References
- Anderson, P. and Kedersha, N. (2008). Stress granules: the Tao of RNA triage. Trends Biochem. Sci. 33, 141-150. https://doi.org/10.1016/j.tibs.2007.12.003
- Cozen, A.E., Quartley, E., Holmes, A.D., Hrabeta-Robinson, E., Phizicky, E.M., and Lowe, T.M. (2015). ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat. Methods 12, 879-884. https://doi.org/10.1038/nmeth.3508
- Dang, Y., Kedersha, N., Low, W.K., Romo, D., Gorospe, M., Kaufman, R., Anderson, P., and Liu, J.O. (2006). Eukaryotic initiation factor 2alpha-independent pathway of stress granule induction by the natural product pateamine A. J. Biol. Chem. 281, 32870-32878. https://doi.org/10.1074/jbc.M606149200
- Elkordy, A., Mishima, E., Niizuma, K., Akiyama, Y., Fujimura, M., Tominaga, T., and Abe, T. (2018). Stress-induced tRNA cleavage and tiRNA generation in rat neuronal PC12 cells. J. Neurochem. 146, 560-569. https://doi.org/10.1111/jnc.14321
- Emara, M.M., Ivanov, P., Hickman, T., Dawra, N., Tisdale, S., Kedersha, N., Hu, G.F., and Anderson, P. (2010). Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J. Biol. Chem. 285, 10959-10968. https://doi.org/10.1074/jbc.M109.077560
- Evdokimova, V., Ruzanov, P., Imataka, H., Raught, B., Svitkin, Y., Ovchinnikov, L.P., and Sonenberg, N. (2001). The major mRNA-associated protein YB-1 is a potent 5' cap-dependent mRNA stabilizer. EMBO J. 20, 5491-5502. https://doi.org/10.1093/emboj/20.19.5491
- Farny, N.G., Kedersha, N.L., and Silver, P.A. (2009). Metazoan stress granule assembly is mediated by P-eIF2alpha-dependent and -independent mechanisms. RNA 15, 1814-1821. https://doi.org/10.1261/rna.1684009
- Fricker, R., Brogli, R., Luidalepp, H., Wyss, L., Fasnacht, M., Joss, O., Zywicki, M., Helm, M., Schneider, A., Cristodero, M., et al. (2019). A tRNA half modulates translation as stress response in Trypanosoma brucei. Nat. Commun. 10, 118. https://doi.org/10.1038/s41467-018-07949-6
- Fu, H., Feng, J., Liu, Q., Sun, F., Tie, Y., Zhu, J., Xing, R., Sun, Z., and Zheng, X. (2009). Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett. 583, 437-442. https://doi.org/10.1016/j.febslet.2008.12.043
- Gebetsberger, J., Wyss, L., Mleczko, A.M., Reuther, J., and Polacek, N. (2017). A tRNA-derived fragment competes with mRNA for ribosome binding and regulates translation during stress. RNA Biol. 14, 1364-1373. https://doi.org/10.1080/15476286.2016.1257470
- Gebetsberger, J., Zywicki, M., Kunzi, A., and Polacek, N. (2012). tRNAderived fragments target the ribosome and function as regulatory non-coding RNA in haloferax volcanii. Archaea 2012, 260909.
- Goodarzi, H., Liu, X., Nguyen, H.C.B., Zhang, S., Fish, L., and Tavazoie, S.F. (2015). Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell 161, 790-802. https://doi.org/10.1016/j.cell.2015.02.053
- Gupta, N., Singh, A., Zahra, S., and Kumar, S. (2018). PtRFdb: a database for plant transfer RNA-derived fragments. Database (Oxford) 2018, 1-8. https://doi.org/10.1093/database/bay092
- Guzzi, N., Ciesla, M., Ngoc, P.C.T., Lang, S., Arora, S., Dimitriou, M., Pimkova, K., Sommarin, M.N.E., Munita, R., Lubas, M., et al. (2018). Pseudouridylation of tRNA-derived fragments steers translational control in stem cells. Cell 173, 1204-1216. https://doi.org/10.1016/j.cell.2018.03.008
- Haiser, H.J., Karginov, F.V., Hannon, G.J., and Elliot, M.A. (2008). Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor. Nucleic Acids Res. 36, 732-741. https://doi.org/10.1093/nar/gkm1096
- Haussecker, D., Huang, Y., Lau, A., Parameswaran, P., Fire, A.Z., and Kay, M.A. (2010). Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16, 673-695. https://doi.org/10.1261/rna.2000810
- Ivanov, P., Emara, M.M., Villen, J., Gygi, S.P., and Anderson, P. (2011). Angiogenin-induced tRNA fragments inhibit translation initiation. Mol. Cell 43, 613-623. https://doi.org/10.1016/j.molcel.2011.06.022
- Ivanov, P., O'Day, E., Emara, M.M., Wagner, G., Lieberman, J., and Anderson, P. (2014). G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments. Proc. Natl. Acad. Sci. U. S. A. 111, 18201-18206. https://doi.org/10.1073/pnas.1407361111
- Jochl, C., Rederstorff, M., Hertel, J., Stadler, P.F., Hofacker, I.L., Schrettl, M., Haas, H., and Huttenhofer, A. (2008). Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res. 36, 2677-2689. https://doi.org/10.1093/nar/gkn123
- Keam, S.P., Sobala, A., Ten Have, S., and Hutvagner, G. (2017). tRNA-derived RNA fragments associate with human multisynthetase complex (MSC) and modulate ribosomal protein translation. J. Proteome Res. 16, 413-420. https://doi.org/10.1021/acs.jproteome.6b00267
- Kim, H.K., Fuchs, G., Wang, S., Wei, W., Zhang, Y., Park, H., Roy-Chaudhuri, B., Li, P., Xu, J., Chu, K., et al. (2017). A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature 552, 57-62. https://doi.org/10.1038/nature25005
- Kumar, P., Anaya, J., Mudunuri, S.B., and Dutta, A. (2014a). 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. 12, 78. https://doi.org/10.1186/s12915-014-0078-0
- Kumar, P., Kuscu, C., and Dutta, A. (2016). Biogenesis and function of transfer RNA-related fragments (tRFs). Trends Biochem. Sci. 41, 679-689. https://doi.org/10.1016/j.tibs.2016.05.004
- Kumar, P., Mudunuri, S.B., Anaya, J., and Dutta, A. (2014b). tRFdb: a database for transfer RNA fragments. Nucleic Acids Res. 43, D141-D145. https://doi.org/10.1093/nar/gku1138
- Lee, S.R. and Collins, K. (2005). Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. J. Biol. Chem. 280, 42744-42749. https://doi.org/10.1074/jbc.M510356200
- Lee, Y.S., Shibata, Y., Malhotra, A., and Dutta, A. (2009). A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev. 23, 2639-2649. https://doi.org/10.1101/gad.1837609
- Levitz, R., Chapman, D., Amitsur, M., Green, R., Snyder, L., and Kaufmann, G. (1990). The optional E. coli prr locus encodes a latent form of phage T4-induced anticodon nuclease. EMBO J. 9, 1383-1389. https://doi.org/10.1002/j.1460-2075.1990.tb08253.x
- Luo, S., He, F., Luo, J., Dou, S., Wang, Y., Guo, A., and Lu, J. (2018). Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response. Nucleic Acids Res. 46, 5250-5268. https://doi.org/10.1093/nar/gky189
- Lyons, S.M., Achorn, C., Kedersha, N.L., Anderson, P.J., and Ivanov, P. (2016). YB-1 regulates tiRNA-induced Stress Granule formation but not translational repression. Nucleic Acids Res. 44, 6949-6960. https://doi.org/10.1093/nar/gkw418
- Lyons, S.M., Gudanis, D., Coyne, S.M., Gdaniec, Z., and Ivanov, P. (2017). Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs. Nat. Commun. 8, 1127. https://doi.org/10.1038/s41467-017-01278-w
- Mleczko, A.M., Celichowski, P., and Bakowska-Zywicka, K. (2018). Transfer RNA-derived fragments target and regulate ribosome-associated aminoacyl-transfer RNA synthetases. Biochim. Biophys. Acta Gene Regul. Mech. 1861, 647-656. https://doi.org/10.1016/j.bbagrm.2018.06.001
- Nekrasov, M.P., Ivshina, M.P., Chernov, K.G., Kovrigina, E.A., Evdokimova, V.M., Thomas, A.A.M., Hershey, J.W.B., and Ovchinnikov, L.P. (2003). The mRNA-binding protein YB-1 (p50) prevents association of the eukaryotic initiation factor eIF4G with mRNA and inhibits protein synthesis at the initiation stage. J. Biol. Chem. 278, 13936-13943. https://doi.org/10.1074/jbc.M209145200
- Panas, M.D., Ivanov, P., and Anderson, P. (2016). Mechanistic insights into mammalian stress granule dynamics. J. Cell Biol. 215, 313-323. https://doi.org/10.1083/jcb.201609081
- Phizicky, E.M. and Hopper, A.K. (2010). tRNA biology charges to the front. Genes Dev. 24, 1832-1860. https://doi.org/10.1101/gad.1956510
- Pliatsika, V., Loher, P., Magee, R., Telonis, A.G., Londin, E., Shigematsu, M., Kirino, Y., and Rigoutsos, I. (2018). MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res. 46, D152-D159. https://doi.org/10.1093/nar/gkx1075
- Robledo, S., Idol, R.A., Crimmins, D.L., Ladenson, J.H., Mason, P.J., and Bessler, M. (2008). The role of human ribosomal proteins in the maturation of rRNA and ribosome production. RNA 14, 1918-1929. https://doi.org/10.1261/rna.1132008
- Schimmel, P. (2017). The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat. Rev. Mol. Cell Biol. 19, 45-58. https://doi.org/10.1038/nrm.2017.77
- Telonis, A.G., Loher, P., Honda, S., Jing, Y., Palazzo, J., Kirino, Y., and Rigoutsos, I. (2015). Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget 6, 24797-24822. https://doi.org/10.18632/oncotarget.4695
- Thompson, D.M., Lu, C., Green, P.J., and Parker, R. (2008). tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14, 2095-2103. https://doi.org/10.1261/rna.1232808
- Yamasaki, S., Ivanov, P., Hu, G.F., and Anderson, P. (2009). Angiogenin cleaves tRNA and promotes stress-induced translational repression. J. Cell Biol. 185, 35-42. https://doi.org/10.1083/jcb.200811106
- Zhang, S., Sun, L., and Kragler, F. (2009). The phloem-delivered RNA pool contains small noncoding RNAs and interferes with translation. Plant Physiol. 150, 378-387. https://doi.org/10.1104/pp.108.134767
- Zheng, G., Qin, Y., Clark, W.C., Dai, Q., Yi, C., He, C., Lambowitz, A.M., and Pan, T. (2015). Efficient and quantitative high-throughput tRNA sequencing. Nat. Methods 12, 835-837. https://doi.org/10.1038/nmeth.3478
- Zheng, L.L., Xu, W.L., Liu, S., Sun, W.J., Li, J.H., Wu, J., Yang, J.H., and Qu, L.H. (2016). tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. Nucleic Acids Res. 44, W185-W193. https://doi.org/10.1093/nar/gkw414
Cited by
- Small RNA Sequencing Reveals Transfer RNA-derived Small RNA Expression Profiles in Retinal Neovascularization vol.17, pp.12, 2020, https://doi.org/10.7150/ijms.46209
- Novel Links between TORC1 and Traditional Non-Coding RNA, tRNA vol.11, pp.9, 2019, https://doi.org/10.3390/genes11090956
- Non-Coding RNAs as Cancer Hallmarks in Chronic Lymphocytic Leukemia vol.21, pp.18, 2019, https://doi.org/10.3390/ijms21186720
- Elucidating the Role of Serum tRF-31-U5YKFN8DYDZDD as a Novel Diagnostic Biomarker in Gastric Cancer (GC) vol.11, 2019, https://doi.org/10.3389/fonc.2021.723753
- Research progress on the tsRNA classification, function, and application in gynecological malignant tumors vol.7, pp.1, 2019, https://doi.org/10.1038/s41420-021-00789-2
- Dnmt2-null sperm block maternal transmission of a paramutant phenotype† vol.105, pp.3, 2021, https://doi.org/10.1093/biolre/ioab086
- Regulatory roles of tRNA-derived RNA fragments in human pathophysiology vol.26, 2019, https://doi.org/10.1016/j.omtn.2021.06.023
- Multiple targets identified with genome wide profiling of small RNA and mRNA expression are linked to fracture healing in mice vol.15, 2019, https://doi.org/10.1016/j.bonr.2021.101115
- Deciphering the tRNA-derived small RNAs: origin, development, and future vol.13, pp.1, 2019, https://doi.org/10.1038/s41419-021-04472-3