title: Chromatin topology is coupled to Polycomb group protein subnuclear organization.
abstract: The genomes of metazoa are organized at multiple scales. Many proteins that regulate genome architecture, including Polycomb group (PcG) proteins, form subnuclear structures. Deciphering mechanistic links between protein organization and chromatin architecture requires precise description and mechanistic perturbations of both. Using super-resolution microscopy, here we show that PcG proteins are organized into hundreds of nanoscale protein clusters. We manipulated PcG clusters by disrupting the polymerization activity of the sterile alpha motif (SAM) of the PcG protein Polyhomeotic (Ph) or by increasing Ph levels. Ph with mutant SAM disrupts clustering of endogenous PcG complexes and chromatin interactions while elevating Ph level increases cluster number and chromatin interactions. These effects can be captured by molecular simulations based on a previously described chromatin polymer model. Both perturbations also alter gene expression. Organization of PcG proteins into small, abundant clusters on chromatin through Ph SAM polymerization activity may shape genome architecture through chromatin interactions.
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Ajazul H
authors.initials: AH
authors.lastname: Wani
authors.affiliation: Howard Hughes Medical Institute, Harvard University Cambridge, Cambridge, Massachusetts 02138, USA.|Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.|Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Alistair N
authors.initials: AN
authors.lastname: Boettiger
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Schorderet
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.
authors.forename: Ayla
authors.initials: A
authors.lastname: Ergun
authors.affiliation: Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.
authors.forename: Christine
authors.initials: C
authors.lastname: Münger
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.|Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Ruslan I
authors.initials: RI
authors.lastname: Sadreyev
authors.affiliation: Howard Hughes Medical Institute, Harvard University Cambridge, Cambridge, Massachusetts 02138, USA.|Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.|Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhuang
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Kingston
authors.affiliation: Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.|Département de biochimie et medécine moléculaire, Université de Montréal, Montréal, Québec, Canada.
authors.forename: Nicole J
authors.initials: NJ
authors.lastname: Francis
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004330:Drosophila; D029721:Drosophila Proteins / Q000378:metabolism*; D005455:Fluorescent Antibody Technique; D042581:Intranuclear Space / Q000378:metabolism*; D008853:Microscopy; D056004:Molecular Dynamics Simulation; D061848:Optical Imaging; D063150:Polycomb Repressive Complex 1 / Q000378:metabolism*; D063146:Polycomb-Group Proteins / Q000378:metabolism; D011108:Polymers; D020836:Protein Structure, Quaternary; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D063146:Polycomb-Group Proteins; D011108:Polymers; C072820:ph-d protein, Drosophila; D063150:Polycomb Repressive Complex 1