Computational prediction of efficient splice sites for trans-splicing ribozymes

RNA

Volumn 18, Issue 3, 2012, Pages 590-602

  Meluzzi, Dario ^a,b   Olson, Karen E ^a   Dolan, Gregory F ^a   Arya, Gaurav ^b   Müller, Ulrich F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Free energy; Group I intron; Ribozyme; Secondary structure; Trans splicing

Indexed keywords

CHLORAMPHENICOL ACETYLTRANSFERASE; MESSENGER RNA; RIBOZYME;

ARTICLE; ENERGY; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; EXON; PREDICTION; PRIORITY JOURNAL; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN UNFOLDING; RNA HYBRIDIZATION; RNA SPLICING; RNA TRANSCRIPTION; TRANS ISOMER;

COMPUTATIONAL BIOLOGY; NUCLEIC ACID CONFORMATION; RNA SPLICE SITES; RNA, CATALYTIC; RNA, MESSENGER; TRANS-SPLICING; TRANSCRIPTION, GENETIC;

EID: 84857437446     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.029884.111     Document Type: Article

References (78)

1. Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA. 2004. Crystal structure of a self-splicing group I intron with both exons. Nature 430: 45-50. (Pubitemid 38915218)
2. Ayre BG, Kohler U, Goodman HM, Haseloff J. 1999. Design of highly specific cytotoxins by using trans-splicing ribozymes. Proc Natl Acad Sci 96: 3507-3512. (Pubitemid 29168939)
3. Backofen R, Hess WR. 2010. Computational prediction of sRNAs and their targets in bacteria. RNA Biol 7: 33-42.
4. Bai Y, Gong H, Li H, Vu GP, Lu S, Liu F. 2011. Oral delivery of RNase P ribozymes by Salmonella inhibits viral infection in mice. Proc Natl Acad Sci 108: 3222-3227.
5. Been MD, Cech TR. 1986. One binding site determines sequence specificity of Tetrahymena pre-rRNA self-splicing, trans-splicing, and RNA enzyme activity. Cell 47: 207-216.
6. Bell MA, Sinha J, Johnson AK, Testa SM. 2004. Enhancing the second step of the trans excision-splicing reaction of a group I ribozyme by exploiting P9.0 and P10 for intermolecular recognition. Biochemistry 43: 4323-4331. (Pubitemid 38445653)
7. Busch A, Richter AS, Backofen R. 2008. IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 24: 2849-2856.
8. Bustin SA. 2000. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25: 169-193.
9. Byun J, Lan N, Long M, Sullenger BA. 2003. Efficient and specific repair of sickle beta-globin RNA by trans-splicing ribozymes. RNA 9: 1254-1263. (Pubitemid 37151679)
10. Campbell TB, Cech TR. 1995. Identification of ribozymes within a ribozyme library that efficiently cleave a long substrate RNA. RNA 1: 598-609.
11. Carter JR, Keith JH, Barde PV, Fraser TS, Fraser MJ Jr. 2010. Targeting of highly conserved Dengue virus sequences with anti- Dengue virus trans-splicing group I introns. BMC Mol Biol 11: 84. doi: 10.1186/1471-2199-11- 84.
12. Cech TR, Damberger SH, Gutell RR. 1994. Representation of the secondary and tertiary structure of group I introns. Nat Struct Biol 1: 273-280. (Pubitemid 24974851)
13. Chan JH, Lim S, Wong WS. 2006. Antisense oligonucleotides: From design to therapeutic application. Clin Exp Pharmacol Physiol 33: 533-540.
14. Condon A, Jabbari H. 2009. Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges. Theor Comput Sci 410: 294-301.
15. Ding Y, Lawrence CE. 2001. Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res 29: 1034-1046. (Pubitemid 32186188)
16. Dotson PP II, Johnson AK, Testa SM. 2008. Tetrahymena thermophila and Candida albicans group I intron-derived ribozymes can catalyze the trans-excision-splicing reaction. Nucleic Acids Res 36: 5281-5289.
17. Doudna JA, Cormack BP, Szostak JW. 1989. RNA structure, not sequence, determines the 5′ splice-site specificity of a group I intron. Proc Natl Acad Sci 86: 7402-7406. (Pubitemid 19254465)
18. Einvik C, Fiskaa T, Lundblad EW, Johansen S. 2004. Optimization and application of the group I ribozyme trans-splicing reaction. Methods Mol Biol 252: 359-371.
19. Far RK, Leppert J, Frank K, Sczakiel G. 2005. Technical improvements in the computational target search for antisense oligonucleotides. Oligonucleotides 15: 223-233. (Pubitemid 41395999)
20. Fiskaa T, Birgisdottir AB. 2010. RNA reprogramming and repair based on trans-splicing group I ribozymes. New Biotechnol 27: 194-203.
21. Fiskaa T, Lundblad EW, Henriksen JR, Johansen SD, Einvik C. 2006. RNA reprogramming of alpha-mannosidase mRNA sequences in vitro by myxomycete group IC1 and IE ribozymes. FEBS J 273: 2789-2800.
22. Gao Y, Liu XL, Li XR. 2011. Research progress on siRNA delivery with nonviral carriers. Int J Nanomedicine 6: 1017-1025.
23. Golden BL, Kim H, Chase E. 2005. Crystal structure of a phage Twort group I ribozyme-product complex. Nat Struct Mol Biol 12: 82-89. (Pubitemid 40082921)
24. Guo F, Gooding AR, Cech TR. 2004. Structure of the Tetrahymena ribozyme: Base triple sandwich and metal ion at the active site. Mol Cell 16: 351-362. (Pubitemid 39504790)
25. Guo P, Coban O, Snead NM, Trebley J, Hoeprich S, Guo S, Shu Y. 2010. Engineering RNA for targeted siRNA delivery and medical application. Adv Drug Deliv Rev 62: 650-666.
26. Haugen P, Andreassen M, Birgisdottir AB, Johansen S. 2004. Hydrolytic cleavage by a group I intron ribozyme is dependent on RNA structures not important for splicing. Eur J Biochem 271: 1015-1024. (Pubitemid 38299655)
27. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. 1994. Fast folding and comparison of RNA secondary structures. Monatsh Chem 125: 167-188.
28. Inoue T, Sullivan FX, Cech TR. 1985. Intermolecular exon ligation of the rRNA precursor of Tetrahymena: Oligonucleotides can function as 5′ exons. Cell 43: 431-437. (Pubitemid 16213268)
29. Inoue T, Sullivan FX, Cech TR. 1986. New reactions of the ribosomal RNA precursor of Tetrahymena and the mechanism of self-splicing. J Mol Biol 189: 143-165.
30. Johnson AK, Sinha J, Testa SM. 2005. Trans insertion-splicing: Ribozyme-catalyzed insertion of targeted sequences into RNAs. Biochemistry 44: 10702-10710. (Pubitemid 41098247)
31. Jones JT, Lee SW, Sullenger BA. 1996. Tagging ribozyme reaction sites to follow trans-splicing in mammalian cells. Nat Med 2: 643-648. (Pubitemid 26191950)
32. Jung HS, Lee SW. 2005. Re-engineering of carcinoembryonic antigen RNA with the group I intron of Tetrahymena thermophila by targeted trans-splicing. J Microbiol Biotechnol 15: 1408-1413.
33. Jung HS, Lee SW. 2006. Ribozyme-mediated selective killing of cancer cells expressing carcinoembryonic antigen RNA by targeted transsplicing. Biochem Biophys Res Commun 349: 556-563.
34. Karbstein K, Carroll KS, Herschlag D. 2002. Probing the Tetrahymena group I ribozyme reaction in both directions. Biochemistry 41: 11171-11183. (Pubitemid 35034019)
35. Kay PS, Inoue T. 1987. Catalysis of splicing-related reactions between dinucleotides by a ribozyme. Nature 327: 343-346. (Pubitemid 17075091)
36. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. 2007. The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284. (Pubitemid 47482690)
37. Kim A, Ban G, Song MS, Bae CD, Park J, Lee SW. 2007. Selective regression of cells expressing mouse cytoskeleton-associated protein 2 transcript by trans-splicing ribozyme. Oligonucleotides 17: 95-103. (Pubitemid 46651431)
38. Kohler U, Ayre BG, Goodman HM, Haseloff J. 1999. Trans-splicing ribozymes for targeted gene delivery. J Mol Biol 285: 1935-1950. (Pubitemid 29078162)
39. Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR. 1982. Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31: 147-157. (Pubitemid 13215202)
40. Kwon BS, Jung HS, Song MS, Cho KS, Kim SC, Kimm K, Jeong JS, Kim IH, Lee SW. 2005. Specific regression of human cancer cells by ribozyme-mediated targeted replacement of tumor-specific transcript. Mol Ther 12: 824-834. (Pubitemid 41614477)
41. Lan N, Howrey RP, Lee SW, Smith CA, Sullenger BA. 1998. Ribozyme-mediated repair of sickle beta-globin mRNAs in erythrocyte precursors. Science 280: 1593-1596. (Pubitemid 28277702)
42. Lan N, Rooney BL, Lee SW, Howrey RP, Smith CA, Sullenger BA. 2000. Enhancing RNA repair efficiency by combining transsplicing ribozymes that recognize different accessible sites on a target RNA. Mol Ther 2: 245-255.
43. Layton DM, Bundschuh R. 2005. A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation. Nucleic Acids Res 33: 519-524. (Pubitemid 40360981)
44. Lee SJ, Lee SW, Jeong JS, Kim IH. 2010. In vivo reprogramming of human telomerase reverse transcriptase (hTERT) by trans-splicing ribozyme to target tumor cells. Methods Mol Biol 629: 307-321.
45. Lehnert V, Jaeger L, Michel F, Westhof E. 1996. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymena thermophila ribozyme. Chem Biol 3: 993-1009. (Pubitemid 27058823)
46. Lipchock SV, Strobel SA. 2008. A relaxed active site after exon ligation by the group I intron. Proc Natl Acad Sci 105: 5699-5704. (Pubitemid 351758435)
47. Long MB, Sullenger BA. 1999. Evaluating group I intron catalytic efficiency in mammalian cells. Mol Cell Biol 19: 6479-6487. (Pubitemid 29441833)
48. Lu ZJ, Mathews DH. 2008. Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Res 36: 640-647. (Pubitemid 351250454)
49. Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH. 1999. Predicting oligonucleotide affinity to nucleic acid targets. RNA 5: 1458-1469.
50. McCaskill JS. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105-1119. (Pubitemid 20145703)
51. Milligan JF, Uhlenbeck OC. 1989. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol 180: 51-62. (Pubitemid 20039565)
52. Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 15: 8783-8798.
53. Mitov MI, Greaser ML, Campbell KS. 2009. GelBandFitter-A computer program for analysis of closely spaced electrophoretic and immunoblotted bands. Electrophoresis 30: 848-851.
54. Pan J, Thirumalai D, Woodson SA. 1997. Folding of RNA involves parallel pathways. J Mol Biol 273: 7-13. (Pubitemid 27460208)
55. Park Y-H, Jung H-S, Kwon B-S, Lee S-W. 2003. Replacement of thymidine phosphorylase RNA with group I intron of Tetrahymena thermophila by targeted trans-splicing. J Microbiol 41: 340-344. (Pubitemid 38125429)
56. Phylactou LA, Darrah C, Wood MJ. 1998. Ribozyme-mediated transsplicing of a trinucleotide repeat. Nat Genet 18: 378-381.
57. Pichon C, Felden B. 2008. Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics 24: 2807-2813.
58. Rogers CS, Vanoye CG, Sullenger BA, George AL Jr. 2002. Functional repair of a mutant chloride channel using a trans-splicing ribozyme. J Clin Invest 110: 1783-1789. (Pubitemid 36076485)
59. Ryu KJ, Lee SW. 2003. Identification of the most accessible sites to ribozymes on the hepatitis C virus internal ribosome entry site. J Biochem Mol Biol 36: 538-544.
60. Ryu KJ, Kim JH, Lee SW. 2003. Ribozyme-mediated selective induction of new gene activity in hepatitis C virus internal ribosome entry site-expressing cells by targeted trans-splicing. Mol Ther 7: 386-395.
61. Scott WG. 2007. Ribozymes. Curr Opin Struct Biol 17: 280-286. (Pubitemid 47028596)
62. Shadle SE, Allen DF, Guo H, Pogozelski WK, Bashkin JS, Tullius TD. 1997. Quantitative analysis of electrophoresis data: Novel curve fitting methodology and its application to the determination of a protein-DNA binding constant. Nucleic Acids Res 25: 850-860. (Pubitemid 27299843)
63. Shao Y, Wu Y, Chan CY, McDonough K, Ding Y. 2006. Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation. Nucleic Acids Res 34: 5660-5669. (Pubitemid 44742453)
64. Shao Y, Chan CY, Maliyekkel A, Lawrence CE, Roninson IB, Ding Y. 2007a. Effect of target secondary structure on RNAi efficiency. RNA 13: 1631-1640. (Pubitemid 47481671)
65. Shao Y, Wu S, Chan CY, Klapper JR, Schneider E, Ding Y. 2007b. A structural analysis of in vitro catalytic activities of hammerhead ribozymes. BMC Bioinformatics 8: 469. doi: 10.1186/1471-2105-8-469.
66. Shi X, Mollova ET, Pljevaljcic G, Millar DP, Herschlag D. 2009. Probing the dynamics of the P1 helix within the Tetrahymena group I intron. J Am Chem Soc 131: 9571-9578.
67. Sullenger BA, Cech TR. 1994. Ribozyme-mediated repair of defective mRNA by targeted, trans-splicing. Nature 371: 619-622. (Pubitemid 24315745)
68. Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J, Hofacker IL. 2008. The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol 26: 578-583. (Pubitemid 351668044)
69. Thomas CE, Ehrhardt A, Kay MA. 2003. Progress and problems with the use of viral vectors for gene therapy. Nat Rev Genet 4: 346-358. (Pubitemid 36538359)
70. Thomas M, Lieberman J, Lal A. 2010. Desperately seeking microRNA targets. Nat Struct Mol Biol 17: 1169-1174.
71. Thompson AJ, Herrin DL. 1991. In vitro self-splicing reactions of the chloroplast group I intron Cr.LSU from Chlamydomonas reinhardtii and in vivo manipulation via gene-replacement. Nucleic Acids Res 19: 6611-6618. (Pubitemid 21913097)
72. van der Horst G, Inoue T. 1993. Requirements of a group I intron for reactions at the 3′ splice site. J Mol Biol 229: 685-694. (Pubitemid 23068044)
73. Walton SP, Stephanopoulos GN, Yarmush ML, Roth CM. 1999. Prediction of antisense oligonucleotide binding affinity to a structured RNA target. Biotechnol Bioeng 65: 1-9. (Pubitemid 29406765)
74. Walton SP, Wu M, Gredell JA, Chan C. 2010. Designing highly active siRNAs for therapeutic applications. FEBS J 277: 4806-4813.
75. Wang JY, Drlica K. 2004. Computational identification of antisense oligonucleotides that rapidly hybridize to RNA. Oligonucleotides 14: 167-175. (Pubitemid 39362484)
76. Waring RB, Towner P, Minter SJ, Davies RW. 1986. Splice-site selection by a self-splicing RNA of Tetrahymena. Nature 321: 133-139. (Pubitemid 16022016)
77. Watanabe T, Sullenger BA. 2000. Induction of wild-type p53 activity in human cancer cells by ribozymes that repair mutant p53 transcripts. Proc Natl Acad Sci 97: 8490-8494. (Pubitemid 30639700)
78. Zarrinkar PP, Sullenger BA. 1998. Probing the interplay between the two steps of group I intron splicing: Competition of exogenous guanosine with omega G. Biochemistry 37: 18056-18063. (Pubitemid 29023962)