Antisense oligonucleotides capable of promoting specific target mRNA reduction via competing RNase H1-dependent and independent mechanisms

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Vickers, Timothy A ^a   Crooke, Stanley T ^a  

^a ISIS PHARMACEUTICALS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; COPPER ZINC SUPEROXIDE DISMUTASE; MESSENGER RNA; RIBONUCLEASE H; RIBONUCLEASE HI; RNA PRECURSOR;

ARTICLE; BIOTINYLATION; CONTROLLED STUDY; HUMAN; HUMAN CELL; INTRON; POLYADENYLATION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN RNA BINDING; PROTEIN STABILITY; PROTEIN TARGETING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA CLEAVAGE; RNA PROCESSING; RNA SPLICING; SITE DIRECTED MUTAGENESIS; WESTERN BLOTTING; GENETICS; HELA CELL LINE; METABOLISM; TUMOR CELL LINE;

CELL LINE, TUMOR; HELA CELLS; HUMANS; INTRONS; OLIGONUCLEOTIDES, ANTISENSE; RIBONUCLEASE H; RNA PRECURSORS; RNA, MESSENGER;

EID: 84907829489     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0108625     Document Type: Article

References (40)

1. Crooke ST (1999) Molecular mechanisms of action of antisense drugs. Biochim, Biophys Acta 1489:30-42.
2. Crouch RJ, Dirksen M-L (1985) Ribonucleases H. In: Linn SM, Roberts RJ, editors. Nucleases. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. pp. 211-241.
3. Cerritelli SM, Crouch RJ (2009) Ribonuclease H: the enzymes in eukaryotes. FEBS Journal 276:1494-1505.
4. Wu H, Lima WF, Crooke ST (1999) Properties of cloned and expressed human RNase H1. Journal of Biological Chemistry 274:28270-28278.
5. Wu H, Lima WF, Zhang H, Fan A, Sun H, et al. (2004) Determination of the Role of the Human RNase H1 in the Pharmacology of DNA-like Antisense Drugs. Journal of Biological Chemistry 279:17181-17189.
6. Bennett CF, Swayze EE (2010) RNA Targeting Therapeutics: Molecular Mechanisms of Antisense Oligonucleotides as a Therapeutic Platform. Annual Review of Pharmacology and Toxicology 50:259-293.
7. Sharp PA (2009) The Centrality of RNA. Cell 136:577-580.
8. Vickers TA, Zhang H, Graham MJ, Lemonidis KM, Zhao C, et al. (2006) Modification of MyD88 mRNA Splicing and Inhibition of IL-1beta Signaling in Cell Culture and in Mice with a 29-O-Methoxyethyl-Modified Oligonucleotide. Journal of Immunology 176:3652-3661.
9. Hua Y, Vickers TA, Baker BF, Bennett CF, Krainer AR (2007) Enhancement of SMN2 Exon 7 Inclusion by Antisense Oligonucleotides Targeting the Exon. PLoS Biol 5:e73.
10. Hua Y, Vickers TA, Okunola HL, Bennett CF, Krainer AR (2008) Antisense Masking of an hnRNP A1/A2 Intronic Splicing Silencer Corrects SMN2 Splicing in Transgenic Mice American Journal of Human Genetics 82:834-848.
11. Rigo F, Hua Y, Chun SJ, Prakash TP, Krainer AR, et al. (2012) Synthetic oligonucleotides recruit ILF2/3 to RNA transcripts to modulate splicing. Nature Chemical Biology 8:555-561.
12. Crooke ST, Vickers TA, Lima W, Wu H (2007) Mechanisms of Antisense Drug Action, an Introduction. In: Crooke ST, editor. Antisense Drug Discovery: Principles, Strategies, and Applications (ed Stanley T Crooke) 2nd Ed: CRC Press, Taylor & Francis Group. pp. 3-46.
13. Baker BF, Miraglia L, Hagedorn CH (1992) Modulation of eucaryotic initiation factor-4E binding to 59-capped oligoribonucleotides by modified anti-sense oligonucleotides. Journal of Biological Chemistry 267:11495-11499.
14. Baker BF, Lot SS, Condon TP, Cheng-Flournoy S, Lesnik EA, et al. (1997) 29-O-(2-Methoxy) ethyl-modified anti-intercellular adhesion molecule 1 (ICAM-1) oligonucleotides selectively increase the ICAM-1 mRNA level and inhibit formation of the ICAM-1 translation initiation complex in human umbilical vein endothelial cells. Journal of Biological Chemistry 272:11994-12000.
15. Vickers TA, Wyatt JR, Burckin T, Bennett CF, Freier SM (2001) Fully modified 29 MOE oligonucleotides redirect polyadenylation. Nucleic Acids Research 29:1293-1299.
16. Vickers TA, Baker BF, Cook PD, Zounes M, Buckheit RW Jr, et al. (1991) Inhibition of HIV-LTR gene expression by oligonucleotides targeted to the TAR element. Nucleic Acids Research 19:3359-3368.
17. Wu H, Sun H, Liang X, Lima WF, Crooke ST (2013) Human RNase H1 Is Associated with Protein P32 and Is Involved in Mitochondrial Pre-rRNA Processing. PLoS ONE 8:e71006.
18. Liang X-h, Shen W, Sun H, Prakash T, Crooke ST (2014) TCP1 complex proteins interact with phosphorothioate oligonucleotides and can co-localize in oligonucleotide-induced nuclear bodies in mammalian cells. Nucleic Acids Research 42:7819-7832.
19. Baker BF, Lot SS, Condon TP, Cheng-Flournoy S, Lesnik EA, et al. (1997) a29-O-(2-methoxy) ethyl-modified anti-intercellular adhesion molecule 1 (ICAM-1) oligonucleotides selectively increase the ICAM-1 mRNA level and inhibit formation of the ICAM-1 translation initiation complex in human umbilical vein endothelial cells. Journal of Biological Chemistry 272:11994-12000.
20. Lima WF, Vickers TA, Nichols J, Li C, Crooke ST (2014) Defining the factors that contribute to on-target specificity for antisense oligonucleotides. PLoS ONE 9:e101752.
21. Winer J, Kwang C, Jung S, Shackel I, Williams PM (1999) Development and Validation of Real-Time Quantitative Reverse Transcriptase6Polymerase Chain Reaction for Monitoring Gene Expression in Cardiac Myocytes in Vitro. Anal Biochem 270:41-49.
22. Hashimoto JG, Beadles-Bohling AS, Wiren KM (2004) Comparison of RiboGreen and 18S rRNA quantitation for normalizing real-time RT-PCR expression analysis. BioTechniques 36:58-60.
23. Vickers TA, Lima WF, Nichols JG, Crooke ST (2007) Reduced levels of Ago2 expression result in increased siRNA competition in mammalian cells. Nucleic Acids Research 35:6598-6610.
24. Cook PD (1993) Medicinal chemistry strategies for antisense research. In: Crooke ST, Lebleu B, editors. Antisense Research and Applications. Boca Raton: CRC Press. pp. 149-187.
25. Kogoma T, Subia NL, von Meyenburg K (1985) Function of ribonuclease H in initiation of DNA replication in Escherichia coli K-12. Mol Gen Genet 200:103-109.
26. Sproat BS, Lamond AI (1993) 2'-O-alkyloligoribonucleotides. In: Crooke ST, Lebleu B, editors. Antisense Res App. Boca Raton: CRC Press. pp. 351-362.
27. Monia BP, Johnston JF, Sasmor H, Cummins LL (1996) Nuclease resistance and antisense activity of modified oligonucleotides targeted to Ha-ras. Journal of Biological Chemistry 271:14533-14540.
28. Matunis MJ, Xing J, Dreyfuss G (1994) The hnRNP F protein: unique primary structure, nucleic acid-binding properties, and subcellular localization. Nucleic Acids Research 22:1059-1067.
29. Chaudhury A, Chander P, Howe PH (2010) Heterogeneous nuclear ribonucleoproteins (hnRNPs) in cellular processes: Focus on hnRNP E1's multifunctional regulatory roles. RNA 16:1449-1462.
30. Pastor T, Pagani F (2011) Interaction of hnRNPA1/A2 and DAZAP1 with an Alu-Derived Intronic Splicing Enhancer Regulates ATM Aberrant Splicing. PLoS Biol 6:e23349.
31. Hodges D, Crooke ST (1995) Inhibition of splicing of wild-type and mutated luciferase-adenovirus pre-mRNA by antisense oligonucleotides. Molecular Pharmacology 48:905-918.
32. McKay R, Miraglia L, Cummins L, Owens S, Sasmor H, et al. (1999) Characterization of a potent and specific class of antisense oligonucleotide inhibitors of human PKC-a expression. Journal of Biological Chemistry 274:1715-1722.
33. Monia BP, Lesnik EA, Gonzalez C, Lima WF, McGee D, et al. (1993) Evaluation of 2' modified oligonucleotides containing deoxy gaps as antisense inhibitors of gene expression. Journal of Biological Chemistry 268:14514-14522.
34. Talukdar I, Sen S, Urbano R, Thompson J, Yates JR III, et al. (2011) hnRNP A1 and hnRNP F Modulate the Alternative Splicing of Exon 11 of the Insulin Receptor Gene. PLoS ONE 6:e27869.
35. Tang X, Kane V, Morré D, Morré DJ (2011) hnRNP F directs formation of an exon 4 minus variant of tumor-associated NADH oxidase (ENOX2). Molecular and Cellular Biochemistry 357:55-63.
36. Chou M-Y, Rooke N, Turck CW, Black DL (1999) hnRNP H Is a Component of a Splicing Enhancer Complex That Activates a c-src Alternative Exon in Neuronal Cells. Molecular and Cellular Biology 19:69-77.
37. Lima WF, Rose JB, Nichols JG, Wu H, Migawa MT, et al. (2007) Human RNase H1 Discriminates between Subtle Variations in the Structure of the Heteroduplex Substrate. Molecular Pharmacology 71:83-91.
38. Wu H, Lima WF, Crooke ST (1999) Properties of Cloned and Expressed Human RNase H1. Journal of Biological Chemistry 274:28270-28278.
39. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, et al. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494-498.
40. Caplen NJ, Parrish S, Imani F, Fire A, Morgan RA (2001) Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci USA 98:9742-9747.