دورية أكاديمية
In silico approach for the identification of tRNA-derived small non-coding RNAs in SARS-CoV infection.
| العنوان: | In silico approach for the identification of tRNA-derived small non-coding RNAs in SARS-CoV infection. |
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| المؤلفون: | Ajmeriya S; Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India., Bharti DR; Trinity Translation Medicine Institute, Trinity College Dublin, The University of Dublin, Dublin, Ireland., Kumar A; ICMR-AIIMS Computational Genomics Center, Division of Biomedical Informatics, Division, Indian Council of Medical Research, Ansari Nagar, New Delhi, India., Rana S; ICMR-AIIMS Computational Genomics Center, Division of Biomedical Informatics, Division, Indian Council of Medical Research, Ansari Nagar, New Delhi, India., Singh H; ICMR-AIIMS Computational Genomics Center, Division of Biomedical Informatics, Division, Indian Council of Medical Research, Ansari Nagar, New Delhi, India., Karmakar S; Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India. subhradip.k@aiims.edu. |
| المصدر: | Journal of applied genetics [J Appl Genet] 2024 May; Vol. 65 (2), pp. 403-413. Date of Electronic Publication: 2024 Mar 21. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Springer Country of Publication: England NLM ID: 9514582 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2190-3883 (Electronic) Linking ISSN: 12341983 NLM ISO Abbreviation: J Appl Genet Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 2011- : Cheshire, United Kingdom : Springer Original Publication: Poznań, Poland : Institute of Plant Genetics, Polish Academy of Sciences, 1995- |
| مواضيع طبية MeSH: | Virus Diseases* , Severe acute respiratory syndrome-related coronavirus*/genetics, Mice ; Animals ; RNA, Transfer/genetics ; RNA, Transfer/metabolism |
| مستخلص: | tsRNAs (tRNA-derived small non-coding RNAs), including tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been implicated in some viral infections, such as respiratory viral infections. However, their involvement in SARS-CoV infection is completely unknown. A comprehensive analysis was performed to determine tsRNA populations in a mouse model of SARS-CoV-infected samples containing the wild-type and attenuated viruses. Data from the Gene Expression Omnibus (GEO) dataset at NCBI (accession ID GSE90624 ) was used for this study. A count matrix was generated for the tRNAs. Differentially expressed tRNAs, followed by tsRNAs derived from each significant tRNAs at different conditions and time points between the two groups WT(SARS-CoV-MA15-WT) vs Mock and ΔE (SARS-CoV-MA15-ΔE) vs Mock were identified. Notably, significantly differentially expressed tRNAs at 2dpi but not at 4dpi. The tsRNAs originating from differentially expressed tRNAs across all the samples belonging to each condition (WT, ΔE, and Mock) were identified. Intriguingly, tRFs (tRNA-derived RNA fragments) exhibited higher levels compared to tiRNAs (tRNA-derived stress-induced RNAs) across all samples associated with WT SARS-CoV strain compared to ΔE and mock-infected samples. This discrepancy suggests a non-random formation of tsRNAs, hinting at a possible involvement of tsRNAs in SARS-CoV viral infection. (© 2024. The Author(s), under exclusive licence to Institute of Plant Genetics Polish Academy of Sciences.) |
| References: | 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. (PMID: 10.1016/J.MOLCEL.2005.10.03616387656) 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. (PMID: 10.1016/J.FEBSLET.2014.09.001252206754339185) 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. (PMID: 10.1016/J.TIBS.2016.03.003270688034884153) Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297. https://doi.org/10.1016/S0092-8674(04)00045-5. (PMID: 10.1016/S0092-8674(04)00045-514744438) 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. (PMID: 10.1371/JOURNAL.PPAT.1004242249920364081823) 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. (PMID: 10.1093/NAR/GKV130926673694) 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. (PMID: 10.3390/NCRNA5010007306466096468702) 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. (PMID: 10.1128/JVI.01467-0617108030) 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. (PMID: 10.1038/MT.2015.124261562444817927) 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. (PMID: 10.1074/jbc.M109.077560201299162856301) 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. (PMID: 10.1016/J.FEBSLET.2008.12.04319114040) 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. (PMID: 10.1186/S12864-017-4031-9) Grundhoff A, Sullivan CS (2011) Virus-encoded microRNAs. Virology 411:325. https://doi.org/10.1016/J.VIROL.2011.01.002. (PMID: 10.1016/J.VIROL.2011.01.00221277611) 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. (PMID: 10.1093/NAR/GKM109618084030) Hunter JD (2007) Matplotlib: a 2D graphics environment. Comput Sci Eng 9:90–95. https://doi.org/10.1109/MCSE.2007.55. (PMID: 10.1109/MCSE.2007.55) 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. (PMID: 10.1101/GAD.118740415082526) Jiang H, Wong WH (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24:2395. https://doi.org/10.1093/BIOINFORMATICS/BTN429. (PMID: 10.1093/BIOINFORMATICS/BTN429186977692562015) 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. (PMID: 10.1186/S12915-014-0078-0) 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. (PMID: 10.1128/MCB.19.7.49271037354284300) 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. (PMID: 10.1074/JBC.M51035620016272149) 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. (PMID: 10.1101/GAD.1837609199331532779758) 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. (PMID: 10.3390/GENES905024629748504) 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. (PMID: 10.1186/S13059-014-0550-8) 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. (PMID: 10.1016/J.CHOM.2017.01.015282162515662013) 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. (PMID: 10.1038/S41422-018-0013-Y294639005939049) 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. (PMID: 10.1073/PNAS.1001984107/-/DCSUPPLEMENTAL205344712895093) 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. (PMID: 10.1371/JOURNAL.PPAT.0030005) 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. (PMID: 10.1128/JVI.02823-13244035823993537) 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. (PMID: 10.3389/FGENE.2023.1216890/BIBTEX3741560310322155) 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. (PMID: 10.1038/srep07675) 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. (PMID: 10.1016/J.TIBS.2018.09.00730297206) 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. (PMID: 10.4137/GRSB.S29411264010984567038) Thompson DM, Parker R (2009) Stressing out over tRNA cleavage. Cell 138:215–219. https://doi.org/10.1016/J.CELL.2009.07.001. (PMID: 10.1016/J.CELL.2009.07.00119632169) 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. (PMID: 10.1101/GAD.259077.115257925954378190) 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. https://doi.org/10.1371/JOURNAL.PBIO.0030189. (PMID: 10.1371/JOURNAL.PBIO.003018915828860) Wang Q, Lee I, Ren J et al (2013) Identification and functional characterization of tRNA-derived RNA fragments (tRFs) in respiratory syncytial virus infection. Molecular Therapy 21:368. https://doi.org/10.1038/MT.2012.237. (PMID: 10.1038/MT.2012.23723183536) Weng KF, Hung CT, Hsieh PT et al (2014) A cytoplasmic RNA virus generates functional viral small RNAs and regulates viral IRES activity in mammalian cells. Nucleic Acids Res 42:12789. https://doi.org/10.1093/NAR/GKU952. (PMID: 10.1093/NAR/GKU952253525514227785) Yamasaki S, Ivanov P, Hu GF, Anderson P (2009) Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol 185:35. https://doi.org/10.1083/JCB.200811106. (PMID: 10.1083/JCB.200811106193328862700517) Yu X, Xie Y, Zhang S et al (2021) tRNA-derived fragments: mechanisms underlying their regulation of gene expression and potential applications as therapeutic targets in cancers and virus infections. Theranostics 11:461–469. https://doi.org/10.7150/thno.51963. (PMID: 10.7150/thno.51963333914867681095) |
| فهرسة مساهمة: | Keywords: Coronavirus; Deep sequencing; SARS-CoV; sncRNA; tRFs; tiRNAs |
| المشرفين على المادة: | 9014-25-9 (RNA, Transfer) |
| تواريخ الأحداث: | Date Created: 20240322 Date Completed: 20240411 Latest Revision: 20240411 |
| رمز التحديث: | 20240411 |
| DOI: | 10.1007/s13353-024-00853-4 |
| PMID: | 38514586 |
| قاعدة البيانات: | MEDLINE |
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Full Text Finder | تدمد: | 2190-3883 |
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| DOI: | 10.1007/s13353-024-00853-4 |