Nuclear and cytoplasmic RNA exosomes and PELOTA1 prevent miRNA-induced secondary siRNA production in Arabidopsis

Abstract Amplification of short interfering RNA (siRNAs) via RNA-dependent RNA polymerases (RdRPs) is of fundamental importance in RNA silencing. Plant microRNA (miRNA) action generally does not involve engagement of RdRPs, in part thanks to a poorly understood activity of the cytoplasmic exosome ad...

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Bibliographic Details
Published in:Nucleic acids research 2022-02, Vol.50 (3), p.1396-1415
Main Authors: Vigh, Maria L, Bressendorff, Simon, Thieffry, Axel, Arribas-Hernández, Laura, Brodersen, Peter
Format: Article
Language:English
Subjects:
Arabidopsis - genetics
Arabidopsis - metabolism
Exosome Multienzyme Ribonuclease Complex - genetics
Gene regulation, Chromatin and Epigenetics
MicroRNAs - genetics
RNA Interference
RNA, Double-Stranded
RNA, Small Interfering - genetics
RNA-Induced Silencing Complex - metabolism
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Summary:Abstract Amplification of short interfering RNA (siRNAs) via RNA-dependent RNA polymerases (RdRPs) is of fundamental importance in RNA silencing. Plant microRNA (miRNA) action generally does not involve engagement of RdRPs, in part thanks to a poorly understood activity of the cytoplasmic exosome adaptor SKI2. Here, we show that inactivation of the exosome subunit RRP45B and SKI2 results in similar patterns of miRNA-induced siRNA production. Furthermore, loss of the nuclear exosome adaptor HEN2 leads to secondary siRNA production from miRNA targets largely distinct from those producing siRNAs in ski2. Importantly, mutation of the Release Factor paralogue PELOTA1 required for subunit dissociation of stalled ribosomes causes siRNA production from miRNA targets overlapping with, but distinct from, those affected in ski2 and rrp45b mutants. We also show that in exosome mutants, miRNA targets can be sorted into producers and non-producers of illicit secondary siRNAs based on trigger miRNA levels and miRNA:target affinity rather than on presence of 5′-cleavage fragments. We propose that stalled RNA-Induced Silencing Complex (RISC) and ribosomes, but not mRNA cleavage fragments released from RISC, trigger siRNA production, and that the exosome limits siRNA amplification by reducing RISC dwell time on miRNA target mRNAs while PELOTA1 does so by reducing ribosome stalling.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkab1289