Biogenesis of diverse plant phasiRNAs involves an miRNA-trigger and Dicer-processing

Abstract

It has been almost 30 years since RNA interference (RNAi) was shown to silence genes via double-stranded RNAs (dsRNAs) in Caenorhabditis elegans (Fire et al. 1998). 20-30-nucleotide (nt) small non-coding RNAs are a key element of the RNAi machinery. Recently, phased small interfering RNAs (phasiRNAs), small RNAs that are generated from a long RNA precursor at intervals of 21 to 26-nt, have been identified in plants and animals. In Drosophila, phasiRNAs are generated by the endonuclease, Zucchini (Zuc), in germlines. These phasiRNAs, known as one of PIWI-interacting RNAs (piRNAs), mainly repress transposable elements. Similarly, reproduction-specific phasiRNAs have been identified in the family Poaceae, although DICER LIKE (DCL) protein-dependent phasiRNA biogenesis in rice is distinct from piRNA biogenesis in animals. In plants, phasiRNA biogenesis is initiated when 22-nt microRNAs (miRNAs) cleave single-stranded target RNAs. Subsequently, RNA-dependent RNA polymerase (RDR) forms dsRNAs from the cleaved RNAs, and dsRNAs are further processed by DCLs into 21 to 24-nt phasiRNAs. Finally, the phasiRNAs are loaded to ARGONAUTE (AGO) proteins to induce RNA-silencing. There are diverse types of phasiRNA precursors and the miRNAs that trigger the biogenesis. Their expression patterns also differ among plant species, suggesting that species-specific combinations of these triggers dictate the spatio-temporal pattern of phasiRNA biogenesis during development, or in response to environmental stimuli.

Keywords: 22-nt miRNAs; ARGONAUTE; DCL-processing; Reproduction; phasiRNAs; tasiRNAs.

Fig. 1

A model for phasi/tasiRNA biogenesis in gymnosperms, dicots, and monocots. In plant phasi/tasiRNA biogenesis, (1) phasiRNA precursor transcripts are cleaved by 22-nt miRNA, (2) (RDR)-dependent dsRNAs are synthesized, (3) DCL-dependent processing results in phasiRNAs and (4) their loading onto AGO proteins. The phasiRNA pathway is conserved in gymnosperms, dicots, and monocots. In gymnosperms, there are miR482/miR2118-triggered phasiRNAs derived from both coding-RNAs (NB-LRRs, etc.) and non-coding RNAs (reproductive lincRNAs). The phasiRNA pathway, involving miR482/miR2118-triggered coding-RNAs (NB-LRRs), is also conserved in dicots. In contrast, miR482/miR2118-triggered phasiRNAs generated from reproductive lincRNAs are conserved in monocots