Cis-Elements and Trans-Acting Factors Involved in CFTR Exon 9 Alternative Splicing

Alternative splicing of human cystic fibrosis transmembrane conductance regulator (CFTR) exon 9 is regulated by a combination of cis-acting elements distributed through the exon and both flanking introns. Several studies have identified at 3' end of intron 8 a regulatory element that is composed by a polymorphic (TG)m(T)n repeated sequence. Variations at this polymorphic locus are associated with the alternative splicing of exon 9, which results in a non-functional CFTR protein. In our previous studies, we identified TDP43 as the factor that specifically binds to the (TG)m sequence. In this thesis we demonstrate, using transient transfection experiment with a minigene system, that overexpression of TDP43 results in an increase of exon 9 skipping. This effect is more pronounced with concomitant overexpression of SF2/ ASP SR protein previously shown to inhibit CFTR exon 9 inclusion. Moreover, antisense inhibition of endogenous TDP43 expression results in increased inclusion of exon 9. The clinical and biological relevance of this finding in viva is demonstrated by our characterization of a CF patient carrying a (TG)10T9(Delta F508)/(TG)13(T)3 genotype leading to a disease-causing high proportion of exon skipping in the allele with non mutated coding sequence. We have also previously shown the presence of a splicing inhibitory element (ISS) in the intron 9. The binding of SR proteins to the ISS modulates, together with other trans-acting factors, the level of exon 9 inclusion. In this thesis we studied the region of intron 9 from the 5' splice site until the ISS. This region presents a peculiar arrangement of polypyrimidine-rich elements and we demonstrated that one of these (PY2) acts as a splicing enhancer. In fact, mutations introduced in this PY2 element -cause a decrease in exon 9 inclusion. While the factor that binds to this pyrimidine-rich enhancer element is still unknown, we provide evidence for an involvement of polypyrimidine tract binding protein (PTB) on the modulation of exon 9 inclusion. The functional effect of PTB that we report is linked to the binding of the protein to elements in CFTR intron 9. Exonic sequences are also involved in the modulation of the alternative splicing of exon 9. In fact, for the first time, we studied the effect of several natural and site-directed mutants distributed on the entire exon and we demonstrate that in some instances this mutations induce significant changes in pre-mRNA splicing, with different degree of exon skipping and inclusion. The effect of this mutations is also modulate by the length of the polymorphic (TG)m(T)n tract at 3' end of intron 9. We also identified a critical regulatory element which contains two adjacent sequences with enhancer and silencer activity. We defined this element having overlapping enhancer and silencer properties Composit Exonic Regulatory Element of Splicing (CERES). The analysis of several site directed mutants spanning the region between nucleotides 144 and 157 showed that the functional characterization of the element cannot be simply defined by the mutated position but also by the type of nucleotide substitution. All together the results reported in this thesis shed light into the regulation of the CFTR exon 9 alternative splicing. The new cis-acting elements and trans-acting factors that we have identified point to an unexpected complexity of this system that needs further investigation. In addiction, it is certain that this is not a unique situation and that exonic and intronic splicing elements widespread in all genes and currently accepted splicing models will have to be correct.