Article | Published:

Transcription-generated torsional stress destabilizes nucleosomes

Nature Structural & Molecular Biology volume 21, pages 8894 (2014) | Download Citation

Abstract

As RNA polymerase II (Pol II) transcribes a gene, it encounters an array of well-ordered nucleosomes. How it traverses through this array in vivo remains unresolved. One model proposes that torsional stress generated during transcription destabilizes nucleosomes ahead of Pol II. Here, we describe a method for high-resolution mapping of underwound DNA, using next-generation sequencing, and show that torsion is correlated with gene expression in Drosophila melanogaster cells. Accumulation of torsional stress, through topoisomerase inhibition, results in increased Pol II at transcription start sites. Whereas topoisomerase I inhibition results in increased nascent RNA transcripts, topoisomerase II inhibition causes little change. Despite the different effects on Pol II elongation, topoisomerase inhibition results in increased nucleosome turnover and salt solubility within gene bodies, thus suggesting that the elongation-independent effects of torsional stress on nucleosome dynamics contributes to the destabilization of nucleosomes.

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Acknowledgements

We thank A. Marty (Fred Hutchinson Cancer Research Center Genomics Shared Resource) for Illumina sequencing; F. Steiner, F. Yang, C. Weber and S. Ramachandran for critical comments; and J. Henikoff for help on sequencing data analysis. This work was supported by the US National Science Foundation Graduate Research Fellowship under grant no. DGE-0718124 (S.S.T.), by the US National Institutes of Health grant U01 HG004274 (S.H.) and by the Howard Hughes Medical Institute (S.H.).

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Affiliations

  1. Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

    • Sheila S Teves
    •  & Steven Henikoff
  2. Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA.

    • Sheila S Teves
  3. Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

    • Steven Henikoff

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Contributions

S.S.T. and S.H. conceived of the project. S.S.T. designed and performed experiments. S.S.T. and S.H. analyzed data and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Steven Henikoff.

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DOI

https://doi.org/10.1038/nsmb.2723