BACKGROUND: Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Over 1800 CFTR mutations have been reported, and about 12% of mutations are believed to impair pre-mRNA splicing. Given that several synthetic, non-splice-junction synonymous substitutions have been reported to alter splicing in CFTR, we predicted that naturally occurring synonymous substitutions may be erroneously classified as functionally neutral. METHODS: Computational tools were used to predict the effect of synonymous substitutions on CFTR pre-mRNA splicing. The functional consequences of selected substitutions were evaluated using a minigene splicing assay. RESULTS: Two synonymous mutations were shown to have a dramatic effect on CFTR pre-mRNA splicing, and consequently could alter protein integrity and phenotypic outcome. CONCLUSIONS: Traditional methods of mutation analysis overlook splicing defects that occur at internal positions in coding exons, especially synonymous substitutions. We show that bioinformatics tools and minigene splicing assays are a potent combination to prioritize and identify mutations that cause aberrant CFTR pre-mRNA splicing. Published by Elsevier B.V.
BACKGROUND:Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Over 1800 CFTR mutations have been reported, and about 12% of mutations are believed to impair pre-mRNA splicing. Given that several synthetic, non-splice-junction synonymous substitutions have been reported to alter splicing in CFTR, we predicted that naturally occurring synonymous substitutions may be erroneously classified as functionally neutral. METHODS: Computational tools were used to predict the effect of synonymous substitutions on CFTR pre-mRNA splicing. The functional consequences of selected substitutions were evaluated using a minigene splicing assay. RESULTS: Two synonymous mutations were shown to have a dramatic effect on CFTR pre-mRNA splicing, and consequently could alter protein integrity and phenotypic outcome. CONCLUSIONS: Traditional methods of mutation analysis overlook splicing defects that occur at internal positions in coding exons, especially synonymous substitutions. We show that bioinformatics tools and minigene splicing assays are a potent combination to prioritize and identify mutations that cause aberrant CFTR pre-mRNA splicing. Published by Elsevier B.V.
Authors: Neeraj Sharma; Patrick R Sosnay; Anabela S Ramalho; Christopher Douville; Arianna Franca; Laura B Gottschalk; Jeenah Park; Melissa Lee; Briana Vecchio-Pagan; Karen S Raraigh; Margarida D Amaral; Rachel Karchin; Garry R Cutting Journal: Hum Mutat Date: 2014-09-10 Impact factor: 4.878
Authors: Min Tang; Maria Eugenia Alaniz; Daniel Felsky; Badri Vardarajan; Dolly Reyes-Dumeyer; Rafael Lantigua; Martin Medrano; David A Bennett; Philip L de Jager; Richard Mayeux; Ismael Santa-Maria; Christiane Reitz Journal: Neurol Genet Date: 2020-06-08
Authors: Patrick R Sosnay; Karen R Siklosi; Fredrick Van Goor; Kyle Kaniecki; Haihui Yu; Neeraj Sharma; Anabela S Ramalho; Margarida D Amaral; Ruslan Dorfman; Julian Zielenski; David L Masica; Rachel Karchin; Linda Millen; Philip J Thomas; George P Patrinos; Mary Corey; Michelle H Lewis; Johanna M Rommens; Carlo Castellani; Christopher M Penland; Garry R Cutting Journal: Nat Genet Date: 2013-08-25 Impact factor: 38.330
Authors: Anya T Joynt; Taylor A Evans; Matthew J Pellicore; Emily F Davis-Marcisak; Melis A Aksit; Alice C Eastman; Shivani U Patel; Kathleen C Paul; Derek L Osorio; Alyssa D Bowling; Calvin U Cotton; Karen S Raraigh; Natalie E West; Christian A Merlo; Garry R Cutting; Neeraj Sharma Journal: PLoS Genet Date: 2020-10-21 Impact factor: 5.917