ArticleNucleic acids research2021
Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 20 citations in OpenAlex.
- Interpretable distillation reveals that deep learning splicing models suffer from pervasive confounders and blind spots.Genome biology · 2026Article
- predNMD: prediction of nonsense-mediated mRNA decay for improved clinical variant pathogenicity classification.bioRxiv : the preprint server for biology · 2026Article
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- Genomic stop codon scanning reveals quantitative principles of nonsense-mediated mRNA decay.bioRxiv : the preprint server for biology · 2025Article
- Plans within plans: post-transcriptional regulation governs macrophage responses.Trends in immunology · 2025Review
- Assessing Splicing Variants in the PAX6 Gene: A Comprehensive Minigene Approach.Journal of cellular and molecular medicine · 2025Article
- Novel mutation leading to splice donor loss in a conserved site ofJournal of medical genetics · 2024Article
- Selection on synonymous sites: the unwanted transcript hypothesis.Nature reviews. Genetics · 2024Review
- Assessing the reliability of point mutation as data augmentation for deep learning with genomic data.BMC bioinformatics · 2024Article
- Escaping from CRISPR-Cas-mediated knockout: the facts, mechanisms, and applications.Cellular & molecular biology letters · 2024Review
- Novel biallelic mutations in TMEM126B cause splicing defects and lead to Leigh-like syndrome with severe complex I deficiency.Journal of human genetics · 2023Article
- In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue.PLoS genetics · 2022Article
- Predictive functional, statistical and structural analysis ofFrontiers in molecular biosciences · 2022Article
- Twelve exonic variants in theFrontiers in genetics · 2022Article
- T-G-A Deficiency Pattern in Protein-Coding Genes and Its Potential Reason.Frontiers in microbiology · 2022Article
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcripts containing premature termination codons (PTCs) can be subject to nonsense-associated alternative splicing (NAS). Two models have been evoked to explain this, scanning and splice motif disruption. The latter postulates that exonic cis motifs, such as exonic splice enhancers (ESEs), are disrupted by nonsense mutations. We employ genome-wide transcriptomic and k-mer enrichment methods to scrutinize this model. First, we show that ESEs are prone to disruptive nonsense mutations owing to their purine richness and paucity of TGA, TAA and TAG. The motif model correctly predicts that NAS rates should be low (we estimate 5-30%) and approximately in line with estimates for the rate at which random point mutations disrupt splicing (8-20%). Further, we find that, as expected, NAS-associated PTCs are predictable from nucleotide-based machine learning approaches to predict splice disruption and, at least for pathogenic variants, are enriched in ESEs. Finally, we find that both in and out of frame mutations to TAA, TGA or TAG are associated with exon skipping. While a higher relative frequency of such skip-inducing mutations in-frame than out of frame lends some credence to the scanning model, these results reinforce the importance of considering splice motif modulation to understand the etiology of PTC-associated disease.
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