HuD Regulates mRNA-circRNA-miRNA Networks in the Mouse Striatum Linked to Neuronal Development and Drug Addiction.

Michela Dell’Orco,Janet L Neisewander,Shobana Sekar,Amir Elyaderani,Nora I Perrone-Bizzozero,Winnie S Liang,Annika Vannan,Gregory Powell

doi:10.3390/biology10090939

Michela Dell’Orco, Janet L Neisewander + Show 6 more

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https://doi.org/10.3390/biology10090939

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Abstract

Simple SummaryGene expression controls all aspects of life, including that of humans. Genes are expressed by copying the information stored in the DNA into RNA molecules, and this process is regulated in part by multiple RNA-binding proteins (RBPs). One such protein, HuD, plays a critical role in the development of neurons and has been implicated in childhood brain tumors, neurodegenerative disorders (Parkinson’s, Alzheimer’s, and ALS), and drug abuse. In addition, HuD participates in neuronal remodeling mechanisms in the mature brain and promotes regeneration of peripheral nerves. HuD primarily binds to transcribed messenger RNAs, which are then stabilized for translation into proteins. However, recent studies demonstrate that HuD also regulates the expression of non-coding RNAs, such as circular RNAs (circRNAs) and microRNAs (miRNAs). In this study, we examined the role of HuD in the control of non-coding RNA expression in the mouse striatum, a brain region associated both with normal behaviors and pathological conditions such as drug abuse. Our results show that HuD regulates mRNA-circRNA-miRNA networks involved in the expression of genes associated with brain development and remodeling of neuronal connections. These findings suggest the possibility of new mechanisms controlling brain development, neurodegenerative diseases, and substance use disorders.The RNA-binding protein HuD (a.k.a., ELAVL4) is involved in neuronal development and synaptic plasticity mechanisms, including addiction-related processes such as cocaine conditioned-place preference (CPP) and food reward. The most studied function of this protein is mRNA stabilization; however, we have recently shown that HuD also regulates the levels of circular RNAs (circRNAs) in neurons. To examine the role of HuD in the control of coding and non-coding RNA networks associated with substance use, we identified sets of differentially expressed mRNAs, circRNAs and miRNAs in the striatum of HuD knockout (KO) mice. Our findings indicate that significantly downregulated mRNAs are enriched in biological pathways related to cell morphology and behavior. Furthermore, deletion of HuD altered the levels of 15 miRNAs associated with drug seeking. Using these sets of data, we predicted that a large number of upregulated miRNAs form competing endogenous RNA (ceRNA) networks with circRNAs and mRNAs associated with the neuronal development and synaptic plasticity proteins LSAMP and MARK3. Additionally, several downregulated miRNAs form ceRNA networks with mRNAs and circRNAs from MEF2D, PIK3R3, PTRPM and other neuronal proteins. Together, our results indicate that HuD regulates ceRNA networks controlling the levels of mRNAs associated with neuronal differentiation and synaptic physiology.

Highlights

RNA-binding proteins (RBPs) play multiple roles in the post-transcriptional regulation of gene expression, from mRNA localization and metabolism to translation
This finding is in agreement with the decreases in HuB mRNA, which is a target of HuD, in the brains of mice overexpressing HuD [43], suggesting that these proteins are regulated in an opposite manner in neurons
As HuD is expressed in neurons, we compared the list of downregulated mRNAs with a set of medium spiny neuron (MSN)-expressed transcripts [44] and found that about 79% are expressed in MSNs (Table S1d)

Summary

Introduction

RNA-binding proteins (RBPs) play multiple roles in the post-transcriptional regulation of gene expression, from mRNA localization and metabolism to translation. These proteins are important in neurons where mRNAs are transported to dendrites and axons for localized translation [1,2,3]. HuD and other Hu proteins are the best-known mRNA stabilizers [9,10]. These proteins bind to AU-rich elements (AREs) in the 3 UTR of mRNAs, thereby increasing their half-life. Binding to the same element controls mRNA transport and local translation [11]. Hu proteins are known to compete with microRNAs for the regulation of gene expression [12]

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