Poison exon splicing in the human brain: a new paradigm for understanding and targeting neurological disorders

Poison exons (PE) are highly conserved exons whose inclusion creates premature termination codons (PTCs) and triggers nonsense-mediated decay (NMD) of the mature transcript. Despite their important role in post-transcriptional regulation, PEs remain poorly annotated due to the lack of systematic transcriptome-wide approaches. Here, we comprehensively investigate the function of PEs in the human brain under physiological and pathological conditions. A comparative analysis of 957 eukaryotic transcriptomes revealed that humans exhibit the highest enrichment of NMD-targeted isoforms. By annotating all splicing events that generate PTCs, we found 12,014 PEs in the human genome. Using GTEx and BrainSpan RNA-seq dataset, we compared PE splicing across tissues and developmental stages and identified 117 PEs uniquely found in the human brain, 1,214 PEs with brain-specific differential splicing, and 1,610 PEs differentially spliced during brain development. By integrating ClinVar variant annotations with SpliceAI predictions, we identified 1,877 pathogenic variants associated with neurological disorders that are predicted to affect the splicing of 891 PEs, and we functionally validated the impact of a subset of them using CRISPR prime-editing in human cells. Our findings highlight PEs as pivotal regulators of gene expression in the human brain and support the therapeutic targeting of PE splicing in neurological diseases.