RNA-seq analysis of AS-NMD targets in developing mouse neurons

The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) has been shown to modulate the expression of numerous genes. Previous studies have identified several examples of this regulation in developing neurons. However, the systems-level effects of AS-NMD in this context have been poorly understood. To this end, we performed a longitudinal analysis of gene expression in mouse embryonic stem cells undergoing induced neuronal differentiation, as well as primary neural cells. To improve the detection of NMD-sensitive splice forms, some of the samples were treated with the translation inhibitor cycloheximide or separated into nuclear and cytoplasmic fractions. Our analyses uncovered hundreds of AS-NMD events with significant potential to regulate their host genes. Notably, these events were significantly overrepresented in developmentally downregulated genes. Particularly strong enrichment was detected for alternative cassette exons that trigger NMD upon their inclusion into mature mRNA. Overall, this study extends our understanding of the molecular mechanisms underlying neuronal differentiation and highlights the importance of post-transcriptional regulation gene expression in orchestrating this intricate process.