Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis

Abstract

Small RNAs are central players in RNA silencing, yet their cytoplasmic compartmentalization and the effects it may have on their activities have not been studied at the genomic scale. Here we report that Arabidopsis microRNAs (miRNAs) and small interfering RNAs (siRNAs) are distinctly partitioned between the endoplasmic reticulum (ER) and cytosol. All miRNAs are associated with membrane-bound polysomes (MBPs) as opposed to polysomes in general. The MBP association is functionally linked to a deeply conserved and tightly regulated activity of miRNAs – production of phased siRNAs (phasiRNAs) from select target RNAs. The phasiRNA precursor RNAs, thought to be noncoding, are on MBPs and are occupied by ribosomes in a manner that supports miRNA-triggered phasiRNA production, suggesting that ribosomes on the rough ER impact siRNA biogenesis. This study reveals global patterns of cytoplasmic partitioning of small RNAs and expands the known functions of ribosomes and ER.DOI: http://dx.doi.org/10.7554/eLife.22750.001

Polysomes, Stress Granules, and Processing Bodies: A Dynamic Triumvirate Controlling Cytoplasmic mRNA Fate and Function

“…Notably, MBP association of AtAGO1 is required for miRNA-triggered production of phased secondary small interfering RNAs (phasiRNAs) from select RNAs (e.g. TRANS-ACTING SIRNA [TAS] transcripts; Li et al, 2016). This is corroborated by the presence of two proteins required for phasiRNA biogenesis, SUPPRESSOR OF GENE SILENCING3 (SGS3) and RNA-DEPENDENT RNA POLYMERASE6, in specific granules called siRNA bodies that reside on the cytoplasmic side of membrane compartments (Jouannet et al, 2012).…”

The ‘how’ and ‘where’ of plant microRNAs

“…Mutants of MOS2 and Elongator subunits have a reduced number of dicing bodies, whereas those of PINP1 , NOT2 and DBR1 have more dicing bodies than the wild-type; thus, opposite effects are observed, although all of the above mutants have compromised miRNA levels (Wang et al ., 2013; X. Wu et al ., 2013; Fang et al ., 2015; Qiao et al ., 2015; Z. Li et al ., 2016).…”

“…Thus, sequence complementarity is not the factor that dictates the mode of action in which plant miRNAs engage. Emerging findings of miRNA target transcripts bound by ribosomes or ribosomes on the endoplasmic reticulum (ER) (Hou et al ., 2016; S. Li et al ., 2016; Yu et al ., 2016) imply that translation inhibition may occur at a larger number of miRNA targets than expected.…”

Arabidopsis ALA1 and ALA2 Mediate RNAi-Based Antiviral Immunity

“…miRNA-guided cleavage can also occur on ER membrane-bound polysomes (Li et al, 2016). These studies take ER into a central stage of small RNAs-mediated silencing (Ma et al, 2013; Li et al, 2016).…”

“…miRNA-guided cleavage can also occur on ER membrane-bound polysomes (Li et al, 2016). These studies take ER into a central stage of small RNAs-mediated silencing (Ma et al, 2013; Li et al, 2016). On the other hand, viruses recruit ER membrane and manipulate lipid synthesis, transport and metabolism to form a circumstance essential for viral replication and morphogenesis (Fernández de Castro et al, 2016).…”