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:

RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription

Nature volume 435, pages 1275–1279 (2005)Cite this article

A Retraction to this article was published on 13 October 2005

Abstract

RNA interference (RNAi) acts on long double-stranded RNAs (dsRNAs) in a variety of eukaryotes to generate small interfering RNAs that target homologous messenger RNA, resulting in their destruction. This process is widely used to ‘knock-down’ the expression of genes of interest to explore phenotypes1,2,3. In plants3,4,5, fission yeast6,7,8, ciliates9,10, flies11 and mammalian cells12,13, short interfering RNAs (siRNAs) also induce DNA or chromatin modifications at the homologous genomic locus, which can result in transcriptional silencing or sequence elimination14. siRNAs may direct DNA or chromatin modification by siRNA–DNA interactions at the homologous locus4,5. Alternatively, they may act by interactions between siRNA and nascent transcript15,16. Here we show that in fission yeast (Schizosaccharomyces pombe), chromatin modifications are only directed by RNAi if the homologous DNA sequences are transcribed. Furthermore, transcription by exogenous T7 polymerase is not sufficient. Ago1, a component of the RNAi effector RISC/RITS complex, associates with target transcripts and RNA polymerase II. Truncation of the regulatory carboxy-terminal domain (CTD) of RNA pol II disrupts transcriptional silencing, indicating that, like other RNA processing events17,18,19, RNAi-directed chromatin modification is coupled to transcription.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: Transcription of siRNA target is required to effect silent chromatin assembly.
Figure 2: Transcription by T7 polymerase is not sufficient for RNAi-directed chromatin modification.
Figure 3: RNA pol II CTD truncation affects centromeric silent chromatin.
Figure 4: Association of Ago1 with chromatin is RNase sensitive and dependent on transcription and pol II.

Similar content being viewed by others

References

  1. Hannon, G. J. & Rossi, J. J. Unlocking the potential of the human genome with RNA interference. Nature 431, 371–378 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  2. Mello, C. C. & Conte, D. Jr. Revealing the world of RNA interference. Nature 431, 338–342 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  3. Baulcombe, D. RNA silencing in plants. Nature 431, 356–363 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  4. Jones, L., Ratcliff, F. & Baulcombe, D. C. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Curr. Biol. 11, 747–757 (2001)

    Article  CAS  PubMed  Google Scholar 

  5. Mette, M. F., Aufsatz, W., van der Winden, J., Matzke, M. A. & Matzke, A. J. Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 19, 5194–5201 (2000)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  7. Schramke, V. & Allshire, R. Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301, 1069–1074 (2003)

    Article  ADS  CAS  PubMed  Google Scholar 

  8. Lippman, Z. & Martienssen, R. The role of RNA interference in heterochromatic silencing. Nature 431, 364–370 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  9. Mochizuki, K., Fine, N. A., Fujisawa, T. & Gorovsky, M. A. Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in Tetrahymena. Cell 110, 689–699 (2002)

    Article  CAS  PubMed  Google Scholar 

  10. Mochizuki, K. & Gorovsky, M. A. Small RNAs in genome rearrangement in Tetrahymena. Curr. Opin. Genet. Dev. 14, 181–187 (2004)

    Article  CAS  PubMed  Google Scholar 

  11. Pal-Bhadra, M. et al. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303, 669–672 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  12. Kawasaki, H. & Taira, K. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature 431, 211–217 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  13. Morris, K. V., Chan, S. W., Jacobsen, S. E. & Looney, D. J. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305, 1289–1292 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  14. Matzke, M. A. & Birchler, J. A. RNAi-mediated pathways in the nucleus. Nature Rev. Genet. 6, 24–35 (2005)

    Article  CAS  PubMed  Google Scholar 

  15. Martienssen, R. A. Maintenance of heterochromatin by RNA interference of tandem repeats. Nature Genet. 35, 213–214 (2003)

    Article  CAS  PubMed  Google Scholar 

  16. Grewal, S. I. & Moazed, D. Heterochromatin and epigenetic control of gene expression. Science 301, 798–802 (2003)

    Article  ADS  CAS  PubMed  Google Scholar 

  17. Orphanides, G. & Reinberg, D. A unified theory of gene expression. Cell 108, 439–451 (2002)

    Article  CAS  PubMed  Google Scholar 

  18. Proudfoot, N. New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr. Opin. Cell Biol. 16, 272–278 (2004)

    Article  CAS  PubMed  Google Scholar 

  19. Reed, R. Coupling transcription, splicing and mRNA export. Curr. Opin. Cell Biol. 15, 326–331 (2003)

    Article  CAS  PubMed  Google Scholar 

  20. Noma, K. et al. RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nature Genet. 36, 1174–1180 (2004)

    Article  CAS  PubMed  Google Scholar 

  21. Verdel, A. et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  22. Partridge, J. F., Borgstrom, B. & Allshire, R. C. Distinct protein interaction domains and protein spreading in a complex centromere. Genes Dev. 14, 783–791 (2000)

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Partridge, J. F., Scott, K. S., Bannister, A. J., Kouzarides, T. & Allshire, R. C. cis-acting DNA from fission yeast centromeres mediates histone H3 methylation and recruitment of silencing factors and cohesin to an ectopic site. Curr. Biol. 12, 1652–1660 (2002)

    Article  CAS  PubMed  Google Scholar 

  24. Motamedi, M. R. et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119, 789–802 (2004)

    Article  CAS  PubMed  Google Scholar 

  25. Sugiyama, T., Cam, H., Verdel, A., Moazed, D. & Grewal, S. I. RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production. Proc. Natl Acad. Sci. USA 102, 152–157 (2005)

    Article  ADS  CAS  PubMed  Google Scholar 

  26. Aranda, A. & Proudfoot, N. Transcriptional termination factors for RNA polymerase II in yeast. Mol. Cell 7, 1003–1011 (2001)

    Article  CAS  PubMed  Google Scholar 

  27. Scafe, C., Nonet, M. & Young, R. A. RNA polymerase II mutants defective in transcription of a subset of genes. Mol. Cell. Biol. 10, 1010–1016 (1990)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Herr, A. J., Jensen, M. B., Dalmay, T. & Baulcombe, D. C. RNA polymerase IV directs silencing of endogenous DNA. Science 308, 118–120 (2005)

    Article  ADS  CAS  PubMed  Google Scholar 

  29. Onodera, Y. et al. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120, 613–622 (2005)

    Article  CAS  PubMed  Google Scholar 

  30. Pidoux, A. L., Richardson, W. & Allshire, R. C. Sim4: a novel fission yeast kinetochore protein required for centromeric silencing and chromosome segregation. J. Cell Biol. 161, 295–307 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank members of the Allshire laboratory for advice, discussion and comments on the manuscript; E. Bayne for the model; P. Dunoyer and O. Voinnet for help with siRNA detection; T. Jenuwein for anti-H3K9me2 serum; and other members of the EC FP6 ‘The Epigenome’ Network for input. This research was supported by funding from the Wellcome Trust to R.C.A., who is a Wellcome Trust Principal Research Fellow.

Author information

Authors and Affiliations

  1. Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, King's Buildings, University of Edinburgh, EH9 3JR, Edinburgh, UK

    Vera Schramke, Daniel M. Sheedy & Robin C. Allshire

  2. Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York, 11724, USA

    Ahmet M. Denli & Gregory J. Hannon

  3. Karolinska Institutet, Department of Biosciences/Department of Natural Sciences, University College Sodertorn, Alfred Nobel's Allé 7, S-141 89, Huddinge, Sweden

    Carolina Bonila & Karl Ekwall

Authors
  1. Vera Schramke
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Daniel M. Sheedy
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ahmet M. Denli
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Carolina Bonila
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Karl Ekwall
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Gregory J. Hannon
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Robin C. Allshire
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Robin C. Allshire.

Ethics declarations

Competing interests

Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

This contains Supplementary Figures S1-S3 and Supplementary Tables 1-3 (DOC 299 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Schramke, V., Sheedy, D., Denli, A. et al. RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription. Nature 435, 1275–1279 (2005). https://doi.org/10.1038/nature03652

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature03652

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced 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