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

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.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [1]; ORCiD logo [6]; ORCiD logo [3]; ORCiD logo [5]; ORCiD logo [7]
  1. Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
  2. Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States
  3. Department of Physics, University of California, San Diego, San Diego, United States
  4. Department of Physics, University of California, Berkeley, Berkeley, United States
  5. Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
  6. Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
  7. Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States, Department of Physics, University of California, Berkeley, Berkeley, United States, Jason L Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, United States, Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
Publication Date:
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1545911
Alternate Identifier(s):
OSTI ID: 1545912
Grant/Contract Number:  
Nanomachine Program under Contract DE-AC02-05CH11231
Resource Type:
Published Article
Journal Name:
eLife
Additional Journal Information:
Journal Name: eLife Journal Volume: 8; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
English

Citation Formats

Chen, Zhijie, Gabizon, Ronen, Brown, Aidan I., Lee, Antony, Song, Aixin, Díaz-Celis, César, Kaplan, Craig D., Koslover, Elena F., Yao, Tingting, and Bustamante, Carlos. High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier. United States: N. p., 2019. Web. doi:10.7554/eLife.48281.
Chen, Zhijie, Gabizon, Ronen, Brown, Aidan I., Lee, Antony, Song, Aixin, Díaz-Celis, César, Kaplan, Craig D., Koslover, Elena F., Yao, Tingting, & Bustamante, Carlos. High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier. United States. doi:10.7554/eLife.48281.
Chen, Zhijie, Gabizon, Ronen, Brown, Aidan I., Lee, Antony, Song, Aixin, Díaz-Celis, César, Kaplan, Craig D., Koslover, Elena F., Yao, Tingting, and Bustamante, Carlos. Wed . "High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier". United States. doi:10.7554/eLife.48281.
@article{osti_1545911,
title = {High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier},
author = {Chen, Zhijie and Gabizon, Ronen and Brown, Aidan I. and Lee, Antony and Song, Aixin and Díaz-Celis, César and Kaplan, Craig D. and Koslover, Elena F. and Yao, Tingting and Bustamante, Carlos},
abstractNote = {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.},
doi = {10.7554/eLife.48281},
journal = {eLife},
number = ,
volume = 8,
place = {United States},
year = {2019},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.7554/eLife.48281

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Works referenced in this record:

Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules
journal, February 1996


Structural insight into nucleosome transcription by RNA polymerase II with elongation factors
journal, February 2019


Effect of force on mononucleosomal dynamics
journal, October 2006

  • Mihardja, S.; Spakowitz, A. J.; Zhang, Y.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 43
  • DOI: 10.1073/pnas.0607526103

H2A.Z: View from the Top
journal, February 2008


The FACT Complex Travels with Elongating RNA Polymerase II and Is Important for the Fidelity of Transcriptional Initiation In Vivo
journal, October 2003


Entropic elasticity of lambda-phage DNA
journal, September 1994


Histone H2A variants in nucleosomes and chromatin: more or less stable?
journal, September 2012

  • Bonisch, C.; Hake, S. B.
  • Nucleic Acids Research, Vol. 40, Issue 21
  • DOI: 10.1093/nar/gks865

Genome-Wide Dynamics of Htz1, a Histone H2A Variant that Poises Repressed/Basal Promoters for Activation through Histone Loss
journal, October 2005


Histone chaperone FACT action during transcription through chromatin by RNA polymerase II
journal, April 2013

  • Hsieh, F. -K.; Kulaeva, O. I.; Patel, S. S.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 19
  • DOI: 10.1073/pnas.1222198110

Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads
journal, November 1992


Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates
journal, July 2018


H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes
journal, September 2016

  • Rudnizky, Sergei; Bavly, Adaiah; Malik, Omri
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12958

Structure of transcribing RNA polymerase II-nucleosome complex
journal, December 2018


Nucleosome Remodeling Induced by RNA Polymerase II
journal, March 2002


Characterization of Photoactivated Singlet Oxygen Damage in Single-Molecule Optical Trap Experiments
journal, October 2009


Subnucleosomal Structures and Nucleosome Asymmetry across a Genome
journal, December 2014


FACT Facilitates Transcription-Dependent Nucleosome Alteration
journal, August 2003


Revealing transient structures of nucleosomes as DNA unwinds
journal, July 2014

  • Chen, Yujie; Tokuda, Joshua M.; Topping, Traci
  • Nucleic Acids Research, Vol. 42, Issue 13
  • DOI: 10.1093/nar/gku562

Power spectrum analysis for optical tweezers
journal, March 2004

  • Berg-Sørensen, Kirstine; Flyvbjerg, Henrik
  • Review of Scientific Instruments, Vol. 75, Issue 3
  • DOI: 10.1063/1.1645654

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome
journal, January 2009

  • Hall, Michael A.; Shundrovsky, Alla; Bai, Lu
  • Nature Structural & Molecular Biology, Vol. 16, Issue 2
  • DOI: 10.1038/nsmb.1526

Structural basis of the nucleosome transition during RNA polymerase II passage
journal, October 2018


Crystal structure of the nucleosome core particle at 2.8 Å resolution
journal, September 1997

  • Luger, Karolin; Mäder, Armin W.; Richmond, Robin K.
  • Nature, Vol. 389, Issue 6648
  • DOI: 10.1038/38444

Nucleosomal Elements that Control the Topography of the Barrier to Transcription
journal, November 2012


Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of Poly(dT) and Poly(dA) 1 1Edited by B. Honig
journal, January 1999

  • Mills, Janine B.; Vacano, Elsi; Hagerman, Paul J.
  • Journal of Molecular Biology, Vol. 285, Issue 1
  • DOI: 10.1006/jmbi.1998.2287

Full molecular trajectories of RNA polymerase at single base-pair resolution
journal, January 2018

  • Righini, Maurizio; Lee, Antony; Cañari-Chumpitaz, Cristhian
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 6
  • DOI: 10.1073/pnas.1719906115

The construction of customized nucleosomal arrays
journal, March 2016


Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility
journal, March 2015


Functions of FACT in Breaking the Nucleosome and Maintaining Its Integrity at the Single-Nucleosome Level
journal, July 2018


Stretching DNA with optical tweezers
journal, March 1997


High-Resolution Dual-Trap Optical Tweezers with Differential Detection: An Introduction
journal, October 2009

  • Bustamante, C.; Chemla, Y. R.; Moffitt, J. R.
  • Cold Spring Harbor Protocols, Vol. 2009, Issue 10
  • DOI: 10.1101/pdb.top60

New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
journal, February 1998


Generation of nonhydrolyzable ubiquitin–histone mimics
journal, December 2014


Histone octamer rearranges to adapt to DNA unwrapping
journal, December 2017

  • Bilokapic, Silvija; Strauss, Mike; Halic, Mario
  • Nature Structural & Molecular Biology, Vol. 25, Issue 1
  • DOI: 10.1038/s41594-017-0005-5

Force fluctuations impact kinetics of biomolecular systems
journal, July 2012


Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates
journal, December 2017


Ubiquitination of histone H2B regulates chromatin dynamics by enhancing nucleosome stability
journal, September 2009

  • Chandrasekharan, M. B.; Huang, F.; Sun, Z. -W.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 39
  • DOI: 10.1073/pnas.0907862106

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase
journal, March 2014


Sequence-Resolved Detection of Pausing by Single RNA Polymerase Molecules
journal, June 2006


Paused RNA polymerase II inhibits new transcriptional initiation
journal, May 2017

  • Shao, Wanqing; Zeitlinger, Julia
  • Nature Genetics, Vol. 49, Issue 7
  • DOI: 10.1038/ng.3867

H2B Ubiquitylation Acts as a Barrier to Ctk1 Nucleosomal Recruitment Prior to Removal by Ubp8 within a SAGA-Related Complex
journal, July 2007


Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss
journal, October 2013

  • Sheinin, Maxim Y.; Li, Ming; Soltani, Mohammad
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms3579

Chaperoning Histones during DNA Replication and Repair
journal, January 2010


A New Fluorescence Resonance Energy Transfer Approach Demonstrates That the Histone Variant H2AZ Stabilizes the Histone Octamer within the Nucleosome
journal, March 2004

  • Park, Young-Jun; Dyer, Pamela N.; Tremethick, David J.
  • Journal of Biological Chemistry, Vol. 279, Issue 23
  • DOI: 10.1074/jbc.M313152200

Replicating nucleosomes
journal, August 2015


Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II
journal, July 2009


Transcribing through the nucleosome
journal, December 2014

  • Teves, Sheila S.; Weber, Christopher M.; Henikoff, Steven
  • Trends in Biochemical Sciences, Vol. 39, Issue 12
  • DOI: 10.1016/j.tibs.2014.10.004

Genome-wide function of H2B ubiquitylation in promoter and genic regions
journal, November 2011


Nucleosomal arrangement affects single-molecule transcription dynamics
journal, October 2016

  • Fitz, Veronika; Shin, Jaeoh; Ehrlich, Christoph
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 45
  • DOI: 10.1073/pnas.1602764113

Regions of variant histone His2AvD required for Drosophila development
journal, June 1999

  • Clarkson, Michael John; Wells, Julian R. E.; Gibson, Frank
  • Nature, Vol. 399, Issue 6737
  • DOI: 10.1038/21436

Histone Variant H2A.Z and RNA Polymerase II Transcription Elongation
journal, February 2011

  • Santisteban, M. S.; Hang, M.; Smith, M. M.
  • Molecular and Cellular Biology, Vol. 31, Issue 9
  • DOI: 10.1128/MCB.01346-10

Ultrahigh-resolution optical trap with single-fluorophore sensitivity
journal, February 2011

  • Comstock, Matthew J.; Ha, Taekjip; Chemla, Yann R.
  • Nature Methods, Vol. 8, Issue 4
  • DOI: 10.1038/nmeth.1574

Nucleosomes Can Form a Polar Barrier to Transcript Elongation by RNA Polymerase II
journal, November 2006


Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism
journal, September 2013

  • Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Liu, Shixin
  • eLife, Vol. 2
  • DOI: 10.7554/eLife.00971

Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements
journal, January 1999