Discrimination of the Expression of Paralogous microRNA Precursors That Share the Same Major Mature Form

Abstract

BackgroundMicroRNAs (miRNAs) are a class of small non-coding RNAs generated from endogenous transcripts that form hairpin structures. The hairpin precursor is processed into two mature miRNAs that form major/minor duplexes. Mature miRNAs regulate gene expression by cleaving mRNA or repressing protein translation. Numerous miRNAs have been discovered via deep sequencing. Many miRNAs are produced from multiple genome sites. These miRNAs are grouped into paralogous families of miRNAs that generate the same major mature form within organisms. Currently, no method of distinguishing the expression of these miRNAs is available.ResultsIn the present study, strategies were developed to discriminate and quantify the expression of paralogous miRNA precursors. First, paralogous miRNA precursors that were differentially expressed in tissues were identified through analysis of the coexpression scores of their major and minor forms based on deep sequencing data. Then the precursors were identified by monitoring the expression of their host gene or minor form using real-time PCR. Finally, precursors were identified by assessing the expression of clusters of miRNA members. These approaches were used to distinguish miR-128-1 and miR-128-2 as well as miR-194-1 and miR-194-2. The mechanism of transcription related to the differential expression of miR-194-1 and miR-194-2 was also investigated.ConclusionThis is the first report to distinguish paralogous miRNA copies by analyzing the expression of major-minor pairs, the host gene, and miRNA clusters. Discriminating paralogous precursors can provide useful information for investigating the mechanisms that regulate miRNA gene expression under different physiological and pathological conditions.

Probiotic‐derived nanoparticles inhibit ALD through intestinal miR194 suppression and subsequent FXR activation

“…Consistent with this study, we found that alcohol feeding increased serum exosomal miR192 but not miR194 levels (Figure 3C), further suggesting a local regulation of ileal miR194 by alcohol. We also found that the expression of both primary‐miR194‐2 ( pri‐miR194‐2 ) and primary‐miR194‐1 ( pri‐miR194‐1 ) in the ileum was increased by alcohol feeding, but the increase of pri‐miR194‐2 was more pronounced (Figure 3C), which is the major contributor to the expression of miR194 in the gastrointestinal tract 20. These results suggest partial transcriptional regulation of miR194 expression in the intestine by alcohol.…”

“…We also found that the expression of both primary-miR194-2 (pri-miR194-2) and primary-miR194-1 (pri-miR194-1) in the ileum was increased by alcohol feeding, but the increase of pri-miR194-2 was more pronounced (Figure 3C), which is the major contributor to the expression of miR194 in the gastrointestinal tract. [20] These results suggest partial transcriptional regulation of miR194 expression in the intestine by alcohol. Interestingly, intestinal mucus-derived exosomes contain miR194, and it was significantly increased by alcohol feeding (Figure S5A).…”

Overexpression of Drosha, DiGeorge syndrome critical region gene 8 (DGCR8), and Dicer mRNAs in the pathogenesis of psoriasis

“…MicroRNAs (miRNAs) are endogenous small noncoding RNAs of 19~23 nucleotides (nt), which are diverse in sequence and expression patterns, suggesting that they may participate in a wide range of genetic regulatory pathways . They regulate gene expression through mRNA cleavage and translational repression by binding to the 3′ untranslated region of the target miRNA . To date, nearly 2700 miRNA genes have been identified in the human genome .…”