DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Journal Article · · Nature Structural & Molecular Biology
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.

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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1490278
Journal Information:
Nature Structural & Molecular Biology, Vol. 25, Issue 2; ISSN 1545-9993
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 132 works
Citation information provided by
Web of Science

References (85)

Characterization of nucleosome core particles containing histone proteins made in bacteria 1 1Edited by A. Klug journal September 1997
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 journal November 2016
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
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
Prevention of overfitting in cryo-EM structure determination journal July 2012
Appion: An integrated, database-driven pipeline to facilitate EM image processing journal April 2009
Automated molecular microscopy: The new Leginon system journal July 2005
Jarid2 and PRC2, partners in regulating gene expression journal February 2010
Molecular architecture of human polycomb repressive complex 2 journal October 2012
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
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy journal February 2017
3D-DART: a DNA structure modelling server journal May 2009
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
The SANT domain: a unique histone-tail-binding module?
  • Boyer, Laurie A.; Latek, Robert R.; Peterson, Craig L.
  • Nature Reviews Molecular Cell Biology, Vol. 5, Issue 2, p. 158-163 https://doi.org/10.1038/nrm1314
journal February 2004
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
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
Understanding the language of Lys36 methylation at histone H3 journal January 2012
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
Features and development of Coot journal March 2010
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
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
AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2 journal March 2009
Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity journal October 2012
Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation journal April 2008
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
Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA journal October 2017
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
Reconstitution of Nucleosome Core Particles from Recombinant Histones and DNA book January 2003
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs journal October 2008
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
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome journal December 2019
Red light-induced structure changes in phytochrome A from Pisum sativum journal February 2021
Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder journal April 2021
Structures of human PRC2 with its cofactors AEBP2 and JARID2 text January 2018
A Bayesian view on cryo-EM structure determination conference May 2012
Substrate Preferences of the EZH2 Histone Methyltransferase Complex text January 2006
Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation text January 2008
New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning journal February 1998
The Site-Specific Installation of Methyl-Lysine Analogs into Recombinant Histones journal March 2007
HOTAIR Lifts Noncoding RNAs to New Levels journal June 2007
Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy journal October 2003
Automated molecular microscopy: The new Leginon system journal July 2005
Bsoft: Image processing and molecular modeling for electron microscopy journal January 2007
Appion: An integrated, database-driven pipeline to facilitate EM image processing journal April 2009
DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy journal May 2009
iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates journal November 2013
Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks journal May 2011
Post-translational modifications of tau protein: Implications for Alzheimer's disease journal March 2011
Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation journal April 2008
Role of the polycomb protein EED in the propagation of repressive histone marks journal September 2009
The structural basis of modified nucleosome recognition by 53BP1 journal July 2016
Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure journal April 2017
Prevention of overfitting in cryo-EM structure determination journal July 2012
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs journal October 2008
The SANT domain: a unique histone-tail-binding module?
  • Boyer, Laurie A.; Latek, Robert R.; Peterson, Craig L.
  • Nature Reviews Molecular Cell Biology, Vol. 5, Issue 2, p. 158-163 https://doi.org/10.1038/nrm1314
journal February 2004
Understanding the language of Lys36 methylation at histone H3 journal January 2012
Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity journal October 2012
Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA journal October 2017
AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2 journal March 2009
3D-DART: a DNA structure modelling server journal May 2009
Nucleosome-binding activities within JARID2 and EZH1 regulate the function of PRC2 on chromatin journal December 2013
A Bayesian view on cryo-EM structure determination conference May 2012
Substrate Preferences of the EZH2 Histone Methyltransferase Complex text January 2006

Cited By (26)

Polycomb Repressive Complex 2: Modulator Development for Functional Regulation of a Multiprotein Complex by Using Structural Information journal July 2019
Cryo-EM in drug discovery: achievements, limitations and prospects journal June 2018
Sperm-inherited H3K27me3 impacts offspring transcription and development in C. elegans journal March 2019
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
Structural basis of nucleosome recognition and modification by MLL methyltransferases journal September 2019
Nucleosome structure and dynamics are coming of age journal December 2018
RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2 journal March 2019
G-tract RNA removes Polycomb repressive complex 2 from genes journal September 2019
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
Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1 journal September 2018
PRC2 is high maintenance journal May 2019
Regulation of histone methylation by automethylation of PRC2 journal September 2019
An inter‐dimer allosteric switch controls NMDA receptor activity journal November 2018
Polycomb Assemblies Multitask to Regulate Transcription journal June 2019
The EZH2 SANT1 Domain is a Histone Reader Providing Sensitivity to the Modification State of the H4 Tail journal February 2018
The cryo-EM resolution revolution and transcription complexes journal October 2018
Theoretical analysis of Polycomb-Trithorax systems predicts that poised chromatin is bistable and not bivalent journal May 2019
Cryo-EM structure of the human MLL1 core complex bound to the nucleosome journal December 2019
G-tracts give PRC2 the boot journal October 2019
Chromatin fiber structural motifs as regulatory hubs of genome function? journal April 2019
Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1 journal September 2018
Lysine Acetyltransferase Inhibitors From Natural Sources journal August 2020