Pumilio differentially binds to mRNA 3’ UTR isoforms to regulate localization of synaptic proteins

In neuronal cells, the regulation of RNA is crucial for the spatiotemporal control of gene expression, but how the correct localization, levels, and function of synaptic proteins are achieved is not well understood. In this study, we globally investigate the role of alternative 3’ UTRs in regulating RNA localization in the synaptic regions of the Drosophila brain. We identify direct mRNA targets of the translational repressor Pumilio, finding that mRNAs bound by Pumilio encode proteins enriched in synaptosomes. Pumilio differentially binds to RNA isoforms of the same gene, favoring long, neuronal 3’ UTRs. These longer 3’ UTRs tend to remain in the neuronal soma, whereas shorter UTR isoforms localize to the synapse. In cultured pumilio mutant neurons, severe axon outgrowth defects were accompanied by mRNA isoform mislocalization, and proteins encoded by these Pumilio targets displayed excessive abundance at synaptic boutons. Our study identifies an important and widespread mechanism for the spatiotemporal regulation of protein function in neurons.