In plants, the known microRNAs (miRNAs) are produced as ∼21 nucleotide (nt) duplexes from their precursors by Dicer-like 1 (DCL1). They are incorporated into Argonaute 1 (AGO1) protein to regulate target gene expression primarily through mRNA cleavage. We report here the discovery of a class of miRNAs in the model monocot rice (Oryza sativa). These are 24 nt in length and require another member of the Dicer family, DCL3, for their biogenesis. The 24 nt long miRNAs (lmiRNAs) are loaded into AGO4 clade proteins according to hierarchical rules, depending on the upstream biogenesis machinery and the 5′-terminal nucleotide. We demonstrated that lmiRNAs direct DNA methylation at loci from which they are produced as well as in trans at their target genes and play roles in gene regulation. Considered together, our findings define a miRNA pathway that mediates DNA methylation.
Highlights
► There are DCL3-dependent 24 nt long miRNAs (lmiRNAs) in rice ► LmiRNAs are sorted into AGO4 clade proteins ► MicroRNA sorting depends on the biogenesis machinery and the 5′ end nucleotide ► LmiRNAs direct target DNA methylation and play roles in gene regulation
