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Mechanisms of Action of tRNA-derived Small RNAs and Their Potential Roles in Related Diseases |
LIAO Tian-ci,ZHENG Ting,SHEN Lin-yuan,ZHAO Ye,NIU Li-li,ZHANG Shun-hua,ZHU Li**() |
College of Animal Science and Technology, Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China |
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Abstract Recently, tRNA-derived small RNAs (tsRNAs) were gradually recognized as a novel and potential non-coding RNAs (ncRNAs).There are mainly two types of tsRNAs, including tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs), which differ in the cleavage position of the precursor or mature tRNA transcript. Emerging evidence suggests that tsRNAs are implicated in various cellular processes, including translational inhibition, gene silencing, and ribosome biogenesis. They also play an important role in the development of related diseases such as cancer, neurodegeneration, metabolic diseases and viral infections. This review summarizes the functions and mechanisms of action of tsRNAs, the potential application of tsRNAs in related diseases,and the current problems and puts forward future research directions.
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Received: 12 August 2021
Published: 07 April 2022
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Corresponding Authors:
Li ZHU
E-mail: zhuli7508@163.com
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[1] |
Kirchner S, Ignatova Z. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nature Reviews Genetics, 2015, 16(2):98-112.
doi: 10.1038/nrg3861
|
|
|
[2] |
Phizicky E M, Hopper A K. tRNA biology charges to the front. Genes & Development, 2010, 24(17):1832-1860.
doi: 10.1101/gad.1956510
|
|
|
[3] |
Schimmel P. The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nature Reviews Molecular Cell Biology, 2018, 19(1):45-58.
doi: 10.1038/nrm.2017.77
pmid: 28875994
|
|
|
[4] |
Borek E, Baliga B S, Gehrke C W, et al. High turnover rate of transfer RNA in tumor tissue. Cancer Research, 1977, 37(9):3362-3366.
pmid: 884680
|
|
|
[5] |
Li S Q, Xu Z P, Sheng J H. tRNA-derived small RNA: a novel regulatory small non-coding RNA. Genes, 2018, 9(5):246.
doi: 10.3390/genes9050246
|
|
|
[6] |
Elkordy A, Mishima E, Niizuma K, et al. Stress-induced tRNA cleavage and tiRNA generation in rat neuronal PC12 cells. Journal of Neurochemistry, 2018, 146(5):560-569.
doi: 10.1111/jnc.14321
pmid: 29431851
|
|
|
[7] |
Shigematsu M, Kirino YM. tRNA-derived short non-coding RNA as interacting partners of argonaute proteins. Gene Regulation and Systems Biology, 2015, 9:27-33.
doi: 10.4137/GRSB.S29411
pmid: 26401098
|
|
|
[8] |
Kuscu C, Kumar P, Kiran M, et al. tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner. RNA, 2018, 24(8):1093-1105.
doi: 10.1261/rna.066126.118
|
|
|
[9] |
Zhu X L, Li T, Cao Y, et al. tRNA-derived fragments tRF(GlnCTG) induced by arterial injury promote vascular smooth muscle cell proliferation. Molecular Therapy - Nucleic Acids, 2021, 23:603-613.
|
|
|
[10] |
Kumar P, Kuscu C, Dutta A. Biogenesis and function of transfer RNA-related fragments (tRFs). Trends in Biochemical Sciences, 2016, 41(8):679-689.
doi: 10.1016/j.tibs.2016.05.004
|
|
|
[11] |
Kumar P, Mudunuri S B, Anaya J, et al. tRFdb: a database for transfer RNA fragments. Nucleic Acids Research, 2015, 43(D1):D141-D145.
doi: 10.1093/nar/gku1138
|
|
|
[12] |
Emara M M, Ivanov P, Hickman T, et al. Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. Journal of Biological Chemistry, 2010, 285(14):10959-10968.
doi: 10.1074/jbc.M109.077560
|
|
|
[13] |
Lyons S M, Kharel P, Akiyama Y, et al. eIF4G has intrinsic G-quadruplex binding activity that is required for tiRNA function. Nucleic Acids Research, 2020, 48(11):6223-6233.
doi: 10.1093/nar/gkaa336
|
|
|
[14] |
Sobala A, Hutvagner G. Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells. RNA Biology, 2013, 10(4):553-563.
doi: 10.4161/rna.24285
|
|
|
[15] |
Maute R L, Schneider C, Sumazin P, et al. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. PNAS, 2013, 110(4):1404-1409.
doi: 10.1073/pnas.1206761110
pmid: 23297232
|
|
|
[16] |
Tao E W, Wang H L, Cheng W Y, et al. A specific tRNA half, 5'tiRNA-His-GTG, responds to hypoxia via the HIF1α/ANG axis and promotes colorectal cancer progression by regulating LATS2. Journal of Experimental & Clinical Cancer Research: CR, 2021, 40(1):67.
|
|
|
[17] |
Pan X Q, Geng X M, Liu Y, et al. Transfer RNA fragments in the kidney in hypertension. Hypertension (Dallas, Tex : 1979), 2021, 77(5):1627-1637.
|
|
|
[18] |
Wang Q R, Lee I, Ren J P, et al. Identification and functional characterization of tRNA-derived RNA fragments (tRFs) in respiratory syncytial virus infection. Molecular Therapy: the Journal of the American Society of Gene Therapy, 2013, 21(2):368-379.
doi: 10.1038/mt.2012.237
|
|
|
[19] |
Kim H K, Fuchs G, Wang S C, et al. A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature, 2017, 552(7683):57-62.
doi: 10.1038/nature25005
|
|
|
[20] |
Kim H K, Xu J P, Chu K, et al. A tRNA-derived small RNA regulates ribosomal protein S28 protein levels after translation initiation in humans and mice. Cell Reports, 2019, 29(12):3816-3824, e4.
doi: 10.1016/j.celrep.2019.11.062
|
|
|
[21] |
Zhang X, He X, Liu C, et al. IL-4 inhibits the biogenesis of an epigenetically suppressive PIWI-interacting RNA to upregulate CD1a molecules on monocytes/dendritic cells. Journal of Immunology (Baltimore, Md : 1950), 2016, 196(4):1591-1603.
doi: 10.4049/jimmunol.1500805
|
|
|
[22] |
Kazimierczyk M, Jędroszkowiak A, Kowalczykiewicz D, et al. tRNA-derived fragments from the Sus scrofa tissues provide evidence of their conserved role in mammalian development. Biochemical and Biophysical Research Communications, 2019, 520(3):514-519.
doi: S0006-291X(19)31951-5
pmid: 31610915
|
|
|
[23] |
Wang Z J, Xiang L, Shao J J, et al. The 3' CCACCA sequence of tRNAAla(UGC) is the motif that is important in inducing Th1-like immune response, and this motif can be recognized by Toll-like receptor 3. Clinical and Vaccine Immunology: CVI, 2006, 13(7):733-739.
doi: 10.1128/CVI.00019-06
|
|
|
[24] |
Pawar K, Shigematsu M, Sharbati S, et al. Infection-induced 5'-half molecules of tRNAHisGUG activate Toll-like receptor 7. PLoS Biology, 2020, 18(12):e3000982.
doi: 10.1371/journal.pbio.3000982
|
|
|
[25] |
Shao Y, Sun Q L, Liu X M, et al. tRF-Leu-CAG promotes cell proliferation and cell cycle in non-small cell lung cancer. Chemical Biology & Drug Design, 2017, 90(5):730-738.
|
|
|
[26] |
Goodarzi H, Liu X H, Nguyen H C B, et al. Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell, 2015, 161(4):790-802.
doi: 10.1016/j.cell.2015.02.053
pmid: 25957686
|
|
|
[27] |
Saikia M, Jobava R, Parisien M, et al. Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress. Molecular and Cellular Biology, 2014, 34(13):2450-2463.
doi: 10.1128/MCB.00136-14
|
|
|
[28] |
Yamasaki S, Ivanov P, Hu G F, et al. Angiogenin cleaves tRNA and promotes stress-induced translational repression. The Journal of Cell Biology, 2009, 185(1):35-42.
doi: 10.1083/jcb.200811106
|
|
|
[29] |
Donovan J, Rath S, Kolet-Mandrikov D, et al. Rapid RNase L-driven arrest of protein synthesis in the dsRNA response without degradation of translation machinery. RNA (New York, NY), 2017, 23(11):1660-1671.
doi: 10.1261/rna.062000.117
|
|
|
[30] |
Ivanov P, Emara M M, Villen J, et al. Angiogenin-induced tRNA fragments inhibit translation initiation. Molecular Cell, 2011, 43(4):613-623.
doi: 10.1016/j.molcel.2011.06.022
pmid: 21855800
|
|
|
[31] |
Ivanov P, O’Day E, Emara M M, et al. G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments. PNAS, 2014, 111(51):18201-18206.
doi: 10.1073/pnas.1407361111
pmid: 25404306
|
|
|
[32] |
Kumar P, Anaya J, Mudunuri S B, et al. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biology, 2014, 12:78.
doi: 10.1186/s12915-014-0078-0
|
|
|
[33] |
Haussecker D, Huang Y, Lau A, et al. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA (New York, NY), 2010, 16(4):673-695.
doi: 10.1261/rna.2000810
|
|
|
[34] |
Couvillion M T, Bounova G, Purdom E, et al. A Tetrahymena piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus. Molecular Cell, 2012, 48(4):509-520.
doi: 10.1016/j.molcel.2012.09.010
pmid: 23084833
|
|
|
[35] |
Dhahbi J M, Spindler S R, Atamna H, et al. 5' tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction. BMC Genomics, 2013, 14:298.
doi: 10.1186/1471-2164-14-298
|
|
|
[36] |
Zhang Y F, Zhang Y, Shi J C, et al. Identification and characterization of an ancient class of small RNAs enriched in serum associating with active infection. Journal of Molecular Cell Biology, 2014, 6(2):172-174.
doi: 10.1093/jmcb/mjt052
|
|
|
[37] |
Chen Q, Yan M H, Cao Z H, et al. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science (New York, NY), 2016, 351(6271):397-400.
doi: 10.1126/science.aad7977
|
|
|
[38] |
Huang Y, Ge H, Zheng M J, et al. Serum tRNA-derived fragments (tRFs) as potential candidates for diagnosis of nontriple negative breast cancer. Journal of Cellular Physiology, 2020, 235(3):2809-2824.
doi: 10.1002/jcp.29185
pmid: 31535382
|
|
|
[39] |
Han X Y, Cai L, Lu Y, et al. Identification of tRNA-derived fragments and their potential roles in diabetic cataract rats. Epigenomics, 2020, 12(16):1405-1418.
doi: 10.2217/epi-2020-0193
|
|
|
[40] |
Zhu J J, Cheng M L, Zhao X K. A tRNA-derived fragment (tRF-3001b) aggravates the development of nonalcoholic fatty liver disease by inhibiting autophagy. Life Sciences, 2020, 257:118125.
doi: 10.1016/j.lfs.2020.118125
|
|
|
[41] |
Yeung M L, Bennasser Y, Watashi K, et al. Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid. Nucleic Acids Research, 2009, 37(19):6575-6586.
doi: 10.1093/nar/gkp707
pmid: 19729508
|
|
|
[42] |
Deng J F, Ptashkin R N, Chen Y, et al. Respiratory syncytial virus utilizes a tRNA fragment to suppress antiviral responses through a novel targeting mechanism. Molecular Therapy : the Journal of the American Society of Gene Therapy, 2015, 23(10):1622-1629.
doi: 10.1038/mt.2015.124
|
|
|
[43] |
Huh D, Passarelli M C, Gao J, et al. A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression. The EMBO Journal, 2021, 40(2):e106696.
|
|
|
[44] |
Luan N, Mu Y L, Mu J Y, et al. Dicer1 promotes colon cancer cell invasion and migration through modulation of tRF-20-MEJB5Y13 expression under hypoxia. Frontiers in Genetics, 2021, 12:638244.
doi: 10.3389/fgene.2021.638244
|
|
|
[45] |
Yang C, Lee M, Song G, et al. tRNA(Lys)-derived fragment alleviates cisplatin-induced apoptosis in prostate cancer cells. Pharmaceutics, 2021, 13(1):55.
doi: 10.3390/pharmaceutics13010055
|
|
|
[46] |
Vaupel P, Höckel M, Mayer A. Detection and characterization of tumor hypoxia using pO2 histography. Antioxidants & Redox Signaling, 2007, 9(8):1221-1235.
|
|
|
[47] |
Keith B, Simon M C. Hypoxia-inducible factors, stem cells, and cancer. Cell, 2007, 129(3):465-472.
doi: 10.1016/j.cell.2007.04.019
|
|
|
[48] |
Cui Y Y, Huang Y, Wu X W, et al. Hypoxia-induced tRNA-derived fragments, novel regulatory factor for doxorubicin resistance in triple-negative breast cancer. Journal of Cellular Physiology, 2019, 234(6):8740-8751.
doi: 10.1002/jcp.v234.6
|
|
|
[49] |
Skeparnias I, Anastasakis D, Grafanaki K, et al. Contribution of miRNAs, tRNAs and tRFs to aberrant signaling and translation deregulation in lung cancer. Cancers, 2020, 12(10):3056.
doi: 10.3390/cancers12103056
|
|
|
[50] |
Skalsky R L, Cullen B R. Viruses, microRNAs, and host interactions. Annual Review of Microbiology, 2010, 64:123-141.
doi: 10.1146/micro.2010.64.issue-1
|
|
|
[51] |
Taxis T M, Bauermann F V, Ridpath J F, et al. Analysis of tRNA halves (tsRNAs) in serum from cattle challenged with bovine viral diarrhea virus. Genetics and Molecular Biology, 2019, 42(2):374-379.
doi: 10.1590/1678-4685-gmb-2018-0019
|
|
|
[52] |
Blanco S, Dietmann S, Flores J V, et al. Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. The EMBO Journal, 2014, 33(18):2020-2039.
doi: 10.15252/embj.201489282
|
|
|
[53] |
Schaefer M, Pollex T, Hanna K, et al. RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. Genes & Development, 2010, 24(15):1590-1595.
doi: 10.1101/gad.586710
|
|
|
[54] |
Greenway M J, Andersen P M, Russ C, et al. ANG mutations segregate with familial and ‘sporadic’ amyotrophic lateral sclerosis. Nature Genetics, 2006, 38(4):411-413.
pmid: 16501576
|
|
|
[55] |
van Es M A, Schelhaas H J, van Vught P W J, et al. Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis. Annals of Neurology, 2011, 70(6):964-973.
doi: 10.1002/ana.22611
|
|
|
[56] |
Dou R, Zhang X L, Xu X D, et al. Mesenchymal stem cell exosomal tsRNA-21109 alleviate systemic lupus erythematosus by inhibiting macrophage M1 polarization. Molecular Immunology, 2021, 139:106-114.
doi: 10.1016/j.molimm.2021.08.015
|
|
|
[57] |
Taxis T M, Kehrli M E, D’orey-Branco R, et al. Association of transfer RNA fragments in white blood cells with antibody response to bovine leukemia virus in Holstein cattle. Frontiers in Genetics, 2018, 9:236.
doi: 10.3389/fgene.2018.00236
|
|
|
[58] |
Li S Q, Chen Y D, Sun D S, et al. Angiogenin prevents progranulin A9D mutation-induced neuronal-like cell apoptosis through cleaving tRNAs into tiRNAs. Molecular Neurobiology, 2018, 55(2):1338-1351.
doi: 10.1007/s12035-017-0396-7
|
|
|
[59] |
Zhang Z Y, Zhang C H, Yang J J, et al. Genome-wide analysis of hippocampal transfer RNA-derived small RNAs identifies new potential therapeutic targets of Bushen Tiansui formula against Alzheimer’s disease. Journal of Integrative Medicine, 2021, 19(2):135-143.
doi: 10.1016/j.joim.2020.12.005
|
|
|
[60] |
Honda S, Loher P, Shigematsu M, et al. Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. PNAS, 2015, 112(29):E3816-E3825.
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