFs) in Bladder Cancer: Increased 5'-tRF-LysCTT Results in Disease Early Progression and Patients' Poor Treatment Outcome. Cancers (Basel) 2020; 12:cancers12123661. [PMID: 33291319 PMCID: PMC7762106 DOI: 10.3390/cancers12123661] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/24/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Bladder cancer (BlCa) management relies on lifelong surveillance strategies with invasive interventions that adversely affect patients’ quality-of-life and lead to a high economic burden for healthcare systems. Exploitation of bladder tumors’ molecular background could lead to modern precision medicine. tRNA-derived fragments (tRFs), rather than degradation debris, are novel functional small ncRNAs that have emerged as key regulators of cellular homeostasis. This is the first study of the clinical utility of tRFs in BlCa. Using in silico analysis of the TCGA-BLCA project, we identified 5′-tRF-LysCTT (5′-tRF of tRNALysCTT) to be significantly deregulated in BlCa, and we have studied its clinical value in our cohort of 230 BlCa patients. Elevated 5′-tRF-LysCTT levels were significantly associated with aggressive tumor phenotype as well as early disease progression and poor treatment outcome. Integration of 5′-tRF-LysCTT with established disease markers resulted in superior prediction of patients’ prognosis, supporting personalized treatment and monitoring decisions. Abstract The heterogeneity of bladder cancer (BlCa) prognosis and treatment outcome requires the elucidation of tumors’ molecular background towards personalized patients’ management. tRNA-derived fragments (tRFs), although originally considered as degradation debris, represent a novel class of powerful regulatory non-coding RNAs. In silico analysis of the TCGA-BLCA project highlighted 5′-tRF-LysCTT to be significantly deregulated in bladder tumors, and 5′-tRF-LysCTT levels were further quantified in our screening cohort of 230 BlCa patients. Recurrence and progression for non-muscle invasive (NMIBC) patients, as well as progression and patient’s death for muscle-invasive (MIBC) patients, were used as clinical endpoint events. TCGA-BLCA were used as validation cohort. Bootstrap analysis was performed for internal validation and the clinical net benefit of 5′-tRF-LysCTT on disease prognosis was assessed by decision curve analysis. Elevated 5′-tRF-LysCTT was associated with unfavorable disease features, and significant higher risk for early progression (multivariate Cox: HR = 2.368; p = 0.033) and poor survival (multivariate Cox: HR = 2.151; p = 0.032) of NMIBC and MIBC patients, respectively. Multivariate models integrating 5′-tRF-LysCTT with disease established markers resulted in superior risk-stratification specificity and positive prediction of patients’ progression. In conclusion, increased 5′-tRF-LysCTT levels were strongly associated with adverse disease outcome and improved BlCa patients’ prognostication.
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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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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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80
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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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Wnuk M, Slipek P, Dziedzic M, Lewinska A. The Roles of Host 5-Methylcytosine RNA Methyltransferases during Viral Infections. Int J Mol Sci 2020; 21:E8176. [PMID: 33142933 PMCID: PMC7663479 DOI: 10.3390/ijms21218176] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic 5-methylcytosine RNA methyltransferases catalyze the transfer of a methyl group to the fifth carbon of a cytosine base in RNA sequences to produce 5-methylcytosine (m5C). m5C RNA methyltransferases play a crucial role in the maintenance of functionality and stability of RNA. Viruses have developed a number of strategies to suppress host innate immunity and ensure efficient transcription and translation for the replication of new virions. One such viral strategy is to use host m5C RNA methyltransferases to modify viral RNA and thus to affect antiviral host responses. Here, we summarize the latest findings concerning the roles of m5C RNA methyltransferases, namely, NOL1/NOP2/SUN domain (NSUN) proteins and DNA methyltransferase 2/tRNA methyltransferase 1 (DNMT2/TRDMT1) during viral infections. Moreover, the use of m5C RNA methyltransferase inhibitors as an antiviral therapy is discussed.
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Affiliation(s)
- Maciej Wnuk
- Department of Biotechnology, Institute of Biology and Biotechnology, University of Rzeszow, 35-310 Rzeszow, Poland; (P.S.); (M.D.)
| | | | | | - Anna Lewinska
- Department of Biotechnology, Institute of Biology and Biotechnology, University of Rzeszow, 35-310 Rzeszow, Poland; (P.S.); (M.D.)
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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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83
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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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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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Abstract
We report a systematic unbiased analysis of small RNA molecule expression in 11 different tissues of the model organism mouse. We discovered uncharacterized noncoding RNA molecules and identified that ∼30% of total noncoding small RNA transcriptome are distributed across the body in a tissue-specific manner with some also being sexually dimorphic. Distinct distribution patterns of small RNA across the body suggest the existence of tissue-specific mechanisms involved in noncoding RNA processing. Small noncoding RNAs (ncRNAs) play a vital role in a broad range of biological processes both in health and disease. A comprehensive quantitative reference of small ncRNA expression would significantly advance our understanding of ncRNA roles in shaping tissue functions. Here, we systematically profiled the levels of five ncRNA classes (microRNA [miRNA], small nucleolar RNA [snoRNA], small nuclear RNA [snRNA], small Cajal body-specific RNA [scaRNA], and transfer RNA [tRNA] fragments) across 11 mouse tissues by deep sequencing. Using 14 biological replicates spanning both sexes, we identified that ∼30% of small ncRNAs are distributed across the body in a tissue-specific manner with some also being sexually dimorphic. We found that some miRNAs are subject to “arm switching” between healthy tissues and that tRNA fragments are retained within tissues in both a gene- and a tissue-specific manner. Out of 11 profiled tissues, we confirmed that brain contains the largest number of unique small ncRNA transcripts, some of which were previously annotated while others are identified in this study. Furthermore, by combining these findings with single-cell chromatin accessibility (scATAC-seq) data, we were able to connect identified brain-specific ncRNAs with their cell types of origin. These results yield the most comprehensive characterization of specific and ubiquitous small RNAs in individual murine tissues to date, and we expect that these data will be a resource for the further identification of ncRNAs involved in tissue function in health and dysfunction in disease.
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86
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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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87
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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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88
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Tosar JP, Cayota A. Extracellular tRNAs and tRNA-derived fragments. RNA Biol 2020; 17:1149-1167. [PMID: 32070197 PMCID: PMC7549618 DOI: 10.1080/15476286.2020.1729584] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 01/08/2023] Open
Abstract
Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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89
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Xie Y, Yao L, Yu X, Ruan Y, Li Z, Guo J. Action mechanisms and research methods of tRNA-derived small RNAs. Signal Transduct Target Ther 2020; 5:109. [PMID: 32606362 PMCID: PMC7326991 DOI: 10.1038/s41392-020-00217-4] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/07/2020] [Accepted: 06/13/2020] [Indexed: 02/07/2023] Open
Abstract
tRNA-derived small RNAs (tsRNAs), including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), are small regulatory RNAs processed from mature tRNAs or precursor tRNAs. tRFs and tiRNAs play biological roles through a variety of mechanisms by interacting with proteins or mRNA, inhibiting translation, and regulating gene expression, the cell cycle, and chromatin and epigenetic modifications. The establishment and application of research technologies are important in understanding the biological roles of tRFs and tiRNAs. To study the molecular mechanisms of tRFs and tiRNAs, researchers have used a variety of bioinformatics and molecular biology methods, such as microarray analysis, real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR); Northern blotting; RNA sequencing (RNA-seq); cross-linking, ligation and sequencing of hybrids (CLASH); and photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP). This paper summarizes the classification, action mechanisms, and roles of tRFs and tiRNAs in human diseases and the related signal transduction pathways, targeted therapies, databases, and research methods associated with them.
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Affiliation(s)
- Yaoyao Xie
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Lipeng Yao
- Ningbo College of Health Sciences, Ningbo, 315000, Zhejiang, China
| | - Xiuchong Yu
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Yao Ruan
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Zhe Li
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China.
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90
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Zeng T, Hua Y, Sun C, Zhang Y, Yang F, Yang M, Yang Y, Li J, Huang X, Wu H, Fu Z, Li W, Yin Y. Relationship between tRNA-derived fragments and human cancers. Int J Cancer 2020; 147:3007-3018. [PMID: 32427348 DOI: 10.1002/ijc.33107] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
tRNA-derived fragments, a class of small noncoding RNAs (sncRNAs), have been identified in numerous studies in recent years. tRNA-derived fragments are classified into two main groups, including tRNA halves (tiRNAs) and tRNA-derived small RNA fragments (tRFs), according to different cleavage positions of the precursor or mature tRNAs. Instead of random tRNA degradation debris, a growing body of evidence has shown that tRNA-derived fragments are precise products of specific tRNA modifications and play important roles in biological activities, such as regulating protein translation, affecting gene expression, and altering immune signaling. Recently, the relations between tRNA-derived fragments and the occurrence of human diseases, especially cancers, have generated wide interest. It has been demonstrated that tRNA-derived fragments are involved in cancer cell proliferation, metastasis, progression and survival. In this review, we will describe the biogenesis of tRNA-derived fragments, the distinct expression and function of tRNA-derived fragments in the development of cancers, and their emerging roles as diagnostic and prognostic biomarkers and precise targets of future treatments.
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Affiliation(s)
- Tianyu Zeng
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yijia Hua
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chunxiao Sun
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuchen Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fan Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mengzhu Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yiqi Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Wu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ziyi Fu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Nanjing Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated of Nanjing Medical University, Nanjing, China
| | - Wei Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yongmei Yin
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
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91
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Jehn J, Treml J, Wulsch S, Ottum B, Erb V, Hewel C, Kooijmans RN, Wester L, Fast I, Rosenkranz D. 5' tRNA halves are highly expressed in the primate hippocampus and might sequence-specifically regulate gene expression. RNA (NEW YORK, N.Y.) 2020; 26:694-707. [PMID: 32144192 PMCID: PMC7266158 DOI: 10.1261/rna.073395.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
Fragments of mature tRNAs have long been considered as mere degradation products without physiological function. However, recent reports show that tRNA-derived small RNAs (tsRNAs) play prominent roles in diverse cellular processes across a wide spectrum of species. Contrasting the situation in other small RNA pathways the mechanisms behind these effects appear more diverse, more complex, and are generally less well understood. In addition, surprisingly little is known about the expression profiles of tsRNAs across different tissues and species. Here, we provide an initial overview of tsRNA expression in different species and tissues, revealing very high levels of 5' tRNA halves (5' tRHs) particularly in the primate hippocampus. We further modulated the regulation capacity of selected 5' tRHs in human cells by transfecting synthetic tsRNA mimics ("overexpression") or antisense-RNAs ("inhibition") and identified differentially expressed transcripts based on RNA-seq. We then used a novel k-mer mapping approach to dissect the underlying targeting rules, suggesting that 5' tRHs silence genes in a sequence-specific manner, while the most efficient target sites align to the mid-region of the 5' tRH and are located within the CDS or 3' UTR of the target. This amends previous observations that tsRNAs guide Argonaute proteins to silence their targets via a miRNA-like 5' seed match and suggests a yet unknown mechanism of regulation. Finally, our data suggest that some 5' tRHs that are also able to sequence-specifically stabilize mRNAs as up-regulated mRNAs are also significantly enriched for 5' tRH target sites.
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Affiliation(s)
- Julia Jehn
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Jana Treml
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Svenja Wulsch
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Benjamin Ottum
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Verena Erb
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Charlotte Hewel
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Roxana N Kooijmans
- Primate Brain Bank, Netherlands Institute for Neuroscience, 1105 BA Amsterdam, The Netherlands
| | - Laura Wester
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Isabel Fast
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
- Senckenberg Centre for Human Genetics, 60314 Frankfurt am Main, Germany
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92
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Kuncha SK, Venkadasamy VL, Amudhan G, Dahate P, Kola SR, Pottabathini S, Kruparani SP, Shekar PC, Sankaranarayanan R. Genomic innovation of ATD alleviates mistranslation associated with multicellularity in Animalia. eLife 2020; 9:58118. [PMID: 32463355 PMCID: PMC7302879 DOI: 10.7554/elife.58118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
The emergence of multicellularity in Animalia is associated with increase in ROS and expansion of tRNA-isodecoders. tRNA expansion leads to misselection resulting in a critical error of L-Ala mischarged onto tRNAThr, which is proofread by Animalia-specific-tRNA Deacylase (ATD) in vitro. Here we show that in addition to ATD, threonyl-tRNA synthetase (ThrRS) can clear the error in cellular scenario. This two-tier functional redundancy for translation quality control breaks down during oxidative stress, wherein ThrRS is rendered inactive. Therefore, ATD knockout cells display pronounced sensitivity through increased mistranslation of threonine codons leading to cell death. Strikingly, we identify the emergence of ATD along with the error inducing tRNA species starting from Choanoflagellates thus uncovering an important genomic innovation required for multicellularity that occurred in unicellular ancestors of animals. The study further provides a plausible regulatory mechanism wherein the cellular fate of tRNAs can be switched from protein biosynthesis to non-canonical functions. The first animals evolved around 750 million years ago from single-celled ancestors that were most similar to modern-day organisms called the Choanoflagellates. As animals evolved they developed more complex body plans consisting of multiple cells organized into larger structures known as tissues and organs. Over time cells also evolved increased levels of molecules called reactive oxygen species, which are involved in many essential cell processes but are toxic at high levels. Animal cells also contain more types of molecules known as transfer ribonucleic acids, or tRNAs for short, than Choanoflagellate cells and other single-celled organisms. These molecules deliver building blocks known as amino acids to the machinery that produces new proteins. To ensure the proteins are made correctly, it is important that tRNAs deliver specific amino acids to the protein-building machinery in the right order. Each type of tRNA usually only pairs with a specific type of amino acid, but sometimes the enzymes involved in this process can make mistakes. Therefore, cells contain proofreading enzymes that help remove incorrect amino acids on tRNAs. One such enzyme – called ATD – is only found in animals. Experiments in test tubes reported that ATD removes an amino acid called alanine from tRNAs that are supposed to carry threonine, but its precise role in living cells remained unclear. To address this question, Kuncha et al. studied proofreading enzymes in human kidney cells. The experiments showed that, in addition to ATD, a second enzyme known as ThrRS was also able to correct alanine substitutions for threonines on tRNAs. However, reactive oxygen species inactivated the proofreading ability of ThrRS, suggesting ATD plays an essential role in correcting errors in cells containing high levels of reactive oxygen species. These findings suggest that as organisms evolved multiple cells and the levels of tRNA and oxidative stress increased, this led to the appearance of a new proofreading enzyme. Further studies found that ATD originated around 900 million years ago, before Choanoflagellates and animals diverged, indicating these enzymes might have helped to shape the evolution of animals. The next step following on from this work will be to understand the role of ATD in the cells of organs that are known to have particularly high levels of reactive oxygen species, such as testis and ovaries.
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Affiliation(s)
- Santosh Kumar Kuncha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | | | - Priyanka Dahate
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sankara Rao Kola
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - P Chandra Shekar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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93
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The potential role of tRNAs and small RNAs derived from tRNAs in the occurrence and development of systemic lupus erythematosus. Biochem Biophys Res Commun 2020; 527:561-567. [PMID: 32423797 DOI: 10.1016/j.bbrc.2020.04.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Emerging evidence has shown the involvement of dysregulated transfer RNAs (tRNAs) and small RNAs derived from transfer RNAs (tsRNAs) in the pathophysiology of human diseases. The role of tRNAs and tsRNAs in systemic lupus erythematosus (SLE) remains unclear. Therefore, this study aims to investigate the possible regulatory roles of tRNAs and tsRNAs in the pathological mechanism of SLE. METHODS Total RNA was extracted from peripheral blood mononuclear cells (PBMCs) of 20 SLE patients and 20 normal controls (NCs) to obtain tRNAs and tsRNAs, followed by tRNA and tsRNA expression profiling by the NextSeq system. Target genes were predicted by informatics analysis. Subsequently, to explore the function of messenger RNA (mRNA) in these target genes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the Cytoscape plug-in BinGo, the DAVID database, and Cytoscape software. RESULTS A total of 101 tRNAs and 355 tsRNAs were found to be differentially expressed in SLE patients versus NCs by RNA microarray. GO analysis revealed that the altered target genes of the selected tRNAs and tsRNAs were most enriched similarly in immune response and the immune system process. Moreover, KEGG pathway analysis demonstrated that altered target genes of tRNAs were most enriched in systemic lupus erythematosus, while the altered target genes of tsRNAs were most enriched in the T cell receptor signalling pathway, Th1 and Th2 cell differentiation and primary immunodeficiency. These pathways may be related to the initiation of SLE. CONCLUSION Our results provide a novel perspective for studying the tRNA-related and tsRNA-related pathogenesis of SLE.
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94
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Gonskikh Y, Gerstl M, Kos M, Borth N, Schosserer M, Grillari J, Polacek N. Modulation of mammalian translation by a ribosome-associated tRNA half. RNA Biol 2020; 17:1125-1136. [PMID: 32223506 PMCID: PMC7549673 DOI: 10.1080/15476286.2020.1744296] [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] [Indexed: 01/03/2023] Open
Abstract
Originally considered futile degradation products, tRNA-derived RNA fragments (tdRs) have been shown over the recent past to be crucial players in orchestrating various cellular functions. Unlike other small non-coding RNA (ncRNA) classes, tdRs possess a multifaceted functional repertoire ranging from regulating transcription, apoptosis, RNA interference, ribosome biogenesis to controlling translation efficiency. A subset of the latter tdRs has been shown to directly target the ribosome, the central molecular machine of protein biosynthesis. Here we describe the function of the mammalian tRNAPro 5ʹ half, a 35 residue long ncRNA associated with ribosomes and polysomes in several mammalian cell lines. Addition of tRNAPro halves to mammalian in vitro translation systems results in global translation inhibition and concomitantly causes the upregulation of a specific low molecular weight translational product. This tRNAPro 5ʹ half-dependent translation product consists of both RNA and amino acids. Transfection of the tRNAPro half into HeLa cells leads to the formation of the same product in vivo. The migration of this product in acidic gels, the insensitivity to copper sulphate treatment, the resistance to 3ʹ polyadenylation, and the association with 80S monosomes indicate that the accumulated product is peptidyl-tRNA. Our data thus suggest that binding of the tRNAPro 5ʹ half to the ribosome leads to ribosome stalling and to the formation of peptidyl-tRNA. Our findings revealed a so far unknown functional role of a tdR thus further enlarging the functional heterogeneity of this emerging class of ribo-regulators.
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Affiliation(s)
- Yulia Gonskikh
- Department of Chemistry and Biochemistry, University of Bern , Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern , Bern, Switzerland
| | - Matthias Gerstl
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences , Vienna, Austria
| | - Martin Kos
- Biochemistry Center, University of Heidelberg , Heidelberg, Germany
| | - Nicole Borth
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences , Vienna, Austria
| | - Markus Schosserer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences , Vienna, Austria
| | - Johannes Grillari
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences , Vienna, Austria.,Christian Doppler Laboratory on Biotechnology of Skin Aging , Vienna, Austria.,Ludwig Boltzmann Institute for Experimental and Clinical Traumatology , Vienna, Austria
| | - Norbert Polacek
- Department of Chemistry and Biochemistry, University of Bern , Bern, Switzerland
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95
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Circulating Small Noncoding RNAs Have Specific Expression Patterns in Plasma and Extracellular Vesicles in Myelodysplastic Syndromes and Are Predictive of Patient Outcome. Cells 2020; 9:cells9040794. [PMID: 32224889 PMCID: PMC7226126 DOI: 10.3390/cells9040794] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are hematopoietic stem cell disorders with large heterogeneity at the clinical and molecular levels. As diagnostic procedures shift from bone marrow biopsies towards less invasive techniques, circulating small noncoding RNAs (sncRNAs) have become of particular interest as potential novel noninvasive biomarkers of the disease. We aimed to characterize the expression profiles of circulating sncRNAs of MDS patients and to search for specific RNAs applicable as potential biomarkers. We performed small RNA-seq in paired samples of total plasma and plasma-derived extracellular vesicles (EVs) obtained from 42 patients and 17 healthy controls and analyzed the data with respect to the stage of the disease, patient survival, response to azacitidine, mutational status, and RNA editing. Significantly higher amounts of RNA material and a striking imbalance in RNA content between plasma and EVs (more than 400 significantly deregulated sncRNAs) were found in MDS patients compared to healthy controls. Moreover, the RNA content of EV cargo was more homogeneous than that of total plasma, and different RNAs were deregulated in these two types of material. Differential expression analyses identified that many hematopoiesis-related miRNAs (e.g., miR-34a, miR-125a, and miR-150) were significantly increased in MDS and that miRNAs clustered on 14q32 were specifically increased in early MDS. Only low numbers of circulating sncRNAs were significantly associated with somatic mutations in the SF3B1 or DNMT3A genes. Survival analysis defined a signature of four sncRNAs (miR-1237-3p, U33, hsa_piR_019420, and miR-548av-5p measured in EVs) as the most significantly associated with overall survival (HR = 5.866, p < 0.001). In total plasma, we identified five circulating miRNAs (miR-423-5p, miR-126-3p, miR-151a-3p, miR-125a-5p, and miR-199a-3p) whose combined expression levels could predict the response to azacitidine treatment. In conclusion, our data demonstrate that circulating sncRNAs show specific patterns in MDS and that their expression changes during disease progression, providing a rationale for the potential clinical usefulness of circulating sncRNAs in MDS prognosis. However, monitoring sncRNA levels in total plasma or in the EV fraction does not reflect one another, instead, they seem to represent distinctive snapshots of the disease and the data should be interpreted circumspectly with respect to the type of material analyzed.
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96
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Zhu P, Yu J, Zhou P. Role of tRNA-derived fragments in cancer: novel diagnostic and therapeutic targets tRFs in cancer. Am J Cancer Res 2020; 10:393-402. [PMID: 32195016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/02/2020] [Indexed: 09/28/2022] Open
Abstract
Recent studies have revealed that tRNAs are not always the terminal molecules and small RNA fragments can be mapped to precursor tRNA sequences or mature tRNA sequences. tRNA-derived fragments (tRFs) are a novel class of small RNAs in miRNA-size found in a diverse range of organisms and can be the source of small regulatory RNAs, a previously unanticipated concept. tRFs have a diverse range of effects on cells involving in cell differentiation and homeostasis. They play a critical role in pathological processes, particularly in cancer, and therefore can modulate complicated regulatory networks. Recent studies on the role of tRFs in tumorigenesis suggest that they are promising targets for diagnosis and therapeutics. Improvement in experimental and computational approaches permit a greater understanding of the regulatory networks and will have a significant impact on both basic and clinical research.
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Affiliation(s)
- Ping Zhu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai 200032, China
| | - Jerry Yu
- Department of Medicine, University of Louisville Louisville 40292, Kentucky, USA
| | - Ping Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai 200032, China
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97
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Rosace D, López J, Blanco S. Emerging roles of novel small non-coding regulatory RNAs in immunity and cancer. RNA Biol 2020; 17:1196-1213. [PMID: 32186461 DOI: 10.1080/15476286.2020.1737442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The term small non-coding RNAs (ncRNAs) refers to all those RNAs that even without encoding for a protein, can play important functional roles. Transfer RNA and ribosomal RNA-derived fragments (tRFs and rRFs, respectively) are an emerging class of ncRNAs originally considered as simple degradation products, which though play important roles in stress responses, signalling, or gene expression. They control all levels of gene expression regulating transcription and translation and affecting RNA processing and maturation. They have been linked to pivotal cellular processes such as self-renewal, differentiation, and proliferation. For this reason, mis-regulation of this novel class of ncRNAs can lead to various pathological processes such as neurodegenerative and development diseases, metabolism and immune system disorders, and cancer. In this review, we summarise the classification, biogenesis, and functions of tRFs and rRFs with a special focus on their role in immunity and cancer.
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Affiliation(s)
- Domenico Rosace
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| | - Judith López
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| | - Sandra Blanco
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
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98
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Guzzi N, Bellodi C. Novel insights into the emerging roles of tRNA-derived fragments in mammalian development. RNA Biol 2020; 17:1214-1222. [PMID: 32116113 PMCID: PMC7549657 DOI: 10.1080/15476286.2020.1732694] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
tRNA-derived fragments or tRFs were long considered merely degradation intermediates of full-length tRNAs; however, emerging research is highlighting unanticipated new and highly distinct functions in epigenetic control, metabolism, immune activity and stem cell fate commitment. Importantly, recent studies suggest that RNA epitranscriptomic modifications may provide an additional regulatory layer that dynamically directs tRF activity in stem and cancer cells. In this review, we explore current work illustrating unanticipated roles of tRFs in mammalian stem cells with a focus on the impact of post-transcriptional RNA modifications for the biogenesis and function of this growing class of small noncoding RNAs.
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Affiliation(s)
- Nicola Guzzi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University , Lund, Sweden
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University , Lund, Sweden
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99
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Lalande S, Merret R, Salinas-Giegé T, Drouard L. Arabidopsis tRNA-derived fragments as potential modulators of translation. RNA Biol 2020; 17:1137-1148. [PMID: 31994438 DOI: 10.1080/15476286.2020.1722514] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transfer RNA-derived fragments (tRFs) exist in all branches of life. They are involved in RNA degradation, regulation of gene expression, ribosome biogenesis. In archaebacteria, kinetoplastid, yeast, and human cells, they were also shown to regulate translation. In Arabidopsis, the tRFs population fluctuates under developmental or environmental conditions but their functions are yet poorly understood. Here, we show that populations of long (30-35 nt) or short (19-25 nt) tRFs produced from Arabidopsis tRNAs can inhibit in vitro translation of a reporter gene. Analysing a series of oligoribonucleotides mimicking natural tRFs, we demonstrate that only a limited set of tRFs possess the ability to affect protein synthesis. Out of a dozen of tRFs, only two deriving from tRNAAla(AGC) and tRNAAsn(GUU) strongly attenuate translation in vitro. Contrary to human tRF(Ala), the 4 Gs present at the 5' extremity of Arabidopsis tRF(Ala) are not implicated in this inhibition while the G18 and G19 residues are essential. Protein synthesis inhibition by tRFs does not require complementarity with the translated mRNA but, having the capability to be associated with polyribosomes, tRFs likely act as general modulation factors of the translation process in plants.
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Affiliation(s)
- Stéphanie Lalande
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg , Strasbourg, France
| | - Rémy Merret
- Université de Perpignan Via Domitia , Perpignan, France
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg , Strasbourg, France
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg , Strasbourg, France
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100
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Carvalho Barbosa C, Calhoun SH, Wieden HJ. Non-coding RNAs: what are we missing? Biochem Cell Biol 2020; 98:23-30. [DOI: 10.1139/bcb-2019-0037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Over the past two decades, the importance of small non-coding RNAs (sncRNAs) as regulatory molecules has become apparent in all three domains of life (archaea, bacteria, eukaryotes). In fact, sncRNAs play an important role in the control of gene expression at both the transcriptional and the post-transcriptional level, with crucial roles in fine-tuning cell responses during internal and external stress. Multiple pathways for sncRNA biogenesis and diverse mechanisms of regulation have been reported, and although biogenesis and mechanisms of sncRNAs in prokaryotes and eukaryotes are different, remarkable similarities exist. Here, we briefly review and compare the major sncRNA classes that act post-transcriptionally, and focus on recent discoveries regarding the ribosome as a target of regulation and the conservation of these mechanisms between prokaryotes and eukaryotes.
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Affiliation(s)
- Cristina Carvalho Barbosa
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Sydnee H. Calhoun
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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