The Coding and Small Non-coding Hippocampal Synaptic RNAome
Open Access
- 31 May 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Molecular Neurobiology
- Vol. 58 (6), 2940-2953
- https://doi.org/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.Funding Information
- Projekt DEAL
This publication has 59 references indexed in Scilit:
- STAR: ultrafast universal RNA-seq alignerBioinformatics, 2012
- The Local Transcriptome in the Synaptic Neuropil Revealed by Deep Sequencing and High-Resolution ImagingNeuron, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal cladesNucleic Acids Research, 2011
- Mechanisms of dendritic mRNA transport and its role in synaptic taggingThe EMBO Journal, 2011
- A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expressionThe EMBO Journal, 2010
- Microfluidic Local Perfusion Chambers for the Visualization and Manipulation of SynapsesNeuron, 2010
- Somatodendritic microRNAs identified by laser capture and multiplex RT-PCRRNA, 2007
- Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cellsNature, 2007
- Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction NetworksGenome Research, 2003