High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier

  1. Zhijie Chen
  2. Ronen Gabizon
  3. Aidan I Brown
  4. Antony Lee
  5. Aixin Song
  6. Cesar Diaz-Celis
  7. Craig D Kaplan
  8. Elena F Koslover
  9. Tingting Yao  Is a corresponding author
  10. Carlos Bustamante  Is a corresponding author
  1. University of California, Berkeley, United States
  2. University of California, San Diego, United States
  3. Colorado State University, United States
  4. University of Pittsburgh, United States

Abstract

Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. A high-resolution description of the barrier topography, its modulation by epigenetic modifications, and their effects on Pol II nucleosome crossing dynamics, is still missing. Here, we obtain topographic and transcriptional (Pol II residence time) maps of canonical, H2A.Z, and monoubiquitinated H2B (uH2B) nucleosomes at near base-pair resolution and accuracy. Pol II crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression.

Data availability

Matlab scripts for processing unzipping curves and hopping data has been deposited in github at https://github.com/lenafabr/dataprocessDNAunzippingRaw data is available from Dryad https://doi.org/10.5061/dryad.8sb6h8nFurther information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Carlos J. Bustamante (carlosb@berkeley.edu).

The following data sets were generated

Article and author information

Author details

  1. Zhijie Chen

    Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1376-5750
  2. Ronen Gabizon

    Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Aidan I Brown

    Department of Physics, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Antony Lee

    Department of Physics, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2193-5369
  5. Aixin Song

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Cesar Diaz-Celis

    Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Craig D Kaplan

    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Elena F Koslover

    Department of Physics, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4139-9209
  9. Tingting Yao

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
    For correspondence
    Tingting.Yao@Colostate.edu
    Competing interests
    The authors declare that no competing interests exist.
  10. Carlos Bustamante

    Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States
    For correspondence
    carlosb@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2970-0073

Funding

National Institute of General Medical Sciences (R01GM032543)

  • Carlos Bustamante

National Institute of General Medical Sciences (R01GM071552)

  • Carlos Bustamante

National Institute of General Medical Sciences (R01GM098401)

  • Tingting Yao

National Institute of General Medical Sciences (R01GM097260)

  • Craig D Kaplan

Basic Energy Sciences (Nanomachine Program under Contract DE-AC02-05CH11231)

  • Carlos Bustamante

Alfred P. Sloan Foundation (FG-2018-10394)

  • Elena F Koslover

Burroughs Wellcome Fund (Collaborative Research Travel Grant)

  • Tingting Yao

Howard Hughes Medical Institute

  • Carlos Bustamante

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Taekjip Ha, Johns Hopkins University, United States

Publication history

  1. Received: May 8, 2019
  2. Accepted: July 30, 2019
  3. Accepted Manuscript published: July 31, 2019 (version 1)
  4. Version of Record published: September 13, 2019 (version 2)

Copyright

© 2019, Chen et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Zhijie Chen
  2. Ronen Gabizon
  3. Aidan I Brown
  4. Antony Lee
  5. Aixin Song
  6. Cesar Diaz-Celis
  7. Craig D Kaplan
  8. Elena F Koslover
  9. Tingting Yao
  10. Carlos Bustamante
(2019)
High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier
eLife 8:e48281.
https://doi.org/10.7554/eLife.48281
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