Concordant and Discordant Regulation of Target Genes by miR-31 and Its Isoforms

Abstract

It has been shown that imprecise cleavage of a primary or precursor RNA by Drosha or Dicer, respectively, may yield a group of microRNA (miRNA) variants designated as “isomiR”. Variations in the relative abundance of isoforms for a given miRNA among different species and different cell types beg the question whether these isomiRs might regulate target genes differentially. We compared the capacity of three miR-31 isoforms (miR-31-H, miR-31-P, and miR-31-M), which differ only slightly in their 5′- and/or 3′-end sequences, to regulate several known targets and a predicted target, Dicer. Notably, we found isomiR-31s displayed concordant and discordant regulation of 6 known target genes. Furthermore, we validated a predicted target gene, Dicer, to be a novel target of miR-31 but only miR-31-P could directly repress Dicer expression in both MCF-7 breast cancer cells and A549 lung cancer cells, resulting in their enhanced sensitivity to cisplatin, a known attribute of Dicer knockdown. This was further supported by reporter assay using full length 3′-untranslated region (UTR) of Dicer. Our findings not only revealed Dicer to be a direct target of miR-31, but also demonstrated that isomiRs displayed similar and disparate regulation of target genes in cell-based systems. Coupled with the variations in the distribution of isomiRs among different cells or conditions, our findings support the possibility of fine-tuning gene expression by miRNAs.

Regulation of Huntingtin Gene Expression by miRNA-137, -214, -148a, and Their Respective isomiRs

“…Specifically, targets for the canonical miRNAs were compared with the targets of the miRNAs with seed regions shifted by −1, +1, and +2 nt. This analysis revealed that the number of predicted targets changed, but apart from unique targets, many genes were still predicted as targets for both miRNAs and isomiRs, confirming that isomiRs might share certain common mRNA targets but not all mRNA targets [36]. These results are also consistent with the suggestion that isomiRs function cooperatively to target common biological pathways [30].…”

“…Specifically, one variant of miR-101 [35] and two isomiRs of miR-133 [31] and miR-31 [36] have been investigated. In these reports, the isomiRs were less effective than their canonical analogs [35] or exhibited differences in effectiveness depending on the regulated target [31].…”

“…Differential mRNA targeting was demonstrated in the case of two prevalent 5′ isomiRs of the key cardiac regulator miR-133a [31]. Three miR-31 isoforms that differed only slightly in their 5′- and/or 3′-end sequences were compared (namely, hsa-miR-31, ptr-miR-31, and mmu-miR-31), implicating isomiR-31s in the concordant and discordant regulation of six known target genes [36]. …”

IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies

“…File 10), which in turn suggests that in addition to the miRBase reference the isomiR variants can also be functionally active. One possible implication of this observation could be that the different isomiRs from the same precursor arm can work cooperatively to repress target genes or that they have slightly different targeting profiles that permit an increased diversity of the targeted transcripts [10, 20-22]. …”

Distinctive Profile of IsomiR Expression and Novel MicroRNAs in Rat Heart Left Ventricle

“…The distribution of isomiRs indicates that they are not randomly generated, and may have (patho)physiological importance [56]–[58]. Indeed, specific isomiRs have been shown to be functional and to have target gene repertoires that differ from those of their corresponding canonical miRNAs [59], [60]. Recent data suggests the possibility of isomiR-specific gene targeting in the heart [61], [62].…”