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:

RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II

Nature volume 479, pages 135–138 (2011)Cite this article

Subjects

Abstract

Heterochromatin comprises tightly compacted repetitive regions of eukaryotic chromosomes. The inheritance of heterochromatin through mitosis requires RNA interference (RNAi), which guides histone modification1 during the DNA replication phase of the cell cycle2. Here we show that the alternating arrangement of origins of replication and non-coding RNA in pericentromeric heterochromatin results in competition between transcription and replication in Schizosaccharomyces pombe. Co-transcriptional RNAi releases RNA polymerase II (Pol II), allowing completion of DNA replication by the leading strand DNA polymerase, and associated histone modifying enzymes3 that spread heterochromatin with the replication fork. In the absence of RNAi, stalled forks are repaired by homologous recombination without histone modification.

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 and replication of pericentromeric heterochromatin in fission yeast.
Figure 2: RNA interference and DNA replication restrict RNA polymerase II accumulation and prevent DNA damage.
Figure 3: Replication fork stalling during heterochromatin replication.
Figure 4: Replication-coupled transcriptional silencing through histone modification and RNAi.

Similar content being viewed by others

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Gene Expression Omnibus

Data deposits

Genomics data and analysis are available from the Gene Expression Omnibus accession number GSE30837. Individual cDNA sequences are available from GenBank with accession numbers JN388396–JN388565.

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  ADS  CAS  Google Scholar 

  2. Kloc, A., Zaratiegui, M., Nora, E. & Martienssen, R. RNA interference guides histone modification during the S phase of chromosomal replication. Curr. Biol. 18, 490–495 (2008)

    Article  CAS  Google Scholar 

  3. Li, F., Martienssen, R. & Cande, W. Z. Coordination of DNA replication and histone modification by the Rik1–Dos2 complex. Nature 475, 244–248 (2011)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  5. Motamedi, M. R. et al. HP1 proteins form distinct complexes and mediate heterochromatic gene silencing by nonoverlapping mechanisms. Mol. Cell 32, 778–790 (2008)

    Article  CAS  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. Irvine, D. V. et al. Argonaute slicing is required for heterochromatic silencing and spreading. Science 313, 1134–1137 (2006)

    Article  ADS  CAS  Google Scholar 

  8. Svejstrup, J. Q. The interface between transcription and mechanisms maintaining genome integrity. Trends Biochem. Sci. 35, 333–338 (2010)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  10. Djupedal, I. et al. RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev. 19, 2301–2306 (2005)

    Article  CAS  Google Scholar 

  11. 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 

  12. Rosonina, E., Kaneko, S. & Manley, J. L. Terminating the transcript: breaking up is hard to do. Genes Dev. 20, 1050–1056 (2006)

    Article  CAS  Google Scholar 

  13. 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 

  14. Bühler, M., Haas, W., Gygi, S. P. & Moazed, D. RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell 129, 707–721 (2007)

    Article  Google Scholar 

  15. Murakami, H. et al. Ribonuclease activity of Dis3 is required for mitotic progression and provides a possible link between heterochromatin and kinetochore function. PLoS ONE 2, e317 (2007)

    Article  ADS  Google Scholar 

  16. Smith, J. G. et al. Replication of centromere II of Schizosaccharomyces pombe . Mol. Cell. Biol. 15, 5165–5172 (1995)

    Article  CAS  Google Scholar 

  17. Hayashi, M. T., Takahashi, T. S., Nakagawa, T., Nakayama, J. & Masukata, H. The heterochromatin protein Swi6/HP1 activates replication origins at the pericentromeric region and silent mating-type locus. Nature Cell Biol. 11, 357–362 (2009)

    Article  CAS  Google Scholar 

  18. Lambert, S., Watson, A., Sheedy, D. M., Martin, B. & Carr, A. M. Gross chromosomal rearrangements and elevated recombination at an inducible site-specific replication fork barrier. Cell 121, 689–702 (2005)

    Article  CAS  Google Scholar 

  19. Shimmoto, M. et al. Interactions between Swi1-Swi3, Mrc1 and S phase kinase, Hsk1 may regulate cellular responses to stalled replication forks in fission yeast. Genes Cells 14, 669–682 (2009)

    Article  CAS  Google Scholar 

  20. Segurado, M., Gomez, M. & Antequera, F. Increased recombination intermediates and homologous integration hot spots at DNA replication origins. Mol. Cell 10, 907–916 (2002)

    Article  CAS  Google Scholar 

  21. Minca, E. C. & Kowalski, D. Multiple Rad5 activities mediate sister chromatid recombination to bypass DNA damage at stalled replication forks. Mol. Cell 38, 649–661 (2010)

    Article  CAS  Google Scholar 

  22. Deshpande, A. M. & Newlon, C. S. DNA replication fork pause sites dependent on transcription. Science 272, 1030–1033 (1996)

    Article  ADS  CAS  Google Scholar 

  23. Scott, K. C., Merrett, S. L. & Willard, H. F. A heterochromatin barrier partitions the fission yeast centromere into discrete chromatin domains. Curr. Biol. 16, 119–129 (2006)

    Article  CAS  Google Scholar 

  24. Lambert, S. et al. Homologous recombination restarts blocked replication forks at the expense of genome rearrangements by template exchange. Mol. Cell 39, 346–359 (2010)

    Article  CAS  Google Scholar 

  25. Groth, A., Rocha, W., Verreault, A. & Almouzni, G. Chromatin challenges during DNA replication and repair. Cell 128, 721–733 (2007)

    Article  CAS  Google Scholar 

  26. Pirngruber, J., Shchebet, A. & Johnsen, S. A. Insights into the function of the human P-TEFb component CDK9 in the regulation of chromatin modifications and co-transcriptional mRNA processing. Cell Cycle 8, 3636–3642 (2009)

    Article  CAS  Google Scholar 

  27. Zhang, K. et al. Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA. Science 331, 1624–1627 (2011)

    Article  ADS  CAS  Google Scholar 

  28. Ghazal, G. et al. Yeast RNase III triggers polyadenylation-independent transcription termination. Mol. Cell 36, 99–109 (2009)

    Article  CAS  Google Scholar 

  29. Washburn, R. S. & Gottesman, M. E. Transcription termination maintains chromosome integrity. Proc. Natl Acad. Sci. USA 108, 792–797 (2011)

    Article  ADS  CAS  Google Scholar 

  30. Pauler, F. M., Koerner, M. V. & Barlow, D. P. Silencing by imprinted noncoding RNAs: is transcription the answer? Trends Genet. 23, 284–292 (2007)

    Article  CAS  Google Scholar 

  31. Moreno, S., Klar, A. & Nurse, P. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe . Methods Enzymol. 194, 795–823 (1991)

    Article  CAS  Google Scholar 

  32. Sallés, F. J., Richards, W. G. & Strickland, S. Assaying the polyadenylation state of mRNAs. Methods 17, 38–45 (1999)

    Article  Google Scholar 

  33. Zaratiegui, M. et al. CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR. Nature 469, 112–115 (2011)

    Article  ADS  CAS  Google Scholar 

  34. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008)

    Article  Google Scholar 

Download references

Acknowledgements

We thank D. Roh and T. Volpe for isolating cDNA clones. D.V.I. was supported by a NHMRC CJ Martin Postdoctoral Research Fellowship. M.Z. was supported by a fellowship from the Spanish Ministry of Science. This work was supported by grants BFU2008-01919 and Consolider-Ingenio CSD2007-00015 from the Spanish Ministry of Science and Innovation to F.A., and NIH R01 GM076396 to W.Z.C. and R.A.M.

Author information

Author notes

  1. Mikel Zaratiegui, Danielle V. Irvine, Anna Kloc, Fei Li & Derek Goto

    Present address: Present addresses: Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA (M.Z.); Yale Stem Cell Center, Yale University, New Haven, Connecticut 06520, USA (A.K.); Creative Research Initiative Sousei, Hokkaido University, 001-0021 Sapporo, Japan (D.G.); Department of Biology, New York University, New York, New York 10003, USA (F.L.); Murdoch Children’s Research Institute, University of Melbourne, Melbourne, Victoria 3052, Australia (D.V.I.).,

Authors and Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA

    Mikel Zaratiegui, Stephane E. Castel, Danielle V. Irvine, Anna Kloc, Jie Ren, An-Yun Chang, Derek Goto, Benoit Arcangioli & Robert A. Martienssen

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

    Stephane E. Castel & Robert A. Martienssen

  3. Molecular and Cellular Biology, University of California Berkeley, Berkeley, 94720, USA

    Fei Li & W. Zacheus Cande

  4. Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, Salamanca 37007, Spain

    Elisa de Castro, Laura Marín & Francisco Antequera

  5. Molecular and Cell Biology program, Stony Brook University, Stony Brook, 11794, New York, USA

    An-Yun Chang

  6. Institut Pasteur, Paris, France

    Benoit Arcangioli

Authors
  1. Mikel Zaratiegui
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stephane E. Castel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Danielle V. Irvine
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Anna Kloc
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jie Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Fei Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Elisa de Castro
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Laura Marín
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. An-Yun Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Derek Goto
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. W. Zacheus Cande
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Francisco Antequera
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Benoit Arcangioli
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Robert A. Martienssen
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

S.C., D.V.I., A.K., J.R. contributed equally to this work and are listed in alphabetical order. M.Z., S.C., D.V.I., A.K., J.R., F.L., E.d.C., L.M., A.-Y.C. and D.G. performed experiments, and S.C. analysed the data. W.Z.C., F.A., B.A. and R.A.M. designed experiments and R.A.M. and M.Z. wrote the manuscript.

Corresponding author

Correspondence to Robert A. Martienssen.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Tables 1-4, Supplementary Figures 1-5 with legends and additional references. (PDF 5439 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zaratiegui, M., Castel, S., Irvine, D. et al. RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature 479, 135–138 (2011). https://doi.org/10.1038/nature10501

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature10501

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