Conserved and highly expressed tRNA derived fragments in zebrafish

BMC Molecular Biology

Volumn 16, Issue 1, 2015, Pages

  Soares, Ana Raquel ^a   Fernandes, Noémia ^a   Reverendo, Marisa ^a   Araújo, Hugo Rafael ^b   Oliveira, José Luís ^b   Moura, Gabriela M R ^a   Santos, Manuel A S ^a  

^a UNIVERSITY OF AVEIRO   (Portugal)

^b UNIVERSITY OF AVEIRO   (Portugal)

Author keywords

Small non coding RNAs; TRNA derived fragments; TRNAs; Zebrafish

Indexed keywords

DICER; TRANSFER RNA; REGULATORY RNA SEQUENCE; RIBONUCLEASE III; SMALL UNTRANSLATED RNA;

ADULT; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; COLORECTAL CANCER; CONTROLLED STUDY; DATA MINING; DEVELOPMENT; EMBRYO; GENE EXPRESSION; GENE SILENCING; HUMAN; IN VITRO STUDY; INFECTION; NEXT GENERATION SEQUENCING; NONHUMAN; RNA INTERFERENCE; VERTEBRATE; ZEBRA FISH; ANIMAL; CELL LINE; COLORECTAL TUMOR; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; MOUSE; NIH 3T3 CELL LINE; NUCLEOTIDE SEQUENCE; REGULATORY RNA SEQUENCE; SEQUENCE ANALYSIS;

ANIMALS; BASE SEQUENCE; CELL LINE; COLORECTAL NEOPLASMS; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; NIH 3T3 CELLS; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RIBONUCLEASE III; RNA INTERFERENCE; RNA, SMALL UNTRANSLATED; RNA, TRANSFER; SEQUENCE ANALYSIS, RNA; ZEBRAFISH;

EID: 84951822589     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/s12867-015-0050-8     Document Type: Article

References (45)

1. Kim VN, Han J, Siomi MC. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol. 2009;10(2):126-39.
2. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116(2):281-97.
3. Burnside J, Ouyang M, Anderson A, Bernberg E, Lu C, Meyers BC, Green PJ, Markis M, Isaacs G, Huang E et al. Deep sequencing of chicken microRNAs. Bmc Genom. 2008;9:185.
4. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 2007;129(7):1401-14.
5. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008;18(4):610-21.
6. Sunkar R, Zhou XF, Zheng Y, Zhang WX, Zhu JK. Identification of novel and candidate miRNAs in rice by high throughput sequencing. Bmc Plant Biol. 2008;8:25.
7. Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, van den Elst H, Filippov DV, Blaser H, Raz E, Moens CB, et al. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell. 2007;129(1):69-82.
8. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell. 2006;127(6):1193-207.
9. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T. The small RNA profile during Drosophila melanogaster development. Dev Cell. 2003;5(2):337-50.
10. Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, Green PJ, Barton GJ, Hutvagner G. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA. 2009;15(12):2147-60.
11. Lee YS, Shibata Y, Malhotra A, Dutta A. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev. 2009;23(22):2639-49.
12. Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, et al. Hidden layers of human small RNAs. BMC Genom. 2008;9:157.
13. Burroughs AM, Ando Y, Hoon ML, Tomaru Y, Suzuki H, Hayashizaki Y, Daub CO. 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(1):158-77.
14. Wang Q, Lee I, Ren J, Ajay SS, Lee YS, Bao X. Identification and functional characterization of tRNA-derived RNA fragments (tRFs) in respiratory syncytial virus infection. Mol Ther J Am Soc Gene Ther. 2013;21(2):368-79.
15. Keam SP, Young PE, McCorkindale AL, Dang TH, Clancy JL, Humphreys DT, Preiss T, Hutvagner G, Martin DI, Cropley JE, et al. The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells. Nucleic Acids Res. 2014;42(14):8984-95.
16. Sobala A, Hutvagner G. Small RNAs derived from the 5′ end of tRNA can inhibit protein translation in human cells. RNA Biol. 2013;10(4):553-63.
17. Maute RL, Schneider C, Sumazin P, Holmes A, Califano A, Basso K, Dalla-Favera R. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proc Natl Acad Sci USA. 2013;110(4):1404-9.
18. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA. 2010;16(4):673-95.
19. Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 2008;22(20):2773-85.
20. 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(2):437-42.
21. Thompson DM, Parker R. The RNase Rny1p cleaves tRNAs and promotes cell death during oxidative stress in Saccharomyces cerevisiae. J Cell Biol. 2009;185(1):43-50.
22. Lee SR, Collins K. Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. J Biol Chem. 2005;280(52):42744-9.
23. Yamasaki S, Ivanov P, Hu GF, Anderson P. Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol. 2009;185(1):35-42.
24. Emara MM, Ivanov P, Hickman T, Dawra N, Tisdale S, Kedersha N, Hu GF, Anderson P. Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J Biol Chem. 2010;285(14):10959-68.
25. Ivanov P, Emara MM, Villen J, Gygi SP, Anderson P. Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell. 2011;43(4):613-23.
26. Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, Moura GR, Santos MAS. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. Bmc Genom. 2009;10:195.
27. Li Z, Ender C, Meister G, Moore PS, Chang Y, John B. Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res. 2012;40(14):6787-99.
28. Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 2006;22(4):500-3.
29. Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009;37(Database issue):D93-97.
30. Noren Hooten N, Fitzpatrick M, Wood WH, 3rd, De S, Ejiogu N, Zhang Y, Mattison JA, Becker KG, Zonderman AB, Evans MK. Age-related changes in microRNA levels in serum. Aging. 2013;5(10):725-40.
31. Stark TJ, Arnold JD, Spector DH, Yeo GW. High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection. J Virol. 2012;86(1):226-35.
32. Farazi TA, Horlings HM, Ten Hoeve JJ, Mihailovic A, Halfwerk H, Morozov P, Brown M, Hafner M, Reyal F, van Kouwenhove M, et al. MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer Res. 2011;71(13):4443-53.
33. Liao JY, Ma LM, Guo YH, Zhang YC, Zhou H, Shao P, Chen YQ, Qu LH. 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(5):e10563.
34. Phizicky EM, Hopper AK. tRNA biology charges to the front. Genes Dev. 2010;24(17):1832-60.
35. Jeffries CD, Fried HM, Perkins DO. Nuclear and cytoplasmic localization of neural stem cell microRNAs. RNA. 2011;17(4):675-86.
36. Huang V, Li LC. miRNA goes nuclear. RNA Biol. 2012;9(3):269-73.
37. Wei C, Salichos L, Wittgrove CM, Rokas A, Patton JG. Transcriptome-wide analysis of small RNA expression in early zebrafish development. RNA. 2012;18(5):915-29.
38. Gong B, Lee YS, Lee I, Shelite TR, Kunkeaw N, Xu G, Lee K, Jeon SH, Johnson BH, Chang Q, et al. Compartmentalized, functional role of angiogenin during spotted fever group rickettsia-induced endothelial barrier dysfunction: evidence of possible mediation by host tRNA-derived small noncoding RNAs. BMC Infect Dis. 2013;13:285.
39. Thompson DM, Lu C, Green PJ, Parker R. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA. 2008;14(10):2095-103.
40. Nicoli S, Knyphausen CP, Zhu LJ, Lakshmanan A, Lawson ND. miR-221 is required for endothelial tip cell behaviors during vascular development. Dev Cell. 2012;22(2):418-29.
41. Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S, Hammond SM, Bartel DP, Schier AF. MicroRNAs regulate brain morphogenesis in zebrafish. Science. 2005;308(5723):833-8.
42. Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, Moura GR, Santos MA. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genom. 2009;10:195.
43. De Pietri Tonelli D, Calegari F, Fei JF, Nomura T, Osumi N, Heisenberg CP, Huttner WB. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 2006;41(6):727-32.
44. Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes Dev. 2009;23(5):619-32.
45. Edgar R, Domrachev M, Lash AE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30(1):207-10.