Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping

Abstract

Mutations that affect splicing of precursor messenger RNAs play a major role in the development of hereditary diseases. Most splicing mutations have been found to eliminate GT or AG dinucleotides that define the 5 0 and 3 0 ends of introns, leading to exon skipping or cryptic splice-site activation. Although accurate description of the mis-spliced transcripts is critical for predicting phenotypic consequences of these alterations, their exact nature in affected individuals cannot often be determined experimentally. Using a comprehensive collection of exons that sustained cryptic splice-site activation or were skipped as a result of splice-site mutations, we have developed a multivariate logistic discrimination procedure that distinguishes the two aberrant splicing outcomes from DNA sequences. The new algorithm was validated using an independent sample of exons and implemented as a free online utility termed CRYP-SKIP (http://www.dbass.org.uk/cryp-skip/). The web application takes up one or more mutated alleles, each consisting of one exon and flanking intronic sequences, and provides a list of important predictor variables and their values, the overall probability of activating cryptic splice vs exon skipping, and the location and intrinsic strength of predicted cryptic splice sites in the input sequence. These results will facilitate phenotypic prediction of splicing mutations and provide further insights into splicing enhancer and silencer elements and their relative importance for splice-site selection in vivo.

PITX2 and FOXC1 spectrum of mutations in ocular syndromes

“…This is expected to lead to cryptic splice site activation or exon skipping, and to result in the production of an aberrant protein product or decreased protein production. Analysis by the CRYP-SKIP program 27 (http://cryp-skip.img.cas.cz/) identifies three 3 0 splice sites with a predicted strength of Z0.5 (out of 1.0). Utilization of any one of these three sites would be predicted to cause deletion of 233, 430, or 866 nucleotides, respectively, all resulting in frameshift and truncation of the PITX2 protein.…”

“…Several previously reported polymorphisms were observed in both patient and control populations. Genomic analysis identified deletions involving the FOXC1-coding region in three probands with ARS (cases [25][26][27] as well as the case of De Hauwere syndrome (case 28) 22 (Table 2, Figure 3). Deletion size ranged from at least 0.98 Mb to at least 1.5 Mb, deleting between 2 and 11 genes.…”

Prediction of single‐nucleotide substitutions that result in exon skipping: identification of a splicing silencer inBRCA1exon 6

“…The new online tools are publicly available and should facilitate detection of DNA variants that alter splicing if carried out in conjunction with other tools that assess the strength of natural splice sites [Senapathy et al, 1990;Yeo and Burge, 2004] and branch points [Kol et al, 2005]. Similar algorithms have been recently applied to distinguish exon skipping and cryptic splice site activation ab initio [Divina et al, 2009].…”

Pick one, but be quick: 5′ splice sites and the problems of too many choices

“…Ab initio predictions of mutation severity by 59ss scoring methods are largely accurate; i.e., the higher the difference in scores between the wild-type and mutant 59ss, the more severe the mutation. Predicting the precise consequence of the mutation is far more difficult, although recent analyses have shown some progress (Wimmer et al 2007;Divina et al 2009). …”