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The efficacy of gene silencing by plant microRNAs (miRNAs) is generally assumed to be predominantly determined by their abundance. In Arabidopsis the highly abundant miRNA, miR159, acts as a molecular “switch” in vegetative tissues completely silencing the expression of two  GAMYB-like  genes,  MYB33  and  MYB65 . Here, we show that miR159 has a diminished silencing efficacy in the seed. Using reporter gene constructs, we determined that  MIR159  and  MYB33  are co-transcribed in the aleurone and embryo of germinating seeds. However in contrast to vegetative tissues,  MYB33  is not completely silenced. Instead, miR159 appears to shape the spatio-temporal expression pattern of MYB33 during seed germination. Transcript profiling in a time course during seed germination in wild-type and a  mir159  mutant in which miR159 is almost absent, revealed that transcript levels of the  GAMYB-like  genes were similar between these two genotypes during germination, but much higher in the  mir159  mutant once germination had completed. This attenuation in the silencing of the  GAMYB-like  genes was not explained by a decrease in mature miR159 levels, which remained constant at all time points during seed germination. We propose that miR159 acts as a tuner of  GAMYB-like  levels in Arabidopsis germinating seeds and that the activity of this miRNA is attenuated in the seed compared to vegetative tissues. This implies that the efficacy of miRNA-mediated silencing is not solely determined by miRNA abundance and target transcript levels, but is being determined through additional mechanisms.

MicroRNA159 Can Act as a Switch or Tuning MicroRNA Independently of Its Abundance in Arabidopsis