The Coding and Small Non-coding Hippocampal Synaptic RNAome

Robert Epple,Sarah Köster,Momchil Ninov,Gerrit Brehm,Tea Berulava,Rezaul Islam,Andre Fischer,Dennis Krüger

doi:10.1007/s12035-021-02296-y

Abstract

Neurons are highly compartmentalized cells that depend on local protein synthesis. Messenger RNAs (mRNAs) have thus been detected in neuronal dendrites, and more recently in the pre- and postsynaptic compartments as well. Other RNA species such as microRNAs have also been described at synapses where they are believed to control mRNA availability for local translation. A combined dataset analyzing the synaptic coding and non-coding RNAome via next-generation sequencing approaches is, however, still lacking. Here, we isolate synaptosomes from the hippocampus of young wild-type mice and provide the coding and non-coding synaptic RNAome. These data are complemented by a novel approach for analyzing the synaptic RNAome from primary hippocampal neurons grown in microfluidic chambers. Our data show that synaptic microRNAs control almost the entire synaptic mRNAome, and we identified several hub microRNAs. By combining the in vivo synaptosomal data with our novel microfluidic chamber system, our findings also support the hypothesis that part of the synaptic microRNAome may be supplied to neurons via astrocytes. Moreover, the microfluidic system is suitable for studying the dynamics of the synaptic RNAome in response to stimulation. In conclusion, our data provide a valuable resource and point to several important targets for further research.

Highlights

Neurons are highly compartmentalized cells that form chemical synapses, and the plasticity of such synapses is a key process underlying cognitive function
To complement the data and address the question as to the origin of synaptic RNAs, we developed a novel microfluid chamber that allowed us to grow primary hippocampal neurons that form synapses in a pre-defined compartment [20] and enabled us to isolate the synaptic compartments from these chambers using a novel device we call SNIDER (SyNapse Isolation DevicE by Refined Cutting)
Functional pathway analysis showed that the Messenger RNAs (mRNAs) found in our synaptosomal preparations represent key pathways linked to synaptic function and plasticity (Fig. 1d)

Summary

Introduction

Neurons are highly compartmentalized cells that form chemical synapses, and the plasticity of such synapses is a key process underlying cognitive function. Mol Neurobiol (2021) 58:2940–2953 by the corresponding neurons and RNAs that might be transferred to synapses from other cell types. This issue is becoming increasingly important since there is emerging evidence on intercellular RNA transport and data that support the hypothesis that glia cells, for example, provide neurons with RNA [18, 19]. To complement the data and address the question as to the origin of synaptic RNAs, we developed a novel microfluid chamber that allowed us to grow primary hippocampal neurons that form synapses in a pre-defined compartment [20] and enabled us to isolate the synaptic compartments from these chambers using a novel device we call SNIDER (SyNapse Isolation DevicE by Refined Cutting). After the synaptic compartments were isolated, we performed RNA sequencing. We show that this novel microfluid chamber is suitable for assaying the dynamics of the synaptic RNAome in response to stimulation

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