TAS3-derived short-interfering RNAs confer cleavage of mRNAs in rice

Plant TRANS-ACTING SIRNA3 (TAS3)-derived short-interfering RNAs (siRNAs) include tasiR-ARFs, which are functionally conserved in targeting AUXIN RESPONSE FACTOR (ARF) genes, and a set of non-tasiR-ARF siRNAs, which have rarely been studied. In this study, TAS3 siRNAs were systematically characterized in rice (Oryza sative). Small RNA-seq results showed that an overwhelming majority of TAS3 siRNAs belong to the non-tasiR-ARF group, while tasiR-ARFs occupy a diminutive fraction. Phylogenetic analysis of TAS3 genes across dicot and monocot plants revealed that the siRNA-generating regions were highly conserved in grass species, especially in the oryzoideae. Target genes were identified for not only tasiR-ARFs but also non-tasiR-ARF siRNAs by analyzing rice degradome datasets, and some of these siRNA-target interactions were experimentally confirmed in rice tas3 mutants. Consistent with altered expression of target genes, phenotypic variations were observed for mutants in three TAS3 loci in comparison to wild-type rice. The regulatory role of ribosomes in the TAS3 siRNA-target interactions was further revealed by the fact that TAS3 siRNA-mediated target cleavage, in particular tasiR-ARFs targeting ARF2/3/14/15, occurred extensively in rice polysome samples. Altogether our study sheds new insights into TAS3 genes in plants and expand our knowledge about rice TAS3 siRNA-target interactions. 12 samples in total, 3 replicates for WT, tas3a1, tas3b1,tas3c1