Transcriptomic analysis identifies synapse-enriched lncRNAs required for glutamatergic synapse development and fear memory consolidation.

Regulatory functions of lncRNAs in neurons have been majorly limited to the nucleus. The identity of synaptic lncRNAs and their functional roles associated with synapse development and plasticity are poorly understood. Transcriptomic analysis from synaptoneurosomes identified 94 synapse-enriched lncRNAs from the mouse hippocampus. We find Pvt1 to be a specific regulator of excitatory, not inhibitory, synapse development. Synapse-specific loss of Pvt1 regulates synaptic activity and the downregulation of mRNAs pertinent to synapse development. We also report a synapse-centric role for an uncharacterized lncRNA; 2410006H16Rik (SynLAMP); in translation and memory formation. SynLAMP demonstrates enhanced localization to the synapse following fear conditioning and regulates dendritic translation by sequestering the translation repressor FUS; acting as a molecular decoy. Synapse-specific knockdown of SynLAMP inhibits the localised, activity-dependent translation of CamK2a, a FUS target. SynLAMP RNAi occludes fear-memory formation. Comprehensively, our study highlights that de novo activity of lncRNAs are involved in diverse synaptic functions.