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Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II

Nature Structural & Molecular Biology volume 16, pages 1272–1278 (2009)Cite this article

Abstract

Transcription of eukaryotic genes by RNA polymerase II (Pol II) is typically accompanied by nucleosome survival and minimal exchange of histones H3 and H4. The mechanism of nucleosome survival and recovery of chromatin structure remains obscure. Here we show how transcription through chromatin by Pol II is uniquely coupled with nucleosome survival. Structural modeling and functional analysis of the intermediates of transcription through a nucleosome indicated that when Pol II approaches an area of strong DNA-histone interactions, a small intranucleosomal DNA loop (zero-size or Ø-loop) containing transcribing enzyme is formed. During formation of the Ø-loop, the recovery of DNA-histone interactions behind Pol II is tightly coupled with their disruption ahead of the enzyme. This coupling is a distinct feature of the Pol II–type mechanism that allows further transcription through the nucleosome, prevents nucleosome translocation and minimizes displacement of H3 and H4 histones from DNA during enzyme passage.

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Figure 1: Promoter-distal high-affinity nucleosome positioning sequences dictate the high nucleosomal barrier to transcription by Pol II.
Figure 2: A model of an intranucleosomal Pol II containing a DNA Ø-loop.
Figure 3: RNAP forms an intranucleosomal Ø-loop at position +49.
Figure 4: Structures of the key intermediates formed during transcription through a nucleosome by Pol II.
Figure 5: Removal of the promoter-proximal H2A-H2B dimer results in Pol II arrest in the +45 region of the nucleosome.
Figure 6: A feedback mechanism allows survival of histones H3 and H4 during Pol II transcription.

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Acknowledgements

We thank J. Widom (Northwestern University) for plasmids containing the nucleosome positioning sequences, G. Zheng for making the movie, and D. Clark, M. Gartenberg, J. Hayes and D. Luse for suggestions and critical reading of the manuscript. This work was supported by US National Science Foundation 0549593 and National Institutes of Health (NIH) GM58650 grants to V.M.S., NIH GM74252 and GM74840 grants to D.G.V., and NIH GM067153 grant to I.A.

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Author notes

  1. Olga I Kulaeva and Daria A Gaykalova: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Pharmacology, University of Medicine and Dentistry of New Jersey–Robert Wood Johnson Medical School, Piscataway, New Jersey, USA

    Olga I Kulaeva, Daria A Gaykalova, Nikolai A Pestov, Viktor V Golovastov & Vasily M Studitsky

  2. Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, Birmingham, Alabama, USA

    Dmitry G Vassylyev

  3. Department of Microbiology, The Ohio State University, Columbus, Ohio, USA

    Irina Artsimovitch

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Contributions

O.I.K. designed and constructed some templates, designed and performed transcription experiments using Pol II; D.A.G. performed characterization and footprinting of the elongation complexes; N.A.P. performed restriction enzyme mapping of the elongation complexes; V.V.G. designed and constructed some templates and performed initial walking experiments; D.G.V. conducted docking; I.A. purified GreB and contributed to writing the manuscript; V.M.S. purified histones and donor chromatin, designed the study, interpreted results and wrote the manuscript.

Corresponding author

Correspondence to Vasily M Studitsky.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Discussion and Supplementary Methods (PDF 1637 kb)

Supplementary Video 1

Transcription through a nucleosomes by RNA polymerase II. (GIF 3692 kb)

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Kulaeva, O., Gaykalova, D., Pestov, N. et al. Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II. Nat Struct Mol Biol 16, 1272–1278 (2009). https://doi.org/10.1038/nsmb.1689

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