A highly expressed miR-101 isomiR is a functional silencing small RNA

Abstract

BackgroundMicroRNAs (miRNAs) are short non-coding regulatory RNAs that control gene expression usually producing translational repression and gene silencing. High-throughput sequencing technologies have revealed heterogeneity at length and sequence level for the majority of mature miRNAs (IsomiRs). Most isomiRs can be explained by variability in either Dicer1 or Drosha cleavage during miRNA biogenesis at 5’ or 3’ of the miRNA (trimming variants). Although isomiRs have been described in different tissues and organisms, their functional validation as modulators of gene expression remains elusive. Here we have characterized the expression and function of a highly abundant miR-101 5’-trimming variant (5’-isomiR-101).ResultsThe analysis of small RNA sequencing data in several human tissues and cell lines indicates that 5’-isomiR-101 is ubiquitously detected and a highly abundant, especially in the brain. 5’-isomiR-101 was found in Ago-2 immunocomplexes and complementary approaches showed that 5’-isomiR-101 interacted with different members of the silencing (RISC) complex. In addition, 5’-isomiR-101 decreased the expression of five validated miR-101 targets, suggesting that it is a functional variant. Both the binding to RISC members and the degree of silencing were less efficient for 5’-isomiR-101 compared with miR-101. For some targets, both miR-101 and 5’-isomiR-101 significantly decreased protein expression with no changes in the respective mRNA levels. Although a high number of overlapping predicted targets suggest similar targeted biological pathways, a correlation analysis of the expression profiles of miR-101 variants and predicted mRNA targets in human brains at different ages, suggest specific functions for miR-101- and 5’-isomiR-101.ConclusionsThese results suggest that isomiRs are functional variants and further indicate that for a given miRNA, the different isomiRs may contribute to the overall effect as quantitative and qualitative fine-tuners of gene expression.

Divergent target recognition by coexpressed 5′-isomiRs of miR-142-3p and selective viral mimicry

“…2A,B). This suggests that these 5-isomiRs represent distinct regulatory entities and is in stark contrast to other reports, which concluded that 5 ′ -isomiRs mostly share their targets (Cloonan et al 2011;Llorens et al 2013).…”

“…Thus, miR-223 5 ′ -isomiR expression appears to broaden the overall range of miR-223 targets. The prediction that 5 ′ -isomiR expression can impact miRNA target ranges is further supported by the confirmation of small sets of differentially regulated targets for an aberrant miR-307 5 ′ -isomiR in flies (Fukunaga et al 2012) and for transfected 5 ′ -isomiRs of miR-133a, miR-101, and miR-9 (Humphreys et al 2012;Llorens et al 2013;Tan et al 2014). On the other hand, it has been suggested that 5 ′ -isomiRs have highly overlapping targets (Cloonan et al 2011;Llorens et al 2013) and could therefore act redundantly, to increase the effective miRNA dosage or reduce offtarget effects (Cloonan et al 2011).…”

Construction of regulatory networks mediated by small RNAs responsive to abiotic stresses in rice (Oryza sativa)

“…The sequence variants of the miRNAs termed isomiRs were discovered in recent years (Guo et al, 2012;Li et al, 2012;Llorens et al, 2013). In animals, some of the isomiRs have been demonstrated to have biological roles (Cloonan et al, 2011).…”

IsomiRs: A New Approach to Cancer Study

“…Advanced research from NGS (next-generation sequencing) suggests isomiRs are multiple distinct mature miRNAs that arise from the same hairpin arm and 5' or 3' ends of their sequences and are different from canonical miRNAs in public databases such as miRBase (9). Moreover, recent studies have shown variation in cleavage site for DROSHA and DICER1 enzymes or even other miRNAs processing enzymes or posttranscriptional editing which lead to sequence modification in miRNAs (1) that are classified as "trimming variants" (10). Further evidences have shown there are another group of isomiRs that stem from Argonaute 2(AGO2) cleavage independent of Dicer.…”