Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

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.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

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).

References

  1. Slotkin, R. K. & Martienssen, R. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8, 272–285 (2007).

    Article  CAS  PubMed  Google Scholar 

  2. Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461–472 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Borges, F. & Martienssen, R. A. The expanding world of small RNAs in plants. Nat. Rev. Mol. Cell Biol. 16, 727–741 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Fultz, D., Choudury, S. G. & Slotkin, R. K. Silencing of active transposable elements in plants. Curr. Opin. Plant Biol. 27, 67–76 (2015).

    Article  CAS  PubMed  Google Scholar 

  5. Cho, J. Transposon-derived non-coding RNAs and their function in plants. Front. Plant Sci. 9, 600 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Baeg, K., Iwakawa, H. O. & Tomari, Y. The poly(A) tail blocks RDR6 from converting self mRNAs into substrates for gene silencing. Nat. Plants 3, 17036 (2017).

    Article  PubMed  Google Scholar 

  7. Kumakura, N. et al. SGS3 and RDR6 interact and colocalize in cytoplasmic SGS3/RDR6-bodies. FEBS Lett. https://doi.org/10.1016/j.febslet.2009.03.055 (2009).

  8. Catoni, M. et al. DNA sequence properties that predict susceptibility to epiallelic switching. EMBO J. 36, 617–628 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Tatarinova, T., Elhaik, E. & Pellegrini, M. Cross-species analysis of genic GC3 content and DNA methylation patterns. Genome Biol. Evol. 5, 1443–1456 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Luo, Z. & Chen, Z. Improperly terminated, unpolyadenylated mRNA of sense transgenes is targeted by RDR6-mediated RNA silencing in Arabidopsis. Plant Cell 19, 943–958 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Szádeczky-Kardoss, I., Gál, L., Auber, A., Taller, J. & Silhavy, D. The No-go decay system degrades plant mRNAs that contain a long A-stretch in the coding region. Plant Sci. 275, 19–27 (2018).

    Article  PubMed  Google Scholar 

  12. Yang, F. et al. The RNA surveillance complex Pelo-Hbs1 is required for transposon silencing in the Drosophila germline. EMBO Rep. 16, 965–974 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zhao, D. et al. Analysis of ribosome-associated mRNAs in rice reveals the importance of transcript size and GC content in translation. G3 (Bethesda) 7, 203–219 (2017).

    Article  CAS  PubMed  Google Scholar 

  14. Vongs, A., Kakutani, T., Martienssen, R. A. & Richards, E. J. Arabidopsis thaliana DNA methylation mutants. Science 260, 1926–1928 (1993).

    Article  CAS  PubMed  Google Scholar 

  15. Hu, L. et al. Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proc. Natl Acad. Sci. USA 111, 10642–10647 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Hou, C. Y. et al. Global analysis of truncated RNA ends reveals new insights into ribosome stalling in plants. Plant Cell 28, 2398–2416 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Creasey, K. M. et al. MiRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature 508, 411–415 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Ikeuchi, K. et al. Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways. EMBO J. 38, e100276 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  19. McCue, A. D., Nuthikattu, S., Reeder, S. H. & Slotkin, R. K. Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. PLoS Genet. 8, e1002474 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Jouannet, V. et al. Cytoplasmic Arabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for ta-siRNA biogenesis. EMBO J. 31, 1704–1713 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Chantarachot, T. & Bailey-Serres, J. Polysomes, stress granules, and processing bodies: a dynamic triumvirate controlling cytoplasmic mRNA fate and function. Plant Physiol. 176, 254–269 (2018).

    Article  CAS  PubMed  Google Scholar 

  22. Wang, J. et al. A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 174, 688–699 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Maharana, S. et al. RNA buffers the phase separation behavior of prion-like RNA binding proteins. Science https://doi.org/10.1126/science.aar7366 (2018).

  24. Wheeler, J. R. et al. The stress granule transcriptome reveals principles of mRNA accumulation in stress granules. Mol. Cell 68, 808–820 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  25. Namkoong, S., Ho, A., Woo, Y. M., Kwak, H. & Lee, J. H. Systematic characterization of stress-induced RNA granulation. Mol. Cell https://doi.org/10.1016/j.molcel.2018.02.025 (2018).

  26. Jain, S. et al. ATPase-modulated stress granules contain a diverse proteome and substructure. Cell 164, 487–498 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Schwach, F., Vaistij, F. E., Jones, L. & Baulcombe, D. C. An RNA-dependent RNA polymerase prevents meristem invasion by potato virus X and is required for the activity but not the production of a systemic silencing signal. Plant Physiol. 138, 1842–1852 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Sidorenko, L. V. et al. GC-rich coding sequences reduce transposon-like, small RNA-mediated transgene silencing. Nat. Plants 3, 875–884 (2017).

    Article  CAS  PubMed  Google Scholar 

  29. Hu, S. et al. SAMHD1 Inhibits LINE-1 retrotransposition by promoting stress granule formation. PLoS Genet. 11, e1005367 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  30. Ahl, V., Keller, H., Schmidt, S. & Weichenrieder, O. Retrotransposition and crystal structure of an Alu RNP in the ribosome-stalling conformation. Mol. Cell 60, 715–727 (2015).

    Article  CAS  PubMed  Google Scholar 

  31. Li, Z. et al. The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements. Genome Biol. https://doi.org/10.1186/s13059-019-1746-8 (2019).

  32. Sanchez, D. H. & Paszkowski, J. Heat-induced release of epigenetic silencing reveals the concealed role of an imprinted plant gene. PLoS Genet. https://doi.org/10.1371/journal.pgen.1004806 (2014).

  33. Yoo, S. D., Cho, Y. H. & Sheen, J. Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat. Protoc. 2, 1565–1572 (2007).

    Article  CAS  PubMed  Google Scholar 

  34. Li, Zhen-Yi, Long, R. C., Zhang, T. J., Yang, Q. C. & Kang, J. M. Molecular cloning and characterization of the MsHSP17.7 gene from Medicago sativa L. Mol. Biol. Rep. https://doi.org/10.1007/s11033-016-4008-9 (2016).

  35. Liu, J. et al. An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis. Cell Res. https://doi.org/10.1038/s41422-019-0145-8 (2019).

Download references

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.

Author information

Authors and Affiliations

Authors

Contributions

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.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

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

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

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

Reporting Summary

Supplementary Video 1.

Raw video image of Fig. 3d.

Supplementary Video 2.

Raw video image of Fig. 3e.

Supplementary Data 1.

Statistical source data.

Source data

Source Data Fig. 1.

Statistical source data.

Source Data Fig. 2.

Statistical source data.

Source Data Fig. 3.

Statistical source data.

Source Data Fig. 4.

Statistical source data.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-021-00867-4

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing