Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances

Abstract

Summary Small RNAs are a class of non-coding RNAs that are of great importance in gene expression regulatory networks. Different families of small RNAs are generated via distinct biogenesis pathways. One such family specific to plants is that of phased, secondary siRNAs (phasiRNAs); these require RDR6, DCL4, and (typically) a microRNA (miRNA) trigger for their biogenesis. Protein-encoding genes are an important source of phasi-RNAs. The model legume Medicago truncatula generates phasiRNAs from many PHAS loci, and we aimed to investigate their biogenesis and mechanism by which miRNAs trigger these molecules. We modulated miRNA abundances in transgenic tissues showing that the abundance of phasiRNAs correlates with the levels of both miRNA triggers and the target, precursor transcripts. We identified sets of phasiRNAs or PHAS loci that predominantly and substantially increase in response to miRNA overexpression. In the process of validating targets from miRNA overexpression tissues, we found that in the miRNA-mRNA target pairing, the 3′ terminal nucleotide (the 22nd position), but not the 10th position, is important for phasiRNA production. Mutating the single 3′ terminal nucleotide dramatically diminishes phasiRNA production. Ectopic expression of Medicago NB-LRR-targeting miRNAs in Arabidopsis showed that only a few NB-LRRs are capable of phasiRNA production; our data indicate that this might be due to target inaccessibility determined by sequences flanking target sites. Our results suggest that target accessibility is an important component in miRNA-target interactions that could be utilized in target prediction, and the evolution of mRNA sequences flanking miRNA-target sites may be impacted. Significance Statement We investigated phasiRNA biogenesis in Medicago by bidirectional modulation or ectopic expression of five miRNA triggers, and our work illustrates mechanistic aspects of how miRNAs trigger phasiRNA production from protein-coding transcripts, especially NB-LRRs. Our work demonstrates that a variety of factors that affect phasiRNA production, and we provide new insights into miRNA-target interactions in plants.