Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin. Author Rachel Leicher, Eva Ge, Xingcheng Lin, Matthew Reynolds, Wenjun Xie, Thomas Walz, Bin Zhang, Tom Muir, Shixin Liu Publication Year 2020 Type Journal Article Abstract Polycomb repressive complex 2 (PRC2) installs and spreads repressive histone methylation marks on eukaryotic chromosomes. Because of the key roles that PRC2 plays in development and disease, how this epigenetic machinery interacts with DNA and nucleosomes is of major interest. Nonetheless, the mechanism by which PRC2 engages with native-like chromatin remains incompletely understood. In this work, we employ single-molecule force spectroscopy and molecular dynamics simulations to dissect the behavior of PRC2 on polynucleosome arrays. Our results reveal an unexpectedly diverse repertoire of PRC2 binding configurations on chromatin. Besides reproducing known binding modes in which PRC2 interacts with bare DNA, mononucleosomes, and adjacent nucleosome pairs, our data also provide direct evidence that PRC2 can bridge pairs of distal nucleosomes. In particular, the "1-3" bridging mode, in which PRC2 engages two nucleosomes separated by one spacer nucleosome, is a preferred low-energy configuration. Moreover, we show that the distribution and stability of different PRC2-chromatin interaction modes are modulated by accessory subunits, oncogenic histone mutations, and the methylation state of chromatin. Overall, these findings have implications for the mechanism by which PRC2 spreads histone modifications and compacts chromatin. The experimental and computational platforms developed here provide a framework for understanding the molecular basis of epigenetic maintenance mediated by Polycomb-group proteins. Keywords Structure-Activity Relationship, Humans, Models, Biological, Protein Binding, Mutation, Models, Molecular, Protein Conformation, Methylation, Epigenesis, Genetic, Molecular Dynamics Simulation, Histones, Nucleosomes, Chromatin, Single Molecule Imaging, Polycomb Repressive Complex 2, Heterochromatin, Spectrum Analysis Journal Proc Natl Acad Sci U S A Volume 117 Issue 48 Pages 30465-30475 Date Published 2020 Dec 01 ISSN Number 1091-6490 DOI 10.1073/pnas.2003395117 Alternate Journal Proc Natl Acad Sci U S A PMCID PMC7720148 PMID 33208532 PubMedPubMed CentralGoogle ScholarBibTeXEndNote X3 XML