Transcriptome-wide alternative mRNA splicing analysis reveals post-transcriptional regulation of neuronal differentiation

Abstract Alternative splicing (AS) plays important roles in neuronal development, function, and diseases. Efforts to analyze AS transcriptome-wide in neurons remain limited. We characterized the transcriptome-wide AS changes in SH-SY5Y neuronal differentiation model, which is widely used to study neuronal function and disorders. Our analysis revealed global changes in five AS programs that drive neuronal differentiation. Motif analysis revealed the contribution of RNA binding proteins (RBPs) to the regulation of AS during neuronal development. We focused on the predominant AS program during differentiation, exon skipping (SE) events. Motif analysis revealed motifs for PTB and HuR/ELAVL1 to be the top enriched in SE events, and their protein levels were downregulated after differentiation. shRNA Knockdown of either PTB and HuR were associated with enhanced neuronal differentiation and transcriptome-wide exon skipping events driving the process of differentiation. At the level of gene expression, we observed only modest changes, indicating predominant post-transcriptional effects of PTB and HuR. We also observed that both RBPs altered cellular responses to oxidative stress, in line with the differentiated phenotype observed after KD. Our work characterizes the AS changes in a widely used and important model of neuronal development and neuroscience research and reveals intricate post-transcriptional regulation of neuronal differentiation.