Unique Cell-Type-Specific Distributions and Functions of Brain MicroRNAs

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation of gene expression. The first miRNA was discovered less than 20 years ago in the context of studying Caenorabditis elegans development. The discovery of the second miRNA only 10 years ago led to knowledge that these small regulatory RNAs are widely expressed in eukaryotic organisms and involved in almost all cellular processes. It is generally believed that miRNAs predominantly bind to complementary sequences within the 3' untranslated region (3'UTR) of target mRNAs and promote target degradation and/or inhibit target translation. The central nervous system is composed of four principal cell types: neurons, astrocytes, oligodendrocytes and microglia. Although miRNAs are known to regulate development and adult functions of neural cells, a genome-wide profiling of miRNA expression across the four cell types had not previously been performed. We therefore undertook this challenge and globally compared miRNA expression in the four discrete neural cell types and discovered that they differ extensively in their miRNA profiles. The global impact and mechanistic determinants of miRNAs on gene regulation is of high current interest. Recent studies have shown that miRNAs play an important role in tissue-specific protein expression, most notably during early development and cell specification. In particular, several miRNAs have been shown to have important deterministic roles in neuronal or glial fate development. We expanded the known repertoire of miRNAs functioning in neural cell fate specification by showing that neuron-specific miR-376a and miR-434 promote neuronal differentiation, while glia-specific miR-223, miR-146a, miR-19 and miR-32 inhibit neuronal differentiation. Previous genomic analyses inferred that miRNAs have had a significant impact on the 3'UTR evolution, and noted that mammalian miRNAs typically have expression levels reciprocal to those of their targets. Consistent with the latter, a recent genome-wide study concluded that mammalian miRNAs predominantly lead to degradation of their target mRNAs. However, conflicting views existed as to the relevance of these findings in neural cells, possibly due to the previous lack of cellular resolution of miRNA expression. We addressed this issue on a genome-wide scale by comparing cell-type-specific mRNA and miRNA expression in isolated primary cultures. These analyses showed that, similar to the previously described findings for non-neural tissues and cell types, glial cells show prominent reciprocity of miRNA and predicted target expression and demonstrate functional effects consistent with preventing inappropriate expression of neuron-specific proteins. In contrast, neuron-specific miRNAs surprisingly showed a correlation to the expression of their targets. We further demonstrated that two of these neuron-specific miRNAs, miR-135b and miR-137, regulate the expression of mRNAs encoding important synaptic proteins and that the dynamics of these mRNA-miRNA pairs are regulated in a neural activity-dependent manner. The unexpected finding that neuronal miRNAs have an exceptional positively correlated relationship to their targets adds a new layer of complexity to the current understanding post-transcriptional gene expression regulation by miRNAs. Moreover, additional features of the unique relationships of miRNAs and signaling in neuronal cells suggest how miRNAs may help neurons regulate their highly specialized functions. MiRNAs have also been implicated as modulators of the pathogenesis of neurodegenerative disorders. Interestingly, since one miRNA can regulate the expression of tens or hundreds of genes, manipulating miRNA levels can have broad positive or negative effects on the disease development and progression. We observed that miRNA-22 regulates expression of multiple neurodegeneration-related genes and that enhancing expression of miRNA-22 in models of neurodegeneration has a significant neuroprotective effect. We therefore propose miRNA-22 as a new candidate therapeutic capable of preventing neurodegeneration, which may be of benefit in a number of human afflictions for which there is currently a high unmet medical need.


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