Competing endogenous RNAs in microRNA regulation
As described in the previous section, a single mRNA can contain binding sites for multiple miRNAs. Similarly, a single miRNA can target multiple mRNAs. However, a set of non-coding transcripts that possess miRNA response elements (MREs) similar to target mRNA, bind to the miRNAs and prevent them from acting on target mRNA.108 These non-coding transcripts control the amount of miRNA available for target mRNA, thereby indirectly modulating the target protein expression. RNA transcripts that share a binding site for the same miRNA and regulates each other’s expression by competing for that miRNA are called competing RNAs or ceRNAs. These ceRNAs are present in various forms such as long coding RNAs, circular RNAs, pseudogenes or they could also be protein-coding mRNAs.10 CeRNAs provides an additional layer of complexity to the miRNA mediated gene regulation. Experimental studies indicate that they have major implications in diseases like cancer.109–111 For example, PTENP1 is a pseudogene for PTEN and they share similar MREs in the 3’UTR region. PTENP1 captures miRNAs targeting PTEN and helps in its function as a tumor suppressor. PTENP1 is found to be deleted in various cancers and overexpression of PTENP1 resulted in increased PTEN expression and induced growth inhibition by sequestering the miRNAs.111–113 Several non-coding transcripts that regulate PTEN are found to be expressed in a correlated manner in colon cancer cells, where PTEN expression or copy number is altered.112
Philip et al114 created artificial miRNA sponges with multiple binding sites for miR-20a and found that the addition of miR-20a sponges significantly alters the miR-20a target gene expression.114 Studies also suggest that miRNA activity does not depend on its levels, but the relative abundance of target sites can appreciably influence its activity.9,115–117 However, the ceRNA hypothesis remains controversial because miRNA target sites are usually present in abundance, and alteration in the level of one target mRNA might not considerably affect other miRNA target’s expression level.115,116 Boson et al117quantified the concentration of endogenous target and miRNAs using biochemical techniques such as mRNA-seq, small RNA- ]seq, and iCLIP in mouse cell lines to calculate miRNA: target ratio. They essentially investigated how modulating the ratio using ceRNAs of varying affinity affects miRNA binding.117 They have shown that ceRNAs with high affinity than the target can derepress the miRNA targets only for miRNA families with low miRNA: target ratio. If the miRNA: target ratio is high or the ceRNA affinity is low, then there is no noteworthy effect of ceRNA regulation on the target. They proposed a simple target competition model with hierarchical affinity for targets, which predicts that miRNA: target ratio determines the susceptibility to ceRNA competition at identical level of high affinity ceRNA overexpression.117 However, this aspect of miRNA regulation has to be investigated in a much-detailed manner using theoretical or computational modeling.