Predicted changes in pre-mRNA secondary structure vary in their association with exon skipping for mutations in exons 2, 4, and 8 of the Hprt gene and exon 51 of the fibrillin gene

Mutation Research - Mutation Research Genomics

Volumn 432, Issue 1-2, 2000, Pages 15-32

  Tu, Meihua ^a,b   Tong, Weida ^a   Perkins, Roger ^a   Valentine, Carrie R ^a  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^b PFIZER INC   (United States)

Author keywords

Exon skipping; Exonic splicing enhancers; RNA secondary structure

Indexed keywords

FIBRILLIN; MESSENGER RNA PRECURSOR; THYMIDINE;

ARTICLE; CHINESE HAMSTER; CONTROLLED STUDY; ENERGY; EXON; GENE; GENE LOCUS; GENE SEQUENCE; HUMAN; MUTATION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; RNA SPLICING; RNA STRUCTURE; THERMODYNAMICS;

ANIMALS; BASE SEQUENCE; CELL LINE; CRICETINAE; CRICETULUS; DATABASES, FACTUAL; EXONS; HUMANS; HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE; MICROFILAMENT PROTEINS; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; RNA PRECURSORS;

CRICETINAE;

EID: 0034143612     PISSN: 13835726     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1383-5726(99)00011-4     Document Type: Article

References (54)

1. Valentine C.R. The association of nonsense codons with exon skipping. Mutat. Res. 411:1998;87-117.
2. Reed R., Maniatis T. A role for exon sequences and splice-site proximity in splice-site selection. Cell. 46:1986;681-690.
3. Achsel T., Shimura Y. Factors involved in the activation of pre-mRNA splicing from downstream splicing enhancers. J. Biochem. 120:1996;53-60.
4. Wang Z., Hoffman H.M., Grabowski P.J. Intrinsic U2AF binding is modulated by exon enhancer signals in parallel with changes in splicing activity. RNA. 1:1995;21-35.
5. Sun Q., Mayeda A., Hampson R.K., Krainer A.R., Rottman F.M. General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes Dev. 7:1993;2598-2608.
6. Ramchatesingh J., M Zahler A., Neugebauer K.M., Roth M.B., Cooper R.A. A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer. Mol. Cell. Biol. 15:1995;4898-4907.
7. Cooper T.A., Mattox W. The regulation of splice-site selection, and its role in human disease. Am. J. Hum. Genet. 61:1997;259-266.
8. Valentine C.R., Heflich R.H. The association of nonsense mutation with exon-skipping in hprt mRNA of Chinese hamster ovary cells results from an artifact of RT-PCR. RNA. 3:1997;660-676.
9. Dietz H.C., Kendzior R.J. Jr. Maintenance of an open reading frame as an additional level of scrutiny during splice site selection. Nat. Genet. 8:1994;183-188.
10. Maquat L.E. When cells stop making sense: effects of nonsense codons on RNA metabolism in vertebrate cells. RNA. 1:1995;453-465.
11. Maquat L.E. Defects in RNA splicing and the consequence of shortened translational reading frames. Am. J. Hum. Genet. 59:1996;279-286.
12. Carter M.S., Shulin L., Wilkinson M.F. A splicing-dependent regulatory mechanism that detects translation signals. EMBO J. 15:1996;5965-5975.
13. Li S., Wilkinson M.F. Nonsense surveillance in lymphocytes. Immunity. 8:1998;135-141.
14. Steingrimsdottir H., Rowley G., Dorado G., Cole J., Lehman A.R. Mutations which alter splicing in the human hypoxanthine-guanine phosphoribosyltransferase gene. Nucleic Acids Res. 20:1992;1201-1208.
15. O'Neill J.P., Rogan P.K., Cariello N., Nicklas J.A. Mutations that alter RNA splicing of the human HPRT gene: a review of the spectrum. Mutat. Res. 411:1998;179-214.
16. Hennig E.E., Conney A.H., Wei S.-J. Characterization of hprt mutations induced by the ultimate carcinogenic metabolite of benzo[a]pyrene in Chinese hamster V-79 cells. Cancer Res. 55:1995;1550-1558.
17. Hoffmeyer S., Nürnberger P., Ritter H., Fahsold R., Leistner W., Kaufmann D., Krone W. Nearby stop codons in exons of the neurofibromatosis type 1 gene are disparate splice effectors. Am. J. Hum. Genet. 62:1998;269-277.
18. Cariello N.F., Skopek T.R. Analysis of mutations occurring at the human hprt locus. J. Mol. Biol. 231:1993;41-57.
19. D.H. Mathews, M.E. Burkar, Version 2.52 (1997), http://rna.chem.rochester.edu/RNAstructure.html.
20. Zuker M. On finding all optimal foldings of an RNA molecule. Science. 244:1989;48-52.
21. Jaeger J.A., Turner D.H., Zuker M. Improved predictions of secondary structures for RNA. Proc. Natl. Acad. Sci. USA. 86:1989;7706-7710.
22. Walter A.E., Turner D.H., Kim J., Lyttle M.H., Müller P., Mathews D.H., Zuker M. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl. Acad. Sci. USA. 91:1994;9218-9222.
23. Liu H.-X., Zhang M., Krainer A.R. Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev. 12:1998;1998-2012.
24. Carlo T., Sterner D.A., Berget S.M. An intron splicing enhancer containing a G-rich repeat facilitates inclusion of a vertebrate micro-exon. RNA. 2:1996;342-353.
25. Abrahams J.P., van den Berg M., van Batenburg E., Pleij C. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res. 18:1990;3035-3044.
26. P Gultyaev A. The computer simulation of RNA folding involving pseudoknot formation. Nucleic Acids Res. 19:1991;2489-2494.
27. Lück R., Steger G., Riesner D. Thermodynamic prediction of conserved secondary structure: application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein. J. Mol. Biol. 258:1996;813-826.
28. Hancock J.M., Vogler A.P. Modelling the secondary structures of slippage-prone hypervariable RNA regions: the example of the tiger beetle 18S rRNA variable region V4. Nucleic Acids Res. 26:1998;1689-1699.
29. Wang Y., Killian J., Hamasaki K., Rando R.R. RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities. Biochemistry. 35:1996;12338-12346.
30. Manjanatha M.G., Lindsey L.A., Mittelstaedt R.A., Heflich R.H. Low hprt levels and multiple hprt mRNA species in 6-thioguanine-resistant Chinese hamster cell mutants possessing nonsense mutations. Mutat. Res. 308:1994;65-75.
31. Tanaka K., Watakabe A., Shimura Y. Polypurine sequences within a downstream exon function as a splicing enhancer. Mol. Cell. Biol. 14:1994;1347-1354.
32. Coulter L.R., Landree M.A., Cooper T.A. Identification of a new class of exonic splicing enhancers by in vivo selection. Mol. Cell. Biol. 17:1997;2143-2150.
33. Tian H., Kole R. Selection of novel exon recognition elements from a pool of random sequences. Mol. Cell. Biol. 15:1995;6291-6298.
34. Achsel T., Shimura Y. Factors involved in the activation of pre-mRNA splicing from downstream splicing enhancers. J. Biochem. 120:1996;53-60.
35. A.F. Muro, M. Caputi, R. Pariyarath, F. Pagani, E. Buratti, F.E. Baralle, Regulation of fibronectin EDA exon alternative splicing: Possible role of RNA secondary structure for enhancer display.
36. Morgenthaler P.-M.L., Holzhäuser D. Analysis of mutations induced by 2-amino-1-methyl-6-phenylimidazo[4,5-b](PhIP) in human lymphoblastoid cells. Carcinogenesis. 16:1995;713-718.
37. Yang J.-L., Lin J.-G., Hu M.-C., Wu C.-W. The hprt gene in G1-S and late S phase of diploid human fibroblasts. Cancer Res. 53:1993;2865-2873.
38. Burkhart-Schultz K.J., Thompson C.L., Jones I.M. Spectrum of somatic mutation at the hypoxanthine phosphoribosyltransfrease (hprt) gene of healthy people. Carcinogenesis. 17:1998;1871-1883.
39. Österholm A.-M., Hou S.-M. Splicing mutations at the HPRT locus in human T-lymphocytes in vivo. Environ. Mol. Mutagen. 32:1998;25-32.
40. Nelson S.L., Giver C.R., Grosovsky A.J. Spectrum of X-ray-induced mutations in the human hprt gene. Carcinogenesis. 15:1994;495-502.
41. Papadopoulo D., Laquerbe A., Guillouf C., Moustacchi E. Molecular spectrum of mutations induced at the HPRT locus by a cross-linking agent in human cell lines with different repair capacities. Mutat. Res., DNA Repair. 294:1993;167-177.
42. - diploid human fibroblasts. Carcinogenesis. 15:1994;939-945.
43. Curry J., Rowley G.T., Saddi V., Beare D., Cole J., Glickman B.W. Determination of hprt mutant and mutation frequencies and the molecular characterization of human derived in vivo T-lymphocyte mutants. Environ. Mol. Mutagen. 25:1995;169-179.
44. Rigaud O., Laquerbe A., Moustacchi E. DNA sequence analysis of HPRT mutants induced in human lymphoblastoid cells adapted to ionizing radiation. Radiat. Res. 144:1995;181-189.
45. Yang S.-C., Lin J.-G., Chiou C.-C., Chen L.-Y., Yang J.-L. Mutation specificity of 8-methoxypsoralen plus two doses of UVA irradiation in the hprt gene in diploid human fibroblasts. Carcinogenesis. 15:1994;201-207.
46. Recio L., Simpson D., Cochrane J., Liber H., Skopek T.R. Molecular analysis of hprt mutants induced by 2-cyanoethylene oxide in human lymphoblastoid cells. Mutat. Res. 242:1990;195-208.
47. Valentine C.R., Heflich R.H. Genomic DNA sequencing of mRNA splicing mutants in the hprt gene of Chinese hamster ovary cells. Environ. Mol. Mutagen. 25:1995;85-96.
48. - mutants induced by bleomycin in CHO K1-BH4 cells. Environ. Mol. Mutagen. 32:1998;244-250.
49. Zhang L.-H., Jenssen D. Site specificity of N-methyl-N-nitroso urea-induced transition mutation in the hprt gene. Carcinogenesis. 12:1991;1903-1909.
50. Darè E., Zhang L.-H., Jenssen D., Bianchi V. Molecular analysis of mutations in the hprt gene of V79 hamster fibroblasts: effects of imbalances in the dCTP, dGTP and dTTP pools. J. Mol. Biol. 252:1995;514-521.
51. Zhang L.-H., Vrieling H., van Zeeland A.A., Jenssen D. Spectrum of spontaneously occurring mutations in the hprt gene of V79 Chinese hamster cells. J. Mol. Biol. 223:1992;627-635.
52. R.H. Heflich, unpublished.
53. Dietz H.C., Valle D., Francomano C.A., Kendzior R.J. Jr., Pyeritz R.E., R Cutting G. The skipping of constitutive exons in vivo induced by nonsense mutations. Science. 259:1993;680-683.
54. Liu W., Qian D., Francke U. Silent mutation induces exon skipping of fibrillin-1 gene in Marfan syndrome. Nat. Genet. 16:1997;328-329.