Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons

RNA localization to neuronal dendrites is critical step for long-lasting synaptic potentiation, but there is little consensus regarding which RNAs are localized and the role of alternative isoforms in localization. Using independent RNA-sequencing from soma and dendrites of the same neuron, we deeply profiled the sub-cellular transcriptomes to assess the extent and variability of dendritic RNA localization in individual hippocampal neurons, including an assessment of differential localization of alternative 3UTR isoforms. We identified 2,225 dendritic RNAs, including 298 cases of 3UTR isoform-specific localization. We extensively analyzed the localized RNAs for potential localization motifs, finding that B1 and B2 SINE elements are up to 5.7 times more abundant in localized RNA 3UTRs than non-localized, and also functionally characterized the localized RNAs using protein structure analysis. Finally, we integrate our list of localized RNAs with the literature to provide a comprehensive list of known dendritically localized RNAs as a resource.