The predicted RNA-binding protein regulome of axonal mRNAs

Abstract

Neurons are morphologically complex cells that rely on the compartmentalization of protein expression to develop and maintain their cytoarchitecture. Targeting of RNA transcripts to axons is one of the mechanisms that allows rapid local translation of proteins in response to extracellular signals. 3'; untranslated regions (UTRs) of mRNA are noncoding sequences that play a critical role in determining transcript localization and translation by interacting with specific RNA-binding proteins (RBPs). However, how 3' UTRs contribute to mRNA metabolism and the nature of RBP complexes responsible for these functions remain elusive. We performed 3' end sequencing of RNA isolated from cell bodies and axons of sympathetic neurons exposed to either Nerve Growth factor (NGF) or Neurotrophin 3 (NT-3). NGF and NT-3 are growth factors essential for sympathetic neuron development through distinct signalling mechanisms. Whereas NT-3 acts mostly locally, NGF signal is retrogradely transported from axons to cell bodies. We discovered that both NGF and NT-3 affect transcription and alternative polyadenylation in the nucleus and induce the localization of specific 3'UTR isoforms to axons, including short 3’UTR isoforms found exclusively in axons. The integration of our data with CLIP sequencing data supports a model whereby long 3’UTR isoforms associate with RBP complexes in the nucleus, and upon reaching the axons, are remodelled locally into shorter isoforms. Our findings shed new light into the complex relationship between nuclear polyadenylation, mRNA localisation and local 3'UTR remodelling in developing neurons.