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Abstract
Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their
targets. This is consistent with their primary mode of action being cleavage of target
mRNAs, similar to that induced by perfectly complementary small interfering RNAs (siRNAs).
However, there are natural targets with up to five mismatches. Furthermore, artificial
siRNAs can have substantial effects on so-called off-targets, to which they have only
limited complementarity. By analyzing the transcriptome of plants overexpressing different
miRNAs, we have deduced a set of empirical parameters for target recognition. Compared
to artificial siRNAs, authentic plant miRNAs appear to have much higher specificity,
which may reflect their coevolution with the remainder of the transcriptome. We also
demonstrate that miR172, previously thought to act primarily by translational repression,
can efficiently guide mRNA cleavage, although the effects on steady-state levels of
target transcripts are obscured by strong feedback regulation. This finding unifies
the view of plant miRNA action.