In silico approach for the identification of tRNA-derived small non-coding RNAs in SARS-CoV infection

Alexandrov A, Chernyakov I, Gu W et al (2006) Rapid tRNA decay can result from lack of nonessential modifications. Mol Cell 21:87–96. https://doi.org/10.1016/J.MOLCEL.2005.10.036

Article  CAS  PubMed  Google Scholar 

Anderson P, Ivanov P (2014) tRNA fragments in human health and disease. FEBS Lett 588:4297. https://doi.org/10.1016/J.FEBSLET.2014.09.001

Article  CAS  PubMed  PubMed Central  Google Scholar 

Arimbasseri AG, Maraia RJ (2016) RNA polymerase III Advances: structural and tRNA functional views. Trends Biochem Sci 41:546. https://doi.org/10.1016/J.TIBS.2016.03.003

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297. https://doi.org/10.1016/S0092-8674(04)00045-5

Article  CAS  PubMed  Google Scholar 

Bidet K, Dadlani D, Garcia-Blanco MA (2014) G3BP1, G3BP2 and CAPRIN1 are required for translation of interferon stimulated mRNAs and are targeted by a dengue virus non-coding RNA. PLoS Pathog 10:e1004242. https://doi.org/10.1371/JOURNAL.PPAT.1004242

Article  PubMed  PubMed Central  Google Scholar 

Chan PP, Lowe TM (2016) GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res 44:D184–D189. https://doi.org/10.1093/NAR/GKV1309

Article  CAS  PubMed  Google Scholar 

Damas ND, Fossat N, Scheel TKH (2019) Functional interplay between RNA viruses and non-coding RNA in mammals. Noncoding RNA 5:7. https://doi.org/10.3390/NCRNA5010007

Article  CAS  PubMed  PubMed Central  Google Scholar 

DeDiego ML, Álvarez E, Almazán F et al (2007) A severe acute respiratory syndrome coronavirus that lacks the E gene is attenuated in vitro and in vivo. J Virol 81:1701. https://doi.org/10.1128/JVI.01467-06

Article  CAS  PubMed  Google Scholar 

Deng J, Ptashkin RN, Chen Y et al (2015) Respiratory syncytial virus utilizes a tRNA fragment to suppress antiviral responses through a novel targeting mechanism. Molecular Therapy 23:1622. https://doi.org/10.1038/MT.2015.124

Article  CAS  PubMed  PubMed Central  Google Scholar 

Emara MM, Ivanov P, Hickman T et al (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

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fu H, Feng J, Liu Q et al (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

Article  CAS  PubMed  Google Scholar 

Gebert D, Hewel C, Rosenkranz D (2017) unitas: the universal tool for annotation of small RNAs. BMC Genomics 18:1–14. https://doi.org/10.1186/S12864-017-4031-9

Article  Google Scholar 

Grundhoff A, Sullivan CS (2011) Virus-encoded microRNAs. Virology 411:325. https://doi.org/10.1016/J.VIROL.2011.01.002

Article  CAS  PubMed  Google Scholar 

Haiser HJ, Karginov FV, Hannon GJ, Elliot MA (2008) Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor. Nucleic Acids Res 36:732–741. https://doi.org/10.1093/NAR/GKM1096

Article  CAS  PubMed  Google Scholar 

Hunter JD (2007) Matplotlib: a 2D graphics environment. Comput Sci Eng 9:90–95. https://doi.org/10.1109/MCSE.2007.55

Article  Google Scholar 

Ibba M, Söll D (2004) Aminoacyl-tRNAs: setting the limits of the genetic code. Genes Dev 18:731–738. https://doi.org/10.1101/GAD.1187404

Article  CAS  PubMed  Google Scholar 

Jiang H, Wong WH (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24:2395. https://doi.org/10.1093/BIOINFORMATICS/BTN429

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kumar P, Anaya J, Mudunuri SB, Dutta A (2014) 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 12:1–14. https://doi.org/10.1186/S12915-014-0078-0

Article  CAS  Google Scholar 

Larminie CGC, Sutcliffe JE, Tosh K et al (1999) Activation of RNA polymerase III transcription in cells transformed by simian virus 40. Mol Cell Biol 19:4927. https://doi.org/10.1128/MCB.19.7.4927

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee SR, 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

Article  CAS  PubMed  Google Scholar 

Lee YS, Shibata Y, Malhotra A, Dutta A (2009) A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23:2639. https://doi.org/10.1101/GAD.1837609

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li S, Xu Z, Sheng J (2018) tRNA-derived small RNA: a novel regulatory small non-coding RNA. Genes (Basel) 9:246. https://doi.org/10.3390/GENES9050246

Article  PubMed  Google Scholar 

Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:1–21. https://doi.org/10.1186/S13059-014-0550-8

Article  Google Scholar 

Morales L, Oliveros JC, Fernandez-Delgado R et al (2017) SARS-CoV-encoded small RNAs contribute to infection-associated lung pathology. Cell Host Microbe 21:344. https://doi.org/10.1016/J.CHOM.2017.01.015

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pan T (2018) Modifications and functional genomics of human transfer RNA. Cell Res 28:395–404. https://doi.org/10.1038/S41422-018-0013-Y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Perez JT, Varble A, Sachidanandam R et al (2010) Influenza A virus-generated small RNAs regulate the switch from transcription to replication. Proc Natl Acad Sci U S A 107:11525–11530. https://doi.org/10.1073/PNAS.1001984107/-/DCSUPPLEMENTAL

Article  CAS  PubMed  PubMed Central  Google Scholar 

Roberts A, Deming D, Paddock CD et al (2007) A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice. PLoS Pathog 3:0023–0037. https://doi.org/10.1371/JOURNAL.PPAT.0030005

Article  CAS  Google Scholar 

Ruggero K, Guffanti A, Corradin A et al (2014) 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 88:3612. https://doi.org/10.1128/JVI.02823-13

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ruivinho C, Gama-Carvalho M (2023) Small non-coding RNAs encoded by RNA viruses: old controversies and new lessons from the COVID-19 pandemic. Front Genet 14:1216890. https://doi.org/10.3389/FGENE.2023.1216890/BIBTEX

Article  CAS  PubMed  PubMed Central  Google Scholar 

Selitsky SR, Baran-Gale J, Honda M et al (2015) Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C. Sci Rep 5:1–7. https://doi.org/10.1038/srep07675

Article  CAS  Google Scholar 

Shi J, Zhang Y, Zhou T, Chen Q (2019) tsRNAs: the Swiss Army Knife for translational regulation. Trends Biochem Sci 44:185–189. https://doi.org/10.1016/J.TIBS.2018.09.007

Article  CAS  PubMed  Google Scholar 

Shigematsu M, Kirino Y (2015) tRNA-derived short non-coding RNA as interacting partners of Argonaute proteins. Gene Regul Syst Bio 9:27. https://doi.org/10.4137/GRSB.S29411

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thompson DM, Parker R (2009) Stressing out over tRNA cleavage. Cell 138:215–219. https://doi.org/10.1016/J.CELL.2009.07.001

Article  CAS  PubMed  Google Scholar 

Tycowski KT, Guo YE, Lee N et al (2015) Viral noncoding RNAs: more surprises. Genes Dev 29:567. https://doi.org/10.1101/GAD.259077.115

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vaňáčová Š, Wolf J, Martin G et al (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3:e189.

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