Dicer-Processed Small RNAs: Rules and Exceptions

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Volumn 320, Issue 1, 2013, Pages 35-46

  Langenberger, David ^a,b   Çakir, M Volkan ^a   Hoffmann, Steve ^a,b   Stadler, Peter F ^{a,b,c,d,e,f,g}  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b Bioinformatics Group   (Germany)

^c MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^d FRAUNHOFER INSTITUTE FOR CELL THERAPY AND IMMUNOLOGY   (Germany)

^e UNIVERSITY OF VIENNA   (Austria)

^f UNIVERSITY OF COPENHAGEN   (Denmark)

^g SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEAD BOX PROTEIN; DICER1 PROTEIN, HUMAN; DNA DIRECTED DNA POLYMERASE GAMMA; MICRORNA; RIBONUCLEASE III;

ARTICLE; CELL STRAIN MCF 7; COMPARATIVE STUDY; GENE SILENCING; GENETICS; HUMAN; HUMAN GENOME; METABOLISM;

DEAD-BOX RNA HELICASES; DNA POLYMERASE III; GENE KNOCKDOWN TECHNIQUES; GENOME, HUMAN; HUMANS; MCF-7 CELLS; MICRORNAS; RIBONUCLEASE III;

HOMINIDAE;

EID: 84871822658     PISSN: 15525007     EISSN: 15525015     Source Type: Journal    
DOI: 10.1002/jez.b.22481     Document Type: Article

References (66)

1. Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. 2008. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev 22: 2773-2785.
2. Bernhart SH, Tafer H, Mückstein U, et al. 2006. Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol 1: 3.
3. Blankenberg D, Taylor J, Nekrutenko A, Team TG. 2011. Making whole genome multiple alignments usable for biologists. Bioinformatics 27: 2426-2428.
4. Borchert GM, Holton NW, Williams JD, et al. 2011. Comprehensive analysis of microRNA genomic loci identifies pervasive repetitive-element origins. Mob Genet Elements 1: 8-17.
5. Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J. 2011. Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res 39: 675-686.
6. Canella D, Praz V, Reina JH, Cousin P, Hernandez N. 2010. Defining the RNA polymerase III transcriptome: genome-wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res 20: 710-721.
7. Chan P, Lowe T. 2009. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37: D93-D97.
8. Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ. 2010. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 465: 584-589.
9. Chong MMW, Zhang G, Cheloufi S. et al. 2010. Canonical and alternate functions of the microRNA biogenesis machinery. Genes Dev 24: 1951-1960.
10. Christov CP, Gardiner TJ, Szüts D, Krude T. 2006. Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. Mol Cell Biol 26: 6993-7004.
11. Cifuentes D, Xue H, Taylor DW, et al. 2010. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 328: 1694-1698.
12. Cole C, Sobala A, Lu C, et al. 2009. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 15: 2147-2160.
13. Ebhardt HA, Fedynak A, Fahlman RP. 2010. Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity. Silence 1: 12.
14. Edgar R, Domrachev M, Lash A. 2002. Gene expression omnibus: Ncbi gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
15. Ender C, Krek A, Friedländer MR, et al. 2008. A human snoRNA with microRNA-like functions. Mol Cell 32: 519-528.
16. Findeiß S, Langenberger D, Stadler PF, Hoffmann S. 2011. Traces of post-transcriptional RNA modifications in deep sequencing data. Biol Chem 392: 305-313.
17. Fire A, Xu S, Montgomery MK, et al. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
18. Flynt AS, Greimann JC, Chung WJ, Lima CD, Lai EC. 2010. MicroRNA biogenesis via splicing and exosome-mediated trimming in Drosophila. Mol Cell 38: 900-907.
19. Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. 2012. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 40: 37-52.
20. Gregory RI, Yan KP, Amuthan G, et al. 2004. The Microprocessor complex mediates the genesis of microRNAs. Nature 432: 235-240.
21. Griffiths-Jones S. 2004. The microRNA registry. Nucleic Acids Res 32: D109-D111.
22. Haussecker D, Huang Y, Lau A, et al. 2010. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16: 673-695.
23. Hertel J, Stadler PF. 2006. Hairpins in a haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics 22: e197-e202.
24. Hoffmann S, Otto C, Kurtz S, et al. 2009. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol 5: e1000502.
25. Ji X. 2008. The mechanism of rnase III action: how dicer dices. Curr Top Microbiol Immunol 320: 99-116.
26. Jöchl C, Rederstorff M, Hertel J, et al. 2008. Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein-synthesis. Nucleic Acids Res 36: 2677-2689.
27. Jurka J. 2000. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet 16: 418-420.
28. Karolchik D, Hinrichs A, Furey T, et al. 2004. The UCSC table browser data retrieval tool. Nucleic Acids Res 32: D493-D496.
29. Kawaji H, Nakamura M, Takahashi1 Y, et al. 2008. Hidden layers of human small RNAs. BMC Genomics 9: 157.
30. Kent WJ, Sugnet CW, Furey TS, et al. 2002. The human genome browser at ucsc. Genome Res 12: 996-1006.
31. Lai EC, Tomancak P, Williams RW, Rubin GM. 2003. Computational identification of Drosophila microRNA genes. Genome Biol 4: R42.
32. Langenberger D, Bartschat S, Hertel J, et al. 2011. MicroRNA or not microRNA? In: de Souza ON, Telles GP, Palakal MJ, editors. Advances in bioinformatics and computational biology, 6th Brazilian Symposium on Bioinformatics, BSB 2011, vol. 6832 of Lecture Notes in Computer Science, Berlin, Heidelberg: Springer. p. 1-9.
33. Langenberger D, Bermudez-Santana C, Hertel J, et al. 2009. Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics 25: 2298-2301.
34. Langenberger D, Bermudez-Santana C, Stadler PF, Hoffmann S. 2010. Identification and classification of small RNAs in transcriptome sequence data. Pac Symp Biocomput 15: 80-87.
35. Larkin MA, Blackshields G, Brown NP, et al. 2007. ClustalW and clustalX version 2.0. Bioinformatics 23: 2947-2948.
36. Lee RC, Feinbaum RL, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
37. Lee YS, Shibata Y, Malhotra A, Dutta A. 2009. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23: 2639-2649.
38. Li H, Handsaker B, Wysoker A, et al. 2009. The sequence alignment/map format and samtools. Bioinformatics 25: 2078-2079.
39. Lund E, Güttinger S, Calado A, Dahlberg J, Kutay U. 2004. Nuclear export of microRNA precursors. Science 303: 95-98.
40. Meiri E, Levy A, Benjamin H, et al. 2010. Discovery of microRNAs and other small RNAs in solid tumors. Nucleic Acids Res 38: 6234-6246.
41. Mosig A, Guofeng M, Stadler BMR, Stadler PF. 2007. Evolution of the vertebrate Y RNA cluster. Th Biosci 126: 9-14.
42. Murchison EP, Hannon GJ. 2004. miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr Opin Cell Biol 16: 223-229.
43. Nandy C, Mrázek J, Stoiber H, et al. 2009. Epstein-Barr virus-induced expression of a novel human vault RNA. J Mol Biol 388: 776-784.
44. Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC. 2007. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130: 89-100.
45. Ono M, Scott MS, Yamada K, et al. 2011. Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res 39: 3879-3891.
46. Pan J, Hu H, Zhou Z, et al. 2010. Tumor-suppressive mir-663 gene induces mitotic catastrophe growth arrest in human gastric cancer cells. Oncol Rep 24: 105-112.
47. Parrott AM, Mathews MB. 2007. Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display tissue-restricted distribution. Nucleic Acids Res 35: 6249-6258.
48. Parrott AM, Tsai M, Batchu P, et al. 2011. The evolution and expression of the snaR family of small non-coding RNAs. Nucleic Acids Res 39: 1485-1500.
49. Perreault J, Perreault JP, Boire G. 2007. Ro-associated Y RNAs in metazoans: evolution and diversification. Mol Biol Evol 24: 1678-1689.
50. Persson H, Kvist A, Vallon-Christersson J, et al. 2009. The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs. Nat Cell Biol 11: 1268-1271.
51. Piriyapongsa J, Jordan IK. 2007. A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS ONE 2: e203.
52. Quinlan A, Hall I. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
53. Raha D, Wang Z, Moqtaderi Z, et al. 2010. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci USA 107: 3639-3644.
54. Ruby GJ, Jan CH, Bartell DP. 2007. Intronic microRNA precursors that bypass Drosha processing. Nature 48: 83-86.
55. Scott MS, Avolio F, Ono M, Lamond AI, Barton GJ. 2009. Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput Biol 5: e1000507.
56. Scott MS, Ono M. 2011. From snoRNA to miRNA: dual function regulatory non-coding RNAs. Biochimie 93: 1987-1992.
57. Smalheiser NR, Torvik VI. 2005. Mammalian microRNAs derived from genomic repeats. Trends Genet 21: 322-326.
58. Sobala A, Hutvagner G. 2011. Transfer RNA-derived fragments: origins, processing, and functions. Wiley Interdiscip Rev RNA 2: 853-862.
59. Stadler PF, Chen JJL, Hackermüller J, et al. 2009. Evolution of vault RNAs. Mol Biol Evol 26: 1975-1991.
60. Starega-Roslan J, Krol J, Koscianska E, et al. 2011. Structural basis of microRNA length variety. Nucleic Acids Res 39: 257-268.
61. Taft RJ, Glazov EA, Lassmann T, et al. 2009. Small RNAs derived from snoRNAs. RNA 15: 1233-1240.
62. Thompson DM, Lu C, Green PJ, Parker R. 2008. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14: 2095-2103.
63. Verhagen AP, Pruijn GJ. 2011. Are the Ro RNP-associated Y RNAs concealing microRNAs? Y RNA-derived miRNAs may be involved in autoimmunity. Bioessays 33: 674-682.
64. Yang JS, Lai EC. 2011. Alternative miRNA biogenesis pathways and the interpretation of core miRNA pathway mutants. Mol Cell 43: 892-903.
65. Yi C, Wang Q, Wang L, et al. 2012. MiR-663, a microRNA targeting p21(WAF1/CIP1), promotes the proliferation and tumorigenesis of nasopharyngeal carcinoma. Oncogene 31: 4421-4433.
66. Yuan Z, Sun XS, Liu H, Xie J. 2011. MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes. PLoS ONE 6: e17666.