MicroRNA Expression Profiling Reveals MiRNA Families Regulating Specific Biological Pathways in Mouse Frontal Cortex and Hippocampus

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.

Sex-Biased miRNA Expression in Atlantic Halibut <b><i>(Hippoglossus hippoglossus)</i></b> Brain and Gonads

“…In chicken, sex-dependent differential regulation of the 2 arms of miR-202 has been reported [Bannister et al, 2009]. Similarly, several miRNA families were differentially expressed in 2 regions of mouse brain [Juhila et al, 2011]. In the present study, we found differential expression of miRNAs within families and miRNA arms between tissues and sexes in a teleost, which could result from target preference of miRNAs as it has been previously shown in mammals [Juhila et al, 2011].…”

“…Similarly, several miRNA families were differentially expressed in 2 regions of mouse brain [Juhila et al, 2011]. In the present study, we found differential expression of miRNAs within families and miRNA arms between tissues and sexes in a teleost, which could result from target preference of miRNAs as it has been previously shown in mammals [Juhila et al, 2011]. Alternatively, it can be an effect of variation in post-transcriptional processing and in vivo accumulation or stability of miRNAs [Bail et al, 2010].…”

MicroRNAs and synaptic plasticity—a mutual relationship

“…General profiling by microarrays distinguished the differential expression of miRNAs in different regions of the rodent brain [49,50] with a specific emphasis on the cortex and hippocampus [51,52]. More recently, miRNA expression was also explored under conditions of elevated activity known to induce synaptic plasticity.…”

miR‐204 downregulates EphB2 in aging mouse hippocampal neurons

“…Approximately 50% of mammalian miRNAs are expressed in the brain (Krichevsky et al ., 2003; Somel et al ., 2011), many of which have critical roles in neurogenesis and neuronal development (Giraldez et al ., 2005; De Pietri Tonelli et al ., 2008). A number of hippocampal miRNAs regulate neuronal activity by targeting their downstream genes (Eacker et al ., 2011; Juhila et al ., 2011). For instance, in the miRNA‐mediated synaptic plasticity regulating pathway, miR501 (Hu et al ., 2015), miR223 (Harraz et al ., 2012) and miR134 (Jimenez‐Mateos et al ., 2012) target GluR1, GluR2 and NR2B, and DHX36, respectively.…”