Dynamic endosome-mRNA association drives compartment-specific mRNA localization in neurons

RNA localization is a key mechanism to control protein abundance at the subcellular level. Neurons heavily rely on this process for their proper development and function, but how specific mRNAs reach their site of translation remains poorly understood. Here, we investigated the role of the endosomal pathway in controlling RNA localization and translation in neurons. Through rapid isolation of endosomal compartments followed by RNA sequencing, we first found a vast repertoire of mRNAs associated with endosomes in developing neurons, with functions associated with various organelles and molecular processes. We thus characterized a core endosomal-associated transcriptome as well as specific transcripts that varied depending on the endosomal subtype. Compartment-specific analysis of early endosomal transcriptome and smFISH experiments further revealed that endosomes harbor different mRNAs depending on their subcellular location. The binding of endosomal-related mRNAs was restricted to the soma and by focusing on the transcript encoding for the Early Endosome Associated Protein 1 (EEA1), we discovered that the mRNA is targeted to Golgi-derived EEA1-positive vesicles where its translation regulates the mRNA levels and the presence of EEA1 protein on endosomes. Finally, genetic perturbation of different endosomal trafficking routes was found to lead to distinct changes in the subcellular localization of specific mRNAs in axons and dendrites. Together, our results revealed a key role for endosome-mRNA association in regulating the endosomal proteome as well as a new function for endosomal trafficking in regulating the correct polarized distribution of specific mRNAs during neuronal development.