A retained intron in the 3′-UTR of Calm3 mRNA mediates its Staufen2- and activity-dependent localization to neuronal dendrites

Dendritic localization and hence local mRNA translation contributes to synaptic plasticity in neurons. Staufen2 (Stau2) is a well-known neuronal double-stranded RNA-binding protein (dsRBP) that has been implicated in dendritic mRNA localization. The specificity of Stau2 binding to its target mRNAs remains elusive. Using individual-nucleotide resolution CLIP (iCLIP), we identified significantly enriched Stau2 binding to the 3′-UTRs of 356 transcripts. In 28 (7.9%) of those, binding occurred to a retained intron in their 3′-UTR. The strongest bound 3′-UTR intron was present in the longest isoform of Calmodulin 3 (Calm3_L) mRNA. Calm3_L 3′-UTR contains six Stau2 crosslink clusters, four of which are in this retained 3′-UTR intron. The Calm3_L mRNA localized to neuronal dendrites, while lack of the 3′-UTR intron impaired its dendritic localization. Importantly, Stau2 mediates this dendritic localization via the 3′-UTR intron, without affecting its stability. Also, NMDA-mediated synaptic activity specifically promoted the dendritic mRNA localization of the Calm3_L isoform, while inhibition of synaptic activity reduced it substantially. Together, our results identify the retained intron as a critical element in recruiting Stau2, which then allows for the localization of Calm3_L mRNA to distal dendrites.