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Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe

Nature Structural & Molecular Biology volume 18, pages 94–99 (2011)Cite this article

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Abstract

In the fission yeast S. pombe, the RNA interference (RNAi) pathway is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic silencing of centromeric repeats. Here, we demonstrate that RNAi also functions to repress genomic elements other than constitutive heterochromatin. Using DNA adenine methyltransferase identification (DamID), we show that the RNAi proteins Dcr1 and Rdp1 physically associate with some euchromatic genes, noncoding RNA genes and retrotransposon long terminal repeats, and that this association is independent of the Clr4 histone methyltransferase. Physical association of RNAi with chromatin is sufficient to trigger a silencing response but not to assemble heterochromatin. The mode of silencing at the newly identified RNAi targets is consistent with a co-transcriptional gene silencing model, as proposed earlier, and functions with trace amounts of siRNAs. We anticipate that similar mechanisms could also be operational in other eukaryotes.

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Figure 1: Identification of previously known and novel Swi6 and Rdp1 binding sites by DamID.
Figure 2: Dcr1 physically associates with centromeric chromatin.
Figure 3: Clr4 dependency of Dcr1 or Rdp1 association with chromatin.
Figure 4: Enrichment of Dam fusion proteins at different genomic features.
Figure 5: The S. pombe RNAi machinery contributes to LTR repression.

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References

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

    Article  CAS  Google Scholar 

  2. Volpe, T. et al. RNA interference is required for normal centromere function in fission yeast. Chromosome Res. 11, 137–146 (2003).

    Article  CAS  Google Scholar 

  3. Reinhart, B.J. & Bartel, D.P. Small RNAs correspond to centromere heterochromatic repeats. Science 297, 1831 (2002).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  5. Bühler, M., Verdel, A. & Moazed, D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125, 873–886 (2006).

    Article  Google Scholar 

  6. Bayne, E.H. et al. Stc1: A critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell 140, 666–677 (2010).

    Article  CAS  Google Scholar 

  7. 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  Google Scholar 

  8. 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  CAS  Google Scholar 

  9. Cam, H.P. et al. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat. Genet. 37, 809–819 (2005).

    Article  CAS  Google Scholar 

  10. Emmerth, S. et al. Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly. Dev. Cell 18, 102–113 (2010).

    Article  CAS  Google Scholar 

  11. Sigova, A., Rhind, N. & Zamore, P.D. A single Argonaute protein mediates both transcriptional and posttranscriptional silencing in Schizosaccharomyces pombe. Genes Dev. 18, 2359–2367 (2004).

    Article  CAS  Google Scholar 

  12. Iida, T., Nakayama, J. & Moazed, D. siRNA-mediated heterochromatin establishment requires HP1 and is associated with antisense transcription. Mol. Cell 31, 178–189 (2008).

    Article  CAS  Google Scholar 

  13. Simmer, F. et al. Hairpin RNA induces secondary small interfering RNA synthesis and silencing in trans in fission yeast. EMBO Rep. 11, 112–118 (2010).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  15. Hong, E.J., Villén, J., Gerace, E.L., Gygi, S.P. & Moazed, D. A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3–K9 methyltransferase and is required for RNAi-mediated heterochromatin formation. RNA Biol. 2, 106–111 (2005).

    Article  CAS  Google Scholar 

  16. Sadaie, M., Iida, T., Urano, T. & Nakayama, J. A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast. EMBO J. 23, 3825–3835 (2004).

    Article  CAS  Google Scholar 

  17. Partridge, J.F. et al. Functional separation of the requirements for establishment and maintenance of centromeric heterochromatin. Mol. Cell 26, 593–602 (2007).

    Article  CAS  Google Scholar 

  18. Partridge, J.F. Centromeric chromatin in fission yeast. Front. Biosci. 13, 3896–3905 (2008).

    CAS  PubMed  Google Scholar 

  19. Halic, M. & Moazed, D. Dicer-independent primal RNAs trigger RNAi and heterochromatin formation. Cell 140, 504–516 (2010).

    Article  CAS  Google Scholar 

  20. Bühler, M. & Gasser, S.M. Silent chromatin at the middle and ends: lessons from yeasts. EMBO J. 28, 2149–2161 (2009).

    Article  Google Scholar 

  21. Gullerova, M. & Proudfoot, N.J. Cohesin complex promotes transcriptional termination between convergent genes in S. pombe. Cell 132, 983–995 (2008).

    Article  CAS  Google Scholar 

  22. Bühler, M. RNA turnover and chromatin-dependent gene silencing. Chromosoma 118, 141–151 (2009).

    Article  Google Scholar 

  23. Sadaie, M. et al. Balance between distinct HP1 proteins controls heterochromatin assembly in fission yeast. Mol. Cell. Biol. 23, 6973–6988 (2008).

    Article  Google Scholar 

  24. Bühler, M., Spies, N., Bartel, D.P. & Moazed, D. TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat. Struct. Mol. Biol. 15, 1015–1023 (2008).

    Article  Google Scholar 

  25. Djupedal, I. et al. Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA. EMBO J. 28, 3832–3844 (2009).

    Article  CAS  Google Scholar 

  26. Buker, S.M. et al. Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast. Nat. Struct. Mol. Biol. 14, 200–207 (2007).

    Article  CAS  Google Scholar 

  27. van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat. Biotechnol. 18, 424–428 (2000).

    Article  CAS  Google Scholar 

  28. Bianchi-Frias, D. et al. Hairy transcriptional repression targets and cofactor recruitment in Drosophila. PLoS Biol. 2, E178 (2004).

    Article  Google Scholar 

  29. Bühler, M. & Moazed, D. Transcription and RNAi in heterochromatic gene silencing. Nat. Struct. Mol. Biol. 14, 1041–1048 (2007).

    Article  Google Scholar 

  30. Bowen, N.J., Jordan, I.K., Epstein, J.A., Wood, V. & Levin, H.L. Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. Genome Res. 13, 1984–1997 (2003).

    Article  CAS  Google Scholar 

  31. Mourier, T. & Willerslev, E. Large-scale transcriptome data reveals transcriptional activity of fission yeast LTR retrotransposons. BMC Genomics 11, 167 (2010).

    Article  Google Scholar 

  32. Cam, H.P., Noma, K., Ebina, H., Levin, H.L. & Grewal, S.I. Host genome surveillance for retrotransposons by transposon-derived proteins. Nature 451, 431–436 (2008).

    Article  CAS  Google Scholar 

  33. Anderson, H.E. et al. The fission yeast HIRA histone chaperone is required for promoter silencing and the suppression of cryptic antisense transcripts. Mol. Cell. Biol. 18, 5158–5167 (2009).

    Article  Google Scholar 

  34. Peters, L. & Meister, G. Argonaute proteins: mediators of RNA silencing. Mol. Cell 26, 611–623 (2007).

    Article  CAS  Google Scholar 

  35. Ghildiyal, M. & Zamore, P.D. Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 10, 94–108 (2009).

    Article  CAS  Google Scholar 

  36. Moazed, D. Small RNAs in transcriptional gene silencing and genome defence. Nature 457, 413–420 (2009).

    Article  CAS  Google Scholar 

  37. Law, J.A. & Jacobsen, S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).

    Article  CAS  Google Scholar 

  38. Chapman, E.J. & Carrington, J.C. Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 8, 884–896 (2007).

    Article  CAS  Google Scholar 

  39. Jia, S., Noma, K. & Grewal, S.I. RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins. Science 304, 1971–1976 (2004).

    Article  CAS  Google Scholar 

  40. Kanoh, J., Sadaie, M., Urano, T. & Ishikawa, F. Telomere binding protein Taz1 establishes Swi6 heterochromatin independently of RNAi at telomeres. Curr. Biol. 15, 1808–1819 (2005).

    Article  CAS  Google Scholar 

  41. Bähler, J. et al. Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe. Yeast 14, 943–951 (1998).

    Article  Google Scholar 

  42. Moreno, M.B., Duran, A. & Ribas, J.C. A family of multifunctional thiamine-repressible expression vectors for fission yeast. Yeast 16, 861–872 (2000).

    Article  CAS  Google Scholar 

  43. Vogel, M.J., Peric-Hupkes, D. & van Steensel, B. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat. Protoc. 2, 1467–1478 (2007).

    Article  CAS  Google Scholar 

  44. The R Development Core Team. R: A language and environment for statistical computing. <http://cran.r-project.org> (2004).

  45. Ihaka, R. & Gentleman, R.R. A language for data analysis and graphics. J. Comput. Graph. Statist. 5, 299–314 (1996).

    Google Scholar 

  46. Gentleman, R.C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).

    Article  Google Scholar 

  47. Huber, W., Toedling, J. & Steinmetz, L.M. Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 22, 1963–1970 (2006).

    Article  CAS  Google Scholar 

  48. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

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Acknowledgements

We thank H. Grosshans, A. Peters, F. Mohn and all members of the Bühler lab for critical comments on the manuscript; A.H. Brand for plasmids; B. van Steensel for advice; and H.-R. Hotz for bioinformatics support. We also thank the genomics facility of the Friedrich Miescher Institute for Biomedical Research for array hybridizations. This work was supported by the Swiss National Science Foundation and the Novartis Research Foundation.

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  1. Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland

    Katrina J Woolcock, Dimos Gaidatzis, Tanel Punga & Marc Bühler

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  1. Katrina J Woolcock
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  2. Dimos Gaidatzis
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Contributions

K.J.W. and M.B. designed the research. K.J.W. designed and conducted experiments. D.G. wrote R scripts for data analysis. K.J.W. and D.G. analyzed the DamID data. T.P. conducted experiments. M.B. and K.J.W. analyzed the results and wrote the manuscript.

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Correspondence to Marc Bühler.

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The authors declare no competing financial interests.

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Woolcock, K., Gaidatzis, D., Punga, T. et al. Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe. Nat Struct Mol Biol 18, 94–99 (2011). https://doi.org/10.1038/nsmb.1935

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