Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption

Area of Science:

• Molecular Biology
• Genetics
• Bioinformatics

Background:

• Transcripts with premature termination codons (PTCs) can undergo nonsense-associated alternative splicing (NAS).
• Two models, scanning and splice motif disruption, explain NAS.
• The splice motif disruption model posits that exonic cis motifs, like exonic splice enhancers (ESEs), are disrupted by nonsense mutations.

Purpose of the Study:

• To investigate the role of exonic cis motifs, specifically ESEs, in nonsense-associated alternative splicing (NAS).
• To evaluate the validity of the splice motif disruption model for NAS.
• To understand the contribution of splice motif modulation to PTC-associated diseases.

Main Methods:

• Genome-wide transcriptomic analysis.
• K-mer enrichment methods.
• Nucleotide-based machine learning for splice disruption prediction.

Main Results:

• Exonic splice enhancers (ESEs) are susceptible to disruptive nonsense mutations due to their purine-rich nature and lack of TGA, TAA, and TAG codons.
• Nonsense-associated alternative splicing (NAS) rates are low (5-30%), aligning with estimates for random splicing disruption (8-20%).
• NAS-associated PTCs are predictable using machine learning and enriched in ESEs, particularly for pathogenic variants. Mutations in TAA, TGA, or TAG codons are linked to exon skipping.

Conclusions:

• The splice motif disruption model is supported, highlighting the importance of ESE disruption in NAS.
• While some evidence supports the scanning model, splice motif modulation is critical for understanding PTC-associated disease.
• These findings underscore the significance of considering ESEs and other splice motifs in the context of nonsense-mediated decay and alternative splicing.