Beyond microRNA - Novel RNAs derived from small non-coding RNA and their implication in cancer

Cancer Letters

Volumn 340, Issue 2, 2013, Pages 201-211

  Martens Uzunova, Elena S ^a   Olvedy, Michael ^a   Jenster, Guido ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Cancer; MicroRNA; Next generation sequencing; Non coding RNA; SnoRNA derived RNA (sdRNA); TRNA fragment (tRF)

Indexed keywords

EXPORTIN 5; MICRORNA; RNA POLYMERASE II; SMALL NUCLEOLAR RNA; TRANSCRIPTOME; TRANSFER RNA;

BINDING SITE; BLADDER CARCINOMA; CANCER CELL; CANCER GROWTH; CELL PROLIFERATION; CELL SURVIVAL; COLORECTAL CARCINOMA; DOWN REGULATION; EXOSOME; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; GENETIC TRANSCRIPTION; HETEROCHROMATIN; HUMAN; IN VITRO STUDY; IN VIVO STUDY; INTRON; LUNG NON SMALL CELL CANCER; MALIGNANT TRANSFORMATION; MOLECULAR MECHANICS; NEXT GENERATION SEQUENCING; OXIDATIVE STRESS; PANCREAS CARCINOMA; PRIORITY JOURNAL; RNA INTERFERENCE; RNA SPLICING; SHORT SURVEY; UPREGULATION;

EID: 84887610943     PISSN: 03043835     EISSN: 18727980     Source Type: Journal    
DOI: 10.1016/j.canlet.2012.11.058     Document Type: Review

References (154)

1. J.S. Mattick, I.V. Makunin, Non-coding RNA, Hum. Mol. Genet. 15 Spec No. 1 (2006) R17-R29.
2. 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.
3. Kozomara A., Griffiths-Jones S. MiRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011, 39:D152-157.
4. Iorio M.V., Croce C.M. MicroRNA dysregulation in cancer: diagnostics, monitoring and therapeutics. A comprehensive review. EMBO Mol. Med. 2012, 4:143-159.
5. Mendell Joshua T., Olson Eric N. MicroRNAs in stress signaling and human disease. Cell 2012, 148:1172-1187.
6. Tam O.H., Aravin A.A., Stein P., Girard A., Murchison E.P., Cheloufi S., Hodges E., Anger M., Sachidanandam R., Schultz R.M., Hannon G.J. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 2008, 453:534-538.
7. Watanabe T., Totoki Y., Toyoda A., Kaneda M., Kuramochi-Miyagawa S., Obata Y., Chiba H., Kohara Y., Kono T., Nakano T., Surani M.A., Sakaki Y., Sasaki H. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 2008, 453:539-543.
8. Okamura K., Lai E.C. Endogenous small interfering RNAs in animals. Nat. Rev. Mol. Cell Biol. 2008, 9:673-678.
9. Kim V.N. Small RNAs just got bigger: piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev. 2006, 20:1993-1997.
10. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811.
11. Morris K.V., Chan S.W., Jacobsen S.E., Looney D.J. Small interfering RNA-induced transcriptional gene silencing in human cells. Science (New York, NY) 2004, 305:1289-1292.
12. Moazed D. Small RNAs in transcriptional gene silencing and genome defence. Nature 2009, 457:413-420.
13. Zardo G., Ciolfi A., Vian L., Billi M., Racanicchi S., Grignani F., Nervi C. Transcriptional targeting by microRNA-Polycomb complexes: a novel route in cell fate determination. Cell Cycle 2012, 11:3543-3549.
14. Gagnon K.T., Corey D.R. Argonaute and the nuclear RNAs: new pathways for RNA-mediated control of gene expression. Nucleic Acids Ther. 2012, 22:3-16.
15. Li L.C., Okino S.T., Zhao H., Pookot D., Place R.F., Urakami S., Enokida H., Dahiya R. Small dsRNAs induce transcriptional activation in human cells. Proc. Nat. Acad. Sci. USA 2006, 103:17337-17342.
16. Portnoy V., Huang V., Place R.F., Li L.C. Small RNA and transcriptional upregulation. Wiley interdisciplinary reviews. RNA 2011, 2:748-760.
17. Huang V., Li L.C. MiRNA goes nuclear. RNA Biol. 2012, 9:269-273.
18. Allo M., Buggiano V., Fededa J.P., Petrillo E., Schor I., de la Mata M., Agirre E., Plass M., Eyras E., Elela S.A., Klinck R., Chabot B., Kornblihtt A.R. Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat. Struct. Mol. Biol. 2009, 16:717-724.
19. Gonzalez S., Pisano D.G., Serrano M. Mechanistic principles of chromatin remodeling guided by siRNAs and miRNAs. Cell Cycle 2008, 7:2601-2608.
20. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
21. Kim V.N., Han J., Siomi M.C. Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol. 2009, 10:126-139.
22. Han J., Lee Y., Yeom K.H., Kim Y.K., Jin H., Kim V.N. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 2004, 18:3016-3027.
23. Havens M.A., Reich A.A., Duelli D.M., Hastings M.L. Biogenesis of mammalian microRNAs by a non-canonical processing pathway. Nucleic Acids Res. 2012, 40:4626-4640.
24. Kim V.N. MicroRNA precursors in motion: exportin-5 mediates their nuclear export. Trends Cell Biol. 2004, 14:156-159.
25. Hutvagner G., McLachlan J., Pasquinelli A.E., Balint E., Tuschl T., Zamore P.D. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science (New York, NY) 2001, 293:834-838.
26. Schwarz D.S., Hutvagner G., Du T., Xu Z., Aronin N., Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003, 115:199-208.
27. Khvorova A., Reynolds A., Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003, 115:209-216.
28. * strands into the RNA interference pathway. RNA 2010, 16:43-56.
29. Diederichs S., Haber D.A. Dual role for argonautes in microRNA processing and posttranscriptional regulation of microRNA expression. Cell 2007, 131:1097-1108.
30. Cheloufi S., Dos Santos C.O., Chong M.M., Hannon G.J. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 2010, 465:584-589.
31. Cifuentes D., Xue H., Taylor D.W., Patnode H., Mishima Y., Cheloufi S., Ma E., Mane S., Hannon G.J., Lawson N.D., Wolfe S.A., Giraldez A.J. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science (New York, NY) 2010, 328:1694-1698.
32. Yang J.S., Maurin T., Robine N., Rasmussen K.D., Jeffrey K.L., Chandwani R., Papapetrou E.P., Sadelain M., O'Carroll D., Lai E.C. Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis. Proc. Nat. Acad. Sci. USA 2010, 107:15163-15168.
33. Castanotto D., Lingeman R., Riggs A.D., Rossi J.J. CRM1 mediates nuclear-cytoplasmic shuttling of mature microRNAs. Proc. Nat. Acad. Sci. USA 2009, 106:21655-21659.
34. Weinmann L., Hock J., Ivacevic T., Ohrt T., Mutze J., Schwille P., Kremmer E., Benes V., Urlaub H., Meister G. Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Cell 2009, 136:496-507.
35. Kim D.H., Saetrom P., Snove O., Rossi J.J. MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc. Nat. Acad. Sci. USA 2008, 105:16230-16235.
36. Tan Y., Zhang B., Wu T., Skogerbo G., Zhu X., Guo X., He S., Chen R. Transcriptional inhibition of Hoxd4 expression by miRNA-10a in human breast cancer cells. BMC Mol. Biol. 2009, 10:12.
37. Benhamed M., Herbig U., Ye T., Dejean A., Bischof O. Senescence is an endogenous trigger for microRNA-directed transcriptional gene silencing in human cells. Nat. Cell Biol. 2012, 14:266-275.
38. Place R.F., Li L.C., Pookot D., Noonan E.J., Dahiya R. MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc. Nat. Acad. Sci. USA 2008, 105:1608-1613.
39. Huang V., Place R.F., Portnoy V., Wang J., Qi Z., Jia Z., Yu A., Shuman M., Yu J., Li L.C. Upregulation of Cyclin B1 by miRNA and its implications in cancer. Nucleic Acids Res. 2012, 40:1695-1707.
40. Dieci G., Preti M., Montanini B. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. Genomics 2009, 94:83-88.
41. Filipowicz W., Pogačić V. Biogenesis of small nucleolar ribonucleoproteins. Curr. Opin. Cell Biol. 2002, 14:319-327.
42. Watkins N.J., Bohnsack M.T. The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. Wiley Interdiscipl. Rev.: RNA 2012, 3:397-414.
43. Giorgi C., Fatica A., Nagel R., Bozzoni I. Release of U18 snoRNA from its host intron requires interaction of Nop1p with the Rnt1p endonuclease. EMBO J. 2001, 20:6856-6865.
44. Renzi F., Caffarelli E., Laneve P., Bozzoni I., Brunori M., Vallone B. The structure of the endoribonuclease XendoU: from small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication. Proc. Nat. Acad. Sci. 2006, 103:12365-12370.
45. Laneve P., Gioia U., Ragno R., Altieri F., Di Franco C., Santini T., Arceci M., Bozzoni I., Caffarelli E. The tumor marker human placental protein 11 is an endoribonuclease. J. Biol. Chem. 2008, 283:34712-34719.
46. Henras A.K., Dez C., Henry Y. RNA structure and function in C/D and H/ACA s(no)RNPs. Curr. Opin. Struct. Biol. 2004, 14:335-343.
47. Lafontaine D.L., Bousquet-Antonelli C., Henry Y., Caizergues-Ferrer M., Tollervey D. The box H+ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes Dev. 1998, 12:527-537.
48. Rashid R., Liang B., Baker D.L., Youssef O.A., He Y., Phipps K., Terns R.M., Terns M.P., Li H. Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita. Mol. Cell 2006, 21:249-260.
49. Chen J.-L., Greider C.W. Telomerase RNA structure and function: implications for dyskeratosis congenita. Trends Biochem. Sci. 2004, 29:183-192.
50. Mitchell J.R., Cheng J., Collins K. A box H/ACA small nucleolar RNA-like domain at the human telomerase RNA 3' end. Mol. Cell. Biol. 1999, 19:567-576.
51. Qu G., van Nues R.W., Watkins N.J., Maxwell E.S. The spatial-functional coupling of box C/D and C'/D' RNPs is an evolutionarily conserved feature of the eukaryotic box C/D snoRNP nucleotide modification complex. Mol. Cell. Biol. 2011, 31:365-374.
52. Boisvert F.-M., van Koningsbruggen S., Navascues J., Lamond A.I. The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 2007, 8:574-585.
53. Gardner P.P., Daub J., Tate J.G., Nawrocki E.P., Kolbe D.L., Lindgreen S., Wilkinson A.C., Finn R.D., Griffiths-Jones S., Eddy S.R., Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Res. 2009, 37:D136-140.
54. Bachellerie J.P., Cavaille J., Huttenhofer A. The expanding snoRNA world. Biochimie 2002, 84:775-790.
55. Lowe T.M., Eddy S.R. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25:955-964.
56. Walker S.C., Engelke D.R. Ribonuclease P: the evolution of an ancient RNA enzyme. Crit. Rev. Biochem. Mol. Biol. 2006, 41:77-102.
57. Schiffer S., Rosch S., Marchfelder A. Assigning a function to a conserved group of proteins: the tRNA 3'-processing enzymes. EMBO J. 2002, 21:2769-2777.
58. Yang J.H., Shao P., Zhou H., Chen Y.Q., Qu L.H. DeepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 2010, 38:D123-130.
59. Lizano E., Schuster J., Muller M., Kelso J., Morl M. A splice variant of the human CCA-adding enzyme with modified activity. J. Mol. Biol. 2007, 366:1258-1265.
60. Calvin K., Li H. RNA-splicing endonuclease structure and function. Cell. Mol. Life Sci.: CMLS 2008, 65:1176-1185.
61. J. Popow, A. Schleiffer, J. Martinez, Diversity and roles of (t)RNA ligases, Cell. Mol. Life Sci.: CMLS (2012).
62. Gustilo E.M., Vendeix F.A., Agris P.F. TRNA's modifications bring order to gene expression. Curr. Opin. Microbiol. 2008, 11:134-140.
63. Motorin Y., Helm M. TRNA stabilization by modified nucleotides. Biochemistry 2010, 49:4934-4944.
64. Phizicky E.M., Hopper A.K. TRNA biology charges to the front. Genes Dev. 2010, 24:1832-1860.
65. Hopper A.K., Pai D.A., Engelke D.R. Cellular dynamics of tRNAs and their genes. FEBS Lett. 2010, 584:310-317.
66. Kawaji H., Nakamura M., Takahashi Y., Sandelin A., Katayama S., Fukuda S., Daub C.O., Kai C., Kawai J., Yasuda J., Carninci P., Hayashizaki Y. Hidden layers of human small RNAs. BMC Genom. 2008, 9:157.
67. 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.
68. Taft R.J., Glazov E.A., Lassmann T., Hayashizaki Y., Carninci P., Mattick J.S. Small RNAs derived from snoRNAs. RNA 2009, 15:1233-1240.
69. 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.
70. 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.
71. 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.
72. 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.
73. Brameier M., Herwig A., Reinhardt R., Walter L., Gruber J. Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res. 2011, 39:675-686.
74. Lee S.R., Collins K. Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. J. Biol. Chem. 2005, 280:42744-42749.
75. Li Y., Luo J., Zhou H., Liao J.Y., Ma L.M., Chen Y.Q., Qu L.H. Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia. Nucleic Acids Res. 2008, 36:6048-6055.
76. 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.
77. Kato M., Chen X., Inukai S., Zhao H., Slack F.J. Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans. RNA 2011, 17:1804-1820.
78. Scott M.S., Ono M., Yamada K., Endo A., Barton G.J., Lamond A.I. Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Res. 2012, 40:3676-3688.
79. Kishore S., Khanna A., Zhang Z., Hui J., Balwierz P.J., Stefan M., Beach C., Nicholls R.D., Zavolan M., Stamm S. The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum. Mol. Genet. 2010, 19:1153-1164.
80. Horsthemke B., Wagstaff J. Mechanisms of imprinting of the Prader-Willi/Angelman region. Am. J. Med. Genet. Part A 2008, 146A:2041-2052.
81. Eggermann T. Silver-Russell and Beckwith-Wiedemann syndromes: opposite (epi)mutations in 11p15 result in opposite clinical pictures. Horm. Res. 2009, 71(Suppl 2):30-35.
82. Dong X.Y., Rodriguez C., Guo P., Sun X., Talbot J.T., Zhou W., Petros J., Li Q., Vessella R.L., Kibel A.S., Stevens V.L., Calle E.E., Dong J.T. SnoRNA U50 is a candidate tumor-suppressor gene at 6q14.3 with a mutation associated with clinically significant prostate cancer. Hum. Mol. Genet. 2008, 17:1031-1042.
83. Martens-Uzunova E.S., Jalava S.E., Dits N.F., van Leenders G.J., Moller S., Trapman J., Bangma C.H., Litman T., Visakorpi T., Jenster G. Diagnostic and prognostic signatures from the small non-coding RNA transcriptome in prostate cancer. Oncogene 2012, 31:978-991.
84. Liao J., Yu L., Mei Y., Guarnera M., Shen J., Li R., Liu Z., Jiang F. Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer. Mol. Cancer 2010, 9:198.
85. Mei Y.P., Liao J.P., Shen J., Yu L., Liu B.L., Liu L., Li R.Y., Ji L., Dorsey S.G., Jiang Z.R., Katz R.L., Wang J.Y., Jiang F. Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis. Oncogene 2012, 31:2794-2804.
86. Dong X.Y., Guo P., Boyd J., Sun X., Li Q., Zhou W., Dong J.T. Implication of snoRNA U50 in human breast cancer. J. Genet. Genom. - Yi chuan xue bao 2009, 36:447-454.
87. Askarian-Amiri M.E., Crawford J., French J.D., Smart C.E., Smith M.A., Clark M.B., Ru K., Mercer T.R., Thompson E.R., Lakhani S.R., Vargas A.C., Campbell I.G., Brown M.A., Dinger M.E., Mattick J.S. SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA 2011, 17:878-891.
88. Gee H.E., Buffa F.M., Camps C., Ramachandran A., Leek R., Taylor M., Patil M., Sheldon H., Betts G., Homer J., West C., Ragoussis J., Harris A.L. The small-nucleolar RNAs commonly used for microRNA normalisation correlate with tumour pathology and prognosis. Br. J. Cancer 2011, 104:1168-1177.
89. Tanaka R., Satoh H., Moriyama M., Satoh K., Morishita Y., Yoshida S., Watanabe T., Nakamura Y., Mori S. Intronic U50 small-nucleolar-RNA (snoRNA) host gene of no protein-coding potential is mapped at the chromosome breakpoint t(3;6)(q27;q15) of human B-cell lymphoma. Genes Cells: Devoted Mol. Cell. Mech. 2000, 5:277-287.
90. W. Valleron, E. Laprevotte, E.F. Gautier, C. Quelen, C. Demur, E. Delabesse, X. Agirre, F. Prosper, T. Kiss, P. Brousset, Specific small nucleolar RNA expression profiles in acute leukemia, Leukemia: Off. J. Leukemia Soc. Am. (2012) (Leukemia Research Fund, UK).
91. Ferreira H.J., Heyn H., Moutinho C., Esteller M. CpG island hypermethylation-associated silencing of small nucleolar RNAs in human cancer. RNA Biol. 2012, 9:881-890.
92. Michel C.I., Holley C.L., Scruggs B.S., Sidhu R., Brookheart R.T., Listenberger L.L., Behlke M.A., Ory D.S., Schaffer J.E. Small nucleolar RNAs U32a, U33, and U35a are critical mediators of metabolic stress. Cell Metab. 2011, 14:33-44.
93. 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.
94. 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.
95. 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.
96. Higa-Nakamine S., Suzuki T., Uechi T., Chakraborty A., Nakajima Y., Nakamura M., Hirano N., Suzuki T., Kenmochi N. Loss of ribosomal RNA modification causes developmental defects in zebrafish. Nucleic Acids Res. 2012, 40:391-398.
97. Skreka K., Schafferer S., Nat I.R., Zywicki M., Salti A., Apostolova G., Griehl M., Rederstorff M., Dechant G., Huttenhofer A. Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation. Nucleic Acids Res. 2012, 40:6001-6015.
98. 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.
99. Babiarz J.E., Hsu R., Melton C., Thomas M., Ullian E.M., Blelloch R. A role for noncanonical microRNAs in the mammalian brain revealed by phenotypic differences in Dgcr8 versus Dicer1 knockouts and small RNA sequencing. RNA 2011, 17:1489-1501.
100. Saraiya A.A., Wang C.C. SnoRNA, a novel precursor of microRNA in Giardia lamblia. PLoS Pathog. 2008, 4:e1000224.
101. Li W., Saraiya A.A., Wang C.C. Gene regulation in Giardia lambia involves a putative microRNA derived from a small nucleolar RNA. PLoS Neglected Trop. Dis. 2011, 5:e1338.
102. Hutzinger R., Feederle R., Mrazek J., Schiefermeier N., Balwierz P.J., Zavolan M., Polacek N., Delecluse H.J., Huttenhofer A. Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome. PLoS Pathog. 2009, 5:e1000547.
103. Ono M., Scott M.S., Yamada K., Avolio F., Barton G.J., Lamond A.I. Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res. 2011, 39:3879-3891.
104. Scott M.S., Avolio F., Ono M., Lamond A.I., Barton G.J. Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput. Biol. 2009, 5:e1000507.
105. Jady B.E., Ketele A., Kiss T. Human intron-encoded Alu RNAs are processed and packaged into Wdr79-associated nucleoplasmic box H/ACA RNPs. Genes Develop 2012.
106. Scott M.S., Ono M. From snoRNA to miRNA: dual function regulatory non-coding RNAs. Biochimie 2011, 93:1987-1992.
107. Shen M., Eyras E., Wu J., Khanna A., Josiah S., Rederstorff M., Zhang M.Q., Stamm S. Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. Nucleic Acids Res. 2011, 39:9720-9730.
108. Cassidy S.B., Schwartz S., Miller J.L., Driscoll D.J. Prader-Willi syndrome. Genet. Med.: Off. J. Am. College Med. Genet. 2011.
109. Kishore S., Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science (New York, NY) 2006, 311:230-232.
110. Bortolin-Cavaille M.L., Cavaille J. The SNORD115 (H/MBII-52) and SNORD116 (H/MBII-85) gene clusters at the imprinted Prader-Willi locus generate canonical box C/D snoRNAs. Nucleic Acids Res. 2012, 40:6800-6807.
111. Bazeley P.S., Shepelev V., Talebizadeh Z., Butler M.G., Fedorova L., Filatov V., Fedorov A. SnoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. Gene 2008, 408:172-179.
112. Khanna A., Stamm S. Regulation of alternative splicing by short non-coding nuclear RNAs. RNA Biol. 2010, 7:480-485.
113. Mourtada-Maarabouni M., Pickard M.R., Hedge V.L., Farzaneh F., Williams G.T. GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene 2009, 28:195-208.
114. Goeze A., Schluns K., Wolf G., Thasler Z., Petersen S., Petersen I. Chromosomal imbalances of primary and metastatic lung adenocarcinomas. J. Pathol. 2002, 196:8-16.
115. Yudelevich A. Specific cleavage of an Escherichia coli leucine transfer RNA following bacteriophage T4 infection. J. Mol. Biol. 1971, 60:21-29.
116. Zhao H., Bojanowski K., Ingber D.E., Panigrahy D., Pepper M.S., Montesano R., Shing Y. New role for tRNA and its fragment purified from human urinary bladder carcinoma conditioned medium: inhibition of endothelial cell growth. J. Cell. Biochem. 1999, 76:109-117.
117. 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.
118. Reese T.A., Xia J., Johnson L.S., Zhou X., Zhang W., Virgin H.W. Identification of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts. J. Virol. 2010, 84:10344-10353.
119. 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. 2010, 171:64-73.
120. 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.
121. Sobala A., Hutvagner G. Transfer RNA-derived fragments: origins, processing, and functions. Wiley Interdiscipl. Rev.: RNA 2011, 2:853-862.
122. 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.
123. Thompson D.M., Parker R. Stressing out over tRNA cleavage. Cell 2009, 138:215-219.
124. Mahlab S., Tuller T., Linial M. Conservation of the relative tRNA composition in healthy and cancerous tissues. RNA 2012, 18:640-652.
125. Buchan J.R., Parker R. Eukaryotic stress granules: the ins and outs of translation. Mol. Cell 2009, 36:932-941.
126. Holcik M., Sonenberg N. Translational control in stress and apoptosis. Nat. Rev. Mol. Cell Biol. 2005, 6:318-327.
127. Mei Y., Yong J., Liu H., Shi Y., Meinkoth J., Dreyfuss G., Yang X. TRNA binds to cytochrome c and inhibits caspase activation. Mol. Cell 2010, 37:668-678.
128. 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.
129. Marquet R., Isel C., Ehresmann C., Ehresmann B. TRNAs as primer of reverse transcriptases. Biochimie 1995, 77:113-124.
130. Herschhorn A., Hizi A. Retroviral reverse transcriptases. Cell. Mol. life Sci.: CMLS 2010, 67:2717-2747.
131. Bogerd H.P., Karnowski H.W., Cai X., Shin J., Pohlers M., Cullen B.R. A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs. Mol. Cell 2010, 37:135-142.
132. Diebel K.W., Smith A.L., van Dyk L.F. Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters. RNA 2010, 16:170-185.
133. Wilusz J.E., Freier S.M., Spector D.L. 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 2008, 135:919-932.
134. Parker B.J., Moltke I., Roth A., Washietl S., Wen J., Kellis M., Breaker R., Pedersen J.S. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res. 2011, 21:1929-1943.
135. Couvillion M.T., Sachidanandam R., Collins K. A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo. Genes Dev. 2010, 24:2742-2747.
136. Kim D.H., Villeneuve L.M., Morris K.V., Rossi J.J. Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat. Struct. Mol. Biol. 2006, 13:793-797.
137. Rudinger-Thirion J., Lescure A., Paulus C., Frugier M. Misfolded human tRNA isodecoder binds and neutralizes a 3' UTR-embedded Alu element. Proc. Nat. Acad. Sci. USA 2011, 108:E794-802.
138. Mitchell P.S., Parkin R.K., Kroh E.M., Fritz B.R., Wyman S.K., Pogosova-Agadjanyan E.L., Peterson A., Noteboom J., O'Briant K.C., Allen A., Lin D.W., Urban N., Drescher C.W., Knudsen B.S., Stirewalt D.L., Gentleman R., Vessella R.L., Nelson P.S., Martin D.B., Tewari M. Circulating microRNAs as stable blood-based markers for cancer detection. Proc. Nat. Acad. Sci. USA 2008, 105:10513-10518.
139. Speer J., Gehrke C.W., Kuo K.C., Waalkes T.P., Borek E. TRNA breakdown products as markers for cancer. Cancer 1979, 44:2120-2123.
140. Baraniskin A., Nopel-Dunnebacke S., Ahrens M., Jensen S.G., Zollner H., Maghnouj A., Wos A., Mayerle J., Munding J., Kost D., Reinacher-Schick A., Liffers S., Schroers R., Chromik A.M., Meyer H.E., Uhl W., Klein-Scory S., Weiss F.U., Stephan C., Schwarte-Waldhoff I., Lerch M.M., Tannapfel A., Schmiegel W., Andersen C.L., Hahn S.A. Circulating U2 small nuclear RNA fragments as a novel diagnostic biomarker for pancreatic and colorectal adenocarcinoma. Int. J. Cancer 2012.
141. Lanford R.E., Hildebrandt-Eriksen E.S., Petri A., Persson R., Lindow M., Munk M.E., Kauppinen S., Orum H. Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science (New York, NY) 2010, 327:198-201.
142. Zhang Y., Roccaro A.M., Rombaoa C., Flores L., Obad S., Fernandes S.M., Sacco A., Liu Y., Ngo H., Quang P., Azab A.K., Azab F., Maiso P., Reagan M., Brown J.R., Thai T.-H., Kauppinen S., Ghobrial I.M. LNA-mediated anti-miR-155 silencing in low-grade B-cell lymphomas. Blood 2012, 120:1678-1686.
143. Greenberger L.M., Horak I.D., Filpula D., Sapra P., Westergaard M., Frydenlund H.F., Albaek C., Schroder H., Orum H. A RNA antagonist of hypoxia-inducible factor-1alpha, EZN-2968, inhibits tumor cell growth. Mol. Cancer Ther. 2008, 7:3598-3608.
144. Ono M., Yamada K., Avolio F., Scott M.S., van Koningsbruggen S., Barton G.J., Lamond A.I. Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. Mol. Biol. Cell 2010, 21:1569-1584.
145. Aartsma-Rus A., van Ommen G.J. Antisense-mediated exon skipping: a versatile tool with therapeutic and research applications. RNA 2007, 13:1609-1624.
146. Mowry K.L., Steitz J.A. Identification of the human U7 snRNP as one of several factors involved in the 3' end maturation of histone premessenger RNA's. Science (New York, NY) 1987, 238:1682-1687.
147. Peterlin B.M., Brogie J.E., Price D.H. 7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription. Wiley Interdiscipl. Rev.: RNA 2012, 3:92-103.
148. Ullu E., Murphy S., Melli M. Human 7SL RNA consists of a 140 nucleotide middle-repetitive sequence inserted in an alu sequence. Cell 1982, 29:195-202.
149. Parrott A.M., Tsai M., Batchu P., Ryan K., Ozer H.L., Tian B., Mathews M.B. The evolution and expression of the snaR family of small non-coding RNAs. Nucleic Acids Res. 2011, 39:1485-1500.
150. Christov C.P., Gardiner T.J., Szuts D., Krude T. Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. Mol. Cell. Biol. 2006, 26:6993-7004.
151. Steiner E., Holzmann K., Elbling L., Micksche M., Berger W. Cellular functions of vaults and their involvement in multidrug resistance. Curr. Drug Targets 2006, 7:923-934.
152. Baer M., Nilsen T.W., Costigan C., Altman S. Structure and transcription of a human gene for H1 RNA, the RNA component of human RNase P. Nucleic Acids Res. 1990, 18:97-103.
153. Esakova O., Krasilnikov A.S. Of proteins and RNA: the RNase P/MRP family. RNA 2010, 16:1725-1747.
154. Feng J., Funk W.D., Wang S.S., Weinrich S.L., Avilion A.A., Chiu C.P., Adams R.R., Chang E., Allsopp R.C., Yu J., et al. The RNA component of human telomerase. Science (New York, NY) 1995, 269:1236-1241.