Alternative splicing and disease

Abstract

Almost all protein-coding genes are spliced and their majority is alternatively spliced. Alternative splicing is a key element in eukaryotic gene expression that increases the coding capacity of the human genome and an increasing number of examples illustrates that the selection of wrong splice sites causes human disease. A fine-tuned balance of factors regulates splice site selection. Here, we discuss well-studied examples that show how a disturbance of this balance can cause human disease. The rapidly emerging knowledge of splicing regulation now allows the development of treatment options.

Figure 1. Alternative splicing modes

Constitutive exons are shown as white boxes, introns as vertical lines. Open arrows indicate the 3′ splice site, closed arrows the 5′ splice site. A black box indicates a cassette exon, the most frequent form of alternative splicing. Hatched boxes indicate other splicing modes. Alternative polyadenylation sites and alternate promoters are shown as two other mechanisms to increase mRNA diversity. They are mechanistically different from alternative splicing.

Figure 2. Elements involved in alternative splicing of pre-mRNA

Exons are indicated as boxes, introns as thin lines. Splicing regulator elements (enhancers or silencers) are shown as green or red boxes in exons. The 5′ splice-site (CAGguaagu) and 3′ splice-site (y)10ncagG, as well as the branch point (ynyyray), are indicated (y=c or u, n=a, g, c or u). Upper-case letters refer to nucleotides that remain in the mature mRNA. Two major groups of proteins, hnRNPs (green) and SR or SR related proteins (red), bind to splicing regulator elements; the protein:RNA interaction is indicated by shading. The protein complex assembling around the exon stabilizes binding of spliceosomal copmponents, indicated in blue. For example, SR-proteins can interact with U1 snRNA, which helps in the recognition of the 5′ splice site, as it allows hybridization (thick black line) of the U1 snRNA (black line) with the 5′ splice-site. The formation of the multi-protein:RNA complex allows discrimination between proper splice-sites (bold letters) and cryptic splice-sites (small gt ag) that are frequent in pre-mRNA sequences. Factors at the 3′ splice-site include U2AF, which recognizes pyrimidine rich regions of the 3′ splice-sites, and help stabilize the interaction of U2 snRNP with the adenosine of the branch point.

Figure 3. Disease causing mutations

Exons and introns are indicated as in Figure 2. Arrows indicate repetitive elements. A: Mutation in silencer or enhancer sequences change the interaction between regulatory proteins and pre-mRNA, leading to changes in exon recognition. B: Mutations in splice sites change the interaction with core spliceosomal proteins. C: Due to formation of secondary structures, intronic sequences can be brought close to splice sites, accounting for the effect of some intronic mutations. D: Secondary pre-mRNA structures contribute to exon recognition and their mutations can cause aberrant splicing. E. Expanded repeat elements can sequester splicing regulatory proteins, changing splice site selection in other messages. F. Some snoRNAs regulate splice site selection and their loss can cause disease.