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.

  • Brief Communication
  • Published:

An effect of DNA sequence on nucleosome occupancy and removal

Nature Structural & Molecular Biology volume 18, pages 507–509 (2011)Cite this article

Subjects

Abstract

A barrier phases nucleosomes at the yeast (Saccharomyces cerevisiae) GAL1–GAL10 genes. Here we separate nucleosome positioning from occupancy and show that the degree of occupancy of these phased sites is predictably determined by the underlying DNA sequences. As this occupancy is increased (by sequence alteration), nucleosome removal upon induction is decreased, as is mRNA production. These results explain why promoter sequences have evolved to form nucleosomes relatively inefficiently.

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: Chromatin architecture at the GAL1–GAL10 locus before and after induction.
Figure 2: The effects of increasing nucleosome-forming propensities on nucleosome occupancies at site −1.
Figure 3: Nucleosome removal and mRNA production.

Similar content being viewed by others

References

  1. Floer, M. et al. Cell 141, 407–418 (2010).

    Article  CAS  Google Scholar 

  2. Bryant, G.O. et al. PLoS Biol. 6, 2928–2939 (2008).

    Article  CAS  Google Scholar 

  3. Chung, H.R. et al. PLoS ONE 5, e15754 (2010).

    Article  CAS  Google Scholar 

  4. Locke, G., Tolkunov, D., Moqtaderi, Z., Struhl, K. & Morozov, A.V. Proc. Natl. Acad. Sci. USA 107, 20998–21003 (2010).

    Article  CAS  Google Scholar 

  5. Satchwell, S.C., Drew, H.R. & Travers, A.A. J. Mol. Biol. 191, 659–675 (1986).

    Article  CAS  Google Scholar 

  6. Segal, E. et al. Nature 442, 772–778 (2006).

    Article  CAS  Google Scholar 

  7. Segal, E. & Widom, J. Curr. Opin. Struct. Biol. 19, 65–71 (2009).

    Article  CAS  Google Scholar 

  8. Stein, A., Takasuka, T.E. & Collings, C.K. Nucleic Acids Res. 38, 709–719 (2010).

    Article  CAS  Google Scholar 

  9. Tillo, D. & Hughes, T.R. BMC Bioinformatics 10, 442 (2009).

    Article  Google Scholar 

  10. Rohs, R. et al. Nature 461, 1248–1253 (2009).

    Article  CAS  Google Scholar 

  11. Travers, A.A. & Klug, A. Phil. Trans. R. Soc. Lond. B 317, 537–561 (1987).

    Article  CAS  Google Scholar 

  12. Kaplan, N. et al. Nature 458, 362–366 (2009).

    Article  CAS  Google Scholar 

  13. Takasuka, T.E. & Stein, A. Nucleic Acids Res. 38, 5672–5680 (2010).

    Article  CAS  Google Scholar 

  14. Dechassa, M.L. et al. Mol. Cell 38, 590–602 (2010).

    Article  CAS  Google Scholar 

  15. Ahmad, K. & Henikoff, S. Cell 104, 839–847 (2001).

    Article  CAS  Google Scholar 

  16. Halpern, M.E. et al. Zebrafish 5, 97–110 (2008).

    Article  CAS  Google Scholar 

  17. Mohrmann, L. & Verrijzer, C.P. Biochim. Biophys. Acta 1681, 59–73 (2005).

    Article  CAS  Google Scholar 

  18. Wilson, B., Erdjument-Bromage, H., Tempst, P. & Cairns, B.R. Genetics 172, 795–809 (2006).

    Article  CAS  Google Scholar 

  19. Tillo, D. et al. PLoS ONE 5, e9129 (2010).

    Article  Google Scholar 

  20. Bernstein, B.E., Liu, C.L., Humphrey, E.L., Perlstein, E.O. & Schreiber, S.L. Genome Biol. 5, R62 (2004).

    Article  Google Scholar 

  21. Lee, C.K., Shibata, Y., Rao, B., Strahl, B.D. & Lieb, J.D. Nat. Genet. 36, 900–905 (2004).

    Article  CAS  Google Scholar 

  22. Sekinger, E.A., Moqtaderi, Z. & Struhl, K. Mol. Cell 18, 735–748 (2005).

    Article  CAS  Google Scholar 

  23. Zhang, Y. et al. Nat. Struct. Mol. Biol. 16, 847–852 (2009).

    Article  CAS  Google Scholar 

  24. Ptashne, M. Curr. Biol. 19, R234–R241 (2009).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank E. Segal (Weizmann Institute of Science) and J. Widom (Northwestern University) for the “superbinder” sequence and S. Narayan, G. Berrozpe, A. Gann and D. Rhodes for helpful discussions. This work was supported by US National Institutes of Health grant GM032308 to M.P.

Author information

Author notes

  1. Xin Wang and Gene O Bryant: These authors contributed equally to this work.

Authors and Affiliations

  1. Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA

    Xin Wang, Gene O Bryant, Monique Floer, Dan Spagna & Mark Ptashne

Authors
  1. Xin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gene O Bryant
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Monique Floer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Dan Spagna
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mark Ptashne
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

X.W., G.O.B. and M.P. designed the experiments. X.W., G.O.B. and D.S. performed the experiments. X.W. and G.O.B. analyzed the data. X.W., G.O.B., M.F. and M.P. wrote the paper.

Corresponding author

Correspondence to Mark Ptashne.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figure 1, Supplementary Table 1 and Supplementary Methods (PDF 290 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wang, X., Bryant, G., Floer, M. et al. An effect of DNA sequence on nucleosome occupancy and removal. Nat Struct Mol Biol 18, 507–509 (2011). https://doi.org/10.1038/nsmb.2017

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.2017

This article is cited by

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