The emerging role of minor intron splicing in neurological disorders

Abstract

Pre-mRNA splicing is an essential step in eukaryotic gene expression. Mutations in cis-acting sequence elements within pre-mRNA molecules or trans-acting factors involved in pre-mRNA processing have both been linked to splicing dysfunction that give rise to a large number of human diseases. These mutations typically affect the major splicing pathway, which excises more than 99% of all introns in humans. However, approximately 700-800 human introns feature divergent intron consensus sequences at their 5' and 3' ends and are recognized by a separate pre-mRNA processing machinery denoted as the minor spliceosome. This spliceosome has been studied less than its major counterpart, but has received increasing attention during the last few years as a novel pathomechanistic player on the stage in neurodevelopmental and neurodegenerative diseases. Here, we review the current knowledge on minor spliceosome function and discuss its potential pathomechanistic role and impact in neurodegeneration.

Keywords: ALS; FUS; SMA; TDP-43; minor spliceosome; neurodegeneration; pre-mRNA splicing.

Figure 1. FIGURE 1: Major versus minor intron splicing.

(A) Major (U2-type) and minor (U12-type) introns differ in their cis-acting 5'ss and BPS elements. The (nearly) invariant nucleotides are highlighted in red letters. Non-coloured letters indicate a clear preference for a nucleotide at a given position and potential base parings with the respective snRNAs are depicted. Base modifications of snRNAs are omitted. Minor introns are subdivided into AT-AC or GT-AG minor introns based on their terminal dinucleotides. (B) Major and minor introns are recognized differently by their respective spliceosomes, which assemble on their substrates in a stepwise manner. Major introns are initially recognized by the U1 snRNP binding to the 5’ splice site, SF1 binding to the branch point sequence (BPS) and U2AF2/1 heterodimer recognizing the polypyrimidine tract (PPT) and the 3’ terminal AG dinucleotide, respectively. Recognition of the BPS by the U2 snRNA displaces the SF1 and converts the E complex to complex A. In contrast to the major introns, 5’ss and BPS of minor introns are recognized cooperatively by U11 and U12 of the di-snRNP, respectively, thereby forming the minor intron A complex. The subsequent steps in the splicing process are very similar between the two systems and intron recognition is followed by the association of major and minor tri-snRNPs, respectively, giving rise to (presumably) similar catalytic structures and catalytic steps of splicing.

Figure 2. FIGURE 2: SMN1 and SMN2.

The vast majority of the SMN protein is produced from the SMN1 gene. However, during evolution, humans have acquired a paralogue (SMN2) by gene duplication, but SMN2 produces only approximately 10% of the full-length mRNA. Due to a C to T transition in SMN2 (C to U at RNA level) the first exonic splicing enhancer (ESE) in exon 7 is disrupted and an exonic splicing silencer (ESS) is created, which is bound by hnRNPA1 (A1). Inclusion of exon 7 is further prevented by an A to G transition further downstream in intron 7 (creating an additional hnRNPA1 binding site), and the suboptimal branchpoint (BPS) in intron 6. Hence, exon 7 is mainly skipped leading to the production of an instable C-terminally truncated protein (SMNΔ7) that is rapidly degraded. Cis-acting elements promoting exon inclusion are indicated with green plus signs, while inhibitory elements are marked with red minus signs.

Figure 3. FIGURE 3: Impaired minor intron splicing in SMA and ALS.

Many of the molecular defects observed in patient tissues or disease modelling systems ultimately converge on affecting the spliceosome and minor intron splicing. These include both gain- and loss-of-function mechanisms in the nucleus as well as in the cytoplasm. Defects linked with SMA are indicated with a yellow rectangle, while blue rectangles mark ALS-associated defects.