Global analysis of excitotoxicity-induced alterations in RNA structure and RNA-protein binding in neurons identifies subsets of transcripts and RNA-binding proteins involved in synaptic plasticity and neurodegenerative disorders [PIP-seq]

Our results reveal that NMDA dramatically changes RNA secondary structure at the UTR regions, and that specific RNA structure reduction at the 3’UTR correlates with increased mRNA abundance as assessed by mRNA-Seq. Protein binding sites increase in response to excitotoxicity and, interestingly, different RNA-protein binding in this context defines subsets of transcripts functionally associated with synaptic functions and neurodegenerative disorders. We also identify two RNA motifs enriched in protein binding in the context of excitotoxicity and a list of proteins binding to them in vitro. Accordingly, we observe that two of these RBPs, CELF6 and YBX3 alter their protein levels in response to NMDA treatment, suggesting their involvement in RNA regulation in the context of excitotoxicity. Overall, we describe for the first time the global RNA-protein interactions of primary cortical neurons in baseline conditions and in an in vitro model of excitotoxicity, providing extensive datasets that can be leveraged to bridge the mechanistic gap between two major hallmarks common in multiple neurodegenerative disorders: excitotoxicity and RNA regulation by RBPs