- Paper Report
- Open Access
Polymorphic splice enhacer motifs
- Gerry Wilson1
© Biomed Central Ltd 2001
- Received: 26 July 2001
- Accepted: 26 July 2001
- Published: 26 July 2001
- Exon skipping splice enhancers
- splice enhancers
Exonic polymorphisms may have several consequences: they may be biologically silent or lead to missense or nonsense codons. A nonsense mutation consisting of a guanine to thymine transition at position 6 (G6T) of exon 18 of the BRCA1 gene is associated with skipping of exon 18 in vivo. Potential mechanisms explaining the link between nonsense mutations and RNA processing alterations (nonsense mediated mRNA decay) include a nuclear nonsense codon recognition mechanism. Exonic splice enhancers (ESEs) have been identified that are recognised by serine/arginine-rich (SR) proteins, each of which recognises a distinct but degenerate motif. The authors of this paper have developed a mathematical scoring matrix which predicts the likelihood of interaction between SR proteins and ESEs. Using an SR protein binding matrix, it was predicted that the polymorphism would affect binding of the SF2/ASF protein. The aim of this study was to determine if polymorphisms within ESE motifs result in exon skipping.
The presence of the G6T mutation in exon 18 of a BRCA1 minigene consisting of exons 17, 18 and 19 with short intervening intronic segments led to skipping of exon 18 in the mature transcript. The SR binding motif scores, rather than the type of polymorphism (missense or nonsense), predicted the likelihood of exon skipping. Examination of a database of 50 single-base substitutions which lead to exon skipping in vivo showed that more than half reduced or eliminated at least one high-scoring SR protein binding motif in the mutant allele. This was observed for nonsense, missense and silent mutations.
In vitro translation/splicing, HeLa nuclear extract