A retained intron in the 3'-UTR of Calm3mRNA mediates its Staufen2- and activity-dependent localization to neuronal dendrites

• Published in: EMBO reports 2017-10, Vol.18 (10), p.1762
• Main Authors: Sharangdhar, Tejaswini, Sugimoto, Yoichiro, Heraud-Farlow, Jacqueline, Fernandez-Moya, Sandra M, Ehses, Janina, Ruiz de los Mozos, Igor, Ule, Jernej, Kiebler, Michael A
• Format: Article
• Language: English
• Subjects: 3' Untranslated regions; Calcium-binding protein; Calmodulin; Crosslinking; Dendrites; Dendritic plasticity; Double-stranded RNA; Hippocampus; Introns; Localization; N-Methyl-D-aspartic acid; Neurons; Ribonucleic acid; RNA; RNA-binding protein; Synaptic plasticity
• ISSN: 1469-221X; 1469-3178
• DOI: 10.15252/embr.201744334

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 (Calm3L) mRNA. Calm3L 3'-UTR contains six Stau2 crosslink clusters, four of which are in this retained 3'-UTR intron. The Calm3L 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 Calm3L 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 Calm3L mRNA to distal dendrites. Synopsis This study shows that Stau2 binds 28 transcripts through a retained intron in their 3'-UTR. Stau2 binding to the 3'-UTR intron and synaptic activity both promote the dendritic localization of Calm3mRNA. Stau2 binds to retained introns in 3'-UTRs of several neuronal mRNAs, including Calm3. Stau2 specifically interacts with a retained intron of the long Calm3 mRNA isoform (Calm3L). Stau2 mediates dendritic localization of Calm3L mRNA in mature hippocampal neurons. Synaptic activity induces dendritic localization of Calm3L mRNA.