Frequent Co-Expression of miRNA-5p and -3p Species and Cross-Targeting in Induced Pluripotent Stem Cells

Abstract

Background: A miRNA precursor generally gives rise to one major miRNA species derived from the 5' arm, and are called miRNA-5p. However, more recent studies have shown co-expression of miRNA-5p and -3p, albeit in different concentrations, in cancer cells targeting different sets of transcripts. Co-expression and regulation of the -5p and -3p miRNA species in stem cells, particularly in the reprogramming process, have not been studied.Methods: In this work, we investigated co-expression and regulation of miRNA-5p and -3p species in human induced pluripotent stem cells (iPSCs), mesenchymal stem cells (MSCs) and embryonic stem cells (ESC) using a nanoliter-scale real-time PCR microarray platform that included 1,036 miRNAs.Results: In comparing iPSC and ESC, only 32 miRNAs were found to be differentially expressed, in agreement of the ESC-like nature of iPSC. In the analysis of reprogramming process in iPSCs, 261 miRNAs were found to be differentially expressed compared with the parental MSC and pre-adipose tissue, indicating significant miRNA alternations in the reprogramming process. In iPSC reprogrammed from MSC, there were 88 miRNAs (33.7%), or 44 co-expressed 5p/3p pairs, clearly indicating frequent co-expression of both miRNA species on reprogramming. Of these, 40 pairs were either co-up- or co-downregulated indicating concerted 5p/3p regulation. The 5p/3p species of only 4 pairs were regulated in reverse directions. Furthermore, some 5p/3p species of the same miRNAs were found to target the same transcript and the same miRNA may cross-target different transcripts of proteins of the G1/S transition of the cell cycle; 5p/3p co-targeting was confirmed in stem-loop RT-PCR.Conclusion: The observed cross- and co-regulation by paired miRNA species suggests a fail-proof scheme of miRNA regulation in iPSC, which may be important to iPSC pluripotency.

Changes of Ovarian microRNA Profile in Long-Living Ames Dwarf Mice during Aging

“…Both the -5p and -3p arms of miR-21 were downregulated to a similar extent, which suggests regulation at the level of initial transcription of the miR-21 precursor. In fact, this same pattern of regulation was observed for other seven miRNAs (mmu-miR-29c, mmu-miR-296, mmu-miR-130b, mmu-miR-17, mmu-miR-434, mmu-miR-181c, mmu-miR-132), which further confirms the validity of our analysis and suggests miRNA regulation at the gene expression level [48]. Although it is found at much lower levels, it has been suggested that the 3p arm can also possess regulatory activity [49].…”

Unveiling MYCN regulatory networks in neuroblastoma via integrative analysis of heterogeneous genomics data

“…Interestingly, mir-1307 was differentially expressed under MYCN knockdown, but showed reversed regulation in the 5p/3p species. Although the reverse direction of 5p/3p coexpression has been reported in several studies [56, 57], the mechanism and biological significance of preferred arm selection remains unknown.…”

Lactic Acid Suppresses IL-33–Mediated Mast Cell Inflammatory Responses via Hypoxia-Inducible Factor-1α–Dependent miR-155 Suppression

“…Despite originating from the same transcribed pri-miRNA, it is not unusual for 3p and 5p strands from the same pri-miRNA to be expressed differently in mature form in response to different stimuli. By nature of being complimentary to one another, 3p and 5p strands can have very different targets, eliciting effects with negative or positive feedback on the degradation of these strands (50–52). Additionally, HIF-1α silencing restored miR-155-5p levels, indicating that in mast cells, HIF-1α negatively regulates miR-155-5p expression.…”