An evaluation of detection methods for large lariat RNAs

RNA

Volumn 11, Issue 3, 2005, Pages 323-331

  Coombes, Candice E ^a   Boeke, Jef D ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Lariat; Retrotransposition; RNase protection; Ty1

Indexed keywords

PHOSPHODIESTERASE; RNA;

ANALYTIC METHOD; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; EVALUATION; GEL ELECTROPHORESIS; LONG TERMINAL REPEAT; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; RETROPOSON; RNA ANALYSIS; RNA SPLICING; SACCHAROMYCES CEREVISIAE; TECHNIQUE; TRANSESTERIFICATION;

BASE SEQUENCE; BLOTTING, NORTHERN; DNA PRIMERS; REPETITIVE SEQUENCES, NUCLEIC ACID; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE;

ANIMALIA; SACCHAROMYCES CEREVISIAE;

EID: 13944284088     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7124405     Document Type: Article

References (29)

1. Boeke, J.D., Garfinkel, D.J., Styles, C.A., and Fink, G.R. 1985. Ty elements transpose through an RNA intermediate. Cell 40: 491-500.
2. Boeke, I.D., Eichinger, D., Castrillon, D., and Fink, G.R. 1988. The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1. Mol. Cell Biol. 8: 1432-1442.
3. Chapman, K.B. and Boeke, J.D. 1991. Isolation and characterization of the gene encoding yeast debranching enzyme. Cell 65: 483-492.
4. Chen, C. and Sarnow, P. 1995. Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs. Science 268: 415-417.
5. -. 1998. Internal ribosome entry sites tests with circular mRNAs. Methods Mol. Biol. 77: 355-363.
6. Cheng, Z. and Menees, T.M. 2004. RNA branching and debranching in the yeast retrovirus-like element Ty1. Science 303: 240-243.
7. Chu, V.T., Liu, Q., Podar, M., Perlman, P.S., and Pyle, A.M. 1998. More than one way to splice an RNA: Branching without a bulge and splicing without branching in group II introns. RNA 4: 1186-1202.
8. Collart, M.A. and Olivero, S. 1993. Preparation of yeast RNA. In Current protocols in molecular biology (eds. F.M. Ausbrel et al.), pp. 13.12.1-13.12.5. Wiley, New York.
9. Eichinger, D.J., and Boeke, J.D. 1988. The DNA intermediate in yeast Ty1 element transposition copurifies with virus-like particles: Cell-free Ty1 transposition. Cell 54: 955-966.
10. Elder, R.T., Loh, E.Y., and Davis, R.W. 1983. RNA from the yeast transposable element Ty1 has both ends in the direct repeats, a structure similar to retrovirus RNA. Proc. Natl. Acad. Sci. 80: 2432-2436.
11. Fu, W. and Rein, A. 1993. Maturation of dimeric viral RNA of Moloney murine leukemia virus. J. Virol. 67: 5443-5449.
12. Garfinkel, D.J., Boeke, J.D., and Fink, G.R. 1985. Ty element transposition: Reverse transcriptase and virus-like particles. Cell 42: 507-517.
13. Green, R. and Noller, H.F. 1996. In vitro complementation analysis localizes 23S rRNA posttranscriptional modifications that are required for Escherichia coli 50S ribosomal subunit assembly and function. RNA 2: 1011-1021.
14. Michel, F. and Feray, J.L. 1995. Structure and activities of group II introns. Annu. Rev. Biochem. 64: 435-461.
15. Mules, E.H., Uzun, O., and Gabriel, A. 1998. In vivo Ty1 reverse transcription can generate replication intermediates with untidy ends. J. Virol. 72: 6490-6503.
16. Nam, K., Hudson, R.H.E., Chapman, K.B., Ganeshan, K., Damha, M.J., and Boeke, J.D. 1994. Yeast lariat debranching enzyme: Substrate and sequence specificity. J. Biol. Chem. 269: 20613-20621.
17. Odom, O.W., Schenkenberg, D.L., Garcia, J.A., and Herrin, D.L. 2004. A horizontally acquired group II intron in the chloroplast psbA gene of a psychrophilic Chlamydomonas: In vitro self-splicing and genetic evidence for maturase activity. RNA 10: 1097-1107.
18. Padgett, R.A., Konarska, M.M., Grabowski, P.J., Hardy, S.F., and Sharp, P.A. 1984. Lariat RNAs as intermediates and products in the splicing of messenger RNA precursors. Science 225: 898-903.
19. Padgett, R.A., Konarska, M.M., Aebi, M., Hornig, H., Weissman, C., and Sharp, P.A. 1985. Nonconsensus branch-site sequences in the in vitro splicing of transcripts of mutant rabbit β-globin genes. Proc. Natl. Acad. Sci. 82: 8349-8353.
20. Perlman, P.S. and Boeke, J.D. 2004. Molecular biology. Ring around the retroelement. Science 303: 182-184.
21. Rodriguez, J.R., Pikielny, C.W., and Rosbach, M. 1984. In vivo characterization of yeast mRNA processing intermediates. Cell 39: 603-610.
22. Ruskin, B. and Green, M.R. 1985. An RNA processing activity that debranches RNA lariats. Science 229: 135-140.
23. Ruskin, B., Krainer, A.R., Maniatis, T., and Green, M.R. 1984. Excision of an intact intron as a novel larait structure during pre-mRNA splicing in vitro. Cell 38: 317-331.
24. Salgia, S.R., Singh, S.K., Gurha, P., and Gupta, R. 2003. Two reactions of Haloferax vocanii RNA splicing enzymes: Joining of exons and circularization of introns. RNA 9: 319-330.
25. Tuschl, T., Sharp, P.A., and Bartel, D.P. 2001. A ribozyme selected from variants of U6 snRNA promotes 2′-5′ branch formation. RNA 7: 29-43.
26. Uzun, O. and Gabriel, A. 2001. A Ty1 reverse transcriptase active-site aspartate mutation blocks transposition but not polymerization. J. Virol. 75: 6337-6347.
27. Vogel, J., Hess, W.R., and Borner, T. 1997. Precise branch point mapping and quantification of splicing intermediates. Nucleic Acids Res. 15: 2030-2031.
28. Wang, Y. and Silverman, S.K. 2003. Deoxyribozymes that synthesize branched and lariat RNA. J. Am. Chem. Soc. 125: 6880-6881.
29. Winston, F., Durbin, K.J., and Fink, G.R. 1984. The SPT3 gene is required for normal transcription of Ty1 elements in S. cerevisiae. Cell 39: 675-682.