Identification and functional characterization of tRNA-derived RNA fragments (tRFs) in respiratory syncytial virus infection

Molecular Therapy

Volumn 21, Issue 2, 2013, Pages 368-379

  Wang, Qingrong ^a   Lee, Inhan ^b   Ren, Junping ^a   Ajay, Subramanian Shankar ^c   Lee, Yong Sun ^a   Bao, Xiaoyong ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

^b MiRcore   (United States)

^c NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOGENIN; SMALL UNTRANSLATED RNA; TRANSFER RNA;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; EMBRYO; GENE EXPRESSION PROFILING; GENE MAPPING; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; LUNG ALVEOLUS EPITHELIUM; MOLECULAR CLONING; MOLECULARLY TARGETED THERAPY; NONHUMAN; RESPIRATORY SYNCYTIAL VIRUS INFECTION; RNA ANALYSIS; RNA DEGRADATION; RNA TRANSPORT; VIRUS REPLICATION;

HUMAN RESPIRATORY SYNCYTIAL VIRUS; RESPIRATORY SYNCYTIAL VIRUS; RICE STRIPE VIRUS;

EID: 84873409537     PISSN: 15250016     EISSN: 15250024     Source Type: Journal    
DOI: 10.1038/mt.2012.237     Document Type: Article

References (50)

1. Esteller, M (2011). Non-coding RNAs in human disease. Nat Rev Genet 12: 861-874.
2. Skalsky, RL and Cullen, BR (2010). Viruses, microRNAs, and host interactions. Annu Rev Microbiol 64: 123-141.
3. Tuck, AC and Tollervey, D (2011). RNA in pieces. Trends Genet 27: 422-432.
4. Sobala, A and Hutvagner, G (2011). Transfer RNA-derived fragments: origins, processing, and functions. Wiley Interdiscip Rev RNA 2: 853-862.
5. Emara, MM, Ivanov, P, Hickman, T, Dawra, N, Tisdale, S, Kedersha, N et al. (2010). Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J Biol Chem 285: 10959-10968.
6. Yamasaki, S, Ivanov, P, Hu, GF and Anderson, P (2009). Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol 185: 35-42.
7. Cole, C, Sobala, A, Lu, C, Thatcher, SR, Bowman, A, Brown, JW et al. (2009). Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 15: 2147-2160.
8. Lee, YS, Shibata, Y, Malhotra, A and Dutta, A (2009). A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23: 2639-2649.
9. Haussecker, D, Huang, Y, Lau, A, Parameswaran, P, Fire, AZ and Kay, MA (2010). Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16: 673-695.
10. Hermos, CR, Vargas, SO and McAdam, AJ (2010). Human metapneumovirus. Clin Lab Med 30: 131-148.
11. Papenburg, J and Boivin, G (2010). The distinguishing features of human metapneumovirus and respiratory syncytial virus. Rev Med Virol 20: 245-260.
12. Glezen, WP, Taber, LH, Frank, AL and Kasel, JA (1986). Risk of primary infection and reinfection with respiratory syncytial virus. Am J Dis Child 140: 543-546.
13. Falsey, AR, Hennessey, PA, Formica, MA, Cox, C and Walsh, EE (2005). Respiratory syncytial virus infection in elderly and high-risk adults. N Engl J Med 352: 1749-1759.
14. Martin, JA, Hamilton, BE, Sutton, PD, Ventura, SJ, Menacker, F, Kirmeyer, S et al. (2007). Births: fnal data for 2005. Natl Vital Stat Rep 56: 1-103.
15. Liu, X, Wang, T, Wakita, T and Yang, W (2010). Systematic identifcation of microRNA and messenger RNA profles in hepatitis C virus-infected human hepatoma cells. Virology 398: 57-67.
16. Hess, AM, Prasad, AN, Ptitsyn, A, Ebel, GD, Olson, KE, Barbacioru, C et al. (2011). Small RNA profling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense. BMC Microbiol 11: 45.
17. Boss, IW and Renne, R (2010). Viral miRNAs: tools for immune evasion. Curr Opin Microbiol 13: 540-545.
18. Dölken, L, Pfeffer, S and Koszinowski, UH (2009). Cytomegalovirus microRNAs. Virus Genes 38: 355-364.
19. Pfeffer, S, Zavolan, M, Grässer, FA, Chien, M, Russo, JJ, Ju, J et al. (2004). Identifcation of virus-encoded microRNAs. Science 304: 734-736.
20. Reese, TA, Xia, J, Johnson, LS, Zhou, X, Zhang, W and Virgin, HW (2010). Identifcation of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts. J Virol 84: 10344-10353.
21. Fujishima, K, Sugahara, J, Tomita, M and Kanai, A (2008). Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves. PLoS ONE 3: e1622.
22. Garofalo, R P, Mei, F, Manganaro, M, Espejo, R, Ogra, PL and Reyes, VE (1994). Upregulation of class I major histocompatibility complex (MHC) molecules on respiratory syncytial virus (RSV)-infected airway epithelial cells. Am J Respir Crit Care Med 149: A987.
23. Ren, J, Kolli, D, Liu, T, Xu, R, Garofalo, RP, Casola, A et al. (2011). Human metapneumovirus inhibits IFN-β signaling by downregulating Jak1 and Tyk2 cellular levels. PLoS ONE 6: e24496.
24. Bao, X, Liu, T, Spetch, L, Kolli, D, Garofalo, RP and Casola, A (2007). Airway epithelial cell response to human metapneumovirus infection. Virology 368: 91-101.
25. Zhang, Y, Luxon, BA, Casola, A, Garofalo, RP, Jamaluddin, M and Brasier, AR (2001). Expression of respiratory syncytial virus-induced chemokine gene networks in lower airway epithelial cells revealed by cDNA microarrays. J Virol 75: 9044-9058.
26. Bao, X, Liu, T, Shan, Y, Li, K, Garofalo, RP and Casola, A (2008). Human metapneumovirus glycoprotein G inhibits innate immune responses. PLoS Pathog 4: e1000077.
27. Lee, YS, Nakahara, K, Pham, JW, Kim, K, He, Z, Sontheimer, EJ et al. (2004). Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117: 69-81.
28. Yoo, BH, Bochkareva, E, Bochkarev, A, Mou, TC and Gray, DM (2004). 2'-O-methyl-modifed phosphorothioate antisense oligonucleotides have reduced non-specifc effects in vitro. Nucleic Acids Res 32: 2008-2016.
29. Ideue, T, Hino, K, Kitao, S, Yokoi, T and Hirose, T (2009). Effcient oligonucleotide-mediated degradation of nuclear noncoding RNAs in mammalian cultured cells. RNA 15: 1578-1587.
30. Haeberle, HA, Kuziel, WA, Dieterich, HJ, Casola, A, Gatalica, Z and Garofalo, RP (2001). Inducible expression of infammatory chemokines in respiratory syncytial virus-infected mice: role of MIP-1alpha in lung pathology. J Virol 75: 878-890.
31. Ardelt, W, Mikulski, SM and Shogen, K (1991). Amino acid sequence of an anti-tumor protein from Rana pipiens oocytes and early embryos. Homology to pancreatic ribonucleases. J Biol Chem 266: 245-251.
32. Kaufmann, G (2000). Anticodon nucleases. Trends Biochem Sci 25: 70-74.
33. Suhasini, AN and Sirdeshmukh, R (2006). Transfer RNA cleavages by onconase reveal unusual cleavage sites. J Biol Chem 281: 12201-12209.
34. Akaike, T and Maeda, H (2000). Nitric oxide and virus infection. Immunology 101: 300-308.
35. Bitko, V and Barik, S (2001). An endoplasmic reticulum-specifc stress-activated caspase (caspase-12) is implicated in the apoptosis of A549 epithelial cells by respiratory syncytial virus. J Cell Biochem 80: 441-454.
36. Castelli, J, Wood, KA and Youle, RJ (1998). The 2-5A system in viral infection and apoptosis. Biomed Pharmacother 52: 386-390.
37. Hsieh, LC, Lin, SI, Shih, AC, Chen, JW, Lin, WY, Tseng, CY et al. (2009). Uncovering small RNA-mediated responses to phosphate defciency in Arabidopsis by deep sequencing. Plant Physiol 151: 2120-2132.
38. 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.
39. Lee, SR and Collins, K (2005). Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. J Biol Chem 280: 42744-42749.
40. Haiser, HJ, Karginov, FV, Hannon, GJ and Elliot, MA (2008). Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor. Nucleic Acids Res 36: 732-741.
41. Thompson, DM, Lu, C, Green, PJ and Parker, R (2008). tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14: 2095-2103.
42. Thompson, DM and Parker, R (2009). The RNase Rny1p cleaves tRNAs and promotes cell death during oxidative stress in Saccharomyces cerevisiae. J Cell Biol 185: 43-50.
43. Gerlier, D and Lyles, DS (2011). Interplay between innate immunity and negativestrand RNA viruses: towards a rational model. Microbiol Mol Biol Rev 75: 468-90, second page of table of contents.
44. Bitko, V, Musiyenko, A, Shulyayeva, O and Barik, S (2005). Inhibition of respiratory viruses by nasally administered siRNA. Nat Med 11: 50-55.
45. Zhang, W, Yang, H, Kong, X, Mohapatra, S, San Juan-Vergara, H, Hellermann, G et al. (2005). Inhibition of respiratory syncytial virus infection with intranasal siRNA nanoparticles targeting the viral NS1 gene. Nat Med 11: 56-62.
46. Guerrero-Plata, A, Casola, A and Garofalo, RP (2005). Human metapneumovirus induces a profle of lung cytokines distinct from that of respiratory syncytial virus. J Virol 79: 14992-14997.
47. Ren, J, Liu, T, Pang, L, Li, K, Garofalo, R P, Casola, A et al. (2011). A novel mechanism for the inhibition of interferon regulatory factor-3-dependent gene expression by human respiratory syncytial virus NS1 protein. J Gen Virol 92(Pt 9): 2153-2159.
48. Li, H, Handsaker, B, Wysoker, A, Fennell, T, Ruan, J, Homer, N et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
49. Lee, K, Kunkeaw, N, Jeon, SH, Lee, I, Johnson, BH, Kang, GY et al. (2011). Precursor miR-886, a novel noncoding RNA repressed in cancer, associates with PKR and modulates its activity. RNA 17: 1076-1089.
50. Bannister, R, Rodrigues, D, Murray, EJ, Laxton, C, Westby, M and Bright, H (2010). Use of a highly sensitive strand-specifc quantitative PCR to identify abortive replication in the mouse model of respiratory syncytial virus disease. Virol J 7: 250.