Base-pairing between miRNA and mRNA leads to translational repression or mRNA degradation [2].
Base complementarity between miRNA and mRNA influences the final outcome of the repression (fig. 1 d), in which a perfect base pairing results in target degradation, whereas imperfect base pairing yields sequestration of a target (Bartel 2009).
Using the experimentally validated miRNA targets listed in TarBase, genes involved in mRNA degradation show more negative correlations between miRNA and mRNA expression profiles, comparing with genes involved in translational repression.
Although the binding event behind the translational repression and mRNA degradation is driven primarily by complementarity between miRNA and target sites, computationally predicted target interactions generally generate a large list of targets.
In fact, notwithstanding almost perfect complementarity between miRNA and its target sequence in plants, it has been demonstrated that likewise in animals, non-cleaving repression is a possible mechanism also in the plant kingdom [ 63].
In contrast, when base pairing between miRNA and target mRNA is imperfect, the interaction of the miRNP complex with the target mRNA results in translation repression (Doench et al, 2003).
Additionally, Liang et al. found global correlation between miRNA repression and protein-protein interactions and elucidated the related biological processes of miRNA-regulated PINs [ 18].
Correlations between miRNA and mRNA.
The miRNAs with a single MRE in pRL-VEGF-Con1 and/or pRL-VEGF-Con2 (Table S3) were selected to investigate the relationship between miRNA repression efficiency and the secondary structure of miRNA MRE duplexes.
Since the interaction between miRNAs and viral RNAs also inevitably leads to repression of viral RNA function, we speculate that virus may evolve either to employ cvhRNA networks or to avoid miRNA targeting for optimal fitness within the host.
In contrast, there is very high complementarity between miRNAs and their target mRNAs in plants and the repression of gene expression occurs primarily through the cleavage of mRNA targets (reviewed by [ 12]).
