The function and research methods of tRNA-derived small RNAs (tsRNA)
Received date: 2021-07-16
Revised date: 2021-09-17
Online published: 2021-11-23
Supported by
Supported by the National Natural Science Foundation of China Nos(31902135);Supported by the National Natural Science Foundation of China Nos(31972524);the Sichuan Science and Technology Support Program Nos(2021YJ0265);the Sichuan Science and Technology Support Program Nos(2021YFYZ0007);the Sichuan Science and Technology Support Program Nos(2020YFN0147)
tRNA-derived small RNA (tsRNA), a class of small non-coding RNAs processed from the precursor tRNA or mature tRNA, broadly exist in organisms and have features including high conservation, structural stability and tissue specificity. According to the different paths of biogenesis, tsRNA is classified into two major types, tRNA halves and tRNA-derived RNA fragments (tRFs). Many studies have revealed that the expression of tsRNA is significantly increased under a variety of cellular stress responses, and its involvement in the regulation of stress responses is conserved across different species. tsRNA plays an important role in various biological processes by regulating transcript stability, protein translation and epigenetic processes. Recent researches have shown that tsRNA has the potential as disease biomarkers and therapeutic targets, making it the focus of biomedical research. In this review, we summarize the research on tsRNA from aspects of biogenesis, function and research methods in order to provide a reference for relevant research.
Key words: non-coding RNA; tRNA-derived fragments; tsRNA; tRFs
Jianfeng Ma, Mailin Gan, Li Zhu, Linyuan Shen . The function and research methods of tRNA-derived small RNAs (tsRNA)[J]. Hereditas(Beijing), 2021 , 43(12) : 1107 -1120 . DOI: 10.16288/j.yczz.21-256
| [1] | ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Kara?z U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, L?ytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 2007,447(7146):799-816. |
| [2] | Goodall GJ, Wickramasinghe VO. RNA in cancer. Nat Rev Cancer, 2021,21(1):22-36. |
| [3] | Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA, 2010,16(4):673-695. |
| [4] | Andersen KL, Collins K. Several RNase T2 enzymes function in induced tRNA and rRNA turnover in the ciliate Tetrahymena. Mol Biol Cell, 2012,23(1):36-44. |
| [5] | Rosace D, López J, Blanco S. Emerging roles of novel small non-coding regulatory RNAs in immunity and cancer. RNA Biol, 2020,17(8):1196-1213. |
| [6] | Borek E, Baliga BS, Gehrke CW, Kuo CW, Belman S, Troll W, Waalkes TP. High turnover rate of transfer RNA in tumor tissue. Cancer Res, 1977,37(9):3362-3366. |
| [7] | Speerm J, Gehrkep CW, Kuo KC, Waalkes TP, Borek E. tRNA breakdown products as markers for cancer. Cancer, 1979,44(6):2120-2123. |
| [8] | Saxena SK, Rybak SM, Davey RT Jr, Youle RJ, Ackerman EJ. Angiogenin is a cytotoxic, tRNA-specific ribonuclease in the RNase A superfamily. J Biol Chem, 1992,267(30):21982-21986. |
| [9] | Thompson DM, Lu C, Green PJ, Parker R. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA, 2008,14(10):2095-2103. |
| [10] | Fu HJ, Feng JJ, Liu Q, Sun F, Tie Y, Zhu J, Xing RY, Sun XZ, Zheng XF. Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett, 2009,583(2):437-442. |
| [11] | Liapi E, van Bilsen M, Verjans R, Schroen B. tRNAs and tRNA fragments as modulators of cardiac and skeletal muscle function. Biochim Biophys Acta Mol Cell Res, 2020,1867(3):118465. |
| [12] | Raina M, Ibba M. tRNAs as regulators of biological processes. Front Genet, 2014,5:171. |
| [13] | Maraia RJ, Lamichhane TN. 3′ processing of eukaryotic precursor tRNAs. WIREs RNA, 2011,2(3):362-375. |
| [14] | Zong TY, Yang YY, Zhao H, Li L, Liu MX, Fu XX, Tang GZ, Zhou H, Aung LHH, Li PF, Wang JX, Wang ZB, Yu T. tsRNAs: novel small molecules from cell function and regulatory mechanism to therapeutic targets. Cell Prolif, 2021,54(3):e12977. |
| [15] | Thompson DM, Parker R. The RNase Rny1p cleaves tRNAs and promotes cell death during oxidative stress in Saccharomyces cerevisiae. J Cell Biol, 2009,185(1):43-50. |
| [16] | Saikia M, Krokowski D, Guan BJ, Ivanov P, Parisien M, Hu GF, Anderson P, Pan T, Hatzoglou M. Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J Biol Chem, 2012,287(51):42708-42725. |
| [17] | Su ZL, Kuscu C, Malik A, Shibata E, Dutta A. Angiogenin generates specific stress-induced tRNA halves and is not involved in tRF-3-mediated gene silencing. J Biol Chem, 2019,294(45):16930-16941. |
| [18] | Lee SR, Collins K. Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. J Biol Chem, 2005,280(52):42744-42749. |
| [19] | Fricker R, Brogli R, Luidalepp H, Wyss L, Fasnacht M, Joss O, Zywicki M, Helm M, Schneider A, Cristodero M, Polacek N. A tRNA half modulates translation as stress response in Trypanosoma brucei. Nat Commun, 2019,10(1):118. |
| [20] | Goodarzi H, Liu XH, Nguyen HCB, Zhang S, Fish L, Tavazoie SF. Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell, 2015,161(4):790-802. |
| [21] | Cui YY, Huang Y, Wu XW, Zheng MJ, Xia YQ, Fu ZY, Ge H, Wang S, Xie H. Hypoxia-induced tRNA-derived fragments, novel regulatory factor for doxorubicin resistance in triple-negative breast cancer. J Cell Physiol, 2019,234(6):8740-8751. |
| [22] | Gebetsberger J, Zywicki M, Künzi A, Polacek N. tRNA-derived fragments target the ribosome and function as regulatory non-coding RNA in Haloferax volcanii. Archaea, 2012,2012:260909. |
| [23] | Yamasaki S, Ivanov P, Hu GF, Anderson P. Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol, 2009,185(1):35-42. |
| [24] | Oberbauer V, Schaefer MR. tRNA-derived small RNAs: biogenesis, modification, function and potential impact on human disease development. Genes, 2018,9(12):607. |
| [25] | Guzzi N, Bellodi C. Novel insights into the emerging roles of tRNA-derived fragments in mammalian development. RNA Biol, 2020,17(8):1214-1222. |
| [26] | Ma ZL, Zhou JB, Shao Y, Jafari FA, Qi PF, Li YL. Biochemical properties and progress in cancers of tRNA-derived fragments. J Cell Biochem, 2020,121(3):2058-2063. |
| [27] | Tao EW, Cheng WY, Li WL, Yu J, Gao QY. tiRNAs: A novel class of small noncoding RNAs that helps cells respond to stressors and plays roles in cancer progression. J Cell Physiol, 2020,235(2):683-690. |
| [28] | Prehn JHM, Jirstr?m E. Angiogenin and tRNA fragments in Parkinson’s disease and neurodegeneration. Acta Pharmacol Sin, 2020,41(4):442-446. |
| [29] | Thompson DM, Parker R. Stressing out over tRNA cleavage. Cell, 2009,138(2):215-219. |
| [30] | Li NS, Shan NY, Lu LG, Wang ZH. tRFtarget: a database for transfer RNA-derived fragment targets. Nucleic Acids Res, 2021,49(D1):D254-D260. |
| [31] | Park J, Ahn SH, Shin MG, Kim HK, Chang S. tRNA-derived small RNAs: novel epigenetic regulators. Cancers, 2020,12(10):2773. |
| [32] | Martinez G. tRNA-derived small RNAs: new players in genome protection against retrotransposons. RNA Biol, 2018,15(2):170-175. |
| [33] | Xie YY, Yao LP, Yu XC, Ruan Y, Li Z, Guo JM. Action mechanisms and research methods of tRNA-derived small RNAs. Signal Transduct Tar, 2020,5(1):109. |
| [34] | Zhu LW, Ge JX, Li TW, Shen YJ, Guo JM. tRNA-derived fragments and tRNA halves: the new players in cancers. Cancer Lett, 2019,452:31-37. |
| [35] | Kumar P, Kuscu C, Dutta A. Biogenesis and function of transfer RNA-related fragments (tRFs). Trends Biochem Sci, 2016,41(8):679-689. |
| [36] | Farina NH, Scalia S, Adams CE, Hong DL, Fritz AJ, Messier TL, Balatti V, Veneziano D, Lian JB, Croce CM, Stein GS, Stein JL. Identification of tRNA-derived small RNA (tsRNA) responsive to the tumor suppressor, RUNX1, in breast cancer. J Cell Physiol, 2020,235(6):5318-5327. |
| [37] | Falconi M, Giangrossi M, Zabaleta ME, Wang JB, Gambini V, Tilio M, Bencardino D, Occhipinti S, Belletti B, Laudadio E, Galeazzi R, Marchini C, Amici A. A novel 3′-tRNA Glu -derived fragment acts as a tumor suppressor in breast cancer by targeting nucleolin . FASEB J, 2019,33(12):13228-13240. |
| [38] | Mo DP, Jiang P, Yang YN, Mao XL, Tan XY, Tang X, Wei D, Li B, Wang XM, Tang L, Yan F. A tRNA fragment, 5′-tiRNA Val, suppresses the Wnt/β-catenin signaling pathway by targeting FZD3 in breast cancer . Cancer Lett, 2019,457:60-73. |
| [39] | Zhang F, Shi JX, Wu ZH, Gao P, Zhang WX, Qu BC, Wang X, Song YX, Wang ZN. A 3′-tRNA-derived fragment enhances cell proliferation, migration and invasion in gastric cancer by targeting FBXO47. Arch Biochem Biophys, 2020,690:108467. |
| [40] | Tong LH, Zhang WX, Qu BC, Zhang F, Wu ZH, Shi JX, Chen XW, Song YX, Wang ZN. The tRNA-derived fragment-3017A promotes metastasis by inhibiting NELL2 in human gastric cancer. Front Oncol, 2021,10:570916. |
| [41] | Shen YJ, Xie YY, Yu XC, Zhang SS, Wen QY, Ye GL, Guo JM. Clinical diagnostic values of transfer RNA-derived fragment tRF-19-3L7L73JD and its effects on the growth of gastric cancer cells. J Cancer, 2021,12(11):3230-3238. |
| [42] | Veneziano D, Tomasello L, Balatti V, Palamarchuk A, Rassenti LZ, Kipps TJ, Pekarsky Y, Croce CM. Dysregulation of different classes of tRNA fragments in chronic lymphocytic leukemia. Proc Natl Acad Sci USA, 2019,116(48):24252-24258. |
| [43] | Ruggero K, Guffanti A, Corradin A, Sharma VK, De Bellis G, Corti G, Grassi A, Zanovello P, Bronte V, Ciminale V, D’Agostino DM. Small noncoding RNAs in cells transformed by human t-cell leukemia virus type 1: a role for a tRNA fragment as a primer for reverse transcriptase. J Virol, 2014,88(7):3612-3622. |
| [44] | Honda S, Loher P, Shigematsu M, Palazzo JP, Suzuki R, Imoto I, Rigoutsos I, Kirino Y. Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc Natl Acad Sci USA, 2015,112(29):E3816-E3825. |
| [45] | Yang CW, Lee M, Song G, Lim W. tRNA Lys-derived fragment alleviates cisplatin-induced apoptosis in prostate cancer cells . Pharmaceutics, 2021,13(1):55. |
| [46] | Shao Y, Sun QL, Liu XM, Wang P, Wu RQ, Ma ZL. tRF-Leu-CAG promotes cell proliferation and cell cycle in non-small cell lung cancer. Chem Biol Drug Des, 2017,90(5):730-738. |
| [47] | Balatti V, Nigita G, Veneziano D, Drusco A, Stein GS, Messier TL, Farina NH, Lian JB, Tomasello L, Liu CG, Palamarchuk A, Hart JR, Bell C, Carosi M, Pescarmona E, Perracchio L, Diodoro M, Russo A, Antenucci A, Visca P, Ciardi A, Harris CC, Vogt PK, Pekarsky Y, Croce CM. tsRNA signatures in cancer. Proc Natl Acad Sci USA, 2017,114(30):8071-8076. |
| [48] | Luan N, Chen YQ, Li QS, Mu YL, Zhou Q, Ye X, Deng Q, Ling LM, Wang J, Wang JW. TRF-20-M0NK5Y93 suppresses the metastasis of colon cancer cells by impairing the epithelial-to-mesenchymal transition through targeting Claudin-1. Am J Transl Res, 2021,13(1):124-142. |
| [49] | Huang BQ, Yang HP, Cheng XX, Wang D, Fu SY, Shen WC, Zhang Q, Zhang LJ, Xue ZY, Li Y, Da YR, Yang Q, Li ZS, Liu L, Qiao L, Kong Y, Yao Z, Zhao P, Li M, Zhang RX. tRF/miR-1280 suppresses stem cell-like cells and metastasis in colorectal cancer. Cancer Res, 2017,77(12):3194-3206. |
| [50] | Wu YM, Yang XL, Jiang GM, Zhang HS, Ge LC, Chen F, Li JX, Liu HL, Wang HS. 5′-tRF-GlyGCC: a tRNA- derived small RNA as a novel biomarker for colorectal cancer diagnosis. Genome Med, 2021,13(1):20. |
| [51] | Zhang MM, Li FF, Wang J, He WZ, Li Y, Li HY, Wei ZL, Cao YX. tRNA-derived fragment tRF-03357 promotes cell proliferation, migration and invasion in high-grade serous ovarian cancer. Oncotargets Ther, 2019,12:6371-6383. |
| [52] | Zhou K, Diebel KW, Holy J, Skildum A, Odean E, Hicks DA, Schotl B, Abrahante JE, Spillman MA, Bemis LT. A tRNA fragment, tRF5-Glu, regulates BCAR3 expression and proliferation in ovarian cancer cells. Oncotarget, 2017,8(56):95377-95391. |
| [53] | Papadimitriou M-A, Avgeris M, Levis P, Papasotiriou ECh, Kotronopoulos G, Stravodimos K, Scorilas A. tRNA-derived fragments (tRFs) in bladder cancer: increased 5′-tRF-LysCTT results in disease early progression and patients’ poor treatment outcome. Cancers, 2020,12(12):3661. |
| [54] | He XQ, Yang YY, Wang Q, Wang JR, Li SF, Li CR, Zong TY, Li XL, Zhang Y, Zou YL, Yu T. Expression profiles and potential roles of transfer RNA-derived small RNAs in atherosclerosis. J Cell Mol Med, 2021,25(14):7052-7065. |
| [55] | Meng L, Jiang L, Chen J, Ren HJ, Gao ZQ, Wu F, Wen YY, Yang LJ. Transfer RNA-derived fragment tRF-28-QSZ34KRQ590K in plasma exosomes may be a potential biomarker for atopic dermatitis in pediatric patients. Exp Ther Med, 2021,21(5):489. |
| [56] | Huang P, Tu B, Liao HJ, Huang FZ, Li ZZ, Zhu KY, Dai F, Liu HZ, Zhang TY, Sun CZ. Elevation of plasma tRNA fragments as a promising biomarker for liver fibrosis in nonalcoholic fatty liver disease. Sci Rep, 2021,11(1):5886. |
| [57] | Choi E-J, Wu WZ, Zhang K, Lee I, Kim I-H, Lee YS, Bao XY. 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. |
| [58] | Wu WZ, Lee I, Spratt H, Fang X, Bao XY. tRNA- derived fragments in alzheimer’s disease: implications for new disease biomarkers and neuropathological mechanisms. J Alzheimers Dis, 2021,79(2):793-806. |
| [59] | Magee R, Londin E, Rigoutsos I. TRNA-derived fragments as sex-dependent circulating candidate biomarkers for Parkinson’s disease. Parkinsonism Relat D, 2019,65:203-209. |
| [60] | Li LZ, Liu P, Wang RL, Huang YY, Luo JC, Jiao LQ, Tao Z, Zheng YM, Fan JF, Zhao HP, Han ZP, Luo YM. Pathophysiological significance of neutrophilic transfer RNA-derived small RNAs in asymptomatic moyamoya disease. Cells, 2021,10(5):1086. |
| [61] | Hogg MC, Rayner M, Susdalzew S, Monsefi N, Crivello M, Woods I, Resler A, Blackbourn L, Fabbrizio P, Trolese MC, Nardo G, Bendotti C, van den Berg LH, van Es MA, Prehn JHM. 5′ValCAC tRNA fragment generated as part of a protective angiogenin response provides prognostic value in amyotrophic lateral sclerosis. Brain Commun, 2020, 2(2): fcaa138. |
| [62] | Venkatesh T, Suresh PS, Tsutsumi R. tRFs: miRNAs in disguise. Gene, 2016,579(2):133-138. |
| [63] | Li ZH, Ender C, Meister G, Moore PS, Chang Y, John B. Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res, 2012,40(14):6787-6799. |
| [64] | Kumar P, Anaya J, Mudunuri SB, Dutta A. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol, 2014,12:78. |
| [65] | Sobala A, Hutvagner G. Small RNAs derived from the 5′ end of tRNA can inhibit protein translation in human cells. RNA Biol, 2013,10(4):553-563. |
| [66] | Lafontaine DLJ. Noncoding RNAs in eukaryotic ribosome biogenesis and function. Nat Struct Mol Biol, 2015,22(1):11-19. |
| [67] | Couvillion MT, Bounova G, Purdom E, Speed TP, Collins K. A Tetrahymena piwi bound to mature tRNA 3′ fragments activates the exonuclease Xrn2 for RNA processing in the nucleus. Mol Cell, 2012,48(4):509-520. |
| [68] | Kim HK, Fuchs G, Wang SC, Wei W, Zhang Y, Park H, Roy-Chaudhuri B, Li P, Xu JP, Chu K, Zhang FJ, Chua M-S, So S, Zhang QC, Sarnow P, Kay MA. A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature, 2017,552(7683):57-62. |
| [69] | Kim HK, Xu JP, Chu K, Park H, Jang H, Li P, Valdmanis PN, Zhang QC, Kay MA. A tRNA-derived small RNA regulates ribosomal protein S28 protein levels after translation initiation in humans and mice. Cell Rep, 2019, 29(12): 3816-3824.e4. |
| [70] | Gebetsberger J, Wyss L, Mleczko AM, Reuther J, Polacek N. A tRNA-derived fragment competes with mRNA for ribosome binding and regulates translation during stress. RNA Biol, 2017,14(10):1364-1373. |
| [71] | Lyons SM, Kharel P, Akiyama Y, Ojha S, Dave D, Tsvetkov V, Merrick W, Ivanov P, Anderson P. eIF4G has intrinsic G-quadruplex binding activity that is required for tiRNA function. Nucleic Acids Res, 2020,48(11):6223-6233. |
| [72] | Ivanov P, Emara MM, Villen J, Gygi SP, Anderson P. Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell, 2011,43(4):613-623. |
| [73] | Lyons SM, Gudanis D, Coyne SM, Gdaniec Z, Ivanov P. Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs. Nat Commun, 2017,8(1):1127. |
| [74] | Lyons SM, Achorn C, Kedersha NL, Anderson PJ, Ivanov P. YB-1 regulates tiRNA-induced stress granule formation but not translational repression. Nucleic Acids Res, 2016,44(14):6949-6960. |
| [75] | Yu MQ, Lu BJ, Zhang JS, Ding JW, Liu PY, Lu Y. tRNA-derived RNA fragments in cancer: current status and future perspectives. J Hematol Oncol, 2020,13(1):121. |
| [76] | Ling C, R?nn T. Epigenetics in human obesity and type 2 diabetes. Cell Metab, 2019,29(5):1028-1044. |
| [77] | Iwasaki YW, Siomi MC, Siomi H. PIWI-interacting RNA: its biogenesis and functions. Annu Rev Biochem, 2015,84(1):405-433. |
| [78] | Ozata DM, Gainetdinov I, Zoch A, O’Carroll D, Zamore PD. PIWI-interacting RNAs: small RNAs with big functions. Nat Rev Genet, 2019,20(2):89-108. |
| [79] | Couvillion MT, Sachidanandam R, Collins K. A growth- essential Tetrahymena Piwi protein carries tRNA fragment cargo. Gene Dev, 2010,24(24):2742-2747. |
| [80] | Zhang X, He X, Liu C, Liu J, Hu QF, Pan T, Duan XB, Liu BF, Zhang YW, Chen JL, Ma XR, Zhang X, Luo HH, Zhang H. IL-4 inhibits the biogenesis of an epigenetically suppressive PIWI-interacting RNA To upregulate CD1a molecules on monocytes/dendritic cells. J Immunol, 2016,196(4):1591-1603. |
| [81] | Saze H. Epigenetic regulation of intragenic transposable elements: a two-edged sword. J Biochem, 2018,164(5):323-328. |
| [82] | 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(11):2340-2357. |
| [83] | Schorn AJ, Gutbrod MJ, LeBlanc C, Martienssen R. LTR-Retrotransposon control by tRNA-Derived small RNAs. Cell, 2017,170(1):61-71. |
| [84] | Min B, Park JS, Jeong YS, Jeon K, Kang YK. Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos. Nucleic Acids Res, 2020,48(15):8431-8444. |
| [85] | Fukuda K, Shinkai Y. SETDB1-mediated silencing of retroelements. Viruses, 2020,12(6):596. |
| [86] | Kumar P, Mudunuri SB, Anaya J, Dutta A. tRFdb: a database for transfer RNA fragments. Nucleic Acids Res, 2015,43(D1):D141-D145. |
| [87] | Zheng LL, Xu WL, Liu S, Sun WJ, Li JH, Wu J, Yang JH, Qu LH. tRF2Cancer: a web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. Nucleic Acids Res, 2016,44(W1):W185-W193. |
| [88] | Schuster A, Tang C, Xie YM, Ortogero N, Yuan SQ, Yan W. SpermBase: a database for sperm-borne RNA contents. Biol Reprod, 2016,95(5):99. |
| [89] | Gupta N, Singh A, Zahra S, Kumar S. PtRFdb: a database for plant transfer RNA-derived fragments. Database(Oxford), 2018, 2018: bay063. |
| [90] | Zuo YL, Zhu L, Guo ZX, Liu WR, Zhang JT, Zeng Z, Wu QB, Cheng J, Fu X, Jin Y, Zhao Y, Peng Y. tsRBase: a comprehensive database for expression and function of tsRNAs in multiple species. Nucleic Acids Res, 2021,49(D1):D1038-D1045. |
| [91] | Wang XM, Yang YN, Tan XY, Mao XL, Wei D, Yao YF, Jiang P, Mo DP, Wang T, Yan F. Identification of tRNA-derived fragments expression profile in breast cancer tissues. Curr Genomics, 2019,20(3):199-213. |
| [92] | Xu C, Fu YF. Expression profiles of tRNA-derived fragments and their potential roles in multiple myeloma. Onco Targets Ther, 2021,14:2805-2814. |
| [93] | Benesova S, Kubista M, Valihrach L. Small RNA- sequencing: approaches and considerations for miRNA analysis. Diagnostics, 2021,11(6):964. |
| [94] | Drino A, Oberbauer V, Troger C, Janisiw E, Anrather D, Hartl M, Kaiser S, Kellner S, Schaefer MR. Production and purification of endogenously modified tRNA- derived small RNAs. RNA Biol, 2020,17(8):1104-1115. |
| [95] | Shi JC, Zhang YF, Tan DM, Zhang XD, Yan MH, Zhang Y, Franklin R, Shahbazi M, Mackinlay K, Liu SC, Kuhle B, James ER, Zhang LW, Qu YC, Zhai QW, Zhao WX, Zhao LL, Zhou CC, Gu WF, Murn J, Guo JT, Carrell DT, Wang YS, Chen XM, 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(4):424-436. |
| [96] | Wang JY, Ma G, Li MH, Han X, Xu J, Liang MD, Mao XR, Chen X, Xia TS, Liu XA, Wang S. Plasma tRNA fragments derived from 5′ ends as novel diagnostic biomarkers for early-stage breast cancer. Mol Ther Nucleic Acids, 2020,21:954-964. |
| [97] | Shi HM, Yu MY, Wu Y, Cao YP, Li SW, Qu GT, Gong J, Gan WH, Zhang AQ. tRNA-derived fragments (tRFs) contribute to podocyte differentiation. Biochem Biophys Res Commun, 2020,521(1):1-8. |
| [98] | Lee YS, Shibata Y, Malhotra A, Dutta A. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev, 2009,23(22):2639-2649. |
| [99] | Su ZL, Frost EL, Lammert CR, Przanowska RK, Lukens JR, Dutta A. tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal- immune-activation autism model. RNA Biol, 2020,17(8):1183-1195. |
| [100] | McArdle H, Hogg MC, Bauer S, Rosenow F, Prehn JHM, Adamson K, Henshall DC, Spain E. Quantification of tRNA fragments by electrochemical direct detection in small volume biofluid samples. Sci Rep, 2020,10(1):7516. |
| [101] | Lu TX, Rothenberg ME. MicroRNA. J Allergy Clin Immunol, 2018,141(4):1202-1207. |
| [102] | Shen LY, Tan ZD, Gan ML, Li Q, Chen L, Niu L, Jiang DM, Zhao Y, Wang JY, Li XW, Zhang SH, Zhu L. tRNA-derived small non-coding RNAs as novel epigenetic molecules regulating adipogenesis. Biomolecules, 2019,9(7):274. |
| [103] | Veedu RN, Wengel J. Locked nucleic acids: promising nucleic acid analogs for therapeutic applications. Chem Biodivers, 2010,7(3):536-542. |
| [104] | Torres AG, Reina O, Stephan-Otto Attolini C, Ribas de Pouplana L,. Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments. Proc Natl Acad Sci USA, 2019,116(17):8451-8456. |
| [105] | Green JA, Ansari MY, Ball HC, Haqqi TM. tRNA- derived fragments (tRFs) regulate post-transcriptional gene expression via AGO-dependent mechanism in IL-1β stimulated chondrocytes. Osteoarthritis Cartilage, 2020,28(8):1102-1110. |
| [106] | Kuscu C, Kumar P, Kiran M, Su Z, Malik A, Dutta A. tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner. RNA, 2018,24(8):1093-1105. |
| [107] | Falconi M, Giangrossi M, Zabaleta ME, Wang JB, Gambini V, Tilio M, Bencardino D, Occhipinti S, Belletti B, Laudadio E, Galeazzi R, Marchini C, Amici A. A novel 3′-tRNA Glu -derived fragment acts as a tumor suppressor in breast cancer by targeting nucleolin . FASEB J, 2019,33(12):13228-13240. |
| [108] | Akiyama Y, Kharel P, Abe T, Anderson P, Ivanov P. Isolation and initial structure-functional characterization of endogenous tRNA-derived stress-induced RNAs. RNA Biol, 2020,17(8):1116-1124. |
| [109] | Cho H, Lee W, Kim G-W, Lee S-H, Moon J-S, Kim M, Kim HS, Oh J-W. Regulation of La/SSB-dependent viral gene expression by pre-tRNA 3′ trailer-derived tRNA fragments. Nucleic Acids Res, 2019,47(18):9888-9901. |
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