HuD Is a Neural Translation Enhancer Acting on mTORC1-Responsive Genes and Counteracted by the Y3 Small Non-coding RNA

Toma Tebaldi,Paola Zuccotti,Daniele Peroni,Marcel Köhn,Lisa Gasperini,Valentina Potrich,Veronica Bonazza,Tatiana Dudnakova,Annalisa Rossi,Guido Sanguinetti,Luciano Conti,Paolo Macchi,Vito D’Agostino,Gabriella Viero,David Tollervey,Stefan Hüttelmaier,Alessandro Quattrone

doi:10.1016/j.molcel.2018.06.032

Abstract

SummaryThe RNA-binding protein HuD promotes neurogenesis and favors recovery from peripheral axon injury. HuD interacts with many mRNAs, altering both stability and translation efficiency. We generated a nucleotide resolution map of the HuD RNA interactome in motor neuron-like cells, identifying HuD target sites in 1,304 mRNAs, almost exclusively in the 3′ UTR. HuD binds many mRNAs encoding mTORC1-responsive ribosomal proteins and translation factors. Altered HuD expression correlates with the translation efficiency of these mRNAs and overall protein synthesis, in a mTORC1-independent fashion. The predominant HuD target is the abundant, small non-coding RNA Y3, amounting to 70% of the HuD interaction signal. Y3 functions as a molecular sponge for HuD, dynamically limiting its recruitment to polysomes and its activity as a translation and neuron differentiation enhancer. These findings uncover an alternative route to the mTORC1 pathway for translational control in motor neurons that is tunable by a small non-coding RNA.

Highlights

The intensively studied RNA-binding protein (RBP) human antigen D (HuD)/embryonic lethal, abnormal vision like 4 (ELAVL4) is predominantly expressed in differentiated neurons, as are the other neuronal members of the ELAV family, HuB (ELAVL2) and HuC (ELAVL3)
We adapted the CRAC protocol to be used with mouse motor neuron NSC-34 cells engineered with doxycycline-inducible His-HA tagged HuD
We selected a set of 753 sequences surrounding locations with p value

Summary

Introduction

The intensively studied RNA-binding protein (RBP) human antigen D (HuD)/embryonic lethal, abnormal vision like 4 (ELAVL4) is predominantly expressed in differentiated neurons, as are the other neuronal members (nELAV) of the ELAV family, HuB (ELAVL2) and HuC (ELAVL3). HuD carries three RNA recognition motif (RRM) domains and plays important roles in controlling the fate of many neuronal mRNAs. Functional analyses implicate HuD in the regulation of mRNA stability, alternative splicing, alternative polyadenylation, RNA localization, and translation (Bronicki and Jasmin, 2013). HuD is one of the first markers expressed during neuronal differentiation and plays a fundamental role in controlling neuronal cell fate. Loss of HuD induces increased self-renewal of the neural stem and progenitor cells (Akamatsu et al, 2005), whereas overexpression promotes neurite outgrowth, neurogenesis, and neuronal plasticity (Perrone-Bizzozero and Bolognani, 2002)

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