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Ribosome stalling and SGS3 phase separation prime the epigenetic silencing of transposons

Abstract

Transposable elements (TEs, transposons) are mobile DNAs that can cause fatal mutations1. To suppress their activity, host genomes deploy small interfering RNAs (siRNAs) that trigger and maintain their epigenetic silencing2,3. Whereas 24-nucleotide (nt) siRNAs mediate RNA-directed DNA methylation (RdDM) to reinforce the silent state of TEs3, activated or naive TEs give rise to 21- or 22-nt siRNAs by the RNA-DEPENDENT RNA POLYMERASE 6 (RDR6)-mediated pathway, triggering both RNAi and de novo DNA methylation4,5. This process, which is called RDR6–RdDM, is critical for the initiation of epigenetic silencing of active TEs; however, their specific recognition and the selective processing of siRNAs remain elusive. Here, we suggest that plant transposon RNAs undergo frequent ribosome stalling caused by their unfavourable codon usage. Ribosome stalling subsequently induces RNA truncation and localization to cytoplasmic siRNA bodies, both of which are essential prerequisites for RDR6 targeting6,7. In addition, SUPPRESSOR OF GENE SILENCING 3 (SGS3), the RDR6-interacting protein7, exhibits phase separation both in vitro and in vivo through its prion-like domains, implicating the role of liquid–liquid phase separation in siRNA body formation. Our study provides insight into the host recognition of active TEs, which is important for the maintenance of genome integrity.

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Fig. 1: Reduced translational efficiency of transposons.
Fig. 2: RNA truncation caused by translation inhibition.
Fig. 3: LLPS of SGS3.
Fig. 4: Localization of transposon RNAs to cytoplasmic RGs.

Data availability

The next-generation sequencing data generated in this study are deposited in the SRA repository under PRJNA598331 and summarized in Supplementary Table 2. Public data sets used in this study include PRJNA298638 (rice TRAP-seq)13, SRP043448 (rice small RNA-seq)15 and GSE52952 (Arabidopsis small RNA-seq and degradome-seq)17. The unprocessed raw images for Fig. 3 and Supplementary Fig. 10 are deposited in Figshare (https://doi.org/10.6084/m9.figshare.13627949.v3). Source data are provided with this paper.

Code availability

The custom codes used in this study are deposited in GitHub (https://github.com/JungnamChoLab/CodonOptimality).

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Acknowledgements

We thank Y. He from the Core Facility Centre, CAS Centre for Excellence in Molecular Plant Sciences for technical support with confocal microscopy. Z. He (CAS Centre for Excellence in Molecular Plant Sciences) kindly provided the anti-SGS3 antibody. E.Y.K. is the recipient of a President’s International Fellowship Initiative (PIFI) young staff fellowship (No. 2021FYB0001) from CAS. This work was supported by the Strategic Priority Research Programme of the Chinese Academy of Sciences (grant no. XDB27030209) and the National Natural Science Foundation of China (grant no. 31970518) granted to J.C.

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J.C. conceived the idea and designed the experiments. E.Y.K., Z.L., H.L. and W.F. conducted the experiments. E.Y.K., L.W. and J.C. analysed the data. E.Y.K., L.W. and J.C. drafted the manuscript. J.C. edited and revised the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Jungnam Cho.

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Peer review information Nature Plants thanks Damon Lisch and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–15, Tables 1 and 2, and blots for Supplementary Fig. 11.

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Supplementary Video 1.

Raw video image of Fig. 3d.

Supplementary Video 2.

Raw video image of Fig. 3e.

Supplementary Data 1.

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Source Data Fig. 1.

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Source Data Fig. 2.

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Source Data Fig. 3.

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Kim, E.Y., Wang, L., Lei, Z. et al. Ribosome stalling and SGS3 phase separation prime the epigenetic silencing of transposons. Nat. Plants 7, 303–309 (2021). https://doi.org/10.1038/s41477-021-00867-4

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