Selection of RNA oligonucleotides that can modulate human dicer activity in vitro

Nucleic Acid Therapeutics

Volumn 21, Issue 5, 2011, Pages 333-346

  Tyczewska, Agata ^a   Kurzyńska Kokorniak, Anna ^a   Koralewska, Natalia ^a   Szopa, Aleksandra ^a   Kietrys, Anna M ^a   Wrzesiński, Jan ^a   Twardowski, Tomasz ^a   Figlerowicz, Marek ^a,b  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^b POZNAN UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

DICER; ENZYME INHIBITOR; MICRORNA; OLIGONUCLEOTIDE; RNA; TRANSCRIPTOME;

ALLOSTERISM; ARTICLE; COMPETITIVE INHIBITION; ENZYME ACTIVITY; ENZYME INHIBITION; ENZYME REGULATION; HUMAN; IN VITRO SELECTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; RNA ANALYSIS; RNA CLEAVAGE; RNA ISOLATION; RNA SEQUENCE; RNA SYNTHESIS;

ALLOSTERIC REGULATION; APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BINDING, COMPETITIVE; COMPUTER SIMULATION; DEAD-BOX RNA HELICASES; ENZYME ASSAYS; GENE EXPRESSION REGULATION; HUMANS; MICRORNAS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; RIBONUCLEASE III; SELEX APTAMER TECHNIQUE; TRANSCRIPTOME;

EID: 80054752022     PISSN: 21593337     EISSN: None     Source Type: Journal    
DOI: 10.1089/nat.2011.0304     Document Type: Article

References (42)

1. AMBROS, V. (2003). MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell 113, 673-676. (Pubitemid 36724931)
2. AMBROS, V. (2004). The functions of animal microRNAs. Nature 431, 350-355. (Pubitemid 39265675)
3. ANDERSSON, M.G., HAASNOOT, P.C., XU, N., BERENJIAN, S., BERKHOUT, B., and AKUSJARVI, G. (2005). Suppression of RNA interference by adenovirus virus-associated RNA. J. Virol. 79, 9556-9565. (Pubitemid 41022298)
4. BARTEL, D.P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
5. BERKHOUT, B., and HAASNOOT, J. (2006). The interplay between virus infection and the cellular RNA interference machinery. FEBS Lett. 580, 2896-2902. (Pubitemid 43744478)
6. BERNSTEIN, E., CAUDY, A.A., HAMMOND, S.M., and HAN-NON, G.J. (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363-366. (Pubitemid 32151243)
7. CALIN, G.A., and CROCE, C.M. (2006). MicroRNA signatures in human cancers. Nat. Rev. Cancer 6, 857-866. (Pubitemid 44629897)
8. CARRINGTON, J.C., and AMBROS, V. (2003). Role of micro-RNAs in plant and animal development. Science 301, 336-338. (Pubitemid 36877060)
9. CARTHEW, R.W., and SONTHEIMER, E.J. (2009). Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642-655.
10. ELBASHIR, S.M., LENDECKEL, W., and TUSCHL, T. (2001). RNA interference is mediated by 21-and 22-nucleotide RNAs. Genes Dev. 15, 188-200. (Pubitemid 32107664)
11. ELLINGTON, A.D., and SZOSTAK, J.W. (1990).Invitroselection of RNA molecules that bind specific ligands. Nature 346, 818-822.
12. ESQUELA-KERSCHER, A., and SLACK, F.J. (2006). Oncomirs-microRNAs with a role in cancer. Nat. Rev. Cancer 6, 259-269.
13. FIRE, A., XU, S., MONTGOMERY, M.K., KOSTAS, S.A., DRIVER, S.E., and MELLO, C.C. (1998). Potent and specific ge-netic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811. (Pubitemid 28099681)
14. FRIEDMAN, R.C., FARH, K.K., BURGE, C.B., and BARTEL, D.P. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92-105.
15. HAASNOOT, J., and BERKHOUT, B. (2006). RNA interference: its use as antiviral therapy. Handb. Exp. Pharmacol. 173, 117-150.
16. HAMMOND, S.M., BERNSTEIN, E., BEACH, D., and HAN-NON, G.J. (2000). An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404, 293-296. (Pubitemid 30163547)
17. HENN, A., JOACHIMI, A., GONCALVES, D.P., MONCHAUD, D., TEULADE-FICHOU, M.P., SANDERS, J.K., and HARTIG, J.S. (2008). Inhibition of dicing of guanosine-rich shRNAs by quadruplex-binding compounds. Chembiochem 9, 2722-2729.
18. JACKOWIAK, P., NOWACKA, M., STROZYCKI, P.M., and FIGLEROWICZ, M. (2011). RNA degradome-its biogenesis and functions. Nucleic Acids Res. 39, 7361-7370.
19. JACOBSEN, S.E., RUNNING, M.P., and MEYEROWITZ, E.M. (1999). Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meri-stems. Development 126, 5231-5243. (Pubitemid 30015917)
20. KIM, V.N. (2005). MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6, 376-385. (Pubitemid 40637855)
21. KIM, V.N. (2006). Small RNAs just got bigger: piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev. 20, 1993-1997. (Pubitemid 44157450)
22. KURZYNSKA-KOKORNIAK, A., JACKOWIAK, P., FIGLER-OWICZ, M., and FIGLEROWICZ, M. (2009). Human-and virus-encoded microRNAs as potential targets of antiviral therapy. Mini Rev. Med. Chem. 9, 927-937.
23. LEE, Y., AHN, C., HAN, J., CHOI, H., KIM, J., YIM, J., LEE, J., PROVOST, P., RADMARK, O., KIM, S., and KIM, V.N. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415-419. (Pubitemid 37187272)
24. LIMA, W.F., MURRAY, H., NICHOLS, J.G., WU, H., SUN, H., PRAKASH, T.P., BERDEJA, A.R., GAUS, H.J., and CROOKE, S.T. (2009). Human Dicer binds short single-strand and double-strand RNA with high affinity and interacts with different regions of the nucleic acids. J. Biol. Chem. 284, 2535-2548.
25. MA, E., MACRAE, I.J., KIRSCH, J.F., and DOUDNA, J.A. (2008). Autoinhibition of human dicer by its internal helicase domain. J. Mol. Biol. 380, 237-243.
26. MACRAE, I.J., and DOUDNA, J.A. (2007). Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr. Opin. Struct. Biol. 17, 138-145. (Pubitemid 46240810)
27. MACRAE, I.J., LI, F., ZHOU, K., CANDE, W.Z., and DOUDNA, J.A. (2006a). Structure of Dicer and mechanistic implications for RNAi. Cold Spring Harb. Symp. Quant. Biol. 71, 73-80.
28. MACRAE, I.J., ZHOU, K., LI, F., REPIC, A., BROOKS, A.N., CANDE, W.Z., ADAMS, P.D., and DOUDNA, J.A. (2006b). Structural basis for double-stranded RNA processing by Dicer. Science 311, 195-198. (Pubitemid 43108178)
29. MERCER, T.R., DINGER, M.E., BRACKEN, C.P., KOLLE, G., SZUBERT, J.M., KORBIE, D.J., ASKARIAN-AMIRI, M.E., GARDINER, B.B., GOODALL, G.J., GRIMMOND, S.M., and MATTICK, J.S. (2010). Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res. 20, 1639-1650.
30. OLEJNICZAK, M., GALKA, P., and KRZYZOSIAK, W.J. (2009). Sequence-non-specific effects of RNA interference triggers and microRNA regulators. Nucleic Acids Res. 38, 1-16.
31. PROVOST, P., DISHART, D., DOUCET, J., FRENDEWEY, D., SAMUELSSON, B., and RADMARK, O. (2002a). Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J. 21, 5864-5874. (Pubitemid 35315284)
32. PROVOST, P., SILVERSTEIN, R.A., DISHART, D., WAL-FRIDSSON, J., DJUPEDAL, I., KNIOLA, B., WRIGHT, A., SAMUELSSON, B., RADMARK, O., and EKWALL, K. (2002b). Dicer is required for chromosome segregation and gene silencing in fission yeast cells. Proc. Natl. Acad. Sci. U. S. A. 99, 16648-16653. (Pubitemid 36034027)
33. STAREGA-ROSLAN, J., KROL, J., KOSCIANSKA, E., KO-ZLOWSKI, P., SZLACHCIC, W.J., SOBCZAK, K., and KRZYZOSIAK, W.J. (2010). Structural basis of microRNA length variety. Nucleic Acids Res. 39, 257-268.
34. STOLTENBURG, R., REINEMANN, C., and STREHLITZ, B. (2007). SELEX-a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol. Eng. 24, 381-403. (Pubitemid 47391579)
35. TUERK, C., and GOLD, L. (1990). Systematic evolution of li-gands by exponential enrichment: RNA ligands to bacterio-phage T4 DNA polymerase. Science 249, 505-510.
36. VANCE, V., and VAUCHERET, H. (2001). RNA silencing in plants-defense and counterdefense. Science 292, 2277-2280.
37. VERDEL, A., JIA, S., GERBER, S., SUGIYAMA, T., GYGI, S., GRE-WAL, S.I., and MOAZED, D. (2004). RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672-676. (Pubitemid 38141633)
38. VERMEULEN, A., BEHLEN, L., REYNOLDS, A., WOLFSON, A., MARSHALL, W.S., KARPILOW, J., and KHVOROVA, A. (2005). The contributions of dsRNA structure to Dicer specificity and efficiency. RNA 11, 674-682. (Pubitemid 40594334)
39. WIESEN, J.L., and TOMASI, T.B. (2009). Dicer is regulated by cellular stresses and interferons. Mol. Immunol. 46, 1222-1228.
40. ZAMORE, P.D., TUSCHL, T., SHARP, P.A., and BARTEL, D.P. (2000). RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25-33.
41. ZHANG, H., KOLB, F.A., BRONDANI, V., BILLY, E., and FI-LIPOWICZ, W. (2002). Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21, 5875-5885. (Pubitemid 35315285)
42. ZHANG, H., KOLB, F.A., JASKIEWICZ, L., WESTHOF, E., and FILIPOWICZ, W. (2004). Single processing center models for human Dicer and bacterial RNase III. Cell 118, 57-68. (Pubitemid 38902814)