Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures

n the central nervous system (CNS), the microRNAs (miRNAs), small endogenous RNAs exerting a negative post-transcriptional regulation on mRNA, are involved in major functions, such as neurogenesis, and synaptic plasticity. Moreover, they are essential to define the specific transcriptome of the tissues and cell types. However, few studies were performed to determine the miRNome of the different structures of the rat CNS, even through rat is a major model in neuroscience. We determined the miRNome profile of the hippocampus, the cortex, the striatum, the spinal cord and the olfactory bulb, by small RNA-Seq. Then, we correlated miRNAs expression with their mRNA targets by RT-qPCR. We found a total of 365 known miRNAs and 90 novel miRNAs expressed in the CNS of the rat. Each structure expressed a particular miRNome, and the novel miRNAs seemed to be important in defining structure-specific miRNomes. Differential analysis showed that several miRNAs were specifically enriched/depleted in these CNS structures. Finally, we correlated enriched/depleted miRNA expression with the expression of their mRNA targets and confirmed some of these correlations by RT-qPCR. Altogether, these results suggest the critical role played by these enriched/depleted miRNAs in the transcriptomic and functional identities of CNS structures.