Sensitivity of splice sites to antisense oligonucleotides in vivo

RNA

Volumn 5, Issue 3, 1999, Pages 369-377

  Sierakowska, Halina ^a,d   Sambade, Maria J ^a   Schümperli, Daniel ^b   Kole, Ryszard ^a,c  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF BERN   (Switzerland)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

^d INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

Author keywords

Alternative splicing; pre mRNA splicing; Splicing factors; Splicing mutations

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; BETA GLOBIN; MESSENGER RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; BASE PAIRING; CONSENSUS SEQUENCE; CONTROLLED STUDY; HELA CELL; HUMAN; HUMAN CELL; NUCLEOTIDE METABOLISM; POINT MUTATION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN INTERACTION; RNA SPLICING;

BASE SEQUENCE; GENE EXPRESSION REGULATION; GLOBINS; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDES, ANTISENSE; POINT MUTATION; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER;

EID: 0032979022     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S135583829998130X     Document Type: Article

References (40)

1. Bennett CF. 1998. Use of cationic lipid complexes for antisense oligonucleotide delivery. In: Stein CA, Krieg AM, eds. Applied antisense oligonucleotide technology. New York: Wiley-Liss. pp 129-145.
2. Berget SM. 1995. Exon recognition in vertebrate splicing. J Biol Chem 270:2411-2414.
3. Blencowe BJ, Issner R, Kim J, Mccaw P, Sharp PA. 1995. New proteins related to the Ser-Arg family of splicing factors. RNA 1:852-865.
4. Chen IT, Chasin LA. 1993. Direct selection for mutations affecting specific splice sites in a hamster dihydrofolate reductase minigene. Mol Cell Biol 13:289-300.
5. Cheng T-C, Orkin SH, Antonorakis SE, Potter MJ, Sexton JP, Giardina PJV, Li A, Kazazian HH. 1984. Beta-Thalassemia in Chinese: Use of in vivo RNA analysis and oligonucleotide hybridization in systematic characterization of molecular defects. Proc Natl Acad Sci USA 81:2821-2826.
6. Coulter LR, Landree MA, Cooper TA. 1997. Identification of a new class of exonic splicing enhancers by in vivo selection. Mol Cell Biol 17:2143-2150.
7. Dobkin C, Bank A. 1985. Reversibility of IVS 2 missplicing in a mutant human beta-globin gene. J Biol Chem 260:16332-16337.
8. Dominski Z, Kole R. 1991. Selection of splice sites in pre-mRNAs with short internal exons. Mol Cell Biol 11:6075-6083.
9. Dominski Z, Kole R. 1993. Restoration of correct splicing in thalassemic pre-mRNA by antisense oligonucleotides. Proc Natl Acad Sci USA 90:8673-8677.
10. Dominski Z, Kole R. 1994a. Identification and characterization by antisense oligonucleotides of exon and intron sequences required for splicing. Mol Cell Biol 14:7445-7454.
11. Dominski Z, Kole R. 1994b. Identification of exon sequences involved in splice site selection. J Biol Chem 269:23590-23596.
12. Furdon PJ, Kole R. 1988. The length of the downstream exon and the substitution of specific sequences affect pre-mRNA splicing in vitro. Mol Cell Biol 8:860-866.
13. Gorman L, Suter D, Emerick V, Schümperli D, Kole R. 1998. Stable alteration of pre-mRNA splicing patterns by modified U7 snRNA. Proc Natl Acad Sci USA 95:4929-4934.
14. Hawley-Nelson P, Ciccarone V, Gebeyehu G, Jessee J, Felgner PL. 1993. Lipofectamine reagent: A new, higher efficiency polycationic liposome transfection reagent. Focus 15:73-79.
15. Hertel KJ, Lynch KW, Maniatis T. 1997. Common themes in the function of transcription and splicing enhancers. Curr Opin Cell Biol 9:350-357.
16. Jaeger JA, Turner DH, Zuker M. 1989. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci USA 86:7706-7710.
17. Jones DH, Winistorfer SC. 1992. Recombinant circle PCR and recombination PCR for site-specific mutagenesis without PCR product purification. Biotechniques 12:528-535.
18. Kang S-H, Cho M-J, Kole R. 1998. Up-regulation of luciferase gene expression with antisense oligonucleotides: Implications and applications in functional assay development. Biochemistry 37:6235-6239.
19. Krämer A. 1996. The structure and function of proteins involved in mammalian pre-mRNA splicing. Ann Rev Biochem 65:367-409.
20. Kuo HC, Nasim FH, Grabowski PJ. 1991. Control of alternative splicing by the differential binding of U1 small nuclear ribonucleoprotein particle. Science 251:1045-1050.
21. Manley JL, Tacke R. 1996. SR proteins and splicing control. Genes & Dev 10:1569-1579.
22. McNally LM, McNally MT. 1996. SR protein splicing factors interact with the Rous Sarcoma virus negative regulator of splicing element. J Virol 70:1163-1172.
23. Moore MJ, Query CC, Sharp PA. 1993. Splicing of precursors to mRNA by the spliceosomes. In: Gesteland RF, Atkins JF, eds. RNA world. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. pp 303-358.
24. Neugebauer KM, Stolk JA, Roth MB. 1995. A conserved epitope on a subset of SR proteins defines a larger family of pre-mRNA splicing factors. J Cell Biol 129:899-908.
25. Reed R. 1996. Initial splice site recognition and pairing during pre-mRNA splicing. Curr Opin Gen Dev 6:215-220.
26. Reed R, Maniatis T. 1986. A role for exon sequences and splice-site proximity in splice-site selection. Cell 46:681-690.
27. Robberson BL, Cote GJ, Berget SM. 1990. Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol Cell Biol 10:84-94.
28. Schägger H, von Jagov G. 1987. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem 166:368-379.
29. Schwartz E, Benz EJ. 1995. Thalassemia syndromes. In: Hoffman R, Benz EJ, Shattil SJ, Furie B, Cohen HJ, Silberstein LE, eds. Hematology, basic principles and practice. New York: Churchill Livingstone. pp 586-610.
30. Senapathy P, Shapiro MB, Harris NL. 1990. Splice junctions, branch point sites, and exons: Sequence statistics, identification, and applications to genome project. Methods Enzymol 183:252-278.
31. Sierakowska H, Sambade MJ, Agrawal S, Kole R. 1996. Repair of thalassemic β-globin mRNA by mammalian cells by antisense oligonucleotides. Proc Natl Acad Sci USA 93:12840-12844.
32. Staknis D, Reed R. 1994. SR-proteins promote the first specific recognition of pre-mRNA and are present together with the U1 small nuclear ribonucleoprotein particle in a general splicing enhancer complex. Mol Cell Biol 14:7670-7682.
33. Staley JP, Guthrie C. 1998. Mechanical devices of the spliceosome: Motors, clocks, springs and things. Cell 92:315-326.
34. Sterner DA, Berget SM. 1993. In vivo recognition of a vertebrate mini-exon as an exon-intron-exon unit. Mol Cell Biol 13:2677-2687.
35. Tian H, Kole R. 1995. Selection of novel exon recognition elements from a pool of random sequences. Mol Cell Biol 15:6291-6298.
36. Treisman R, Orkin SH, Maniatis T. 1983. Specific transcription and RNA splicing defects in five cloned beta-thalassaemia genes. Nature 302:591-595.
37. Valcarcel J, Green MR. 1996. The SR protein family: Pleiotropic functions in pre-mRNA splicing. Trends Biochem Sci 21:296-301.
38. Wang J, Manley JL. 1997. Regulation of pre-mRNA splicing in metazoa. Curr Opin Gen Dev 7:205-211.
39. Will CL, Lührmann R. 1997. Protein functions in pre-mRNA splicing. Curr Opin Cell Biol 9:320-328.
40. Wisconsin Package Version 9.1, Genetics Computer Group (GCG), Madison, WI.