In this study, high-throughput miRNA microarray technology with 152 miRNAs selected from miRBase was used to detect miRNA expression in 14 rat tissues. The seven neural tissues selected included olfactory bulb, cortex, hippocampus, brain stem, hypothalamus, spinal cord, and dorsal root ganglion. The tissues selected represented both the central and peripheral nervous systems. The neural miRNA expression profiles were compared with profiles from seven other tissues, including heart, lung, muscle, spleen, testicle, kidney, and liver in order to identify neural-specific miRNAs. Although several studies have previously reported the existence of neural-specific miRNAs, only the striatum, cortex, and hippocampus were selected for these previous analyses. For example, Landgraf et al. [18
] studied the mammalian miRNA expression atlas by sequencing 250 small RNA libraries representing 26 different human and rodent organ systems and cell types, and Wang et al. [21
] used home-made miRNA microarrays to identify the rat lung-specific miRNAs, miR-195 and miR-200c. The number of tissues in this work was up to date the largest rat nerve system related tissue set. The miRNA expression data were integrated with carefully screened functional data from public databases using bioinformatics and bio-statistics based strategies. Tissue-specific miRNA expression profiles were obtained from rat neural and non-neural tissues, and the neural tissue-specific expression profile related miRNAs and their significant target genes. This provided a global view of rat tissue-specific miRNA profiles and their target maps, thus contributing to a better understanding of the role of miRNAs in neural systems. In comparison to the previous studies that investigated neural-specific miRNA expression, we have obtained a more detailed picture of rat tissue miRNA expression profiles using a larger number of neural tissue types. Moreover, based upon our analyses of tissue-specific expression profiles, the resulting signature miRNAs may be used as biomarkers for the classification of tissues from different sources.
After performing the data analysis, we found a total of 30 miRNAs that were specifically expressed in neural tissues. In them, four miRNAs (miR-9, miR-124, miR-128a and miR-128b) were previously reported to be specifically expressed in the cortex and hippocampus in rat [18
]. Comparing with other animals such as mouse or zebrafish, the expression of several miRNAs agrees with previous study. For example, in mouse [14
], miR-10b is highly expressed in spinal cord; miR-124 is widely expressed in brain tissues; miR-200b, miR-128a, miR-128b, miR-429 are specifically expressed in olfactory bulb; miR-200a is highly expressed in olfactory bulb; miR-7b is highly expressed in hypothalamus. Moreover, miR-200b is enriched in zebrafish olfactory bulb; miR-124 and miR-9 expression are detected throughout adult brain [16
]. But more neural specifically expressed miRNAs were found in rat tissues in this study. Although the data were generated from completely different platforms or methods and different miRNA probe sources were used in these studies, several miRNA expression patterns were consistent with previous results, in which the same types of tissues were used in different animal models. Collectively, the data provides convincing evidence that tissue-specific miRNA expression processes and related regulatory mechanisms are highly stable, and may also indicate that the regulatory mechanisms mediated by miRNAs are conserved, and may play a more important role in physiological or pathological processes that previously believed. We identified a number of miRNAs specifically expressed in neural tissue; however, the functions and cell type distributions of most of the miRNAs were not clear. These will be studied in detail in the future.
Furthermore, targets of the specifically expressed miRNAs were mapped to gene function databases, pathway databases, and regulatory networks. This approach clearly illustrated that specifically expressed miRNAs and their targets perform integrated regulatory functions. For example, the fact that a large number of miRNAs were very highly expressed in the olfactory bulb but not in other tissues suggests that more specific combinatory regulation mechanisms may be performed by these miRNAs and their targets. The only enriched GO function in the olfactory bulb is "regulation of cell cycle", which could be affected by processes that modulate the rate or extent of progression through the cell cycle. In the DRG, there are more enriched functions, such as cell migration, cytoskeleton organization, and biogenesis, negative regulation of transcription, and positive regulation of transcription from the RNA polymerase II promoter. The pathways enriched in the DRG are those associated with amyotrophic lateral sclerosis, cytokine-cytokine receptor interactions, glycine, serine and threonine metabolism, seleno-amino acid metabolism, and the adipocytokine signalling pathway. These results imply that as the primary afferent sensory neuron, the DRG takes on a very important role in sensory signal transduction, conduction, and transmission. This study described the neural specifically expressed miRNA target genes, gene ontology and network information. Biological validation experiments needed to be further studied.
In this study, tissue-specific expressed miRNAs were also classified into different groups based on the information regarding miRNA families found on the Sanger website. Groups containing more than one miRNA were selected to compute inter-family and intra-family correlation coefficients. The analyses indicated that there were no significant differences between the correlation coefficients of intra-family and inter-family miRNAs (data not shown). This is not a surprising result, given that compensatory mechanisms of miRNAs are known to exist.
In summary, this study attempted to create a holistic view of rat tissue-specific miRNA expression profiles and combinatorial regulation mechanisms using seven neural tissues and seven non-neural tissues. By integrating the data and information obtained from function enrichment, pathway enrichment, and regulatory networks of tissue-specific miRNA targets, we also obtained regulatory networks mediated by tissue-specific miRNAs in an intuitive manner. Our strategies for extracting significant tissue-specific miRNA expression profiles, approaches for public data integration and extensive curated data sources may serve as valuable tools for the further experimental investigation of regulatory mechanisms of miRNAs in neural systems.