IsomiR expression patterns in canonical and Dicer‑independent microRNAs

Abstract

Multiple microRNA (miRNA) variants, known as isomiRs, are extensively distributed in miRNA loci and predominantly derive from the alternative cleavage of Drosha/Dicer and 3'addition events. The present study aimed to investigate the expression patterns of multiple isomiRs in typical miRNA and Dicer‑independent miRNA loci by conducting evolutionary and expression analysis using public datasets. Although different miRNA maturation processes exist, multiple isomiRs can be detected by similar expression distributions. However, isomiR expression in Dicer‑independent miRNA loci tends to be at a moderate level, particularly for random distribution in the ends that are split by Dicer in the typical miRNA loci. Compared with the mature miRNA locus (dominant miRNA locus), the non‑dominant miRNA locus indicates an expression distribution similar to that of the Dicer‑independent miRNA locus. These results increase the understanding of multiple isomiRs in the progression of diseases.

Figure 1.

An example of multiple isomiRs and their expression patterns. Percentages (%) indicate the percentage of a certain isomiR compared with all detected isomiRs in the miRNA locus. (A) Hsa-mir-30a yields miR-30a-5p and miR-30a-3p with a series of multiple isomiRs via cleavage of Drosha and Dicer. Of these, miR-30a-5p is designated as the mature miRNA, whereas miR-30a-3p was termed the miRNA* sequence. (A-1) Red arrows indicate the annotated canonical miR-30a-3p sequence in the miRBase database, whereas the canonical miR-30a-5p sequence is not dominantly expressed. Only dominantly expressed isomiRs are presented here. Expression patterns from the two miRNA loci are presented in (A-2) and (A-3) using samples of breast cancer. (A-2) Expression distribution of two isomiRs in miR-30a-5p; and (A-3) the expression distribution of three isomiRs in miR-30a-3p. In the miR-30a-5p locus, two dominant isomiRs were identified (>5% in the locus), and four dominant isomiRs were detected in the miR-30a-3p locus. The Y axes in Fig. A-2 and A-3 indicate the expression of relevant isomiR sequences in Fig. A-1. (B) Expression patterns were identified for these dominantly expressed isomiRs using tumor and normal samples with the same sample sizes (n=87). Compared with the expression in (A) in different sample sizes, the expression patterns were considered to be similar. miRNA, microRNAs; BC, breast cancer.

Figure 2.

Phylogenetic trees of Drosha and Dicer. Similar phylogenetic associations are detected based on Drosha and Dicer sequences. hsa, Homo sapiens; ssc, Sus scrofa; mmu, Mus musculus; aca, Anolis carolinensis; gga, Gallus gallus; tgu, Taeniopygia guttata; xtr, Xenopus tropicalis; dre, Danio rerio; NJ, neighbor-joining.

Figure 3.

Multiple isomiRs in miR-451 and variations across different samples. Percentage (%) in the Y-axis indicates the percentage of a certain isomiR compared with all detected isomiRs in the miRNA locus. (A) hsa-miR-451 was identified to undergo Dicer-independent maturation. A similar phenomenon for multiple isomiRs was detected in the miRNA locus. (B) Box plots based on relative expression of isomiRs. According to the most, second and third dominantly expressed isomiRs, isomiRs have a larger degree of variation in tumor samples than normal samples. Compared with miR-30a-5p, the miR-451 locus indicates a moderate level of isomiR expression, which typically involves higher degree of variation in different samples. miR, microRNAs; BC, breast cancer.

Figure 4.

Expression patterns of multiple isomiRs in different miRNA loci and samples. Percentage (%) in the Y-axis indicates the percentage of a specific isomiR compared with all detected isomiRs in the miRNA locus and the X-axis indicates the isomiR types. A total of three miRNA genes, including miR-21, miR-30a and miR-30e, were selected and analyzed due to the fact that miR-#-5p and miR-#-3p were abundantly expressed. Of these, miR-30e-5p was not dominantly expressed (however another strand of miR-30e-3p was upregulated), and miR-451 was also rarely expressed in PRAD and normal samples. Lower expression levels influence the expression pattern of isomiRs. miRNA/miR, microRNA; PRAD, prostate adenocarcinoma; NT, Normal, Matched Tumor; THCA, thyroid carcinoma; TN, Tumor, Matched Normal.

Figure 5.

Variations in isomiRs across different samples using equal sample sizes (n=87). Percentage (%) in the Y-axis indicates the percentage of a specific isomiR compared with all detected isomiRs in the miRNA locus. miR, microRNA; BC, breast cancer.