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

Alternative splicing (AS) plays an important role in neuronal development,
function, and disease. Efforts to analyze the transcriptome of AS neurons
on a wide scale are currently 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
concentrated on the primary alternative splicing program that occurs
during differentiation, specifically on events involving exon skipping
(SE). Motif analysis revealed motifs for Polypyrimidine Tract Binding
Protein 1 (PTB) and ELAV Like RNA Binding Protein 1 (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 was
associated with enhanced neuronal differentiation and transcriptome-wide
exon skipping events that drive 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 either gene knockdown.
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.