In addition, the intracellular localization of virus/host mRNAs and miRNAs, the extent of base pairing complementarity of the competitive RNAs, as well as the time-course of viral RNA expression may also impact ceRNA networks.
In contrast to nucleic acids, which associate according to the rules of base pair complementarity, the intricacies of protein structure do not – normally – allow for an easy mechanism of replication, which presumably explains the evolution of a coded system for their synthesis (for an interesting discussion of the contrasting molecular requirements for replication and catalysis, see [ 12]).
miRNAs function by targeting the 3′ untranslated region (3′UTR) of mRNA with base pair complementarity.
In addition, variations in miRNA response elements (e.g. the seed region of pairing) of viral RNA which inevitably affect base pair complementarity, could thereby influence the interactions between viral and host RNAs.
In a small number of instances, the nine base pair complementarity criteria for target prediction was relaxed somewhat for these double guide sRNAs by allowing G U base pairs and/or a single nucleotide mismatch base pair in the region of complementarity.
These methods search for base pair complementarity between the mature miRNA and 3′-untranslated regions of all mRNAs, allowing for some mismatches (the penalty for mismatches differs between the methods).
These miRNAs bind at their potential target sites within a wide band of energies, bounded on one side by the energy score at perfect WC base pair complementarity and on the other by the score associated with the minimal extent of interaction we consider (e.g. only the seed regions).
The two microsatellites overlap with the miRNA gene of MSHORT1 and could have created a stable hairpin due to base pair complementarity.
The miRNA binds to complementary sequences within the 3′ mRNA tails, although usually only with partial base pair complementarity.
Based on the knowledge that miRNAs control their targets through base pair complementarity, antisense oligonucleotides (ASOs) have been developed to inhibit miRNA function.
