High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier
- University of California, Berkeley, United States
- University of California, San Diego, United States
- Colorado State University, United States
- 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).
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Data from: High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrierDryad Digital Repository, doi:10.5061/dryad.8sb6h8n.
Article and author information
Author details
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
- Taekjip Ha, Johns Hopkins University, United States
Version history
- Received: May 8, 2019
- Accepted: July 30, 2019
- Accepted Manuscript published: July 31, 2019 (version 1)
- 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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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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