Giant hairpins formed by CUG repeats in myotonic dystrophy messenger RNAs might sterically block RNA export through nuclear pores

Journal of Theoretical Biology

Volumn 192, Issue 4, 1998, Pages 505-514

  Koch, K S ^a   Leffert, H L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; CELL NUCLEUS MEMBRANE; MOLECULAR MODEL; MYOTONIC DYSTROPHY; PRIORITY JOURNAL; RNA CONFORMATION; RNA SEQUENCE; RNA TRANSPORT; STEREOSPECIFICITY;

EID: 0032555056     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1998.0679     Document Type: Article

References (35)

1. AOKI, T., KOCH, K. S. & LEFFERT, H. L. (1997). Attenuation of gene expression by a trinucleotide repeat-rich tract from the terminal exon of the rat hepatic polymeric immunoglobulin receptor gene. J. Mol. Biol. 267, 229-236.
2. BAEYENS, K. J., DE BONDT, H. L. & HOLBROOK, S. R. (1995). Structure of an RNA double helix including uracil-uracil base pairs in an internal loop. Nature struct. Biol. 2, 56-62.
3. BROOK, J. D., MCCURRACH, M. E., HARLEY, H. G., BUCKLER, A. J., CHURCH, D., ABURATANI, H. et al. (1992). Molecular basis of myotonic dystrophy: expansion of a trinucleotide (CTG) repeat at the 3′ end of a transcript encoding a protein kinase family member. Cell 68, 799-808.
4. CITOVSKY, V. & ZAMBRYSKI, P. (1993). Transport of nucleic acids through membrane channels: snaking through small holes. Annu. Rev. Microbiol. 47, 167-197.
5. DANEHOLT, B. (1997). A look at messenger RNP moving through the nuclear pore. Cell 88, 585-588.
6. DARLOW, J. M. & LEACH, D. R. (1995). The effects of trinucleotide repeats found in human inherited disorders on palindrome inviability in Escherichia coli suggest hairpin folding preferences in vivo. Genetics 141, 825-832.
7. DAVIS, B. M., MCCURRACH, M. E., TANEJA, K. L., SINGER, R. H. & HOUSMAN, D. E. (1997). Expansion of a CUG trinucleotide repeat in the 3′ untranslated region of myotonic dystrophy protein kinase transcripts results in nuclear retention of transcripts. Proc. Natl. Acad. Sci. U.S.A. 94, 7388-7393.
8. FREIER, S. M., KIEZERK, R., JAEGER, J. A., SUGIMOTO, N., CARUTHERS, M. H., NELSON, T. & TURNER, D. H. (1986). Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. U.S.A. 83, 9373-9377.
9. FU, Y. H., FRIEDMAN, D. L., RICHARDS, S., PEARLMAN, J. A., GIBBS, R. A., PIZZUTI, A. et al. (1993). Decreased expression of myotonin-protein kinase messenger RNA and protein in adult form of myotonic dystrophy. Science 260, 235-238.
10. FU, Y. H., PIZZUTI, A., FENWICK, R. G. JR., KING, J., RAJNARAYAN, S., DUNNE, P. W. et al. (1992). An unstable triplet repeat in a gene related to myotonic muscular dystrophy. Science 255, 1256-1258.
11. GACY, A. M., GOELLNER, G., JURANIC, N., MACURA, S. & MCMURRAY, C. T. (1995). Trinucleotide repeats that expand in human disease form hairpin structures in vitro. Cell 81, 533-540.
12. GORLICH, D. & MATTAJ, I. W. (1996). Nucleocytoplasmic transport. Science 271, 1513-1518.
13. HAMSHERE, M.G., NEWMAN, E. E., ALWAZZAN, M., ATHWAL, B. S. & BROOK, J. D. (1997). Transcriptional abnormality in myotonic dystrophy affects DMPK but not neighboring genes. Proc. Natl. Acad. Sci. U.S.A. 94, 7394-7399.
14. HARPER, P. (1989). Myotonic Dystrophy. London: Saunders.
15. HE, L., KIERZEK, R., SANTALUCIA, J. JR., WALTER, A. E. & TURNER, D. H. (1991). Nearest-neighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text]. Biochemistry 30, 11124-11132.
16. HOFACKER, I. L., FONTANA, W., STADLER, P. F., BONHOEFFER, L. S., TACKER, M. & SCHUSTER, P. (1994). Fast folding and comparison of RNA secondary structures. Chem. Monthly 125, 167-188.
17. JACK, A., LADNER, J. E. & KLUG, A. (1976). Crystallographic refinement of yeast phenylalanine transfer RNA at 2-5 Å resolution. J. Mol. Biol. 108, 619-649.
18. JAEGER, J. A., TURNER, D. H. & ZUKER, M. (1989). Improved predictions of secondary structures for RNA. Proc. Natl. Acad. Sci. U.S.A. 86, 7706-7710.
19. KANG, S., JAWORSKI, A., OHSHIMA, K. & WELLS, R. D. (1995). Expansion and deletion of CTG repeats from human disease genes are determined by the direction of replication in E. coli. Nature Genet. 10, 213-218.
20. KISELEVA, E., GOLDBERG, M. W., DANEHOLT, B. & ALLEN, T. D. (1996). RNP export is mediated by structural reorganization of the nuclear pore basket. J. Mol. Biol. 260, 304-311.
21. KRAHE, R., ASHIZAWA, T., ABBRUZZESE, C., ROEDER, E., CARANGO, P., GIACANELLI, M. et al. (1995). Effect of myotonic dystrophy trinucleotide repeat expansion on DMPK transcription and processing. Genomics 28, 1-14.
22. MAEDA, M., TAFT, C. S., BUSH, E. W., HOLDER, E., BAILEY, W. M., NEVILLE, H. et al. (1995). Identification, tissue-specific expression, and subcellular localization of the 80-and 71-kDa forms of myotonic dystrophy kinase protein. J. Biol. Chem. 270, 20246-20249.
23. MAHADEVAN, M., TSILFIDIS, C., SABOURIN, L., SHUTLER, G., AMEMIYA, C., JANSEN, G. et al. (1992). Myotonic dystrophy mutation: an unstable CTG repeat in the 3′ untranslated region of the gene. Science 255, 1253-1255.
24. MARIAPPAN, S. V., GARCOA, A. E. & GUPTA, G. (1996). Structure and dynamics of the DNA hairpins formed by tandemly repeated CTG triplets associated with myotonic dystrophy. Nucl. Acids Res. 24, 775-783.
25. MATZURA, O. & WENNBORG, A. (1996). RNAdraw: an integrated program for RNA secondary structure calculations and analysis under 32-bit Microsoft Windows. CABIOS 12, 247-249.
26. SHAW, D. J., MCCURRACH, M., RUNDLE, S. A., HARLEY, H. G., CROW, S. R., SOHN, R. et al. (1993). Genomic organization and transcriptional units at the myotonic dystrophy locus. Genomics 18, 673-679.
27. TANEJA, K. L., MCCURRACH, M., SCHALLING, M., HOUSMAN, D. & SINGER, R. H. (1995). Foci of trinucleotide repeat transcripts in nuclei of myotonic dystrophy cells and tissues. J. Cell Biol. 128, 995-1002.
28. TIMCHENKO, L. T., MILLER, J. W., TIMCHENKO, N. A., DEVORE, D. R., DATAR, K. V., LIN, L. et al. (1996). Identification of a (CUG)n triplet repeat RNA-binding protein and its expression in myotonic dystrophy. Nucl. Acids Res. 24, 4407-4414.
29. WAHL, M. C., RAO, S. T. & SUNDARALINGHAM, M. (1996). The structure of r(UUCGCG) has a 5′-UU-overhang exhibiting Hoogsteen-like trans U·U basepairs. Nature struct. Biol. 3, 24-31.
30. WANG, J., PEGORARO, E., MENEGAZZO, E., GENNARELLI, M., HOOP, R. C., ANGELINI, C. & HOFFMAN, E. P. (1995). Myotonic dystrophy: evidence for a possible dominant-negative RNA mutation. Hum. Mol. Genet. 4, 599-606.
31. WANG, Y. H., AMIRHAERI, S., KANG, S., WELLS, R. D. & GRIFFITH, J. D. (1994). Preferential nucleosome assembly at DNA triplet repeats from the myotonic dystrophy gene. Science 265, 669-671.
32. WELLS, R. D. (1996). Molecular basis of genetic instability of triplet repeats. J. Biol. Chem. 271, 2875-2878.
33. YU, A., DILL, J. & MITAS, M. (1995). The purine-rich trinucleotide repeat sequences d(CAG)15 and d(GAC)15 form hairpins. Nucl. Acids Res. 23, 4055-4057.
34. ZUKER, M. & STIEGLER, P. (1981). Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. 9, 133-148.
35. ZUKER, M. (1994). Prediction of secondary structure by energy minimization. In: Computer Analyses of Sequence Data. Methods in Molecular Biology (Griffin, A. M. & Griffin, H.G., eds), pp. 267-294. TOTOWA, N. J.: Humana Press.