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Title: Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes

Abstract

Epigenetic regulation is mediated by protein complexes that couple recognition of chromatin marks to activity or recruitment of chromatin-modifying enzymes. Polycomb repressive complex 2 (PRC2), a gene silencer that methylates lysine 27 of histone H3, is stimulated upon recognition of its own catalytic product and has been shown to be more active on dinucleosomes than H3 tails or single nucleosomes. These properties probably facilitate local H3K27me2/3 spreading, causing heterochromatin formation and gene repression. Here, cryo-EM reconstructions of human PRC2 bound to bifunctional dinucleosomes show how a single PRC2, via interactions with nucleosomal DNA, positions the H3 tails of the activating and substrate nucleosome to interact with the EED subunit and the SET domain of EZH2, respectively. We show how the geometry of the PRC2–DNA interactions allows PRC2 to accommodate varying lengths of the linker DNA between nucleosomes. Furthermore, our structures illustrate how an epigenetic regulator engages with a complex chromatin substrate.

Authors:
ORCiD logo [1];  [1]; ORCiD logo [2]
  1. Univ. of California, Berkeley, CA (United States). California Inst. for Quantitative Biology (QB3); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrative Bio-Imaging Div.
  2. Univ. of California, Berkeley, CA (United States). California Inst. for Quantitative Biology (QB3), Howard Hughes Medical Inst., and Dept. of Molecular and Cell Biology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrative Bio-Imaging Div.
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1490278
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Structural & Molecular Biology
Additional Journal Information:
Journal Volume: 25; Journal Issue: 2; Journal ID: ISSN 1545-9993
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Poepsel, Simon, Kasinath, Vignesh, and Nogales, Eva. Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes. United States: N. p., 2018. Web. doi:10.1038/s41594-018-0023-y.
Poepsel, Simon, Kasinath, Vignesh, & Nogales, Eva. Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes. United States. doi:https://doi.org/10.1038/s41594-018-0023-y
Poepsel, Simon, Kasinath, Vignesh, and Nogales, Eva. Mon . "Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes". United States. doi:https://doi.org/10.1038/s41594-018-0023-y. https://www.osti.gov/servlets/purl/1490278.
@article{osti_1490278,
title = {Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes},
author = {Poepsel, Simon and Kasinath, Vignesh and Nogales, Eva},
abstractNote = {Epigenetic regulation is mediated by protein complexes that couple recognition of chromatin marks to activity or recruitment of chromatin-modifying enzymes. Polycomb repressive complex 2 (PRC2), a gene silencer that methylates lysine 27 of histone H3, is stimulated upon recognition of its own catalytic product and has been shown to be more active on dinucleosomes than H3 tails or single nucleosomes. These properties probably facilitate local H3K27me2/3 spreading, causing heterochromatin formation and gene repression. Here, cryo-EM reconstructions of human PRC2 bound to bifunctional dinucleosomes show how a single PRC2, via interactions with nucleosomal DNA, positions the H3 tails of the activating and substrate nucleosome to interact with the EED subunit and the SET domain of EZH2, respectively. We show how the geometry of the PRC2–DNA interactions allows PRC2 to accommodate varying lengths of the linker DNA between nucleosomes. Furthermore, our structures illustrate how an epigenetic regulator engages with a complex chromatin substrate.},
doi = {10.1038/s41594-018-0023-y},
journal = {Nature Structural & Molecular Biology},
number = 2,
volume = 25,
place = {United States},
year = {2018},
month = {1}
}

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Works referenced in this record:

Characterization of nucleosome core particles containing histone proteins made in bacteria 1 1Edited by A. Klug
journal, September 1997

  • Luger, Karolin; Rechsteiner, Thomas J.; Flaus, Andrew J.
  • Journal of Molecular Biology, Vol. 272, Issue 3
  • DOI: 10.1006/jmbi.1997.1235

Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
journal, November 2016

  • Kimanius, Dari; Forsberg, Björn O.; Scheres, Sjors HW
  • eLife, Vol. 5
  • DOI: 10.7554/eLife.18722

Nucleosome-binding activities within JARID2 and EZH1 regulate the function of PRC2 on chromatin
journal, December 2013


Structures of human PRC2 with its cofactors AEBP2 and JARID2
journal, January 2018


iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates
journal, November 2013

  • Lopéz-Blanco, José Ramón; Chacón, Pablo
  • Journal of Structural Biology, Vol. 184, Issue 2
  • DOI: 10.1016/j.jsb.2013.08.010

Accurate determination of local defocus and specimen tilt in electron microscopy
journal, June 2003


DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy
journal, May 2009

  • Voss, N. R.; Yoshioka, C. K.; Radermacher, M.
  • Journal of Structural Biology, Vol. 166, Issue 2
  • DOI: 10.1016/j.jsb.2009.01.004

Prevention of overfitting in cryo-EM structure determination
journal, July 2012

  • Scheres, Sjors H. W.; Chen, Shaoxia
  • Nature Methods, Vol. 9, Issue 9
  • DOI: 10.1038/nmeth.2115

Appion: An integrated, database-driven pipeline to facilitate EM image processing
journal, April 2009

  • Lander, Gabriel C.; Stagg, Scott M.; Voss, Neil R.
  • Journal of Structural Biology, Vol. 166, Issue 1
  • DOI: 10.1016/j.jsb.2009.01.002

Automated molecular microscopy: The new Leginon system
journal, July 2005

  • Suloway, Christian; Pulokas, James; Fellmann, Denis
  • Journal of Structural Biology, Vol. 151, Issue 1
  • DOI: 10.1016/j.jsb.2005.03.010

Jarid2 and PRC2, partners in regulating gene expression
journal, February 2010


Molecular architecture of human polycomb repressive complex 2
journal, October 2012

  • Ciferri, Claudio; Lander, Gabriel C.; Maiolica, Alessio
  • eLife, Vol. 1
  • DOI: 10.7554/eLife.00005

Asymmetrically Modified Nucleosomes
journal, September 2012


Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure
journal, April 2017


Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
journal, June 2007


Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks
journal, May 2011


Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing
journal, September 2002


The structural basis of modified nucleosome recognition by 53BP1
journal, July 2016

  • Wilson, Marcus D.; Benlekbir, Samir; Fradet-Turcotte, Amélie
  • Nature, Vol. 536, Issue 7614
  • DOI: 10.1038/nature18951

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
journal, February 2017

  • Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul
  • Nature Methods, Vol. 14, Issue 4
  • DOI: 10.1038/nmeth.4193

3D-DART: a DNA structure modelling server
journal, May 2009

  • van Dijk, M.; Bonvin, A. M. J. J.
  • Nucleic Acids Research, Vol. 37, Issue Web Server
  • DOI: 10.1093/nar/gkp287

Bsoft: Image processing and molecular modeling for electron microscopy
journal, January 2007


Role of the polycomb protein EED in the propagation of repressive histone marks
journal, September 2009

  • Margueron, Raphael; Justin, Neil; Ohno, Katsuhito
  • Nature, Vol. 461, Issue 7265
  • DOI: 10.1038/nature08398

The SANT domain: a unique histone-tail-binding module?
journal, February 2004

  • Boyer, Laurie A.; Latek, Robert R.; Peterson, Craig L.
  • Nature Reviews Molecular Cell Biology, Vol. 5, Issue 2, p. 158-163
  • DOI: 10.1038/nrm1314

Gctf: Real-time CTF determination and correction
journal, January 2016


Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2
journal, October 2015


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


Crystal Structures of Nucleosome Core Particles Containing the ‘601’ Strong Positioning Sequence
journal, October 2010

  • Vasudevan, Dileep; Chua, Eugene Y. D.; Davey, Curt A.
  • Journal of Molecular Biology, Vol. 403, Issue 1
  • DOI: 10.1016/j.jmb.2010.08.039

Histone target selection within chromatin: an exemplary case of teamwork
journal, May 2014


A model for transmission of the H3K27me3 epigenetic mark
journal, October 2008

  • Hansen, Klaus H.; Bracken, Adrian P.; Pasini, Diego
  • Nature Cell Biology, Vol. 10, Issue 11
  • DOI: 10.1038/ncb1787

Understanding the language of Lys36 methylation at histone H3
journal, January 2012

  • Wagner, Eric J.; Carpenter, Phillip B.
  • Nature Reviews Molecular Cell Biology, Vol. 13, Issue 2
  • DOI: 10.1038/nrm3274

Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy
journal, October 2003


A Bayesian View on Cryo-EM Structure Determination
journal, January 2012


Visualizing density maps with UCSF Chimera
journal, January 2007

  • Goddard, Thomas D.; Huang, Conrad C.; Ferrin, Thomas E.
  • Journal of Structural Biology, Vol. 157, Issue 1
  • DOI: 10.1016/j.jsb.2006.06.010

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Dense Chromatin Activates Polycomb Repressive Complex 2 to Regulate H3 Lysine 27 Methylation
journal, August 2012


The Site-Specific Installation of Methyl-Lysine Analogs into Recombinant Histones
journal, March 2007


Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking
journal, September 2003

  • Ogura, Toshihiko; Iwasaki, Kenji; Sato, Chikara
  • Journal of Structural Biology, Vol. 143, Issue 3
  • DOI: 10.1016/j.jsb.2003.08.005

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome
journal, October 2008


DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation
journal, October 2017

  • Choi, Jeongyoon; Bachmann, Andreas Linus; Tauscher, Katharina
  • Nature Structural & Molecular Biology, Vol. 24, Issue 12
  • DOI: 10.1038/nsmb.3488

AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2
journal, March 2009

  • Kim, Hana; Kang, Keunsoo; Kim, Joomyeong
  • Nucleic Acids Research, Vol. 37, Issue 9
  • DOI: 10.1093/nar/gkp149

Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity
journal, October 2012

  • Ballaré, Cecilia; Lange, Martin; Lapinaite, Audrone
  • Nature Structural & Molecular Biology, Vol. 19, Issue 12
  • DOI: 10.1038/nsmb.2434

Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation
journal, April 2008

  • McGinty, Robert K.; Kim, Jaehoon; Chatterjee, Champak
  • Nature, Vol. 453, Issue 7196
  • DOI: 10.1038/nature06906

Subunit Contributions to Histone Methyltransferase Activities of Fly and Worm Polycomb Group Complexes
journal, July 2005


Substrate Preferences of the EZH2 Histone Methyltransferase Complex
journal, January 2006

  • Martin, Cyrus; Cao, Ru; Zhang, Yi
  • Journal of Biological Chemistry, Vol. 281, Issue 13
  • DOI: 10.1074/jbc.M513425200

Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA
journal, October 2017

  • Wang, Xueyin; Paucek, Richard D.; Gooding, Anne R.
  • Nature Structural & Molecular Biology, Vol. 24, Issue 12
  • DOI: 10.1038/nsmb.3487

Post-translational modifications of tau protein: Implications for Alzheimer's disease
journal, March 2011


H3K36 Methylation Antagonizes PRC2-mediated H3K27 Methylation
journal, January 2011


Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2
journal, April 2016

  • Justin, Neil; Zhang, Ying; Tarricone, Cataldo
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms11316

SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs
journal, October 2008

  • Shaikh, Tanvir R.; Gao, Haixiao; Baxter, William T.
  • Nature Protocols, Vol. 3, Issue 12
  • DOI: 10.1038/nprot.2008.156

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells
journal, July 2017


Sampling the conformational space of the catalytic subunit of human γ-secretase
journal, December 2015


    Works referencing / citing this record:

    Polycomb Assemblies Multitask to Regulate Transcription
    journal, June 2019


    Polycomb Assemblies Multitask to Regulate Transcription
    journal, June 2019


    Cryo-EM in drug discovery: achievements, limitations and prospects
    journal, June 2018

    • Renaud, Jean-Paul; Chari, Ashwin; Ciferri, Claudio
    • Nature Reviews Drug Discovery, Vol. 17, Issue 7
    • DOI: 10.1038/nrd.2018.77

    Sperm-inherited H3K27me3 impacts offspring transcription and development in C. elegans
    journal, March 2019

    • Kaneshiro, Kiyomi Raye; Rechtsteiner, Andreas; Strome, Susan
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-019-09141-w

    Theoretical analysis of Polycomb-Trithorax systems predicts that poised chromatin is bistable and not bivalent
    journal, May 2019


    H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans
    journal, June 2019


    Cryo-EM structure of the human MLL1 core complex bound to the nucleosome
    journal, December 2019


    Old cogs, new tricks: the evolution of gene expression in a chromatin context
    journal, March 2019

    • Talbert, Paul B.; Meers, Michael P.; Henikoff, Steven
    • Nature Reviews Genetics, Vol. 20, Issue 5
    • DOI: 10.1038/s41576-019-0105-7

    Structural basis of nucleosome recognition and modification by MLL methyltransferases
    journal, September 2019


    Nucleosome structure and dynamics are coming of age
    journal, December 2018

    • Zhou, Keda; Gaullier, Guillaume; Luger, Karolin
    • Nature Structural & Molecular Biology, Vol. 26, Issue 1
    • DOI: 10.1038/s41594-018-0166-x

    RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2
    journal, March 2019

    • Zhang, Qi; McKenzie, Nicholas J.; Warneford-Thomson, Robert
    • Nature Structural & Molecular Biology, Vol. 26, Issue 3
    • DOI: 10.1038/s41594-019-0197-y

    G-tract RNA removes Polycomb repressive complex 2 from genes
    journal, September 2019

    • Beltran, Manuel; Tavares, Manuel; Justin, Neil
    • Nature Structural & Molecular Biology, Vol. 26, Issue 10
    • DOI: 10.1038/s41594-019-0293-z

    The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail
    journal, January 2019


    Chromatin fiber structural motifs as regulatory hubs of genome function?
    journal, April 2019

    • Moraru, Manuela; Schalch, Thomas
    • Essays in Biochemistry, Vol. 63, Issue 1
    • DOI: 10.1042/ebc20180065

    Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1
    journal, September 2018

    • Sauer, Paul V.; Gu, Yajie; Liu, Wallace H.
    • Nucleic Acids Research, Vol. 46, Issue 19
    • DOI: 10.1093/nar/gky823

    PRC2 is high maintenance
    journal, May 2019

    • Yu, Jia-Ray; Lee, Chul-Hwan; Oksuz, Ozgur
    • Genes & Development, Vol. 33, Issue 15-16
    • DOI: 10.1101/gad.325050.119

    Regulation of histone methylation by automethylation of PRC2
    journal, September 2019

    • Wang, Xueyin; Long, Yicheng; Paucek, Richard D.
    • Genes & Development, Vol. 33, Issue 19-20
    • DOI: 10.1101/gad.328849.119

    An inter‐dimer allosteric switch controls NMDA receptor activity
    journal, November 2018

    • Esmenjaud, Jean‐Baptiste; Stroebel, David; Chan, Kelvin
    • The EMBO Journal, Vol. 38, Issue 2
    • DOI: 10.15252/embj.201899894