New type of disease causing mutations: The example of the composite exonic regulatory elements of splicing in CFTR exon 12

Human Molecular Genetics

Volumn 12, Issue 10, 2003, Pages 1111-1120

  Pagani, Franco ^a   Stuani, Cristiana ^a   Tzetis, Maria ^b   Kanavakis, Emmanuel ^b   Efthymiadou, Alexandra ^b   Doudounakis, Stavros ^c   Casals, Teresa ^d   Baralle, Francisco E ^a  

^a INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

^b UNIVERSITY OF ATHENS   (Greece)

^c AGHIA SOPHIA CHILDREN S HOSPITAL   (Greece)

^d Institut de Recerca Oncologica   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ARGININE; ASPARTIC ACID; COMPOSITE EXONIC REGULATORY ELEMENT OF SPLICING; GLYCINE; MESSENGER RNA; REGULATOR PROTEIN; SERINE; TRANSMEMBRANE CONDUCTANCE REGULATOR; UNCLASSIFIED DRUG;

ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; DNA POLYMORPHISM; ENHANCER REGION; EXON; GENE EXPRESSION; GENE MUTATION; GENETIC ANALYSIS; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; NUCLEIC ACID BASE SUBSTITUTION; PATHOGENESIS; PHENOTYPE; PRIORITY JOURNAL; RNA PROCESSING; RNA SPLICING; SINGLE NUCLEOTIDE POLYMORPHISM; SITE DIRECTED MUTAGENESIS;

BASE SEQUENCE; CYSTIC FIBROSIS; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; DNA MUTATIONAL ANALYSIS; GENES, REGULATOR; HUMANS; MOLECULAR SEQUENCE DATA; MUTATION, MISSENSE; RNA SPLICING;

CERES;

EID: 0037899998     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddg131     Document Type: Article

References (42)

1. Mayeda, A. and Krainer, A.R. (1992) Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell, 68, 365-375.
2. Zahler, A.M., Neugebauer, K.M., Lane, W.S. and Roth, M.B. (1993) Distinct functions of SR proteins in alternative pre-mRNA splicing. Science, 260, 219-222.
3. Caceres, J.F., Stamm, S., Helfmman, D.M. and Krainer, A.R. (1994) Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science, 265, 1706-1709.
4. Muro, A.F., Caputi, M., Pariyarath, R., Pagani, F., Buratti, E. and Baralle, F.E. (1999) Regulation of fibronectin EDA exon alternative splicing: possible role of RNA secondary structure for enhancer display. Mol. Cell Biol., 19, 2657-2671.
5. Consortium, I.H.G.S. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
6. Modrek, B. and Lee, C. (2002) A genomic view of alternative splicing. Nat. Genet., 30, 13-19.
7. Ars, E., Serra, E., Garcia, J., Kruyer, H., Gaona, A., Lazaro, C. and Estivill, X. (2000) Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1. Hum. Mol. Genet., 9, 237-247.
8. Teraoka, S.N., Telatar, M., Becker-Catania, S., Liang, T., Onengut, S., Tolun, A., Chessa, L., Sanal, O., Bernatowska, E., Gatti, R.A. and Concannon, P. (1999) Splicing defects in the ataxia-telangiectasia gene, ATM: underlying mutations and consequences. Am. J. Hum. Genet., 64, 1617-1631.
9. Liu, H.X., Cartegni, L., Zhang, M.Q. and Krainer, A.R. (2001) A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nat. Genet., 27, 55-58.
10. Caputi, M., Casari, G., Guenzi, S., Tagliabue, R., Sidoli, A., Melo, C.A. and Baralle, F.E. (1994) A novel bipartite splicing enhancer modulates the differential processing of the human fibronectin EDA exon. Nucl. Acids Res., 22, 1018-1022.
11. Cartegni, L. and Kramer, A.R. (2002) Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat. Genet., 30, 377-384.
12. Delaney, S.J., Rich, D.P., Thomson, S.A., Hargrave, M.R., Lovelock, P.K., Welsh, M.J. and Wainwright, B.J. (1993) Cystic fibrosis transmembrane conductance regulator splice variants are not conserved and fail to produce chloride channels. Nat. Genet., 4, 426-431.
13. Strong, T.V., Smit, L.S., Nasr, S., Wood, D.L., Cole, J.L., Iannuzzi, M.C., Stern, R.C. and Collins, F.S. (1992) Characterization of an intron 12 splice donor mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Hum. Mutat., 1, 380-387.
14. Hull, J., Shackleton, S. and Harris, A. (1993) Abnormal mRNA splicing resulting from three different mutations in the CFTR gene. Hum. Mol. Genet., 2, 689-692.
15. Zielenski, J., Markiewicz, D., Lin, S.P., Huang, F.Y., Yang-Feng, T.L. and Tsui, L.C. (1995) Skipping of exon 12 as a consequence of a point mutation (1898 + 5G→ T) in the cystic fibrosis transmembrane conductance regulator gene found in a consanguineous Chinese family. Clin. Genet., 47, 125-132.
16. Bremer, S., Hoof, T., Wilke, M., Busche, R., Scholte, B., Riordan, J.R., Maass, G. and Tummler, B. (1992) Quantitative expression patterns of multidrug-resistance P-glycoprotein (MDR1) and differentially spliced cystic-fibrosis transmembrane-conductance regulator mRNA transcripts in human epithelia. Eur. J. Biochem., 206, 137-149.
17. Slomski, R., Schloesser, M., Berg, L.P., Wagner, M., Kakkar, V.V., Cooper, D.N. and Reiss, J. (1992) Omission of exon 12 in cystic fibrosis transmembrane conductance regulator (CFTR) gene transcripts. Hum. Genet., 89, 615-619.
18. Hull, J., Shackleton, S. and Harris, A. (1994) Analysis of mutations and alternative splicing patterns in the CFTR gene using mRNA derived from nasal epithelial cells. Hum. Mol. Genet., 3, 1141-1146.
19. Tzetis, M., Efthymiadou, A., Doudounakis, S. and Kanavakis, E. (2001) Qualitative and quantitative analysis of mRNA associated with four putative splicing mutations (621 + 3A→G, 2751 + 2T→A, 296 + 1G→C, 1717-9T→C-D565G) and one nonsense mutation (E822X) in the CFTR gene. Hum. Genet., 109, 592-601.
20. Bienvenu, T., Adjiman, M., Thiounn, N., Jeanpierre, M., Hubert, D., Lepercoq, J., Francoual, C., Wolf, J., Izard, V., Jouannet, P., Kaplan, J.C. and Beldjord, C. (1997) Molecular diagnosis of congenital bilateral absence of the vas deferens: analyses of the CFTR gene in 64 French patients. Ann. Genet., 40, 5-9.
21. Ravnik-Glavac, M., Dean, M. and Glavac, D. (2000) Study of mutant and polyvariant mutant CFTR genes in patients with congenital absence of the vas deferens. Pflugers Arch., 439, R53-55.
22. Pignatti, P.F., Bombieri, C., Marigo, C., Benetazzo, M. and Luisetti, M. (1995) Increased incidence of cystic fibrosis gene mutations in adults with disseminated bronchiectasis. Hum. Mol. Genet., 4, 635-639.
23. Chillon, M., Casals, T., Mercier, B., Bassas, L., Lissens, W., Silber, S., Romey, M.C., Ruiz-Romero, J., Verlingue, C., Claustres, M., Nunes, V., Ferec, C. and Estivill, X. (1995) Mutations in the cystic fibrosis gene in patients with congenital absence of the vas deferens. New Engl. J. Med., 332, 1475-1480.
24. Costes, B., Girodon, E., Ghanem, N., Flori, E., Jardin, A., Soufir, J.C. and Goossens, M. (1995) Frequent occurrence of the CFTR intron 8 (TG)n 5T allele in men with congenital bilateral absence of the vas deferens. Eur. J. Hum. Genet., 3, 285-293.
25. Pagani, F, Buratti, E., Stuani, C., Romano, M., Zuccato, E., Niksic, M., Giglio, L., Faraguna, D. and Baralle, F.E. (2000) Splicing factors induce cystic fibrosis transmembrane regulator exon 9 skipping through a nonevolutionary conserved intronic element. J. Biol. Chem., 275, 21041-21047.
26. Pagani, F., Buratti, E., Stuani, C., Bendix, R., Dork, T. and Baralle, F.E. (2002) A new type of mutation causes a splicing defect in ATM. Nat. Genet., 30, 426-429.
27. Niksic, M., Romano, M., Buratti, E., Pagani, F. and Baralle, F.E. (1999) Functional analysis of cis-acting elements regulating the alternative splicing of human CFTR exon 9. Hum. Mol. Genet., 8, 2339-2349.
28. Kerem, E., Rave-Harel, N., Augarten, A., Madgar, I., Nissim-Rafinia, M., Yahav, Y., Goshen, R., Bentur, L., Rivlin, J., Aviram, M. et al. (1997) A cystic fibrosis transmembrane conductance regulator splice variant with partial penetrance associated with variable cystic fibrosis presentations. Am. J. Respir. Crit. Care Med., 155, 1914-1920.
29. Chiba-Falek, O., Kerem, E., Shoshani, T., Aviram, M., Augarten, A., Bentur, L., Tal, A., Tullis, E., Rahat, A. and Kerem, B. (1998) The molecular basis of disease variability among cystic fibrosis patients carrying the 3849 + 10 kb C→T mutation. Genomics, 53, 276-293.
30. Larriba, S., Bassas, L., Gimenez, J., Ramos, M.D., Segura, A., Nunes, V., Estivill, X. and Casals, T. (1998) Testicular CFTR splice variants in patients with congenital absence of the vas deferens. Hum. Mol. Genet., 7, 1739-1743.
31. Chiba-Falek, O., Parad, R.B., Kerem, E. and Kerem, B. (1999) Variable levels of normal RNA in different fetal organs carrying a cystic fibrosis transmembrane conductance regulator splicing mutation. Am. J. Respir. Crit. Care Med., 159, 1998-2002.
32. Bentley, D. (1999) Coupling RNA polymerase II transcription with pre-mRNA processing. Curr. Opin. Cell Biol., 11, 347-351.
33. Maniatis, T. and Reed, R. (2002) An extensive network of coupling among gene expression machines. Nature, 416, 499-506.
34. Pagani, F., Stuani, C., Zuccato, E., Kornblihtt, A.R. and Baralle, F.E. (2002) Promoter architecture modulates CFTR Exon 9 skipping. J. Biol. Chem., 5, 5.
35. D'Souza, I. and Schellenberg, G.D. (2000) Determinants of 4-repeat tau expression. Coordination between enhancing and inhibitory splicing sequences for exon 10 inclusion. J. Biol. Chem., 275, 17700-17709.
36. Varani, L., Hasegawa, M., Spillantini, M.G., Smith, M.J., Murrell, J.R., Ghetti, B., Klug, A., Goedert, M. and Varani, G. (1999) Structure of tau exon 10 splicing regulatory element RNA and destabilization by mutations of frontotemporal dementia and parkinsonism linked to chromosome 17. Proc. Natl Acad. Sci. USA, 96, 8229-8234.
37. Miller, S.A., Dykes, D.D. and Polesky, H.F. (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucl. Acids Res., 16, 1215.
38. Fanen, P., Ghanem, N., Vidaud, M., Besmond, C., Martin, J., Costes, B., Plassa, F. and Goossens, M. (1992) Molecular characterization of cystic fibrosis: 16 novel mutations identified by analysis of the whole cystic fibrosis conductance transmembrane regulator (CFTR) coding regions and splice site junctions. Genomics, 13, 770-776.
39. Costes, B., Fanen, P., Goossens, M. and Ghanem, N. (1993) A rapid, efficient, and sensitive assay for simultaneous detection of multiple cystic fibrosis mutations. Hum. Mutat., 2, 185-191.
40. Tzetis, M., Kanavakis, E., Antoniadi, T., Doudounakis, S., Adam, G. and Kattamis, C. (1997) Characterization of more than 85% of cystic fibrosis alleles in the Greek population, including five novel mutations. Hum. Genet., 99, 121-125.
41. Buratti, E., Dork, T., Zuccato, E., Pagani, F., Romano, M. and Baralle, F.E. (2001) Nuclear factor TDP-43 and SR proteins promote in vitro and in vivo CFTR exon 9 skipping. EMBO J., 20, 1774-1794.
42. Chomczynski, P. and Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem., 162, 156-159.