U1 adaptors result in reduction of multiple pre-mRNA species principally by sequestering U1snRNP

Nucleic Acids Research

Volumn 39, Issue 10, 2011, Pages

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

^a ISIS PHARMACEUTICALS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA PRECURSOR; OLIGONUCLEOTIDE; SMALL NUCLEAR RIBONUCLEOPROTEIN; ANTISENSE OLIGONUCLEOTIDE; MESSENGER RNA; RNA PRECURSOR; SMALL NUCLEAR RNA; U1 SMALL NUCLEAR RNA;

ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE SILENCING; GENE TARGETING; PRIORITY JOURNAL; RNA PROCESSING; RNA SPLICING; DOWN REGULATION; DRUG ANTAGONISM; HELA CELL; HUMAN; METABOLISM;

DOWN-REGULATION; GENE SILENCING; HELA CELLS; HUMANS; OLIGONUCLEOTIDES; OLIGONUCLEOTIDES, ANTISENSE; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RNA PRECURSORS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA SPLICING; RNA, MESSENGER; RNA, SMALL NUCLEAR;

EID: 79961189939     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr150     Document Type: Article

References (32)

1. Goraczniak, R., Behlke, M.A. and Gunderson, S.I. (2009) Gene silencing by synthetic U1 Adaptors. Nat. Biotechnol., 27, 257-263.
2. Seraphin, B. and Rosbash, M. (1989) Identification of functional U1 snRNA-pre-mRNA complexes committed to spliceosome assembly and splicing. Cell, 59, 349-358. (Pubitemid 19264379)
3. Eperon, I.C., Makarova, O.V., Mayeda, A., Munroe, S.H., Caceres, J.F., Hayward, D.G. and Krainer, A.R. (2000) Selection of alternative 50 splice sites: role of U1 snRNP and models for the antagonistic effects of SF2/ASF and hnRNP A1. Mol. Cell. Biol., 20, 8303-8318.
4. Zhuang, Y. and Weiner, A.M. (1986) A compensatory base change in U1 snRNA suppresses a 50 splice site mutation. Cell, 46, 827-835. (Pubitemid 16027931)
5. Furth, P.A., Choe, W.T., Rex, J.H., Byrne, J.C. and Baker, C.C. (1994) Sequences homologous to 50 splice sites are required for the inhibitory activity of papillomavirus late 30 untranslated regions. Mol. Cell. Biol., 14, 5278-5289.
6. Gunderson, S.I., Polycarpou-Schwarz, M. and Mattaj, I.W. (1998) U1 snRNP Inhibits Pre-mRNA polyadenylation through a direct interaction between U1 70K and poly(A) polymerase. Mol. Cell, 1, 255-264. (Pubitemid 128378666)
7. Roca, X. and Krainer, A.R. (2009) Recognition of atypical 50 splice sites by shifted base-pairing to U1 snRNA. Nat. Struct. Mol. Biol., 16, 176-182.
8. Kaida, D., Berg, M.G., Younis, I., Kasim, M., Singh, L.N., Wan, L. and Dreyfuss, G. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature, 468, 664-669.
9. Baker, B.F., Lot, S.S., Condon, T.P., Cheng-Flournoy, S., Lesnik, E.A., Sasmor, H.M. and Bennett, C.F. (1997) 20-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. J. Biol. Chem., 272, 11994-12000.
10. Vickers, T.A., Zhang, H., Graham, M.J., Lemonidis, K.M., Zhao, C. and Dean, N.M. (2006) Modification of MyD88 mRNA Splicing and Inhibition of IL-1beta Signaling in Cell Culture and in Mice with a 20-O-Methoxyethyl-Modified Oligonucleotide. J. Immunol., 176, 3652-3661. (Pubitemid 43364012)
11. Winer, J., Kwang, C., Jung, S., Shackel, I. and Williams, P.M. (1999) Development and validation of real-time quantitative reverse transcriptase±polymerase chain reaction for monitoring gene expression in cardiac myocytes in vitro. Anal. Biochem., 270, 41-49. (Pubitemid 29230718)
12. Hashimoto, J.G., Beadles-Bohling, A.S. and Wiren, K.M. (2004) Comparison of RiboGreen and 18S rRNA quantitation for normalizing real-time RT-PCR expression analysis. BioTechniques, 36, 58-60.
13. Liang, X.H., Liu, Q. and Fournier, M.J. (2007) rRNA Modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity. Mol. Cell, 28, 965-977. (Pubitemid 350297021)
14. Hua, Y., Vickers, T.A., Baker, B.F., Bennett, C.F. and Krainer, A.R. (2007) Enhancement of SMN2 exon 7 inclusion by antisense oligonucleotides targeting the exon. PLoS Biol., 5, e73.
15. Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
16. Yates, T., Okoniewski, M.J. and Miller, C.J. (2008) X:Map: annotation and visualization of genome structure for affymetrix exon array analysis. Nucleic Acids Res., 36, D780-D786. (Pubitemid 351149823)
17. Okoniewski, M.J. and Miller, C.J. (2008) Comprehensive analysis of affymetrix exon arrays using BioConductor. PLoS Comput. Biol., 4, e6.
18. Smyth, G.K., Yang, Y.H. and Speed, T. (2006) Statistical issues in microarray data analysis. Methods Mol. Biol., 224, 111-136.
19. Benjamini, Y., Drai, D., Elmer, G., Kafkafi, N. and Golani, I. (2001) Controlling the false discovery rate in behavior genetics research. Behav. Brain Res., 125, 279-284. (Pubitemid 33000466)
20. Monia, B.P., Johnston, J.F., Sasmor, H. and Cummins, L.L. (1996) Nuclease resistance and antisense activity of modified oligonucleotides targeted to Ha-ras. J. Biol. Chem., 271, 14533-14540. (Pubitemid 26190357)
21. Cartegni, L. and Krainer, A.R. (2002) Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat. Genet., 30, 377-384.
22. Levin, A.A., Yu, R.Z. and Geary, R.S. (2007) Basic principles of the pharmacokinetics of antisense oligonucleotide drugs. In Stanely Crooke, T. (ed.), Antisense Drug Discovery: Principles, Strategies and Applications. 2nd edn, CRC Press, Taylor & Francis Group, Boca Raton, FL, pp. 183-216.
23. Jackson, A.L., Burchard, J., Schelter, J., Chau, B.N., Cleary, M., Lim, L. and Linsley, P.S. (2006) Widespread siRNA 'off-target' transcript silencing mediated by seed region sequence complementarity. RNA, 12, 1179-1187. (Pubitemid 43990543)
24. Zhuang, Y. and Weiner, A.M. (1986) A compensatory base change in U1 snRNA suppresses a 50 splice site mutation. Cell, 46, 827-835. (Pubitemid 16027931)
25. Cartegni, L., Hastings, M.L., Calarco, J.A., de Stanchina, E. and Krainer, A.R. (2006) Determinants of exon 7 splicing in the spinal muscular atrophy genes, SMN1 and SMN2. Am. J. Hum. Genet., 78, 63-77. (Pubitemid 41833160)
26. Buratti, E., Chivers, M., Kralovicova, J., Romano, M., Baralle, M., Krainer, A.R. and Vorechovsky, I. (2007) Aberrant 50 splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res., 35, 4250-4263. (Pubitemid 47260233)
27. Roca, X., Sachidanandam, R. and Krainer, A.R. (2005) Determinants of the inherent strength of human 50 splice sites. RNA, 11, 683-698. (Pubitemid 40594335)
28. Lim, L.P., Lau, N.C., Garrett-Engele, P., Grimson, A., Schelter, J.M., Castle, J., Bartel, D.P., Linsley, P.S. and Johnson, J.M. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433, 769-773. (Pubitemid 40292988)
29. Monia, B.P., Johnston, J.F., Ecker, D.J., Zounes, M.A., Lima, W.F. and Freier, S.M. (1992) Selective inhibition of mutant Ha-ras mRNA expression by antisense oligonucleotides. J. Biol. Chem., 267, 19954-19962.
30. Vickers, T.A., Koo, S., Bennett, C.F., Crooke, S.T., Dean, N.M. and Baker, B.F. (2003) Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. J. Biol. Chem., 278, 7108-7118. (Pubitemid 36800708)
31. Abad, X., Vera, M., Jung, S.P., Oswald, E., Romero, I., Amin, V., Fortes, P. and Gunderson, S.I. (2008) Requirements for gene silencing mediated by U1 snRNA binding to a target sequence. Nucleic Acids Res., 36, 2338-2352. (Pubitemid 351567007)
32. Wu, H., Lima, W.F. and Crooke, S.T. (1999) Properties of cloned and expressed human RNase H1. J. Biol. Chem., 274, 28270-28278.