The most important requirement for microRNA base pairing with an mRNA target in animal cells is a continuous and perfect complementarity of microRNA nucleotides 2 8, known as the seed region, to the 3' UTR of the target mRNA [19].
In plants, perfect complementarity of miRNAs to their target mRNAs is required to regulate gene expression.
However, considering the perfect complementarity of hairpins in the two miRNAs and low frequency of strand-specific tags especially for hsa-mir-625, it is difficult to assume these two miRNAs as an ideal case of anti-sense miRNA.
In metazoan, the situation is more complex since a perfect complementarity is not necessary for a miRNA to recognize its targets.
Although perfect complementarity is not necessary for effective silencing of expression in animal, specific pattern of seed sequence complementarity have been reported to be effective on the basis of experimentation and prediction.
While supplementary base-pairing outside the 5′ seed has been noted before, to our knowledge, this is the first time that a requirement for supplementary pairing has been shown for target repression even when perfect complementarity in the canonical 5′ seed exists.
The biogenesis of miRNAs in plants is a multi-step enzymatic process involving incorporation of miRNAs into the RNA-induced silencing complex (RISC), and then miRNAs bind target mRNAs to direct for cleavage miRNAs with near perfect complementarity and/or inhibiting translation of those with lower complementarity [ 4- 7].
Pioneering studies in the nematode Caenorhabditis elegans showed that perfect complementarity between miRNAs and their targets is not necessary for silencing (Lee et al., 1993; Wightman et al., 1993).
The most stable combinations of miRNA and the target gene or MIRNA genes were normalized to percent minimum free energy which works well for plant miRNAs because plants possess near perfect complementarity between miRNA and target genes [65], [115].
RNAcofold was included here because it considers intramolecular base pairs resulting in lower energies for sequences that are further away from perfect complementarity.
