Hints of tRNA-derived small RNAs role in RNA silencing mechanisms

Genes

Volumn 3, Issue 4, 2012, Pages 603-614

  Garcia Silva, Maria Rosa ^a   Cabrera Cabrera, Florencia ^a   Güida, Maria Catalina ^a   Cayota, Alfonso ^a,b  

^a INSTITUT PASTEUR DE MONTEVIDEO   (Uruguay)

^b HOSPITAL DE CLÍNICAS   (Uruguay)

Author keywords

RNAi; Small RNAs; tRNAs

Indexed keywords

SMALL INTERFERING RNA; SMALL TRF; TRANSFER RNA; TRANSFER RNA DERIVED SMALL RNA; TRANSFER RNA HALF; UNCLASSIFIED DRUG;

ARABIDOPSIS; ASPERGILLUS FUMIGATUS; BIOGENESIS; CELL CYCLE REGULATION; CELL DIFFERENTIATION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE SILENCING; NONHUMAN; REVIEW; RNA ANALYSIS; RNA CLEAVAGE; RNA INTERFERENCE; RNA PROCESSING; RNA STRUCTURE; RNA TRANSCRIPTION; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; STREPTOMYCES COELICOLOR;

EUKARYOTA;

EID: 84871586107     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes3040603     Document Type: Review

References (42)

1. Ogawa, T.; Tomita, K.; Ueda, T.; Watanabe, K.; Uozumi, T.; Masaki, H. A cytotoxic ribonuclease targeting specific transfer rna anticodons. Science 1999, 283, 2097-2100.
2. Thompson, D.M.; Parker, R. Stressing out over trna cleavage. Cell 2009, 138, 215-219.
3. Fu, H.; Feng, J.; Liu, Q.; Sun, F.; Tie, Y.; Zhu, J.; Xing, R.; Sun, Z.; Zheng, X. Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett. 2009, 583, 437-442.
4. Lee, Y.S.; Shibata, Y.; Malhotra, A.; Dutta, A. A novel class of small rnas: tRNA-derived RNA fragments (tRFs). Genes Dev. 2009, 23, 2639-2649.
5. Haussecker, D.; Huang, Y.; Lau, A.; Parameswaran, P.; Fire, A.Z.; Kay, M.A. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 2010, 16, 673-695.
6. Li, Y.; Luo, J.; Zhou, H.; Liao, J.Y.; Ma, L.M.; Chen, Y.Q.; Qu, L.H. Stress-induced tRNA-derived rRNA: A novel class of small rRNA in the primitive eukaryote giardia lamblia. Nucleic Acids Res. 2008, 36, 6048-6055.
7. Elbarbary, R.A.; Takaku, H.; Uchiumi, N.; Tamiya, H.; Abe, M.; Takahashi, M.; Nishida, H.; Nashimoto, M. Modulation of gene expression by human cytosolic trnase z(l) through 5'-half-tRNA. PLoS One 2009, 4, e5908.
8. Yamasaki, S.; Ivanov, P.; Hu, G.F.; Anderson, P. Angiogenin cleaves tRNA and promotes stress-induced translational repression. J. Cell Biol. 2009, 185, 35-42.
9. Lee, S.R.; Collins, K. Starvation-induced cleavage of the tRNA anticodon loop in tetrahymena thermophila. J. Biol. Chem. 2005, 280, 42744-42749.
10. Haiser, H.J.; Karginov, F.V.; Hannon, G.J.; Elliot, M.A. Developmentally regulated cleavage of trnas in the bacterium streptomyces coelicolor. Nucleic Acids Res. 2008, 36, 732-741.
11. Jochl, C.; Rederstorff, M.; Hertel, J.; Stadler, P.F.; Hofacker, I.L.; Schrettl, M.; Haas, H.; Huttenhofer, A. Small ncRNA transcriptome analysis from aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res. 2008, 36, 2677-2689.
12. Kawaji, H.; Nakamura, M.; Takahashi, Y.; Sandelin, A.; Katayama, S.; Fukuda, S.; Daub, C.O.; Kai, C.; Kawai, J.; Yasuda, J. et al. Hidden layers of human small RNAs. BMC Genomics 2008, 9, 157.
13. Thompson, D.M.; Lu, C.; Green, P.J.; Parker, R. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 2008, 14, 2095-2103.
14. Garcia-Silva, M.R.; Frugier, M.; Tosar, J.P.; Correa-Dominguez, A.; Ronalte-Alves, L.; Parodi-Talice, A.; Rovira, C.; Robello, C.; Goldenberg, S.; Cayota, A. A population of tRNA-derived small RNAs is actively produced in trypanosoma cruzi and recruited to specific cytoplasmic granules. Mol. Biochem. Parasitol. 2011, 171, 64-73.
15. Levitz, R.; Chapman, D.; Amitsur, M.; Green, R.; Snyder, L.; Kaufmann, G. The optional E. Coli prr locus encodes a latent form of phage t4-induced anticodon nuclease. EMBO J. 1990, 9, 1383-1389.
16. Tomita, K.; Ogawa, T.; Uozumi, T.; Watanabe, K.; Masaki, H. A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine trnas at their anticodon loops. Proc. Natl. Acad. Sci. USA 2000, 97, 8278-8283.
17. Emara, M.M.; Ivanov, P.; Hickman, T.; Dawra, N.; Tisdale, S.; Kedersha, N.; Hu, G.F.; Anderson, P. Angiogenin-induced tRNA-derived stress-induced rnas promote stress-induced stress granule assembly. J. Biol. Chem. 2010, 285, 10959-10968.
18. Ivanov, P.; Emara, M.M.; Villen, J.; Gygi, S.P.; Anderson, P. Angiogenin-induced tRNA fragments inhibit translation initiation. Mol. Cell 2011, 43, 613-623.
19. Lee, Y.S.; Pressman, S.; Andress, A.P.; Kim, K.; White, J.L.; Cassidy, J.J.; Li, X.; Lubell, K.; Lim do, H.; Cho, I.S. et al Silencing by small rnas is linked to endosomal trafficking. Nat. Cell Biol. 2009, 11, 1150-1156.
20. Franzen, O.; Arner, E.; Ferella, M.; Nilsson, D.; Respuela, P.; Carninci, P.; Hayashizaki, Y.; Aslund, L.; Andersson, B.; Daub, C.O. The short non-coding transcriptome of the protozoan parasite trypanosoma cruzi. PLoS Negl. Trop. Dis. 2011, 5, e1283.
21. Schaefer, M.; Pollex, T.; Hanna, K.; Tuorto, F.; Meusburger, M.; Helm, M.; Lyko, F. RNA methylation by dnmt2 protects transfer rnas against stress-induced cleavage. Genes Dev. 2010, 24, 1590-1595.
22. Zhang, S.; Sun, L.; Kragler, F. The phloem-delivered RNA pool contains small noncoding RNAs and interferes with translation. Plant Physiol. 2009, 150, 378-387.
23. Garcia Silva, M.R.; Tosar, J.P.; Frugier, M.; Pantano, S.; Bonilla, B.; Esteban, L.; Serra, E.; Rovira, C.; Robello, C.; Cayota, A. Cloning, characterization and subcellular localization of a trypanosoma cruzi argonaute protein defining a new subfamily distinctive of trypanosomatids. Gene 2010, 466, 26-35.
24. Brennecke, J.; Aravin, A.A.; Stark, A.; Dus, M.; Kellis, M.; Sachidanandam, R.; Hannon, G.J. Discrete small RNA-generating loci as master regulators of transposon activity in drosophila. Cell 2007, 128, 1089-1103.
25. Babiarz, J.E.; Ruby, J.G.; Wang, Y.; Bartel, D.P.; Blelloch, R. Mouse es cells express endogenous shrnas, siRNAs, and other microprocessor-independent, dicer-dependent small rnas. Genes Dev. 2008, 22, 2773-2785.
26. Cole, C.; Sobala, A.; Lu, C.; Thatcher, S.R.; Bowman, A.; Brown, J.W.; Green, P.J.; Barton, G.J.; Hutvagner, G. Filtering of deep sequencing data reveals the existence of abundant dicer-dependent small RNAs derived from tRNAs. RNA 2009, 15, 2147-2160.
27. Pederson, T. Regulatory RNAs derived from transfer RNA? RNA 2010, 16, 1865-1869.
28. Sobala, A.; Hutvagner, G. Transfer RNA-derived fragments: Origins, processing, and functions. Wiley Interdiscip. Rev. 2011, 2, 853-862.
29. Liao, J.Y.; Ma, L.M.; Guo, Y.H.; Zhang, Y.C.; Zhou, H.; Shao, P.; Chen, Y.Q.; Qu, L.H. Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of mirnas and tRNA 3' trailers. PLoS One 2010, 5, e10563.
30. Li, Z.; Ender, C.; Meister, G.; Moore, P.S.; Chang, Y.; John, B. Extensive terminal and asymmetric processing of small RNAs from rrnas, snornas, snrnas, and trnas. Nucleic Acids Res. 2012, 40, 6787-6799.
31. Jinek, M.; Doudna, J.A. A three-dimensional view of the molecular machinery of RNA interference. Nature 2009, 457, 405-412.
32. Miyoshi, K.; Miyoshi, T.; Siomi, H. Many ways to generate microrna-like small RNAs: Non-canonical pathways for microrna production. Mol. Genet. Genomics 2010, 284, 95-103.
33. Tuck, A.C.; Tollervey, D. RNA in pieces. Trends Genet. 2011, 27, 422-432.
34. Kim, V.N. Small RNAs: Classification, biogenesis, and function. Mol. Cells 2005, 19, 1-15.
35. Hutvagner, G.; Simard, M.J. Argonaute proteins: Key players in RNA silencing. Nat. Rev. Mol. Cell Biol. 2008, 9, 22-32.
36. Burroughs, A.M.; Ando, Y.; de Hoon, M.J.; Tomaru, Y.; Suzuki, H.; Hayashizaki, Y.; Daub, C.O. Deep-sequencing of human argonaute-associated small RNAs provides insight into miRNA sorting and reveals argonaute association with RNA fragments of diverse origin. RNA Biol. 2011, 8, 158-177.
37. Ender, C.; Krek, A.; Friedlander, M.R.; Beitzinger, M.; Weinmann, L.; Chen, W.; Pfeffer, S.; Rajewsky, N.; Meister, G. A human snorna with microRNA-like functions. Mol. Cell 2008, 32, 519-528.
38. Yeung, M.L.; Bennasser, Y.; Watashi, K.; Le, S.Y.; Houzet, L.; Jeang, K.T. Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: Evidence for the processing of a viral-cellular double-stranded RNA hybrid. Nucleic Acids Res. 2009, 37, 6575-6586.
39. Tamura, M.; Nashimoto, C.; Miyake, N.; Daikuhara, Y.; Ochi, K.; Nashimoto, M. Intracellular mrna cleavage by 3' trnase under the direction of 2'-o-methyl RNA heptamers. Nucleic Acids Res. 2003, 31, 4354-4360.
40. Nakashima, A.; Takaku, H.; Shibata, H.S.; Negishi, Y.; Takagi, M.; Tamura, M.; Nashimoto, M. Gene silencing by the tRNA maturase trnase zl under the direction of small-guide RNA. Gene Ther. 2007, 14, 78-85.
41. Takahashi, M.; Elbarbary, R.A.; Abe, M.; Sato, M.; Yoshida, T.; Yamada, Y.; Tamura, M.; Nashimoto, M. Elimination of specific mirnas by naked 14-nt sgRNAs. PLoS One 2012, 7, e38496.
42. Lee, R.C.; Feinbaum, R.L.; Ambros, V. The C. Elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75, 843-854.