Abstract
MicroRNAs (miRNAs) are small regulatory molecules that cause post-transcriptional gene silencing. Although some miRNAs are known to have region-specific expression patterns in the adult brain, the functional consequences of the region-specificity to the gene regulatory networks of the brain nuclei are not clear. Therefore, we studied miRNA expression patterns by miRNA-Seq and microarrays in two brain regions, frontal cortex (FCx) and hippocampus (HP), which have separate biological functions. We identified 354 miRNAs from FCx and 408 from HP using miRNA-Seq, and 245 from FCx and 238 from HP with microarrays. Several miRNA families and clusters were differentially expressed between FCx and HP, including the miR-8 family, miR-182|miR-96|miR-183 cluster, and miR-212|miR-312 cluster overexpressed in FCx and miR-34 family overexpressed in HP. To visualize the clusters, we developed support for viewing genomic alignments of miRNA-Seq reads in the Chipster genome browser. We carried out pathway analysis of the predicted target genes of differentially expressed miRNA families and clusters to assess their putative biological functions. Interestingly, several miRNAs from the same family/cluster were predicted to regulate specific biological pathways. We have developed a miRNA-Seq approach with a bioinformatic analysis workflow that is suitable for studying miRNA expression patterns from specific brain nuclei. FCx and HP were shown to have distinct miRNA expression patterns which were reflected in the predicted gene regulatory pathways. This methodology can be applied for the identification of brain region-specific and phenotype-specific miRNA-mRNA-regulatory networks from the adult and developing rodent brain.
Highlights
MicroRNAs are highly conserved small regulatory molecules that cause post-transcriptional gene silencing by base pairing with target messenger RNA [1]
Mature mammalian miRNAs bind to their specific target sequences on the 39-untranslated region (UTR) of messenger RNA (mRNA) by imperfect base pairing, leading to mRNA cleavage or translational repression [3,4]
Identification of miRNAs from frontal cortex (FCx) and HP by miRNA-Seq To determine miRNA expression patterns in FCx and HP, we carried out miRNA-Seq using the Illumina Genome Analyzer II
Summary
MicroRNAs (miRNAs) are highly conserved small regulatory molecules that cause post-transcriptional gene silencing by base pairing with target messenger RNA (mRNA) [1]. MiRNAs are processed from primary transcripts into ,70-nt stem-loop precursors in the nucleus by Drosha-DGCR (DiGeorge Critical Region) complex, and further cleaved by the Dicer enzyme in the cytoplasm into ,23-nt functional sequences [2]. Mature mammalian miRNAs bind to their specific target sequences on the 39-untranslated region (UTR) of mRNAs by imperfect base pairing, leading to mRNA cleavage or translational repression [3,4]. MiRNAs have diverse functions in the brain, including regulation of neuronal development and differentiation, synapse formation precursorand plasticity [5,6,7]. MiRNA expression levels seem to be dynamic in the mammalian brain since they are altered by environmental stimuli. It is not surprising that miRNAs have been implicated in the etiology of several brain disorders, including Alzheimer’s disease [10,11], Parkinson’s disease [12], schizophrenia [13], aggressive behavior [14], depression [15], and anxiety disorders [16,17]
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