The Minor Spliceosome Regulates Alternative Splicing of Minor Introns in Neuronal Development and Disease

Expression of ~2% of eukaryotic genes requires the splicing of not just one, but two types of introns: major, as well as minor, introns. These minor introns contain divergent sequences at their splice sites which are recognized by the minor spliceosome (U11, U12, U4atac, U6atac and U5). Since splicing of both intron classes occurs co-transcriptionally, expression of minor intron-containing genes (MIGs) is thought to require the coordinated action of both the major and minor spliceosome. Proper MIG expression is especially important for nervous system development, as underscored by multiple diseases linked to pathogenic variants in minor spliceosome components. To understand this bias of nervous system involvement, I examined tissue-specific splicing of minor introns. To this end, I identified all minor introns in the mouse and human genome and developed new bioinformatics pipelines to study their splicing. Moreover, I identified a subset of MIGs whose aberrant splicing might underlie prevalent symptoms, like microcephaly, observed in minor spliceosome-related diseases. To determine how disrupted minor intron splicing can result in microcephaly we then ablated U11 snRNA in the dorsal telencephalon. U11 loss especially resulted in the death of self-amplifying radial glial cells, through cell cycle defects, DNA damage and p53-mediated apoptosis. This was due to retention and alternative splicing (AS) of minor introns found in genes with crucial roles in cell cycle and led me to explore the mechanism of regulating AS around minor introns. I found that AS is normally repressed through interactions between minor spliceosome component U11-59K and the major spliceosome. Inhibition of the minor spliceosome relieves this repression, resulting in elevated AS in individuals with pathogenic variants in U4atac and U12 snRNA. To test whether disrupted minor intron splicing also plays a role in amyotrophic lateral sclerosis (ALS), we then ubiquitously ablated U11 in juvenile mice and found that they recapitulated most of the pathological hallmarks associated with ALS. In all, I show how the major and minor spliceosome interact to regulate the proper splicing of minor introns in a tissue-specific manner. Moreover, we found that disrupted minor intron splicing affects survival of both neural progenitors and motor neurons

Introns: the “dark matter” of the eukaryotic genome

The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the “dark matter” of the eukaryotic genome and discuss some of the outstanding questions in the field

Disrupted minor intron splicing is prevalent in Mendelian disorders

Abstract Background Splicing is crucial for proper gene expression, and is predominately executed by the major spliceosome. Conversely, 722 introns in 699 human minor intron‐containing genes (MIGs) are spliced by the minor spliceosome. Splicing of these minor introns is disrupted in diseases caused by pathogenic variants in the minor spliceosome, ultimately leading to the aberrant expression of a subset of these MIGs. However, the effect of variants in minor introns and MIGs on diseases remains unexplored. Methods Variants in MIGs and associated clinical manifestations were identified using ClinVar. The HPO database was then used to curate the related symptoms and affected organ systems. Results: We found pathogenic variants in 211 MIGs, which commonly resulted in intellectual disability, seizures and microcephaly. This revealed a subset of MIGs whose aberrant splicing may contribute to the pathogenesis of minor spliceosome‐related diseases. Moreover, we identified 51 pathogenic variants in minor intron splice sites that reduce the splice site strength and can induce alternative splicing. Conclusion These findings highlight that disrupted minor intron splicing has a broader impact on human diseases than previously appreciated. The hope is that this knowledge will aid in the development of therapeutic strategies that incorporate the minor intron splicing pathway