Self-duplexing CUG repeats selectively inhibit mutant huntingtin expression

Nucleic Acids Research

Volumn 41, Issue 22, 2013, Pages 10426-10437

  Fiszer, Agnieszka ^a   Olejniczak, Marta ^a   Galka Marciniak, Paulina ^a   Mykowska, Agnieszka ^a   Krzyzosiak, Wlodzimierz J ^a  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

HUNTINGTIN; REAGENT; SMALL INTERFERING RNA;

ALLELE; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; CUG REPEAT; GENE EXPRESSION; GENE SILENCING; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; HTT GENE; HUMAN; HUMAN CELL; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA INTERFERENCE; STRUCTURE ACTIVITY RELATION;

ALLELES; CELLS, CULTURED; GENETIC VECTORS; HUMANS; HUNTINGTON DISEASE; MUTATION; NERVE TISSUE PROTEINS; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 84890352875     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt825     Document Type: Article

References (43)

1. Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
2. Guo, H., Ingolia, N.T., Weissman, J.S. and Bartel, D.P. (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466, 835-840.
3. Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K. and Tuschl, T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494-498.
4. Liu, J., Carmell, M.A., Rivas, F.V., Marsden, C.G., Thomson, J.M., Song, J.J., Hammond, S.M., Joshua-T. L. and Hannon, G.J. (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305, 1437-1441.
5. Martinez, J., Patkaniowska, A., Urlaub, H., Luhrmann, R. and Tuschl, T. (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell, 110, 563-574.
6. Czech, B. and Hannon, G.J. (2011) Small RNA sorting: matchmaking for Argonautes. Nat. Rev. Genet., 12, 19-31.
7. Zeng, Y., Yi, R. and Cullen, B.R. (2003) MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc. Natl Acad. Sci. USA, 100, 9779-9784.
8. Doench, J.G., Petersen, C.P. and Sharp, P.A. (2003) SiRNAs can function as miRNAs. Genes Dev., 17, 438-442.
9. Saxena, S., Jonsson, Z.O. and Dutta, A. (2003) Small RNAs with imperfect match to endogenous mRNA repress translation. Implications for off-target activity of small inhibitory RNA in mammalian cells. J. Biol. Chem., 278, 44312-44319.
10. Krzyzosiak, W.J., Sobczak, K., Wojciechowska, M., Fiszer, A., Mykowska, A. and Kozlowski, P. (2012) Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target. Nucleic Acids Res., 40, 11-26.
11. Matsui, M. and Corey, D.R. (2012) Allele-selective inhibition of trinucleotide repeat genes. Drug Discov. Today, 17, 443-450.
12. Caplen, N.J., Taylor, J.P., Statham, V.S., Tanaka, F., Fire, A. and Morgan, R.A. (2002) Rescue of polyglutamine-mediated cytotoxicity by double-stranded RNA-mediated RNA interference. Hum. Mol. Genet., 11, 175-184.
13. Fiszer, A., Mykowska, A. and Krzyzosiak, W.J. (2011) Inhibition of mutant huntingtin expression by RNA duplex targeting expanded CAG repeats. Nucleic Acids Res., 39, 5578-5585.
14. Hu, J., Gagnon, K.T., Liu, J., Watts, J.K., Syeda-Nawaz, J., Bennett, C.F., Swayze, E.E., Randolph, J., Chattopadhyaya, J. and Corey, D.R. (2011) Allele-selective inhibition of ataxin-3 (ATX3) expression by antisense oligomers and duplex RNAs. Biol. Chem., 392, 315-325.
15. Hu, J., Liu, J. and Corey, D.R. (2010) Allele-Selective Inhibition of Huntingtin Expression by Switching to an miRNA-like RNAi Mechanism. Chem. Biol., 17, 1183-1188.
16. Hu, J., Matsui, M. and Corey, D.R. (2009) Allele-selective inhibition of mutant huntingtin by peptide nucleic acid-peptide conjugates, locked nucleic acid, and small interfering RNA. Ann. N. Y. Acad. Sci., 1175, 24-31.
17. Hu, J., Matsui, M., Gagnon, K.T., Schwartz, J.C., Gabillet, S., Arar, K., Wu, J., Bezprozvanny, I. and Corey, D.R. (2009) Allele-specific silencing of mutant huntingtin and ataxin-3 genes by targeting expanded CAG repeats in mRNAs. Nat. Biotechnol., 27, 478-484.
18. Miller, V.M., Xia, H., Marrs, G.L., Gouvion, C.M., Lee, G., Davidson, B.L. and Paulson, H.L. (2003) Allele-specific silencing of dominant disease genes. Proc. Natl Acad. Sci. USA, 100, 7195-7200.
19. Xia, H., Mao, Q., Eliason, S.L., Harper, S.Q., Martins, I.H., Orr, H.T., Paulson, H.L., Yang, L., Kotin, R.M. and Davidson, B.L. (2004) RNAi suppresses polyglutamine-induced neurodegeneration in a model of spinocerebellar ataxia. Nat. Med., 10, 816-820.
20. Grimm, D. (2009) Asymmetry in siRNA design. Gene Ther., 16, 827-829.
21. Holen, T., Amarzguioui, M., Babaie, E. and Prydz, H. (2003) Similar behaviour of single-strand and double-strand siRNAs suggests they act through a common RNAi pathway. Nucleic Acids Res., 31, 2401-2407.
22. Schwarz, D.S., Hutvagner, G., Haley, B. and Zamore, P.D. (2002) Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol. Cell, 10, 537-548.
23. Xu, Y., Linde, A., Larsson, O., Thormeyer, D., Elmen, J., Wahlestedt, C. and Liang, Z. (2004) Functional comparison of single-and double-stranded siRNAs in mammalian cells. Biochem. Biophys. Res. Commun., 316, 680-687.
24. Hossbach, M., Gruber, J., Osborn, M., Weber, K. and Tuschl, T. (2006) Gene silencing with siRNA duplexes composed of target-mRNA-complementary and partially palindromic or partially complementary single-stranded siRNAs. RNA Biol., 3, 82-89.
25. McBride, J.L., Boudreau, R.L., Harper, S.Q., Staber, P.D., Monteys, A.M., Martins, I., Gilmore, B.L., Burstein, H., Peluso, R.W., Polisky, B. et al. (2008) Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: implications for the therapeutic development of RNAi. Proc. Natl Acad. Sci. USA, 105, 5868-5873.
26. Koscianska, E., Starega-R. J., Czubala, K. and Krzyzosiak, W.J. (2011) High-resolution northern blot for a reliable analysis of microRNAs and their precursors. ScientificWorldJournal, 11, 102-117.
27. Koscianska, E., Starega-R. J., Sznajder, L.J., Olejniczak, M., Galka-M. P. and Krzyzosiak, W.J. (2011) Northern blotting analysis of microRNAs, their precursors and RNA interference triggers. BMC Mol. Biol., 12, 14.
28. Frank, F., Sonenberg, N. and Nagar, B. (2010) Structural basis for 50-nucleotide base-specific recognition of guide RNA by human AGO2. Nature, 465, 818-822.
29. Sobczak, K., Michlewski, G., de Mezer, M., Kierzek, E., Krol, J., Olejniczak, M., Kierzek, R. and Krzyzosiak, W.J. (2010) Structural diversity of triplet repeat RNAs. J. Biol. Chem., 285, 12755-12764.
30. Chen, P.Y., Weinmann, L., Gaidatzis, D., Pei, Y., Zavolan, M., Tuschl, T. and Meister, G. (2008) Strand-specific 50-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA, 14, 263-274.
31. Olejniczak, M., Galka, P. and Krzyzosiak, W.J. (2010) Sequence-non-specific effects of RNA interference triggers and microRNA regulators. Nucleic Acids Res., 38, 1-16.
32. Evers, M.M., Pepers, B.A., van Deutekom, J.C., Mulders, S.A., den Dunnen, J.T., Aartsma-Rus, A., van Ommen, G.J. and van Roon-Mom, W.M. (2011) Targeting several CAG expansion diseases by a single antisense oligonucleotide. PLoS One, 6, e24308.
33. Fiszer, A., Olejniczak, M., Switonski, P.M., Wroblewska, J.P., Wisniewska-Kruk, J., Mykowska, A. and Krzyzosiak, W.J. (2012) An evaluation of oligonucleotide-based therapeutic strategies for polyQ diseases. BMC Mol. Biol., 13, 6.
34. Kozlowski, P., de Mezer, M. and Krzyzosiak, W.J. (2010) Trinucleotide repeats in human genome and exome. Nucleic Acids Res., 38, 4027-4039.
35. Yu, D., Pendergraff, H., Liu, J., Kordasiewicz, H.B., Cleveland, D.W., Swayze, E.E., Lima, W.F., Crooke, S.T., Prakash, T.P. and Corey, D.R. (2012) Single-stranded RNAs use RNAi to potently and allele-selectively inhibit mutant huntingtin expression. Cell, 150, 895-908.
36. Napierala, M. and Krzyzosiak, W.J. (1997) CUG repeats present in myotonin kinase RNA form metastable 'slippery' hairpins. J. Biol. Chem., 272, 31079-31085.
37. Kierzek, R., Burkard, M.E. and Turner, D.H. (1999) Thermodynamics of single mismatches in RNA duplexes. Biochemistry, 38, 14214-14223.
38. Davis, A.R. and Znosko, B.M. (2010) Positional and neighboring base pair effects on the thermodynamic stability of RNA single mismatches. Biochemistry, 49, 8669-8679.
39. Chi, S.W., Zang, J.B., Mele, A. and Darnell, R.B. (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature, 460, 479-486.
40. Wojciechowska, M. and Krzyzosiak, W.J. (2011) CAG repeat RNA as an auxiliary toxic agent in polyglutamine disorders. RNA Biol., 8, 565-571.
41. Fiszer, A. and Krzyzosiak, W.J. (2013) RNA toxicity in polyglutamine disorders: concepts, models, and progress of research. J. Mol. Med., 91, 683-691.
42. Markham, N.R. and Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res., 33, W577-W581.
43. Patzel, V., Rutz, S., Dietrich, I., Koberle, C., Scheffold, A. and Kaufmann, S.H. (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nat. Biotechnol., 23, 1440-1444.