Aberrant 3′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization

Abstract

The frequency distribution of mutation-induced aberrant 3′ splice sites (3′ss) in exons and introns is more complex than for 5′ splice sites, largely owing to sequence constraints upstream of intron/exon boundaries. As a result, prediction of their localization remains a challenging task. Here, nucleotide sequences of previously reported 218 aberrant 3′ss activated by disease-causing mutations in 131 human genes were compared with their authentic counterparts using currently available splice site prediction tools. Each tested algorithm distinguished authentic 3′ss from cryptic sites more effectively than from de novo sites. The best discrimination between aberrant and authentic 3′ss was achieved by the maximum entropy model. Almost one half of aberrant 3′ss was activated by AG-creating mutations and ∼95% of the newly created AGs were selected in vivo. The overall nucleotide structure upstream of aberrant 3′ss was characterized by higher purine content than for authentic sites, particularly in position −3, that may be compensated by more stringent requirements for positive and negative nucleotide signatures centred around position −11. A newly developed online database of aberrant 3′ss will facilitate identification of splicing mutations in a gene or phenotype of interest and future optimization of splice site prediction tools.

The thermodynamic patterns of eukaryotic genes suggest a mechanism for intron–exon recognition

“…Sequences of 50 bp, flanking the transcript start sites, end sites and splice sites of C. elegans, were obtained from Ensembl (WB220). The list of trans-spliced C. elegans genes was taken from Allen et al 58 Cryptic 3 0 -splice sites and their corresponding authentic 3 0 -splice sites were obtained from DBASS3 33 . BP sequences were obtained from Gao et al 37 Only BPs confirmed by a minimum of three lariat PCR with reverse transcription clones were considered.…”

“…Metazoan transcripts contain large numbers of 'cryptic' splice sites that are inactivated due to suppression from nearby and advantageous authentic splice sites 33 . Mutation of the authentic splice sites activates the cryptic splice sites, leading to aberrant alternative splicing and frequently to genetic disease 34,35 .…”

“…Mutation of the authentic splice sites activates the cryptic splice sites, leading to aberrant alternative splicing and frequently to genetic disease 34,35 . To understand how the thermodynamic profile can influence the splice site selection, we compared DG bias of disease-related cryptic 3 0 -splice sites 33 with their corresponding authentic splice sites. The cryptic splice sites can occur both upstream (in the intron) and downstream (in the exon) of the authentic 3 0 -splice site.…”

“…The cryptic splice sites can occur both upstream (in the intron) and downstream (in the exon) of the authentic 3 0 -splice site. We first analysed 21 cryptic 3 0 -splice sites situated more than 20 bp downstream from the authentic splice sites 33 (Fig. 6a, Supplementary Fig.…”

“…Mutation in the AG consensus of the authentic 3 0 -splice sites could still allow recognition of their upstream unstable regions by the spliceosome and finding of the AG consensus of the cryptic 3 0 -splice sites. We next analysed 15 cryptic sites situated more than 20 bp upstream of the authentic 3 0 -splice site 33 (Fig. 6b, Supplementary Fig.…”